mi.owl
type: Ontology
auto-generated-by: OBO-Edit 2.3.1
date: 15:04:2021 22:57
default-namespace: PSI-MI
has_obo_format_version: 1.2
saved-by: pporras
comment: CVversion: 2.5.5
comment: Each of the top level terms in this file is the root term of an independent controlled vocabulary
comment: Notes:
comment: The PSI MI schema defines short labels for controlled vocabulary terms
comment: The correct use of these vocabularies in the PSI Molecular Interaction XML schema is
comment: The last accession number used in this file is stored in a separate file,
comment: The maintenance of this file is ensured by Luana Licata luana.licata@uniroma2.it and Sandra Orchard orchard@ebi.ac.uk
comment: coverage: This file collect controlled vocabularies describing different aspects of molecular interactions.
comment: formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml.
comment: mapping an element of the PSI Molecular Interaction XML schema.
comment: psi-mi.lastac. It MUST be updated when this file is updated.
comment: publisher: This file is published by the PSI MI working group see http://psidev.info/MI
comment: short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long.

definition
type: AnnotationProperty

Label from MS DeltaMass
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

Drugable
type: AnnotationProperty
comment: Drugable Genome Project
sub property of: subset_property

Alternate label curated by PSI-MI
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

Unique short label curated by PSI-MI
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

PSI-MI slim
type: AnnotationProperty
comment: Subset of PSI-MI
sub property of: subset_property

Alternate label curated by PSI-MOD
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

Unique short label curated by PSI-MOD
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

PSI-MOD slim
type: AnnotationProperty
comment: subset of protein modifications
sub property of: subset_property

Agreed label from MS community
type: AnnotationProperty
has_scope: has_related_synonym
sub property of: synonym_type_property

Alternate name from RESID
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

Misnomer label from RESID
type: AnnotationProperty
has_scope: has_related_synonym
sub property of: synonym_type_property

Name from RESID
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

Systematic name from RESID
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

Alternate name from UniMod
type: AnnotationProperty
has_scope: has_related_synonym
sub property of: synonym_type_property

Description (full_name) from UniMod
type: AnnotationProperty
has_scope: has_related_synonym
sub property of: synonym_type_property

Interim label from UniMod
type: AnnotationProperty
has_scope: has_related_synonym
sub property of: synonym_type_property

Label (title) from UniMod
type: AnnotationProperty
has_scope: has_related_synonym
sub property of: synonym_type_property

Protein feature description from UniProtKB
type: AnnotationProperty
has_scope: has_exact_synonym
sub property of: synonym_type_property

subset_property
type: AnnotationProperty

synonym_type_property
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_scope
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

molecular interaction
type: Class
definition: Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.
has_exact_synonym: mi
has_obo_namespace: PSI-MI
id: MI:0000
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: molecular interaction
annotated property: definition
annotated target: Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.
database_cross_reference: PMID:14755292

Axiom
annotated source: molecular interaction
annotated property: has_exact_synonym
annotated target: mi
has_synonym_type: Unique short label curated by PSI-MI

interaction detection method
type: Class
subclass of: molecular interaction
definition: Method to determine the interaction.
has_exact_synonym: interaction detect
has_obo_namespace: PSI-MI
id: MI:0001
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: interaction detection method
annotated property: definition
annotated target: Method to determine the interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: interaction detection method
annotated property: has_exact_synonym
annotated target: interaction detect
has_synonym_type: Unique short label curated by PSI-MI

participant identification method
type: Class
subclass of: molecular interaction
definition: Method to determine the molecules involved in the interaction.
has_exact_synonym: participant detection
has_exact_synonym: participant ident
has_obo_namespace: PSI-MI
id: MI:0002
in_subset: PSI-MI slim

Axiom
annotated source: participant identification method
annotated property: definition
annotated target: Method to determine the molecules involved in the interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: participant identification method
annotated property: has_exact_synonym
annotated target: participant detection
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: participant identification method
annotated property: has_exact_synonym
annotated target: participant ident
has_synonym_type: Unique short label curated by PSI-MI

feature detection method
type: Class
subclass of: molecular interaction
definition: Method to determine the features of the proteins involved in the interaction.
has_exact_synonym: feature detection
has_obo_namespace: PSI-MI
id: MI:0003
in_subset: PSI-MI slim

Axiom
annotated source: feature detection method
annotated property: definition
annotated target: Method to determine the features of the proteins involved in the interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: feature detection method
annotated property: has_exact_synonym
annotated target: feature detection
has_synonym_type: Unique short label curated by PSI-MI

affinity chromatography technology
type: Class
subclass of: chromatography technology
subclass of: affinity technology
definition: This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins.
has_exact_synonym: Affinity purification
has_exact_synonym: affinity chrom
has_obo_namespace: PSI-MI
id: MI:0004
in_subset: PSI-MI slim

Axiom
annotated source: affinity chromatography technology
annotated property: definition
annotated target: This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins.
database_cross_reference: PMID:7708014

Axiom
annotated source: affinity chromatography technology
annotated property: has_exact_synonym
annotated target: Affinity purification
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: affinity chromatography technology
annotated property: has_exact_synonym
annotated target: affinity chrom
has_synonym_type: Unique short label curated by PSI-MI

alanine scanning
type: Class
subclass of: substitution analysis
definition: This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay.
has_obo_namespace: PSI-MI
id: MI:0005
in_subset: PSI-MI slim

Axiom
annotated source: alanine scanning
annotated property: definition
annotated target: This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay.
database_cross_reference: PMID:14755292

anti bait coimmunoprecipitation
type: Class
subclass of: coimmunoprecipitation
definition: A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample.
has_exact_synonym: anti bait coip
has_obo_namespace: PSI-MI
id: MI:0006
in_subset: PSI-MI slim

Axiom
annotated source: anti bait coimmunoprecipitation
annotated property: definition
annotated target: A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample.
database_cross_reference: PMID:7708014

Axiom
annotated source: anti bait coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: anti bait coip
has_synonym_type: Unique short label curated by PSI-MI

anti tag coimmunoprecipitation
type: Class
subclass of: coimmunoprecipitation
definition: A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available.
has_exact_synonym: anti tag coip
has_obo_namespace: PSI-MI
id: MI:0007
in_subset: PSI-MI slim

Axiom
annotated source: anti tag coimmunoprecipitation
annotated property: definition
annotated target: A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available.
database_cross_reference: PMID:7708014

Axiom
annotated source: anti tag coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: anti tag coip
has_synonym_type: Unique short label curated by PSI-MI

array technology
type: Class
subclass of: affinity technology
definition: In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule.
has_obo_namespace: PSI-MI
id: MI:0008
in_subset: PSI-MI slim

Axiom
annotated source: array technology
annotated property: definition
annotated target: In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule.
database_cross_reference: PMID:14755292

bacterial display
type: Class
subclass of: display technology
subclass of: fluorescence-activated cell sorting
definition: The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells.
has_obo_namespace: PSI-MI
id: MI:0009
in_subset: PSI-MI slim

Axiom
annotated source: bacterial display
annotated property: definition
annotated target: The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells.
database_cross_reference: PMID:10436088
database_cross_reference: PMID:8248129

beta galactosidase complementation
type: Class
subclass of: protein complementation assay
definition: Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment.
has_exact_synonym: beta galactosidase
has_obo_namespace: PSI-MI
id: MI:0010
in_subset: PSI-MI slim

Axiom
annotated source: beta galactosidase complementation
annotated property: definition
annotated target: Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment.
database_cross_reference: PMID:12042868
database_cross_reference: PMID:9237989

Axiom
annotated source: beta galactosidase complementation
annotated property: has_exact_synonym
annotated target: beta galactosidase
has_synonym_type: Unique short label curated by PSI-MI

beta lactamase complementation
type: Class
subclass of: protein complementation assay
definition: This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications.
has_exact_synonym: beta lactamase
has_obo_namespace: PSI-MI
id: MI:0011
in_subset: PSI-MI slim

Axiom
annotated source: beta lactamase complementation
annotated property: definition
annotated target: This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications.
database_cross_reference: PMID:12042868

Axiom
annotated source: beta lactamase complementation
annotated property: has_exact_synonym
annotated target: beta lactamase
has_synonym_type: Unique short label curated by PSI-MI

bioluminescence resonance energy transfer
type: Class
subclass of: fluorescence technology
definition: In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom).
has_exact_synonym: BRET
has_exact_synonym: LRET
has_exact_synonym: bret
has_obo_namespace: PSI-MI
id: MI:0012
in_subset: PSI-MI slim

Axiom
annotated source: bioluminescence resonance energy transfer
annotated property: definition
annotated target: In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom).
database_cross_reference: PMID:10725388
database_cross_reference: PMID:9874787

Axiom
annotated source: bioluminescence resonance energy transfer
annotated property: has_exact_synonym
annotated target: BRET
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: bioluminescence resonance energy transfer
annotated property: has_exact_synonym
annotated target: LRET
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: bioluminescence resonance energy transfer
annotated property: has_exact_synonym
annotated target: bret
has_synonym_type: Unique short label curated by PSI-MI

biophysical
type: Class
subclass of: experimental interaction detection
definition: The application of physical principles and methods to biological experiments.
has_obo_namespace: PSI-MI
id: MI:0013
in_subset: PSI-MI slim

Axiom
annotated source: biophysical
annotated property: definition
annotated target: The application of physical principles and methods to biological experiments.
database_cross_reference: PMID:14755292

adenylate cyclase complementation
type: Class
subclass of: protein complementation assay
definition: Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey.
has_exact_synonym: adenylate cyclase
has_exact_synonym: bacterial two-hybrid
has_obo_namespace: PSI-MI
id: MI:0014
in_subset: PSI-MI slim

Axiom
annotated source: adenylate cyclase complementation
annotated property: definition
annotated target: Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey.
database_cross_reference: PMID:9576956

Axiom
annotated source: adenylate cyclase complementation
annotated property: has_exact_synonym
annotated target: adenylate cyclase
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: adenylate cyclase complementation
annotated property: has_exact_synonym
annotated target: bacterial two-hybrid
has_synonym_type: Alternate label curated by PSI-MI

circular dichroism
type: Class
subclass of: biophysical
definition: Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure.
has_exact_synonym: CD
has_exact_synonym: cd
has_obo_namespace: PSI-MI
id: MI:0016
in_subset: PSI-MI slim

Axiom
annotated source: circular dichroism
annotated property: definition
annotated target: Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure.
database_cross_reference: PMID:11578931

Axiom
annotated source: circular dichroism
annotated property: has_exact_synonym
annotated target: CD
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: circular dichroism
annotated property: has_exact_synonym
annotated target: cd
has_synonym_type: Unique short label curated by PSI-MI

classical fluorescence spectroscopy
type: Class
subclass of: fluorescence technology
definition: Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage.
has_exact_synonym: fluorescence spectr
has_obo_namespace: PSI-MI
id: MI:0017
in_subset: PSI-MI slim

Axiom
annotated source: classical fluorescence spectroscopy
annotated property: definition
annotated target: Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage.
database_cross_reference: PMID:7708014

Axiom
annotated source: classical fluorescence spectroscopy
annotated property: has_exact_synonym
annotated target: fluorescence spectr
has_synonym_type: Unique short label curated by PSI-MI

two hybrid
type: Class
subclass of: transcriptional complementation assay
definition: The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator.
has_exact_synonym: 2 hybrid
has_exact_synonym: 2-hybrid
has_exact_synonym: 2H
has_exact_synonym: 2h
has_exact_synonym: Gal4 transcription regeneration
has_exact_synonym: Y2H
has_exact_synonym: classical two hybrid
has_exact_synonym: two-hybrid
has_exact_synonym: yeast two hybrid
has_obo_namespace: PSI-MI
has_related_synonym: Y-2H
id: MI:0018
in_subset: PSI-MI slim

Axiom
annotated source: two hybrid
annotated property: definition
annotated target: The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator.
database_cross_reference: PMID:10967325
database_cross_reference: PMID:12634794
database_cross_reference: PMID:1946372

Axiom
annotated source: two hybrid
annotated property: has_exact_synonym
annotated target: 2 hybrid
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: two hybrid
annotated property: has_exact_synonym
annotated target: 2-hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: two hybrid
annotated property: has_exact_synonym
annotated target: 2H
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: two hybrid
annotated property: has_exact_synonym
annotated target: 2h
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: two hybrid
annotated property: has_exact_synonym
annotated target: Gal4 transcription regeneration
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: two hybrid
annotated property: has_exact_synonym
annotated target: classical two hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: two hybrid
annotated property: has_exact_synonym
annotated target: two-hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: two hybrid
annotated property: has_exact_synonym
annotated target: yeast two hybrid
has_synonym_type: Alternate label curated by PSI-MI

coimmunoprecipitation
type: Class
subclass of: affinity chromatography technology
definition: In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process.
has_exact_synonym: Co-IP
has_exact_synonym: CoIp
has_exact_synonym: co-immunoprecipitation
has_exact_synonym: coip
has_exact_synonym: immunoprecipitation
has_obo_namespace: PSI-MI
id: MI:0019
in_subset: PSI-MI slim

Axiom
annotated source: coimmunoprecipitation
annotated property: definition
annotated target: In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process.
database_cross_reference: PMID:7708014

Axiom
annotated source: coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: Co-IP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: CoIp
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: co-immunoprecipitation
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: coip
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: immunoprecipitation
has_synonym_type: Alternate label curated by PSI-MI

transmission electron microscopy
type: Class
subclass of: electron microscopy
definition: Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell.
has_exact_synonym: tem
has_obo_namespace: PSI-MI
id: MI:0020
in_subset: PSI-MI slim

Axiom
annotated source: transmission electron microscopy
annotated property: definition
annotated target: Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell.
database_cross_reference: PMID:14755292

Axiom
annotated source: transmission electron microscopy
annotated property: has_exact_synonym
annotated target: tem
has_synonym_type: Unique short label curated by PSI-MI

colocalization by fluorescent probes cloning
type: Class
definition: Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another. OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.
has_exact_synonym: coloc fluoresc probe
has_obo_namespace: PSI-MI
id: MI:0021
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: colocalization by fluorescent probes cloning
annotated property: definition
annotated target: Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another. OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: colocalization by fluorescent probes cloning
annotated property: has_exact_synonym
annotated target: coloc fluoresc probe
has_synonym_type: Unique short label curated by PSI-MI

colocalization by immunostaining
type: Class
definition: The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques. OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.
has_exact_synonym: Immunofluorescence Staining
has_exact_synonym: Immunostaining
has_exact_synonym: coloc immunostaining
has_obo_namespace: PSI-MI
id: MI:0022
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: colocalization by immunostaining
annotated property: definition
annotated target: The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques. OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.
database_cross_reference: PMID:14755292

Axiom
annotated source: colocalization by immunostaining
annotated property: has_exact_synonym
annotated target: Immunofluorescence Staining
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: colocalization by immunostaining
annotated property: has_exact_synonym
annotated target: Immunostaining
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: colocalization by immunostaining
annotated property: has_exact_synonym
annotated target: coloc immunostaining
has_synonym_type: Unique short label curated by PSI-MI

colocalization/visualisation technologies
type: Class
definition: Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type. OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.
has_exact_synonym: coloc visual technol
has_obo_namespace: PSI-MI
id: MI:0023
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: colocalization/visualisation technologies
annotated property: definition
annotated target: Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type. OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.
database_cross_reference: PMID:14755292

Axiom
annotated source: colocalization/visualisation technologies
annotated property: has_exact_synonym
annotated target: coloc visual technol
has_synonym_type: Unique short label curated by PSI-MI

confirmational text mining
type: Class
subclass of: text mining
definition: Text mining is used to support interactions which have been determined by other methods.
has_exact_synonym: conformational tm
has_obo_namespace: PSI-MI
id: MI:0024
in_subset: PSI-MI slim

Axiom
annotated source: confirmational text mining
annotated property: definition
annotated target: Text mining is used to support interactions which have been determined by other methods.
database_cross_reference: PMID:14755292

Axiom
annotated source: confirmational text mining
annotated property: has_exact_synonym
annotated target: conformational tm
has_synonym_type: Unique short label curated by PSI-MI

copurification
type: Class
definition: Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex. OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).
has_obo_namespace: PSI-MI
id: MI:0025
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: copurification
annotated property: definition
annotated target: Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex. OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).
database_cross_reference: PMID:14755292

correlated mutations
type: Class
subclass of: sequence based prediction
subclass of: feature prediction
definition: Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces.
has_obo_namespace: PSI-MI
id: MI:0026
in_subset: PSI-MI slim

Axiom
annotated source: correlated mutations
annotated property: definition
annotated target: Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces.
database_cross_reference: PMID:11933068

cosedimentation
type: Class
subclass of: biochemical
definition: Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact.
has_obo_namespace: PSI-MI
id: MI:0027
in_subset: PSI-MI slim

Axiom
annotated source: cosedimentation
annotated property: definition
annotated target: Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact.
database_cross_reference: PMID:14755292

cosedimentation in solution
type: Class
subclass of: cosedimentation
definition: The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed.
has_exact_synonym: solution sedimentati
has_obo_namespace: PSI-MI
id: MI:0028
in_subset: PSI-MI slim

Axiom
annotated source: cosedimentation in solution
annotated property: definition
annotated target: The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed.
database_cross_reference: PMID:10410796

Axiom
annotated source: cosedimentation in solution
annotated property: has_exact_synonym
annotated target: solution sedimentati
has_synonym_type: Unique short label curated by PSI-MI

cosedimentation through density gradient
type: Class
subclass of: cosedimentation
definition: Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant.
has_exact_synonym: density sedimentation
has_obo_namespace: PSI-MI
id: MI:0029
in_subset: PSI-MI slim

Axiom
annotated source: cosedimentation through density gradient
annotated property: definition
annotated target: Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant.
database_cross_reference: PMID:10410796

Axiom
annotated source: cosedimentation through density gradient
annotated property: has_exact_synonym
annotated target: density sedimentation
has_synonym_type: Unique short label curated by PSI-MI

cross-linking study
type: Class
subclass of: biochemical
definition: Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity.
has_exact_synonym: crosslink
has_obo_namespace: PSI-MI
id: MI:0030
in_subset: PSI-MI slim

Axiom
annotated source: cross-linking study
annotated property: definition
annotated target: Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity.
database_cross_reference: PMID:14755292

Axiom
annotated source: cross-linking study
annotated property: has_exact_synonym
annotated target: crosslink
has_synonym_type: Unique short label curated by PSI-MI

protein cross-linking with a bifunctional reagent
type: Class
subclass of: cross-linking study
definition: Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties.
has_exact_synonym: Label transfer techniques
has_exact_synonym: Photoaffinity labelling
has_exact_synonym: bifunctional agent crosslink
has_obo_namespace: PSI-MI
id: MI:0031
in_subset: PSI-MI slim

Axiom
annotated source: protein cross-linking with a bifunctional reagent
annotated property: definition
annotated target: Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties.
database_cross_reference: PMID:10679368
database_cross_reference: PMID:7708014

Axiom
annotated source: protein cross-linking with a bifunctional reagent
annotated property: has_exact_synonym
annotated target: Label transfer techniques
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein cross-linking with a bifunctional reagent
annotated property: has_exact_synonym
annotated target: Photoaffinity labelling
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein cross-linking with a bifunctional reagent
annotated property: has_exact_synonym
annotated target: bifunctional agent crosslink
has_synonym_type: Unique short label curated by PSI-MI

de novo protein sequencing by mass spectrometry
type: Class
subclass of: protein sequence identification
subclass of: Identification by mass spectrometry
subclass of: experimental feature detection
definition: The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments.
has_exact_synonym: de novo protein sequence
has_obo_namespace: PSI-MI
has_related_synonym: MS/MS
id: MI:0032
in_subset: PSI-MI slim

Axiom
annotated source: de novo protein sequencing by mass spectrometry
annotated property: definition
annotated target: The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments.
database_cross_reference: PMID:10984529

Axiom
annotated source: de novo protein sequencing by mass spectrometry
annotated property: has_exact_synonym
annotated target: de novo protein sequence
has_synonym_type: Unique short label curated by PSI-MI

deletion analysis
type: Class
subclass of: mutation analysis
definition: In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction.
has_obo_namespace: PSI-MI
id: MI:0033
in_subset: PSI-MI slim

Axiom
annotated source: deletion analysis
annotated property: definition
annotated target: In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction.
database_cross_reference: PMID:14755292

display technology
type: Class
subclass of: affinity technology
definition: All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules.
has_obo_namespace: PSI-MI
id: MI:0034
in_subset: PSI-MI slim

Axiom
annotated source: display technology
annotated property: definition
annotated target: All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules.
database_cross_reference: PMID:14755292

docking
type: Class
subclass of: structure based prediction
subclass of: feature prediction from structure
definition: Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions.
has_obo_namespace: PSI-MI
id: MI:0035
in_subset: PSI-MI slim

Axiom
annotated source: docking
annotated property: definition
annotated target: Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions.
database_cross_reference: PMID:11478868
database_cross_reference: PMID:9631301

domain fusion
type: Class
subclass of: genome based prediction
subclass of: sequence based prediction
definition: The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related.
has_exact_synonym: Rosetta Stone
has_obo_namespace: PSI-MI
id: MI:0036
in_subset: PSI-MI slim

Axiom
annotated source: domain fusion
annotated property: definition
annotated target: The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related.
database_cross_reference: PMID:10573422

Axiom
annotated source: domain fusion
annotated property: has_exact_synonym
annotated target: Rosetta Stone
has_synonym_type: Alternate label curated by PSI-MI

domain profile pairs
type: Class
subclass of: experimental knowledge based
subclass of: sequence based prediction
subclass of: feature prediction
definition: This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism.
has_obo_namespace: PSI-MI
id: MI:0037
in_subset: PSI-MI slim

Axiom
annotated source: domain profile pairs
annotated property: definition
annotated target: This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism.
database_cross_reference: PMID:11473021

dynamic light scattering
type: Class
subclass of: light scattering
definition: In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated.
has_exact_synonym: dls
has_obo_namespace: PSI-MI
id: MI:0038
in_subset: PSI-MI slim

Axiom
annotated source: dynamic light scattering
annotated property: definition
annotated target: In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated.
database_cross_reference: PMID:9013660

Axiom
annotated source: dynamic light scattering
annotated property: has_exact_synonym
annotated target: dls
has_synonym_type: Unique short label curated by PSI-MI

edman degradation
type: Class
subclass of: partial identification of protein sequence
definition: In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping.
has_obo_namespace: PSI-MI
id: MI:0039
in_subset: PSI-MI slim

Axiom
annotated source: edman degradation
annotated property: definition
annotated target: In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping.
database_cross_reference: PMID:14755292

electron microscopy
type: Class
subclass of: imaging technique
definition: Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data.
has_exact_synonym: Electron cryomicroscopy
has_exact_synonym: Electron crystallography
has_obo_namespace: PSI-MI
id: MI:0040
in_subset: PSI-MI slim

Axiom
annotated source: electron microscopy
annotated property: definition
annotated target: Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data.
database_cross_reference: PMID:11785754

Axiom
annotated source: electron microscopy
annotated property: has_exact_synonym
annotated target: Electron cryomicroscopy
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: electron microscopy
annotated property: has_exact_synonym
annotated target: Electron crystallography
has_synonym_type: Alternate label curated by PSI-MI

electron nuclear double resonance
type: Class
subclass of: electron resonance
definition: A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency.
has_exact_synonym: ENDOR
has_exact_synonym: endor
has_obo_namespace: PSI-MI
id: MI:0041
in_subset: PSI-MI slim

Axiom
annotated source: electron nuclear double resonance
annotated property: definition
annotated target: A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency.
database_cross_reference: PMID:11817959
database_cross_reference: PMID:11988476
database_cross_reference: PMID:12186859

Axiom
annotated source: electron nuclear double resonance
annotated property: has_exact_synonym
annotated target: ENDOR
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: electron nuclear double resonance
annotated property: has_exact_synonym
annotated target: endor
has_synonym_type: Unique short label curated by PSI-MI

electron paramagnetic resonance
type: Class
subclass of: electron resonance
definition: EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment.
has_exact_synonym: EPR
has_exact_synonym: ESR
has_exact_synonym: epr
has_obo_namespace: PSI-MI
id: MI:0042
in_subset: PSI-MI slim

Axiom
annotated source: electron paramagnetic resonance
annotated property: definition
annotated target: EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment.
database_cross_reference: PMID:11817959

Axiom
annotated source: electron paramagnetic resonance
annotated property: has_exact_synonym
annotated target: EPR
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: electron paramagnetic resonance
annotated property: has_exact_synonym
annotated target: ESR
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: electron paramagnetic resonance
annotated property: has_exact_synonym
annotated target: epr
has_synonym_type: Unique short label curated by PSI-MI

electron resonance
type: Class
subclass of: biophysical
subclass of: experimental feature detection
definition: A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons.
has_obo_namespace: PSI-MI
id: MI:0043
in_subset: PSI-MI slim

Axiom
annotated source: electron resonance
annotated property: definition
annotated target: A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons.
database_cross_reference: PMID:14755292

experimental interaction detection
type: Class
subclass of: interaction detection method
definition: Methods based on laboratory experiments to determine an interaction.
has_exact_synonym: experimental interac
has_obo_namespace: PSI-MI
id: MI:0045
in_subset: PSI-MI slim

Axiom
annotated source: experimental interaction detection
annotated property: has_exact_synonym
annotated target: experimental interac
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: experimental interaction detection
annotated property: definition
annotated target: Methods based on laboratory experiments to determine an interaction.
database_cross_reference: PMID:14755292

experimental knowledge based
type: Class
subclass of: interaction prediction
definition: Predictive algorithms that rely on the information obtained by experimental results.
has_exact_synonym: experimental info
has_obo_namespace: PSI-MI
id: MI:0046
in_subset: PSI-MI slim

Axiom
annotated source: experimental knowledge based
annotated property: definition
annotated target: Predictive algorithms that rely on the information obtained by experimental results.
database_cross_reference: PMID:14755292

Axiom
annotated source: experimental knowledge based
annotated property: has_exact_synonym
annotated target: experimental info
has_synonym_type: Unique short label curated by PSI-MI

far western blotting
type: Class
subclass of: solid phase assay
definition: Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody.
has_exact_synonym: Affinity blotting
has_obo_namespace: PSI-MI
id: MI:0047
in_subset: PSI-MI slim

Axiom
annotated source: far western blotting
annotated property: definition
annotated target: Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody.
database_cross_reference: PMID:7708014

Axiom
annotated source: far western blotting
annotated property: has_exact_synonym
annotated target: Affinity blotting
has_synonym_type: Alternate label curated by PSI-MI

filamentous phage display
type: Class
subclass of: phage display
definition: Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII.
has_exact_synonym: filamentous phage
has_obo_namespace: PSI-MI
id: MI:0048
in_subset: PSI-MI slim

Axiom
annotated source: filamentous phage display
annotated property: definition
annotated target: Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII.
database_cross_reference: PMID:7682645

Axiom
annotated source: filamentous phage display
annotated property: has_exact_synonym
annotated target: filamentous phage
has_synonym_type: Unique short label curated by PSI-MI

filter binding
type: Class
subclass of: solid phase assay
definition: A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody.
has_exact_synonym: Filter overlay assay
has_obo_namespace: PSI-MI
has_related_synonym: dot blot
id: MI:0049
in_subset: PSI-MI slim

Axiom
annotated source: filter binding
annotated property: definition
annotated target: A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody.
database_cross_reference: PMID:7708014

Axiom
annotated source: filter binding
annotated property: has_exact_synonym
annotated target: Filter overlay assay
has_synonym_type: Alternate label curated by PSI-MI

flag tag coimmunoprecipitation
type: Class
definition: The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
has_exact_synonym: flag tag coip
has_obo_namespace: PSI-MI
id: MI:0050
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: flag tag coimmunoprecipitation
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
database_cross_reference: PMID:14755292

Axiom
annotated source: flag tag coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: flag tag coip
has_synonym_type: Unique short label curated by PSI-MI

fluorescence technology
type: Class
subclass of: biophysical
definition: Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds.
has_exact_synonym: fluorescence
has_obo_namespace: PSI-MI
id: MI:0051
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence technology
annotated property: definition
annotated target: Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds.
database_cross_reference: PMID:14755292

Axiom
annotated source: fluorescence technology
annotated property: has_exact_synonym
annotated target: fluorescence
has_synonym_type: Unique short label curated by PSI-MI

fluorescence correlation spectroscopy
type: Class
subclass of: fluorescence technology
definition: FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant.
has_exact_synonym: FCS
has_exact_synonym: fcs
has_obo_namespace: PSI-MI
has_related_synonym: fluctuation correlation specctrometry
id: MI:0052
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence correlation spectroscopy
annotated property: definition
annotated target: FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant.
database_cross_reference: PMID:10733953

Axiom
annotated source: fluorescence correlation spectroscopy
annotated property: has_exact_synonym
annotated target: FCS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescence correlation spectroscopy
annotated property: has_exact_synonym
annotated target: fcs
has_synonym_type: Unique short label curated by PSI-MI

fluorescence polarization spectroscopy
type: Class
subclass of: fluorescence technology
definition: Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled.
has_exact_synonym: FPS
has_exact_synonym: Fluorescence anisotropy
has_exact_synonym: fps
has_obo_namespace: PSI-MI
id: MI:0053
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence polarization spectroscopy
annotated property: definition
annotated target: Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled.
database_cross_reference: PMID:12805227
database_cross_reference: PMID:7708014

Axiom
annotated source: fluorescence polarization spectroscopy
annotated property: has_exact_synonym
annotated target: FPS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescence polarization spectroscopy
annotated property: has_exact_synonym
annotated target: Fluorescence anisotropy
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescence polarization spectroscopy
annotated property: has_exact_synonym
annotated target: fps
has_synonym_type: Unique short label curated by PSI-MI

fluorescence-activated cell sorting
type: Class
subclass of: fluorescence technology
definition: Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels.
has_exact_synonym: FACS
has_exact_synonym: Flow cytometry
has_exact_synonym: facs
has_obo_namespace: PSI-MI
id: MI:0054
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence-activated cell sorting
annotated property: definition
annotated target: Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels.
database_cross_reference: PMID:11988464

Axiom
annotated source: fluorescence-activated cell sorting
annotated property: has_exact_synonym
annotated target: FACS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescence-activated cell sorting
annotated property: has_exact_synonym
annotated target: Flow cytometry
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescence-activated cell sorting
annotated property: has_exact_synonym
annotated target: facs
has_synonym_type: Unique short label curated by PSI-MI

fluorescent resonance energy transfer
type: Class
subclass of: fluorescence technology
definition: FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations.
has_exact_synonym: FRET
has_exact_synonym: FRET analysis
has_exact_synonym: RET
has_exact_synonym: fret
has_obo_namespace: PSI-MI
id: MI:0055
in_subset: PSI-MI slim

Axiom
annotated source: fluorescent resonance energy transfer
annotated property: definition
annotated target: FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations.
database_cross_reference: PMID:11558993

Axiom
annotated source: fluorescent resonance energy transfer
annotated property: has_exact_synonym
annotated target: FRET
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescent resonance energy transfer
annotated property: has_exact_synonym
annotated target: FRET analysis
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescent resonance energy transfer
annotated property: has_exact_synonym
annotated target: RET
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescent resonance energy transfer
annotated property: has_exact_synonym
annotated target: fret
has_synonym_type: Unique short label curated by PSI-MI

full identification by DNA sequencing
type: Class
subclass of: nucleotide sequence identification
subclass of: experimental feature detection
definition: Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data.
has_exact_synonym: full dna sequence
has_obo_namespace: PSI-MI
id: MI:0056
in_subset: PSI-MI slim

Axiom
annotated source: full identification by DNA sequencing
annotated property: definition
annotated target: Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data.
database_cross_reference: PMID:14755292

Axiom
annotated source: full identification by DNA sequencing
annotated property: has_exact_synonym
annotated target: full dna sequence
has_synonym_type: Unique short label curated by PSI-MI

gene neighbourhood
type: Class
subclass of: genome based prediction
definition: Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred.
has_obo_namespace: PSI-MI
id: MI:0057
in_subset: PSI-MI slim

Axiom
annotated source: gene neighbourhood
annotated property: definition
annotated target: Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred.
database_cross_reference: PMID:9787636

genome based prediction
type: Class
subclass of: interaction prediction
definition: Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes.
has_exact_synonym: genome prediction
has_obo_namespace: PSI-MI
id: MI:0058
in_subset: PSI-MI slim

Axiom
annotated source: genome based prediction
annotated property: definition
annotated target: Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes.
database_cross_reference: PMID:14755292

Axiom
annotated source: genome based prediction
annotated property: has_exact_synonym
annotated target: genome prediction
has_synonym_type: Unique short label curated by PSI-MI

gst pull down
type: Class
definition: The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody. OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).
has_obo_namespace: PSI-MI
id: MI:0059
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: gst pull down
annotated property: definition
annotated target: The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody. OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).
database_cross_reference: PMID:14755292

ha tag coimmunoprecipitation
type: Class
definition: The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available. OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
has_exact_synonym: ha tag coip
has_obo_namespace: PSI-MI
id: MI:0060
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: ha tag coimmunoprecipitation
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available. OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
database_cross_reference: PMID:14755292

Axiom
annotated source: ha tag coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: ha tag coip
has_synonym_type: Unique short label curated by PSI-MI

his pull down
type: Class
definition: The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin. OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).
has_obo_namespace: PSI-MI
id: MI:0061
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: his pull down
annotated property: definition
annotated target: The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin. OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).
database_cross_reference: PMID:14755292

his tag coimmunoprecipitation
type: Class
definition: The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
has_exact_synonym: his tag coip
has_obo_namespace: PSI-MI
id: MI:0062
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: his tag coimmunoprecipitation
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
database_cross_reference: PMID:14755292

Axiom
annotated source: his tag coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: his tag coip
has_synonym_type: Unique short label curated by PSI-MI

interaction prediction
type: Class
subclass of: interaction detection method
definition: Computational methods to predict an interaction.
has_exact_synonym: in silico methods
has_exact_synonym: predicted interac
has_obo_namespace: PSI-MI
id: MI:0063
in_subset: PSI-MI slim

Axiom
annotated source: interaction prediction
annotated property: definition
annotated target: Computational methods to predict an interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: interaction prediction
annotated property: has_exact_synonym
annotated target: in silico methods
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: interaction prediction
annotated property: has_exact_synonym
annotated target: predicted interac
has_synonym_type: Unique short label curated by PSI-MI

interologs mapping
type: Class
subclass of: experimental knowledge based
subclass of: sequence based prediction
definition: Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties.
has_exact_synonym: Homology based interaction prediction
has_obo_namespace: PSI-MI
id: MI:0064
in_subset: PSI-MI slim

Axiom
annotated source: interologs mapping
annotated property: definition
annotated target: Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties.
database_cross_reference: PMID:11731503

Axiom
annotated source: interologs mapping
annotated property: has_exact_synonym
annotated target: Homology based interaction prediction
has_synonym_type: Alternate label curated by PSI-MI

isothermal titration calorimetry
type: Class
subclass of: biophysical
definition: Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS.
has_exact_synonym: ITC
has_exact_synonym: itc
has_obo_namespace: PSI-MI
id: MI:0065
in_subset: PSI-MI slim

Axiom
annotated source: isothermal titration calorimetry
annotated property: definition
annotated target: Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS.
database_cross_reference: PMID:11785756

Axiom
annotated source: isothermal titration calorimetry
annotated property: has_exact_synonym
annotated target: ITC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: isothermal titration calorimetry
annotated property: has_exact_synonym
annotated target: itc
has_synonym_type: Unique short label curated by PSI-MI

lambda phage display
type: Class
subclass of: phage display
definition: Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid.
has_exact_synonym: lambda phage
has_obo_namespace: PSI-MI
id: MI:0066
in_subset: PSI-MI slim

Axiom
annotated source: lambda phage display
annotated property: definition
annotated target: Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid.
database_cross_reference: PMID:7682645

Axiom
annotated source: lambda phage display
annotated property: has_exact_synonym
annotated target: lambda phage
has_synonym_type: Unique short label curated by PSI-MI

light scattering
type: Class
subclass of: biophysical
definition: Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam.
has_obo_namespace: PSI-MI
id: MI:0067
in_subset: PSI-MI slim

Axiom
annotated source: light scattering
annotated property: definition
annotated target: Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam.
database_cross_reference: PMID:9013660

mass detection of residue modification
type: Class
subclass of: experimental feature detection
definition: Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies.
has_exact_synonym: modified residue ms
has_obo_namespace: PSI-MI
id: MI:0068
in_subset: PSI-MI slim

Axiom
annotated source: mass detection of residue modification
annotated property: definition
annotated target: Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies.
database_cross_reference: PMID:11395414
database_cross_reference: PMID:11875433

Axiom
annotated source: mass detection of residue modification
annotated property: has_exact_synonym
annotated target: modified residue ms
has_synonym_type: Unique short label curated by PSI-MI

mass spectrometry studies of complexes
type: Class
subclass of: detection by mass spectrometry
definition: Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation.
has_exact_synonym: ms of complexes
has_obo_namespace: PSI-MI
id: MI:0069
in_subset: PSI-MI slim

Axiom
annotated source: mass spectrometry studies of complexes
annotated property: definition
annotated target: Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation.
database_cross_reference: PMID:12057199
database_cross_reference: PMID:12504676

Axiom
annotated source: mass spectrometry studies of complexes
annotated property: has_exact_synonym
annotated target: ms of complexes
has_synonym_type: Unique short label curated by PSI-MI

mobility shift
type: Class
subclass of: experimental feature detection
definition: Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification.
has_obo_namespace: PSI-MI
id: MI:0070
in_subset: PSI-MI slim

Axiom
annotated source: mobility shift
annotated property: definition
annotated target: Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification.
database_cross_reference: PMID:14755292

molecular sieving
type: Class
subclass of: biophysical
subclass of: chromatography technology
definition: In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction.
has_exact_synonym: Gel Filtration
has_exact_synonym: Size Exclusion Chromatography
has_exact_synonym: Sizing column
has_obo_namespace: PSI-MI
id: MI:0071
in_subset: PSI-MI slim

Axiom
annotated source: molecular sieving
annotated property: definition
annotated target: In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction.
database_cross_reference: PMID:7708014

Axiom
annotated source: molecular sieving
annotated property: has_exact_synonym
annotated target: Gel Filtration
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: molecular sieving
annotated property: has_exact_synonym
annotated target: Size Exclusion Chromatography
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: molecular sieving
annotated property: has_exact_synonym
annotated target: Sizing column
has_synonym_type: Alternate label curated by PSI-MI

monoclonal antibody western blot
type: Class
subclass of: western blot
definition: Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology.
has_exact_synonym: monoclonal western
has_obo_namespace: PSI-MI
id: MI:0072
in_subset: PSI-MI slim

Axiom
annotated source: monoclonal antibody western blot
annotated property: definition
annotated target: Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology.
database_cross_reference: PMID:14755292

Axiom
annotated source: monoclonal antibody western blot
annotated property: has_exact_synonym
annotated target: monoclonal western
has_synonym_type: Unique short label curated by PSI-MI

mrna display
type: Class
subclass of: display technology
definition: This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins.
has_obo_namespace: PSI-MI
id: MI:0073
in_subset: PSI-MI slim

Axiom
annotated source: mrna display
annotated property: definition
annotated target: This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins.
database_cross_reference: PMID:11551470

mutation analysis
type: Class
subclass of: experimental feature detection
definition: Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding.
has_obo_namespace: PSI-MI
id: MI:0074
in_subset: PSI-MI slim

Axiom
annotated source: mutation analysis
annotated property: definition
annotated target: Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding.
database_cross_reference: PMID:14755292

myc tag coimmunoprecipitation
type: Class
definition: The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
has_exact_synonym: myc tag coip
has_obo_namespace: PSI-MI
id: MI:0075
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: myc tag coimmunoprecipitation
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
database_cross_reference: PMID:14755292

Axiom
annotated source: myc tag coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: myc tag coip
has_synonym_type: Unique short label curated by PSI-MI

neural network on interface properties
type: Class
subclass of: feature prediction from structure
definition: Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface.
has_exact_synonym: interface predictor
has_obo_namespace: PSI-MI
id: MI:0076
in_subset: PSI-MI slim

Axiom
annotated source: neural network on interface properties
annotated property: definition
annotated target: Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface.
database_cross_reference: PMID:11455607
database_cross_reference: PMID:11874449

Axiom
annotated source: neural network on interface properties
annotated property: has_exact_synonym
annotated target: interface predictor
has_synonym_type: Unique short label curated by PSI-MI

nuclear magnetic resonance
type: Class
subclass of: biophysical
subclass of: experimental feature detection
definition: Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.
has_exact_synonym: NMR
has_exact_synonym: nmr
has_obo_namespace: PSI-MI
id: MI:0077
in_subset: PSI-MI slim

Axiom
annotated source: nuclear magnetic resonance
annotated property: definition
annotated target: Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.
database_cross_reference: PMID:12062432
database_cross_reference: PMID:12120505

Axiom
annotated source: nuclear magnetic resonance
annotated property: has_exact_synonym
annotated target: NMR
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: nuclear magnetic resonance
annotated property: has_exact_synonym
annotated target: nmr
has_synonym_type: Unique short label curated by PSI-MI

nucleotide sequence identification
type: Class
subclass of: experimental feature detection
subclass of: experimental participant identification
definition: Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
has_exact_synonym: nucleotide sequence
has_exact_synonym: sequence cloning
has_obo_namespace: PSI-MI
id: MI:0078
in_subset: PSI-MI slim

Axiom
annotated source: nucleotide sequence identification
annotated property: definition
annotated target: Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleotide sequence identification
annotated property: has_exact_synonym
annotated target: nucleotide sequence
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: nucleotide sequence identification
annotated property: has_exact_synonym
annotated target: sequence cloning
has_synonym_type: Alternate label curated by PSI-MI

other biochemical technologies
type: Class
definition: Experimental methods that could not be assigned to the other large group of technologies. OBSOLETE use biochemical (MI:0401) instead.
has_exact_synonym: other biochemic tech
has_obo_namespace: PSI-MI
id: MI:0079
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: other biochemical technologies
annotated property: definition
annotated target: Experimental methods that could not be assigned to the other large group of technologies. OBSOLETE use biochemical (MI:0401) instead.
database_cross_reference: PMID:14755292

Axiom
annotated source: other biochemical technologies
annotated property: has_exact_synonym
annotated target: other biochemic tech
has_synonym_type: Unique short label curated by PSI-MI

partial DNA sequence identification by hybridization
type: Class
subclass of: partial DNA sequence identification
definition: Genes are recognised by hybridization of a probe with a fragment of the gene sequence.
has_exact_synonym: partial dna sequence hybrid
has_obo_namespace: PSI-MI
id: MI:0080
in_subset: PSI-MI slim

Axiom
annotated source: partial DNA sequence identification by hybridization
annotated property: definition
annotated target: Genes are recognised by hybridization of a probe with a fragment of the gene sequence.
database_cross_reference: PMID:14755292

Axiom
annotated source: partial DNA sequence identification by hybridization
annotated property: has_exact_synonym
annotated target: partial dna sequence hybrid
has_synonym_type: Unique short label curated by PSI-MI

peptide array
type: Class
subclass of: array technology
definition: The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support.
has_obo_namespace: PSI-MI
id: MI:0081
in_subset: PSI-MI slim

Axiom
annotated source: peptide array
annotated property: definition
annotated target: The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support.
database_cross_reference: PMID:11167074

peptide massfingerprinting
type: Class
subclass of: Identification by mass spectrometry
subclass of: partial identification of protein sequence
definition: This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer.
has_exact_synonym: fingerprinting
has_obo_namespace: PSI-MI
id: MI:0082
in_subset: PSI-MI slim

Axiom
annotated source: peptide massfingerprinting
annotated property: definition
annotated target: This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer.
database_cross_reference: PMID:10967324
database_cross_reference: PMID:11752590
database_cross_reference: PMID:11805826

Axiom
annotated source: peptide massfingerprinting
annotated property: has_exact_synonym
annotated target: fingerprinting
has_synonym_type: Unique short label curated by PSI-MI

peptide synthesis
type: Class
subclass of: protein sequence identification
definition: When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs.
has_obo_namespace: PSI-MI
id: MI:0083
in_subset: PSI-MI slim

Axiom
annotated source: peptide synthesis
annotated property: definition
annotated target: When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs.
database_cross_reference: PMID:14755292

phage display
type: Class
subclass of: display technology
definition: Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7).
has_obo_namespace: PSI-MI
id: MI:0084
in_subset: PSI-MI slim

Axiom
annotated source: phage display
annotated property: definition
annotated target: Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7).
database_cross_reference: PMID:10975452
database_cross_reference: PMID:7708014

phylogenetic profile
type: Class
subclass of: genome based prediction
definition: The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified.
has_obo_namespace: PSI-MI
id: MI:0085
in_subset: PSI-MI slim

Axiom
annotated source: phylogenetic profile
annotated property: definition
annotated target: The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified.
database_cross_reference: PMID:10200254

polyclonal antibody western blot
type: Class
subclass of: western blot
definition: Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest.
has_exact_synonym: polyclonal western
has_obo_namespace: PSI-MI
id: MI:0086
in_subset: PSI-MI slim

Axiom
annotated source: polyclonal antibody western blot
annotated property: definition
annotated target: Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest.
database_cross_reference: PMID:14755292

Axiom
annotated source: polyclonal antibody western blot
annotated property: has_exact_synonym
annotated target: polyclonal western
has_synonym_type: Unique short label curated by PSI-MI

predictive text mining
type: Class
subclass of: text mining
definition: Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them.
has_exact_synonym: predictive tm
has_obo_namespace: PSI-MI
id: MI:0087
in_subset: PSI-MI slim

Axiom
annotated source: predictive text mining
annotated property: definition
annotated target: Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them.
database_cross_reference: PMID:11791231

Axiom
annotated source: predictive text mining
annotated property: has_exact_synonym
annotated target: predictive tm
has_synonym_type: Unique short label curated by PSI-MI

primer specific pcr
type: Class
subclass of: partial DNA sequence identification by hybridization
definition: Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs.
has_obo_namespace: PSI-MI
id: MI:0088
in_subset: PSI-MI slim

Axiom
annotated source: primer specific pcr
annotated property: definition
annotated target: Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs.
database_cross_reference: PMID:14755292

protein array
type: Class
subclass of: array technology
definition: The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait.
has_obo_namespace: PSI-MI
id: MI:0089
in_subset: PSI-MI slim

Axiom
annotated source: protein array
annotated property: definition
annotated target: The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait.
database_cross_reference: PMID:10976071
database_cross_reference: PMID:12067604

protein complementation assay
type: Class
subclass of: experimental interaction detection
definition: In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
has_exact_synonym: PCA
has_exact_synonym: complementation
has_obo_namespace: PSI-MI
id: MI:0090
in_subset: PSI-MI slim

Axiom
annotated source: protein complementation assay
annotated property: definition
annotated target: In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
database_cross_reference: PMID:11495741

Axiom
annotated source: protein complementation assay
annotated property: has_exact_synonym
annotated target: PCA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein complementation assay
annotated property: has_exact_synonym
annotated target: complementation
has_synonym_type: Unique short label curated by PSI-MI

chromatography technology
type: Class
subclass of: biochemical
definition: Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC).
has_exact_synonym: chromatography
has_exact_synonym: column chromatography
has_obo_namespace: PSI-MI
id: MI:0091
in_subset: PSI-MI slim

Axiom
annotated source: chromatography technology
annotated property: definition
annotated target: Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC).
database_cross_reference: PMID:14755292

Axiom
annotated source: chromatography technology
annotated property: has_exact_synonym
annotated target: chromatography
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: chromatography technology
annotated property: has_exact_synonym
annotated target: column chromatography
has_synonym_type: Alternate label curated by PSI-MI

protein in situ array
type: Class
subclass of: protein array
definition: Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised.
has_exact_synonym: PISA
has_exact_synonym: pisa
has_obo_namespace: PSI-MI
id: MI:0092
in_subset: PSI-MI slim

Axiom
annotated source: protein in situ array
annotated property: definition
annotated target: Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised.
database_cross_reference: PMID:11470888

Axiom
annotated source: protein in situ array
annotated property: has_exact_synonym
annotated target: PISA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein in situ array
annotated property: has_exact_synonym
annotated target: pisa
has_synonym_type: Unique short label curated by PSI-MI

protein sequence identification
type: Class
subclass of: experimental participant identification
definition: Single amino acid identification along a protein sequence.
has_exact_synonym: protein sequence
has_obo_namespace: PSI-MI
id: MI:0093
in_subset: PSI-MI slim

Axiom
annotated source: protein sequence identification
annotated property: definition
annotated target: Single amino acid identification along a protein sequence.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein sequence identification
annotated property: has_exact_synonym
annotated target: protein sequence
has_synonym_type: Unique short label curated by PSI-MI

protein staining
type: Class
subclass of: experimental feature detection
definition: A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation.
has_obo_namespace: PSI-MI
id: MI:0094
in_subset: PSI-MI slim

Axiom
annotated source: protein staining
annotated property: definition
annotated target: A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation.
database_cross_reference: PMID:12015990

proteinchip(r) on a surface-enhanced laser desorption/ionization
type: Class
subclass of: protein array
definition: ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry.
has_exact_synonym: SELDI ProteinChip
has_exact_synonym: seldi chip
has_obo_namespace: PSI-MI
id: MI:0095
in_subset: PSI-MI slim

Axiom
annotated source: proteinchip(r) on a surface-enhanced laser desorption/ionization
annotated property: definition
annotated target: ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry.
database_cross_reference: PMID:11827829

Axiom
annotated source: proteinchip(r) on a surface-enhanced laser desorption/ionization
annotated property: has_exact_synonym
annotated target: SELDI ProteinChip
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: proteinchip(r) on a surface-enhanced laser desorption/ionization
annotated property: has_exact_synonym
annotated target: seldi chip
has_synonym_type: Unique short label curated by PSI-MI

pull down
type: Class
subclass of: affinity chromatography technology
definition: A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified.
has_obo_namespace: PSI-MI
has_related_synonym: affinity capture
has_related_synonym: pulldown
id: MI:0096
in_subset: PSI-MI slim

Axiom
annotated source: pull down
annotated property: definition
annotated target: A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified.
database_cross_reference: PMID:14755292

reverse ras recruitment system
type: Class
subclass of: protein complementation assay
definition: In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation.
has_exact_synonym: reverse RRS
has_exact_synonym: reverse rrs
has_obo_namespace: PSI-MI
id: MI:0097
in_subset: PSI-MI slim

Axiom
annotated source: reverse ras recruitment system
annotated property: definition
annotated target: In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation.
database_cross_reference: PMID:11160938

Axiom
annotated source: reverse ras recruitment system
annotated property: has_exact_synonym
annotated target: reverse RRS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: reverse ras recruitment system
annotated property: has_exact_synonym
annotated target: reverse rrs
has_synonym_type: Unique short label curated by PSI-MI

ribosome display
type: Class
subclass of: display technology
definition: This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties.
has_obo_namespace: PSI-MI
id: MI:0098
in_subset: PSI-MI slim

Axiom
annotated source: ribosome display
annotated property: definition
annotated target: This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties.
database_cross_reference: PMID:11551470
database_cross_reference: PMID:12167034

scintillation proximity assay
type: Class
subclass of: biophysical
definition: SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present.
has_exact_synonym: RIA Radio Immuno Assay
has_exact_synonym: SPA
has_exact_synonym: spa
has_obo_namespace: PSI-MI
id: MI:0099
in_subset: PSI-MI slim

Axiom
annotated source: scintillation proximity assay
annotated property: definition
annotated target: SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present.
database_cross_reference: PMID:3866247

Axiom
annotated source: scintillation proximity assay
annotated property: has_exact_synonym
annotated target: RIA Radio Immuno Assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: scintillation proximity assay
annotated property: has_exact_synonym
annotated target: SPA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: scintillation proximity assay
annotated property: has_exact_synonym
annotated target: spa
has_synonym_type: Unique short label curated by PSI-MI

sequence based phylogenetic profile
type: Class
subclass of: genome based prediction
subclass of: sequence based prediction
definition: Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs.
has_exact_synonym: sequence phylogeny
has_obo_namespace: PSI-MI
id: MI:0100
in_subset: PSI-MI slim

Axiom
annotated source: sequence based phylogenetic profile
annotated property: definition
annotated target: Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs.
database_cross_reference: PMID:11707606

Axiom
annotated source: sequence based phylogenetic profile
annotated property: has_exact_synonym
annotated target: sequence phylogeny
has_synonym_type: Unique short label curated by PSI-MI

sequence based prediction
type: Class
subclass of: interaction prediction
definition: Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs.
has_exact_synonym: predict from sequenc
has_obo_namespace: PSI-MI
id: MI:0101
in_subset: PSI-MI slim

Axiom
annotated source: sequence based prediction
annotated property: definition
annotated target: Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs.
database_cross_reference: PMID:14755292

Axiom
annotated source: sequence based prediction
annotated property: has_exact_synonym
annotated target: predict from sequenc
has_synonym_type: Unique short label curated by PSI-MI

sequence tag identification
type: Class
subclass of: Identification by mass spectrometry
subclass of: partial identification of protein sequence
definition: This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases.
has_exact_synonym: sequence tag
has_obo_namespace: PSI-MI
has_related_synonym: MS/MS
id: MI:0102
in_subset: PSI-MI slim

Axiom
annotated source: sequence tag identification
annotated property: definition
annotated target: This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases.
database_cross_reference: PMID:10967324
database_cross_reference: PMID:11752590
database_cross_reference: PMID:11805837

Axiom
annotated source: sequence tag identification
annotated property: has_exact_synonym
annotated target: sequence tag
has_synonym_type: Unique short label curated by PSI-MI

southern blot
type: Class
subclass of: partial DNA sequence identification by hybridization
definition: A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
has_obo_namespace: PSI-MI
id: MI:0103
in_subset: PSI-MI slim

Axiom
annotated source: southern blot
annotated property: definition
annotated target: A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
database_cross_reference: PMID:14755292

static light scattering
type: Class
subclass of: light scattering
definition: In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions.
has_exact_synonym: sls
has_obo_namespace: PSI-MI
id: MI:0104
in_subset: PSI-MI slim

Axiom
annotated source: static light scattering
annotated property: definition
annotated target: In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions.
database_cross_reference: PMID:9013660

Axiom
annotated source: static light scattering
annotated property: has_exact_synonym
annotated target: sls
has_synonym_type: Unique short label curated by PSI-MI

structure based prediction
type: Class
subclass of: interaction prediction
definition: Methods based on 3D structure information.
has_exact_synonym: predict from struct
has_obo_namespace: PSI-MI
id: MI:0105
in_subset: PSI-MI slim

Axiom
annotated source: structure based prediction
annotated property: definition
annotated target: Methods based on 3D structure information.
database_cross_reference: PMID:14755292

Axiom
annotated source: structure based prediction
annotated property: has_exact_synonym
annotated target: predict from struct
has_synonym_type: Unique short label curated by PSI-MI

surface patches
type: Class
subclass of: feature prediction from structure
definition: Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions.
has_obo_namespace: PSI-MI
id: MI:0106
in_subset: PSI-MI slim

Axiom
annotated source: surface patches
annotated property: definition
annotated target: Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions.
database_cross_reference: PMID:9299343

surface plasmon resonance
type: Class
subclass of: experimental feature detection
subclass of: biosensor
definition: This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation.
has_exact_synonym: BIAcore(r)
has_exact_synonym: Optical biosensor
has_exact_synonym: spr
has_obo_namespace: PSI-MI
id: MI:0107
in_subset: PSI-MI slim

Axiom
annotated source: surface plasmon resonance
annotated property: definition
annotated target: This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation.
database_cross_reference: PMID:11896282
database_cross_reference: PMID:12120258
database_cross_reference: PMID:16338355

Axiom
annotated source: surface plasmon resonance
annotated property: has_exact_synonym
annotated target: BIAcore(r)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: surface plasmon resonance
annotated property: has_exact_synonym
annotated target: Optical biosensor
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: surface plasmon resonance
annotated property: has_exact_synonym
annotated target: spr
has_synonym_type: Unique short label curated by PSI-MI

t7 phage display
type: Class
subclass of: phage display
definition: T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved.
has_exact_synonym: t7 phage
has_obo_namespace: PSI-MI
id: MI:0108
in_subset: PSI-MI slim
comment: Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1.

Axiom
annotated source: t7 phage display
annotated property: definition
annotated target: T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved.
database_cross_reference: PMID:14755292

Axiom
annotated source: t7 phage display
annotated property: has_exact_synonym
annotated target: t7 phage
has_synonym_type: Unique short label curated by PSI-MI

tap tag coimmunoprecipitation
type: Class
definition: The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676).
has_exact_synonym: tap tag coip
has_obo_namespace: PSI-MI
id: MI:0109
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: tap tag coimmunoprecipitation
annotated property: definition
annotated target: The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676).
database_cross_reference: PMID:10504710

Axiom
annotated source: tap tag coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: tap tag coip
has_synonym_type: Unique short label curated by PSI-MI

text mining
type: Class
subclass of: experimental knowledge based
definition: Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction.
has_obo_namespace: PSI-MI
id: MI:0110
in_subset: PSI-MI slim

Axiom
annotated source: text mining
annotated property: definition
annotated target: Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction.
database_cross_reference: PMID:14755292

dihydrofolate reductase reconstruction
type: Class
subclass of: protein complementation assay
definition: The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled.
has_exact_synonym: dhfr reconstruction
has_obo_namespace: PSI-MI
id: MI:0111
in_subset: PSI-MI slim

Axiom
annotated source: dihydrofolate reductase reconstruction
annotated property: definition
annotated target: The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled.
database_cross_reference: PMID:10318894

Axiom
annotated source: dihydrofolate reductase reconstruction
annotated property: has_exact_synonym
annotated target: dhfr reconstruction
has_synonym_type: Unique short label curated by PSI-MI

ubiquitin reconstruction
type: Class
subclass of: MI 2412
definition: The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
has_exact_synonym: ub reconstruction
has_obo_namespace: PSI-MI
has_related_synonym: membrane yeast two-hybrid
has_related_synonym: myth
has_related_synonym: split-ubiquitin
id: MI:0112
in_subset: PSI-MI slim

Axiom
annotated source: ubiquitin reconstruction
annotated property: definition
annotated target: The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
database_cross_reference: PMID:9560251

Axiom
annotated source: ubiquitin reconstruction
annotated property: has_exact_synonym
annotated target: ub reconstruction
has_synonym_type: Unique short label curated by PSI-MI

western blot
type: Class
subclass of: identification by antibody
subclass of: experimental feature detection
definition: Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane.
has_exact_synonym: Immuno blot
has_obo_namespace: PSI-MI
id: MI:0113
in_subset: PSI-MI slim

Axiom
annotated source: western blot
annotated property: definition
annotated target: Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane.
database_cross_reference: PMID:14755292

Axiom
annotated source: western blot
annotated property: has_exact_synonym
annotated target: Immuno blot
has_synonym_type: Alternate label curated by PSI-MI

x-ray crystallography
type: Class
subclass of: biophysical
subclass of: experimental feature detection
definition: Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions.
has_exact_synonym: X-ray
has_exact_synonym: x-ray diffraction
has_obo_namespace: PSI-MI
has_related_synonym: co-crystallization
has_related_synonym: co-crystallography
id: MI:0114
in_subset: PSI-MI slim

Axiom
annotated source: x-ray crystallography
annotated property: definition
annotated target: Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions.
database_cross_reference: PMID:14755292

Axiom
annotated source: x-ray crystallography
annotated property: has_exact_synonym
annotated target: X-ray
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: x-ray crystallography
annotated property: has_exact_synonym
annotated target: x-ray diffraction
has_synonym_type: Unique short label curated by PSI-MI

yeast display
type: Class
subclass of: display technology
subclass of: fluorescence-activated cell sorting
definition: The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties.
has_obo_namespace: PSI-MI
id: MI:0115
in_subset: PSI-MI slim

Axiom
annotated source: yeast display
annotated property: definition
annotated target: The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties.
database_cross_reference: PMID:9181578

feature type
type: Class
subclass of: molecular interaction
definition: Property of a subsequence that may interfere with the binding of a molecule.
has_obo_namespace: PSI-MI
id: MI:0116
in_subset: PSI-MI slim

Axiom
annotated source: feature type
annotated property: definition
annotated target: Property of a subsequence that may interfere with the binding of a molecule.
database_cross_reference: PMID:14755292

binding-associated region
type: Class
subclass of: biological feature
definition: A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner.
has_broad_synonym: binding site
has_exact_synonym: binding region
has_obo_namespace: PSI-MI
has_related_synonym: binding component
id: MI:0117
in_subset: PSI-MI slim

Axiom
annotated source: binding-associated region
annotated property: definition
annotated target: A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner.
database_cross_reference: PMID:14755292

Axiom
annotated source: binding-associated region
annotated property: has_exact_synonym
annotated target: binding region
has_synonym_type: Unique short label curated by PSI-MI

mutation
type: Class
subclass of: biological feature
definition: A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event.
has_obo_namespace: PSI-MI
id: MI:0118
in_subset: PSI-MI slim

Axiom
annotated source: mutation
annotated property: definition
annotated target: A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event.
database_cross_reference: PMID:14755292

mutation decreasing interaction
type: Class
subclass of: mutation
definition: Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
has_exact_synonym: hotspot
has_exact_synonym: mutation decreasing
has_obo_namespace: PSI-MI
id: MI:0119
in_subset: PSI-MI slim

Axiom
annotated source: mutation decreasing interaction
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
database_cross_reference: PMID:14755292

Axiom
annotated source: mutation decreasing interaction
annotated property: has_exact_synonym
annotated target: hotspot
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: mutation decreasing interaction
annotated property: has_exact_synonym
annotated target: mutation decreasing
has_synonym_type: Unique short label curated by PSI-MI

post translation modification
type: Class
definition: Residue covalent modifications occurring in the specific protein form involved in an interaction. OBSOLETE remap to MOD:00000.
has_exact_synonym: ptm
has_obo_namespace: PSI-MI
id: MI:0120
deprecated: true

Axiom
annotated source: post translation modification
annotated property: definition
annotated target: Residue covalent modifications occurring in the specific protein form involved in an interaction. OBSOLETE remap to MOD:00000.
database_cross_reference: PMID:14755292

Axiom
annotated source: post translation modification
annotated property: has_exact_synonym
annotated target: ptm
has_synonym_type: Unique short label curated by PSI-MI

acetylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00394.
has_obo_namespace: PSI-MI
id: MI:0121
deprecated: true

Axiom
annotated source: acetylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00394.
database_cross_reference: PMID:11125103

n-acetyl-alanine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00050.
has_exact_synonym: (S)-2-(acetylamino)propanoic acid
has_exact_synonym: AAC
has_exact_synonym: N-acetyl-L-alanine
has_exact_synonym: [A:ac]
has_exact_synonym: acetylalanine
has_obo_namespace: PSI-MI
id: MI:0122
deprecated: true

Axiom
annotated source: n-acetyl-alanine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00050.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0041

Axiom
annotated source: n-acetyl-alanine
annotated property: has_exact_synonym
annotated target: (S)-2-(acetylamino)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-alanine
annotated property: has_exact_synonym
annotated target: AAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-alanine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-alanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-alanine
annotated property: has_exact_synonym
annotated target: [A:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-alanine
annotated property: has_exact_synonym
annotated target: acetylalanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-alanine
annotated property: has_exact_synonym
annotated target: acetylalanine
has_synonym_type: Unique short label curated by PSI-MI

n2-acetyl-arginine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00359.
has_exact_synonym: N2-acetyl-L-arginine
has_exact_synonym: RAC
has_exact_synonym: [R:ac]
has_exact_synonym: acetylarginine
has_exact_synonym: alpha-acetylamino-delta-guanidinovaleric acid
has_obo_namespace: PSI-MI
id: MI:0123
deprecated: true

Axiom
annotated source: n2-acetyl-arginine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00359.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0354

Axiom
annotated source: n2-acetyl-arginine
annotated property: has_exact_synonym
annotated target: N2-acetyl-L-arginine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-arginine
annotated property: has_exact_synonym
annotated target: RAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-arginine
annotated property: has_exact_synonym
annotated target: [R:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-arginine
annotated property: has_exact_synonym
annotated target: acetylarginine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-arginine
annotated property: has_exact_synonym
annotated target: acetylarginine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: n2-acetyl-arginine
annotated property: has_exact_synonym
annotated target: alpha-acetylamino-delta-guanidinovaleric acid
has_synonym_type: Alternate label curated by PSI-MI

n-acetyl-asparagine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00780.
has_exact_synonym: N-acetyl-L-asparagine
has_exact_synonym: NAC
has_exact_synonym: [N:ac]
has_exact_synonym: acetylasparagine
has_obo_namespace: PSI-MI
id: MI:0124
deprecated: true

Axiom
annotated source: n-acetyl-asparagine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00780.
database_cross_reference: PMID:11125103

Axiom
annotated source: n-acetyl-asparagine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-asparagine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-asparagine
annotated property: has_exact_synonym
annotated target: NAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-asparagine
annotated property: has_exact_synonym
annotated target: [N:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-asparagine
annotated property: has_exact_synonym
annotated target: acetylasparagine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-aspartic acid
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00051.
has_exact_synonym: (S)-2-(acetylamino)butanedioic acid
has_exact_synonym: DAC
has_exact_synonym: N-acetyl-L-aspartic acid
has_exact_synonym: [D:ac]
has_exact_synonym: acetylaspartate
has_exact_synonym: acetylaspartic acid
has_obo_namespace: PSI-MI
id: MI:0125
deprecated: true

Axiom
annotated source: n-acetyl-aspartic acid
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00051.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0042

Axiom
annotated source: n-acetyl-aspartic acid
annotated property: has_exact_synonym
annotated target: (S)-2-(acetylamino)butanedioic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-aspartic acid
annotated property: has_exact_synonym
annotated target: DAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-aspartic acid
annotated property: has_exact_synonym
annotated target: N-acetyl-L-aspartic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-aspartic acid
annotated property: has_exact_synonym
annotated target: [D:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-aspartic acid
annotated property: has_exact_synonym
annotated target: acetylaspartate
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: n-acetyl-aspartic acid
annotated property: has_exact_synonym
annotated target: acetylaspartic acid
has_synonym_type: Alternate label curated by PSI-MI

n-acetyl-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00052.
has_exact_synonym: (R)-2-acetylamino-3-sulfanylpropanoic acid
has_exact_synonym: 2-acetylamino-3-mercaptopropanoic acid
has_exact_synonym: CAC
has_exact_synonym: N-acetyl-L-cysteine
has_exact_synonym: N-acetylcysteine
has_exact_synonym: [C:ac]
has_exact_synonym: acetylcysteine
has_obo_namespace: PSI-MI
id: MI:0126
deprecated: true

Axiom
annotated source: n-acetyl-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00052.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0043

Axiom
annotated source: n-acetyl-cysteine
annotated property: has_exact_synonym
annotated target: (R)-2-acetylamino-3-sulfanylpropanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-cysteine
annotated property: has_exact_synonym
annotated target: 2-acetylamino-3-mercaptopropanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-cysteine
annotated property: has_exact_synonym
annotated target: CAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-cysteine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-cysteine
annotated property: has_exact_synonym
annotated target: N-acetylcysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-cysteine
annotated property: has_exact_synonym
annotated target: [C:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-cysteine
annotated property: has_exact_synonym
annotated target: acetylcysteine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-glutamine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00054.
has_exact_synonym: (S)-2-acetylamino-5-pentanediamic acid
has_exact_synonym: N-acetyl-L-glutamine
has_exact_synonym: QAC
has_exact_synonym: [Q:ac]
has_exact_synonym: acetylglutamine
has_obo_namespace: PSI-MI
id: MI:0127
deprecated: true

Axiom
annotated source: n-acetyl-glutamine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00054.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0045

Axiom
annotated source: n-acetyl-glutamine
annotated property: has_exact_synonym
annotated target: (S)-2-acetylamino-5-pentanediamic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-glutamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamine
annotated property: has_exact_synonym
annotated target: QAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamine
annotated property: has_exact_synonym
annotated target: [Q:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamine
annotated property: has_exact_synonym
annotated target: acetylglutamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamine
annotated property: has_exact_synonym
annotated target: acetylglutamine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-glutamic acid
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00053.
has_exact_synonym: (S)-2-(acetylamino)pentanedioic acid
has_exact_synonym: EAC
has_exact_synonym: N-acetyl-L-glutamic acid
has_exact_synonym: [E:ac]
has_exact_synonym: acetylglutamate
has_exact_synonym: acetylglutamic acid
has_obo_namespace: PSI-MI
id: MI:0128
deprecated: true

Axiom
annotated source: n-acetyl-glutamic acid
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00053.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0044

Axiom
annotated source: n-acetyl-glutamic acid
annotated property: has_exact_synonym
annotated target: (S)-2-(acetylamino)pentanedioic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamic acid
annotated property: has_exact_synonym
annotated target: EAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamic acid
annotated property: has_exact_synonym
annotated target: N-acetyl-L-glutamic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamic acid
annotated property: has_exact_synonym
annotated target: [E:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamic acid
annotated property: has_exact_synonym
annotated target: acetylglutamate
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: n-acetyl-glutamic acid
annotated property: has_exact_synonym
annotated target: acetylglutamic acid
has_synonym_type: Alternate label curated by PSI-MI

n-acetylglycine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00055.
has_exact_synonym: 2-(acetylamino)ethanoic acid
has_exact_synonym: GAC
has_exact_synonym: N-acetylglycine
has_exact_synonym: [G:ac]
has_exact_synonym: aceturic acid
has_exact_synonym: acetylglycine
has_obo_namespace: PSI-MI
id: MI:0129
deprecated: true

Axiom
annotated source: n-acetylglycine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00055.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0046

Axiom
annotated source: n-acetylglycine
annotated property: has_exact_synonym
annotated target: 2-(acetylamino)ethanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetylglycine
annotated property: has_exact_synonym
annotated target: GAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetylglycine
annotated property: has_exact_synonym
annotated target: N-acetylglycine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetylglycine
annotated property: has_exact_synonym
annotated target: [G:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetylglycine
annotated property: has_exact_synonym
annotated target: aceturic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetylglycine
annotated property: has_exact_synonym
annotated target: acetylglycine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-histidine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00781.
has_exact_synonym: HAC
has_exact_synonym: N-acetyl-L-histidine
has_exact_synonym: [H:ac]
has_exact_synonym: acetylhistidine
has_obo_namespace: PSI-MI
id: MI:0130
deprecated: true

Axiom
annotated source: n-acetyl-histidine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00781.
database_cross_reference: PMID:11125103

Axiom
annotated source: n-acetyl-histidine
annotated property: has_exact_synonym
annotated target: HAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-histidine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-histidine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-histidine
annotated property: has_exact_synonym
annotated target: [H:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-histidine
annotated property: has_exact_synonym
annotated target: acetylhistidine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-isoleucine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00056.
has_exact_synonym: (2S,3S)-2-acetylamino-3-methylpentanoic acid
has_exact_synonym: IAC
has_exact_synonym: N-acetyl-L-isoleucine
has_exact_synonym: [I:ac]
has_exact_synonym: acetylisoleucine
has_obo_namespace: PSI-MI
id: MI:0131
deprecated: true

Axiom
annotated source: n-acetyl-isoleucine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00056.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0047

Axiom
annotated source: n-acetyl-isoleucine
annotated property: has_exact_synonym
annotated target: (2S,3S)-2-acetylamino-3-methylpentanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-isoleucine
annotated property: has_exact_synonym
annotated target: IAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-isoleucine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-isoleucine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-isoleucine
annotated property: has_exact_synonym
annotated target: [I:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-isoleucine
annotated property: has_exact_synonym
annotated target: acetylisoleucine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-isoleucine
annotated property: has_exact_synonym
annotated target: acetylisoleucine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-leucine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00782.
has_exact_synonym: LAC
has_exact_synonym: N-acetyl-L-leucine
has_exact_synonym: [L:ac]
has_exact_synonym: acetylleucine
has_obo_namespace: PSI-MI
id: MI:0132
deprecated: true

Axiom
annotated source: n-acetyl-leucine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00782.
database_cross_reference: PMID:11125103

Axiom
annotated source: n-acetyl-leucine
annotated property: has_exact_synonym
annotated target: LAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-leucine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-leucine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-leucine
annotated property: has_exact_synonym
annotated target: [L:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-leucine
annotated property: has_exact_synonym
annotated target: acetylleucine
has_synonym_type: Unique short label curated by PSI-MI

n2-acetyl-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00057.
has_exact_synonym: (S)-2-acetylamino-6-aminohexanoic acid
has_exact_synonym: KAC
has_exact_synonym: N2-acetyl-L-lysine
has_exact_synonym: N2-acetyllysine
has_exact_synonym: [K:ac]
has_exact_synonym: n2-acetyllysine
has_obo_namespace: PSI-MI
id: MI:0133
deprecated: true

Axiom
annotated source: n2-acetyl-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00057.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0048

Axiom
annotated source: n2-acetyl-lysine
annotated property: has_exact_synonym
annotated target: (S)-2-acetylamino-6-aminohexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-lysine
annotated property: has_exact_synonym
annotated target: KAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-lysine
annotated property: has_exact_synonym
annotated target: N2-acetyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-lysine
annotated property: has_exact_synonym
annotated target: N2-acetyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-lysine
annotated property: has_exact_synonym
annotated target: [K:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n2-acetyl-lysine
annotated property: has_exact_synonym
annotated target: n2-acetyllysine
has_synonym_type: Unique short label curated by PSI-MI

n6-acetyl-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00064.
has_exact_synonym: (S)-2-amino-6-(acetylamino)hexanoic acid
has_exact_synonym: KA6
has_exact_synonym: N(zeta)-acetyllysine
has_exact_synonym: N6-acetyl-L-lysine
has_exact_synonym: [K:N6ac]
has_exact_synonym: epsilon-acetyllysine
has_exact_synonym: n6-acetyllysine
has_obo_namespace: PSI-MI
id: MI:0134
deprecated: true

Axiom
annotated source: n6-acetyl-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00064.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0055

Axiom
annotated source: n6-acetyl-lysine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-6-(acetylamino)hexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-acetyl-lysine
annotated property: has_exact_synonym
annotated target: KA6
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-acetyl-lysine
annotated property: has_exact_synonym
annotated target: N(zeta)-acetyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-acetyl-lysine
annotated property: has_exact_synonym
annotated target: N6-acetyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-acetyl-lysine
annotated property: has_exact_synonym
annotated target: [K:N6ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-acetyl-lysine
annotated property: has_exact_synonym
annotated target: epsilon-acetyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-acetyl-lysine
annotated property: has_exact_synonym
annotated target: n6-acetyllysine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-methionine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00058.
has_exact_synonym: (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid
has_exact_synonym: 2-acetylamino-4-(methylthio)butanoic acid
has_exact_synonym: MAC
has_exact_synonym: N-acetyl-L-methionine
has_exact_synonym: [M:ac]
has_exact_synonym: acetylmethionine
has_exact_synonym: methionamine
has_obo_namespace: PSI-MI
id: MI:0135
deprecated: true

Axiom
annotated source: n-acetyl-methionine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00058.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0049

Axiom
annotated source: n-acetyl-methionine
annotated property: has_exact_synonym
annotated target: (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-methionine
annotated property: has_exact_synonym
annotated target: 2-acetylamino-4-(methylthio)butanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-methionine
annotated property: has_exact_synonym
annotated target: MAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-methionine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-methionine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-methionine
annotated property: has_exact_synonym
annotated target: [M:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-methionine
annotated property: has_exact_synonym
annotated target: acetylmethionine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-methionine
annotated property: has_exact_synonym
annotated target: acetylmethionine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: n-acetyl-methionine
annotated property: has_exact_synonym
annotated target: methionamine
has_synonym_type: Alternate label curated by PSI-MI

n-acetyl-phenylalanine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00784.
has_exact_synonym: FAC
has_exact_synonym: N-acetyl-L-phenylalanine
has_exact_synonym: [F:ac]
has_exact_synonym: acetylphenylalanine
has_obo_namespace: PSI-MI
id: MI:0136
deprecated: true

Axiom
annotated source: n-acetyl-phenylalanine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00784.
database_cross_reference: PMID:11125103

Axiom
annotated source: n-acetyl-phenylalanine
annotated property: has_exact_synonym
annotated target: FAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-phenylalanine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-phenylalanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-phenylalanine
annotated property: has_exact_synonym
annotated target: [F:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-phenylalanine
annotated property: has_exact_synonym
annotated target: acetylphenylalanine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-proline
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00059.
has_exact_synonym: (2S)-1-acetyl-2-pyrrolidinecarboxylic acid
has_exact_synonym: N-acetyl-L-proline
has_exact_synonym: PAC
has_exact_synonym: [P:ac]
has_exact_synonym: acetylproline
has_obo_namespace: PSI-MI
id: MI:0137
deprecated: true

Axiom
annotated source: n-acetyl-proline
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00059.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0050

Axiom
annotated source: n-acetyl-proline
annotated property: has_exact_synonym
annotated target: (2S)-1-acetyl-2-pyrrolidinecarboxylic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-proline
annotated property: has_exact_synonym
annotated target: N-acetyl-L-proline
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-proline
annotated property: has_exact_synonym
annotated target: PAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-proline
annotated property: has_exact_synonym
annotated target: [P:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-proline
annotated property: has_exact_synonym
annotated target: acetylproline
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-proline
annotated property: has_exact_synonym
annotated target: acetylproline
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-serine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00060.
has_exact_synonym: (S)-2-acetylamino-3-hydroxypropanoic acid
has_exact_synonym: N-acetyl-L-serine
has_exact_synonym: N-acetylserine
has_exact_synonym: SAC
has_exact_synonym: [S:ac]
has_exact_synonym: acetylserine
has_obo_namespace: PSI-MI
id: MI:0138
deprecated: true

Axiom
annotated source: n-acetyl-serine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00060.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0051

Axiom
annotated source: n-acetyl-serine
annotated property: has_exact_synonym
annotated target: (S)-2-acetylamino-3-hydroxypropanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-serine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-serine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-serine
annotated property: has_exact_synonym
annotated target: N-acetylserine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-serine
annotated property: has_exact_synonym
annotated target: SAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-serine
annotated property: has_exact_synonym
annotated target: [S:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-serine
annotated property: has_exact_synonym
annotated target: acetylserine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-threonine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00061.
has_exact_synonym: (2S,3R)-2-acetylamino-3-hydroxybutanoic acid
has_exact_synonym: N-acetyl-L-threonine
has_exact_synonym: N-acetylthreonine
has_exact_synonym: TAC
has_exact_synonym: [T:ac]
has_exact_synonym: acetylthreonine
has_obo_namespace: PSI-MI
id: MI:0139
deprecated: true

Axiom
annotated source: n-acetyl-threonine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00061.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0052

Axiom
annotated source: n-acetyl-threonine
annotated property: has_exact_synonym
annotated target: (2S,3R)-2-acetylamino-3-hydroxybutanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-threonine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-threonine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-threonine
annotated property: has_exact_synonym
annotated target: N-acetylthreonine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-threonine
annotated property: has_exact_synonym
annotated target: TAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-threonine
annotated property: has_exact_synonym
annotated target: [T:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-threonine
annotated property: has_exact_synonym
annotated target: acetylthreonine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-tryptophan
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00785.
has_exact_synonym: N-acetyl-L-tryptophan
has_exact_synonym: WAC
has_exact_synonym: [W:ac]
has_exact_synonym: acetyltryptophan
has_obo_namespace: PSI-MI
id: MI:0140
deprecated: true

Axiom
annotated source: n-acetyl-tryptophan
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00785.
database_cross_reference: PMID:11125103

Axiom
annotated source: n-acetyl-tryptophan
annotated property: has_exact_synonym
annotated target: N-acetyl-L-tryptophan
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-tryptophan
annotated property: has_exact_synonym
annotated target: WAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-tryptophan
annotated property: has_exact_synonym
annotated target: [W:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-tryptophan
annotated property: has_exact_synonym
annotated target: acetyltryptophan
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-tyrosine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00062.
has_exact_synonym: (S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid
has_exact_synonym: N-acetyl-L-tyrosine
has_exact_synonym: N-acetyltyrosine
has_exact_synonym: YAC
has_exact_synonym: [Y:ac]
has_exact_synonym: acetyltyrosine
has_obo_namespace: PSI-MI
id: MI:0141
deprecated: true

Axiom
annotated source: n-acetyl-tyrosine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00062.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0053

Axiom
annotated source: n-acetyl-tyrosine
annotated property: has_exact_synonym
annotated target: (S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-tyrosine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-tyrosine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-tyrosine
annotated property: has_exact_synonym
annotated target: N-acetyltyrosine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-tyrosine
annotated property: has_exact_synonym
annotated target: YAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-tyrosine
annotated property: has_exact_synonym
annotated target: [Y:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-tyrosine
annotated property: has_exact_synonym
annotated target: acetyltyrosine
has_synonym_type: Unique short label curated by PSI-MI

n-acetyl-valine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00063.
has_exact_synonym: (S)-2-acetylamino-3-methylbutanoic acid
has_exact_synonym: N-acetyl-L-valine
has_exact_synonym: N-acetylvaline
has_exact_synonym: VAC
has_exact_synonym: [V:ac]
has_exact_synonym: acetylvaline
has_obo_namespace: PSI-MI
id: MI:0142
deprecated: true

Axiom
annotated source: n-acetyl-valine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00063.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0054

Axiom
annotated source: n-acetyl-valine
annotated property: has_exact_synonym
annotated target: (S)-2-acetylamino-3-methylbutanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-valine
annotated property: has_exact_synonym
annotated target: N-acetyl-L-valine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-valine
annotated property: has_exact_synonym
annotated target: N-acetylvaline
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-valine
annotated property: has_exact_synonym
annotated target: VAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-valine
annotated property: has_exact_synonym
annotated target: [V:ac]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-acetyl-valine
annotated property: has_exact_synonym
annotated target: acetylvaline
has_synonym_type: Unique short label curated by PSI-MI

amidated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00674.
has_obo_namespace: PSI-MI
id: MI:0143
deprecated: true

Axiom
annotated source: amidated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00674.
database_cross_reference: PMID:11125103

arginine amide
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00091.
has_exact_synonym: (S)-2-amino-5-guanidinopentanamide
has_exact_synonym: L-arginine amide
has_exact_synonym: RAM
has_exact_synonym: [R:am]
has_exact_synonym: argininamide
has_exact_synonym: arginineamide
has_obo_namespace: PSI-MI
id: MI:0145
deprecated: true

Axiom
annotated source: arginine amide
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00091.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0082

Axiom
annotated source: arginine amide
annotated property: has_exact_synonym
annotated target: (S)-2-amino-5-guanidinopentanamide
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: arginine amide
annotated property: has_exact_synonym
annotated target: L-arginine amide
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: arginine amide
annotated property: has_exact_synonym
annotated target: RAM
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: arginine amide
annotated property: has_exact_synonym
annotated target: [R:am]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: arginine amide
annotated property: has_exact_synonym
annotated target: argininamide
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: arginine amide
annotated property: has_exact_synonym
annotated target: arginineamide
has_synonym_type: Unique short label curated by PSI-MI

formylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00493.
has_obo_namespace: PSI-MI
id: MI:0146
deprecated: true

Axiom
annotated source: formylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00493.
database_cross_reference: PMID:11125103

n-formyl-methionine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00030.
has_exact_synonym: (S)-2-formylamino-4-(methylsulfanyl)butanoic acid
has_exact_synonym: 2-formylamino-4-(methylthio)butanoic acid
has_exact_synonym: MFM
has_exact_synonym: N-formyl-L-methionine
has_exact_synonym: [M:form]
has_exact_synonym: formylmethionine
has_obo_namespace: PSI-MI
id: MI:0147
deprecated: true

Axiom
annotated source: n-formyl-methionine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00030.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0021

Axiom
annotated source: n-formyl-methionine
annotated property: has_exact_synonym
annotated target: (S)-2-formylamino-4-(methylsulfanyl)butanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-formyl-methionine
annotated property: has_exact_synonym
annotated target: 2-formylamino-4-(methylthio)butanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-formyl-methionine
annotated property: has_exact_synonym
annotated target: MFM
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-formyl-methionine
annotated property: has_exact_synonym
annotated target: N-formyl-L-methionine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-formyl-methionine
annotated property: has_exact_synonym
annotated target: [M:form]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-formyl-methionine
annotated property: has_exact_synonym
annotated target: formylmethionine
has_synonym_type: Unique short label curated by PSI-MI

hydroxylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00428.
has_obo_namespace: PSI-MI
id: MI:0148
deprecated: true

Axiom
annotated source: hydroxylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00428.
database_cross_reference: PMID:11125103

lipid modification
type: Class
definition: Residue modification. OBSOLETE remap to MOD:01155.
has_obo_namespace: PSI-MI
id: MI:0150
deprecated: true

Axiom
annotated source: lipid modification
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:01155.
database_cross_reference: PMID:11125103

s-farnesyl-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00111.
has_exact_synonym: (R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid
has_exact_synonym: 2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid
has_exact_synonym: CFN
has_exact_synonym: S-farnesyl-L-cysteine
has_exact_synonym: [C:farn]
has_exact_synonym: farnesylcysteine
has_obo_namespace: PSI-MI
id: MI:0151
deprecated: true

Axiom
annotated source: s-farnesyl-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00111.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0102

Axiom
annotated source: s-farnesyl-cysteine
annotated property: has_exact_synonym
annotated target: (R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-farnesyl-cysteine
annotated property: has_exact_synonym
annotated target: 2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-farnesyl-cysteine
annotated property: has_exact_synonym
annotated target: CFN
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-farnesyl-cysteine
annotated property: has_exact_synonym
annotated target: S-farnesyl-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-farnesyl-cysteine
annotated property: has_exact_synonym
annotated target: [C:farn]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-farnesyl-cysteine
annotated property: has_exact_synonym
annotated target: farnesylcysteine
has_synonym_type: Unique short label curated by PSI-MI

s-geranylgeranyl-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00113.
has_exact_synonym: (R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid
has_exact_synonym: 2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid
has_exact_synonym: CGR
has_exact_synonym: S-geranylgeranyl-L-cysteine
has_exact_synonym: [C:ger]
has_exact_synonym: geranylgeranylcys
has_obo_namespace: PSI-MI
id: MI:0152
deprecated: true

Axiom
annotated source: s-geranylgeranyl-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00113.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0104

Axiom
annotated source: s-geranylgeranyl-cysteine
annotated property: has_exact_synonym
annotated target: (R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-geranylgeranyl-cysteine
annotated property: has_exact_synonym
annotated target: 2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-geranylgeranyl-cysteine
annotated property: has_exact_synonym
annotated target: CGR
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-geranylgeranyl-cysteine
annotated property: has_exact_synonym
annotated target: S-geranylgeranyl-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-geranylgeranyl-cysteine
annotated property: has_exact_synonym
annotated target: [C:ger]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-geranylgeranyl-cysteine
annotated property: has_exact_synonym
annotated target: geranylgeranylcys
has_synonym_type: Unique short label curated by PSI-MI

n-palmitoyl-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00069.
has_exact_synonym: (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid
has_exact_synonym: 2-hexadecanoylamino-3-mercaptopropanoic acid
has_exact_synonym: CPN
has_exact_synonym: N-(1-oxahexadecyl)-L-cysteine
has_exact_synonym: N-palmitoyl-L-cysteine
has_exact_synonym: [C:palm_n]
has_exact_synonym: n-palmitoylcysteine
has_obo_namespace: PSI-MI
id: MI:0153
deprecated: true

Axiom
annotated source: n-palmitoyl-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00069.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0060

Axiom
annotated source: n-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: 2-hexadecanoylamino-3-mercaptopropanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: CPN
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: N-(1-oxahexadecyl)-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: N-palmitoyl-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: [C:palm_n]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: n-palmitoylcysteine
has_synonym_type: Unique short label curated by PSI-MI

s-palmitoyl-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00115.
has_exact_synonym: (R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid
has_exact_synonym: 2-amino-3-(hexadecanoylthio)propanoic acid
has_exact_synonym: CPS
has_exact_synonym: S-palmitoyl-L-cysteine
has_exact_synonym: [C:palm_s]
has_exact_synonym: cysteine hexadecanoate thioester
has_exact_synonym: cysteine palmitate thioester
has_exact_synonym: s-palmitoylcysteine
has_obo_namespace: PSI-MI
id: MI:0154
deprecated: true

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00115.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0106

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: (R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: 2-amino-3-(hexadecanoylthio)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: CPS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: S-palmitoyl-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: [C:palm_s]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: cysteine hexadecanoate thioester
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: cysteine palmitate thioester
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-palmitoyl-cysteine
annotated property: has_exact_synonym
annotated target: s-palmitoylcysteine
has_synonym_type: Unique short label curated by PSI-MI

n-myristoyl-glycine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00068.
has_exact_synonym: GMY
has_exact_synonym: N-myristoyl-glycine
has_exact_synonym: [G:myr]
has_exact_synonym: myristoylglycine
has_obo_namespace: PSI-MI
id: MI:0155
deprecated: true

Axiom
annotated source: n-myristoyl-glycine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00068.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0059

Axiom
annotated source: n-myristoyl-glycine
annotated property: has_exact_synonym
annotated target: GMY
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-myristoyl-glycine
annotated property: has_exact_synonym
annotated target: N-myristoyl-glycine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-myristoyl-glycine
annotated property: has_exact_synonym
annotated target: [G:myr]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-myristoyl-glycine
annotated property: has_exact_synonym
annotated target: myristoylglycine
has_synonym_type: Unique short label curated by PSI-MI

n6-myristoyl-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00087.
has_exact_synonym: (S)-2-amino-6-(tetradecanoylamino)hexanoic acid
has_exact_synonym: KMY
has_exact_synonym: N(zeta)-myristoyllysine
has_exact_synonym: N6-(1-oxotetradecyl)-L-lysine
has_exact_synonym: N6-myristoyl-L-lysine
has_exact_synonym: [K:myr]
has_exact_synonym: epsilon-myristoyllysine
has_exact_synonym: myristoyllysine
has_obo_namespace: PSI-MI
id: MI:0156
deprecated: true

Axiom
annotated source: n6-myristoyl-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00087.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0078

Axiom
annotated source: n6-myristoyl-lysine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-6-(tetradecanoylamino)hexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-myristoyl-lysine
annotated property: has_exact_synonym
annotated target: KMY
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-myristoyl-lysine
annotated property: has_exact_synonym
annotated target: N(zeta)-myristoyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-myristoyl-lysine
annotated property: has_exact_synonym
annotated target: N6-(1-oxotetradecyl)-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-myristoyl-lysine
annotated property: has_exact_synonym
annotated target: N6-myristoyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-myristoyl-lysine
annotated property: has_exact_synonym
annotated target: [K:myr]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-myristoyl-lysine
annotated property: has_exact_synonym
annotated target: epsilon-myristoyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-myristoyl-lysine
annotated property: has_exact_synonym
annotated target: myristoyllysine
has_synonym_type: Unique short label curated by PSI-MI

methylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00427.
has_obo_namespace: PSI-MI
id: MI:0157
deprecated: true

Axiom
annotated source: methylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00427.
database_cross_reference: PMID:11125103

n-methyl-alanine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00070.
has_exact_synonym: (S)-2-methylaminopropanoic acid
has_exact_synonym: AMT
has_exact_synonym: N-methyl-L-alanine
has_exact_synonym: N-methylalanine
has_exact_synonym: [A:meth_n]
has_exact_synonym: methylalanine
has_obo_namespace: PSI-MI
id: MI:0158
deprecated: true

Axiom
annotated source: n-methyl-alanine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00070.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0061

Axiom
annotated source: n-methyl-alanine
annotated property: has_exact_synonym
annotated target: (S)-2-methylaminopropanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-alanine
annotated property: has_exact_synonym
annotated target: AMT
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-alanine
annotated property: has_exact_synonym
annotated target: N-methyl-L-alanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-alanine
annotated property: has_exact_synonym
annotated target: N-methylalanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-alanine
annotated property: has_exact_synonym
annotated target: [A:meth_n]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-alanine
annotated property: has_exact_synonym
annotated target: methylalanine
has_synonym_type: Unique short label curated by PSI-MI

n,n,n-trimethyl-alanine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00071.
has_exact_synonym: (S)-1-carboxy-N,N,N-trimethylethanaminium
has_exact_synonym: (S)-2-(trimethylammonio)propanoic acid
has_exact_synonym: AM3
has_exact_synonym: N,N,N-trimethyl-L-alanine
has_exact_synonym: [A:meth_n3]
has_exact_synonym: trimethylalanine
has_obo_namespace: PSI-MI
id: MI:0159
deprecated: true

Axiom
annotated source: n,n,n-trimethyl-alanine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00071.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0062

Axiom
annotated source: n,n,n-trimethyl-alanine
annotated property: has_exact_synonym
annotated target: (S)-1-carboxy-N,N,N-trimethylethanaminium
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n,n,n-trimethyl-alanine
annotated property: has_exact_synonym
annotated target: (S)-2-(trimethylammonio)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n,n,n-trimethyl-alanine
annotated property: has_exact_synonym
annotated target: AM3
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n,n,n-trimethyl-alanine
annotated property: has_exact_synonym
annotated target: N,N,N-trimethyl-L-alanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n,n,n-trimethyl-alanine
annotated property: has_exact_synonym
annotated target: [A:meth_n3]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n,n,n-trimethyl-alanine
annotated property: has_exact_synonym
annotated target: trimethylalanine
has_synonym_type: Unique short label curated by PSI-MI

omega-n,omega-n-dimethyl-arginine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00077.
has_exact_synonym: (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid
has_exact_synonym: NG,NG-dimethylarginine
has_exact_synonym: RM2
has_exact_synonym: [R:meth_n7]
has_exact_synonym: asymmetric dimethylarginine
has_exact_synonym: dimethylarginine
has_exact_synonym: omega-N,omega-N-dimethyl-L-arginine
has_obo_namespace: PSI-MI
id: MI:0160
deprecated: true

Axiom
annotated source: omega-n,omega-n-dimethyl-arginine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00077.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0068

Axiom
annotated source: omega-n,omega-n-dimethyl-arginine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n,omega-n-dimethyl-arginine
annotated property: has_exact_synonym
annotated target: NG,NG-dimethylarginine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n,omega-n-dimethyl-arginine
annotated property: has_exact_synonym
annotated target: RM2
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n,omega-n-dimethyl-arginine
annotated property: has_exact_synonym
annotated target: [R:meth_n7]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n,omega-n-dimethyl-arginine
annotated property: has_exact_synonym
annotated target: asymmetric dimethylarginine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n,omega-n-dimethyl-arginine
annotated property: has_exact_synonym
annotated target: dimethylarginine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: omega-n,omega-n-dimethyl-arginine
annotated property: has_exact_synonym
annotated target: omega-N,omega-N-dimethyl-L-arginine
has_synonym_type: Alternate label curated by PSI-MI

beta-methylthioaspartic acid
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00237.
has_exact_synonym: (2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid
has_exact_synonym: 3-carboxy-S-methyl-cysteine
has_exact_synonym: 3-methylthio-aspartic acid
has_exact_synonym: DM2
has_exact_synonym: L-beta-methylthioaspartic acid
has_exact_synonym: [D:meth_b]
has_exact_synonym: beta-methylthio-aspartic acid
has_exact_synonym: methylthioaspartate
has_obo_namespace: PSI-MI
id: MI:0161
deprecated: true

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00237.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0232

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: has_exact_synonym
annotated target: (2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: has_exact_synonym
annotated target: 3-carboxy-S-methyl-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: has_exact_synonym
annotated target: 3-methylthio-aspartic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: has_exact_synonym
annotated target: DM2
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: has_exact_synonym
annotated target: L-beta-methylthioaspartic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: has_exact_synonym
annotated target: [D:meth_b]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: has_exact_synonym
annotated target: beta-methylthio-aspartic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: beta-methylthioaspartic acid
annotated property: has_exact_synonym
annotated target: methylthioaspartate
has_synonym_type: Unique short label curated by PSI-MI

n5-methyl-glutamine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00080.
has_exact_synonym: (S)-2-amino-N5-methylpentanediamic acid
has_exact_synonym: N(delta)-methylglutamine
has_exact_synonym: N-methylglutamine
has_exact_synonym: N5-methyl-L-glutamine
has_exact_synonym: QM5
has_exact_synonym: [Q:meth_n5]
has_exact_synonym: gamma-methylglutamine
has_exact_synonym: methylglutamine
has_obo_namespace: PSI-MI
id: MI:0162
deprecated: true

Axiom
annotated source: n5-methyl-glutamine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00080.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0071

Axiom
annotated source: n5-methyl-glutamine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-N5-methylpentanediamic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n5-methyl-glutamine
annotated property: has_exact_synonym
annotated target: N(delta)-methylglutamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n5-methyl-glutamine
annotated property: has_exact_synonym
annotated target: N-methylglutamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n5-methyl-glutamine
annotated property: has_exact_synonym
annotated target: N5-methyl-L-glutamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n5-methyl-glutamine
annotated property: has_exact_synonym
annotated target: QM5
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n5-methyl-glutamine
annotated property: has_exact_synonym
annotated target: [Q:meth_n5]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n5-methyl-glutamine
annotated property: has_exact_synonym
annotated target: gamma-methylglutamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n5-methyl-glutamine
annotated property: has_exact_synonym
annotated target: methylglutamine
has_synonym_type: Unique short label curated by PSI-MI

glutamic acid 5-methyl ester
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00081.
has_exact_synonym: (S)-2-aminopentanedioic acid 5-methyl ester
has_exact_synonym: 5-methyl-L-glutamate
has_exact_synonym: EM5
has_exact_synonym: L-glutamic acid 5-methyl ester
has_exact_synonym: [E:meth_o5]
has_exact_synonym: glutamatemethylester
has_exact_synonym: glutamic acid gamma-methyl ester
has_obo_namespace: PSI-MI
id: MI:0163
deprecated: true

Axiom
annotated source: glutamic acid 5-methyl ester
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00081.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0072

Axiom
annotated source: glutamic acid 5-methyl ester
annotated property: has_exact_synonym
annotated target: (S)-2-aminopentanedioic acid 5-methyl ester
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamic acid 5-methyl ester
annotated property: has_exact_synonym
annotated target: 5-methyl-L-glutamate
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamic acid 5-methyl ester
annotated property: has_exact_synonym
annotated target: EM5
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamic acid 5-methyl ester
annotated property: has_exact_synonym
annotated target: L-glutamic acid 5-methyl ester
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamic acid 5-methyl ester
annotated property: has_exact_synonym
annotated target: [E:meth_o5]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamic acid 5-methyl ester
annotated property: has_exact_synonym
annotated target: glutamatemethylester
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: glutamic acid 5-methyl ester
annotated property: has_exact_synonym
annotated target: glutamic acid gamma-methyl ester
has_synonym_type: Alternate label curated by PSI-MI

n6-methyl-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00085.
has_exact_synonym: (S)-2-amino-6-methylaminohexanoic acid
has_exact_synonym: MLZ
has_exact_synonym: N(zeta)-methyllysine
has_exact_synonym: N6-methyl-L-lysine
has_exact_synonym: [K:meth_1]
has_exact_synonym: epsilon-methyllysine
has_exact_synonym: methyllysine
has_obo_namespace: PSI-MI
id: MI:0165
deprecated: true

Axiom
annotated source: n6-methyl-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00085.
database_cross_reference: PMID:11125103

Axiom
annotated source: n6-methyl-lysine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-6-methylaminohexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-methyl-lysine
annotated property: has_exact_synonym
annotated target: MLZ
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-methyl-lysine
annotated property: has_exact_synonym
annotated target: N(zeta)-methyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-methyl-lysine
annotated property: has_exact_synonym
annotated target: N6-methyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-methyl-lysine
annotated property: has_exact_synonym
annotated target: [K:meth_1]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-methyl-lysine
annotated property: has_exact_synonym
annotated target: epsilon-methyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-methyl-lysine
annotated property: has_exact_synonym
annotated target: methyllysine
has_synonym_type: Unique short label curated by PSI-MI

n6,n6-dimethyl-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00084.
has_exact_synonym: (S)-2-amino-6-dimethylaminohexanoic acid
has_exact_synonym: MLY
has_exact_synonym: N(zeta)-dimethyllysine
has_exact_synonym: N6,N6-dimethyl-L-lysine
has_exact_synonym: [K:meth_2]
has_exact_synonym: dimethyllysine
has_exact_synonym: epsilon-dimethyllysine
has_exact_synonym: lysine derivative Lys(y)
has_obo_namespace: PSI-MI
id: MI:0166
deprecated: true

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00084.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0075

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-6-dimethylaminohexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: has_exact_synonym
annotated target: MLY
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: has_exact_synonym
annotated target: N(zeta)-dimethyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: has_exact_synonym
annotated target: N6,N6-dimethyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: has_exact_synonym
annotated target: [K:meth_2]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: has_exact_synonym
annotated target: dimethyllysine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: has_exact_synonym
annotated target: epsilon-dimethyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6-dimethyl-lysine
annotated property: has_exact_synonym
annotated target: lysine derivative Lys(y)
has_synonym_type: Alternate label curated by PSI-MI

n6,n6,n6-trimethyl-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00083.
has_exact_synonym: (S)-2-amino-6-(trimethylammonio)hexanoic acid
has_exact_synonym: (S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium
has_exact_synonym: M3L
has_exact_synonym: N(zeta)-trimethyllysine
has_exact_synonym: N6,N6,N6-trimethyl-L-lysine
has_exact_synonym: [K:meth_3]
has_exact_synonym: epsilon-trimethyllysine
has_exact_synonym: trimethyllysine
has_obo_namespace: PSI-MI
id: MI:0167
deprecated: true

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00083.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0074

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-6-(trimethylammonio)hexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: has_exact_synonym
annotated target: (S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: has_exact_synonym
annotated target: M3L
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: has_exact_synonym
annotated target: N(zeta)-trimethyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: has_exact_synonym
annotated target: N6,N6,N6-trimethyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: has_exact_synonym
annotated target: [K:meth_3]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: has_exact_synonym
annotated target: epsilon-trimethyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6,n6,n6-trimethyl-lysine
annotated property: has_exact_synonym
annotated target: trimethyllysine
has_synonym_type: Unique short label curated by PSI-MI

n-methyl-methionine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00073.
has_exact_synonym: (S)-2-methylamino-4-(methylsulfanyl)butanoic acid
has_exact_synonym: 2-methylamino-4-(methylthio)butanoic acid
has_exact_synonym: MMT
has_exact_synonym: N-methyl-L-methionine
has_exact_synonym: N-methylmethionine
has_exact_synonym: [M:meth]
has_exact_synonym: methylmethionine
has_obo_namespace: PSI-MI
id: MI:0168
deprecated: true

Axiom
annotated source: n-methyl-methionine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00073.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0064

Axiom
annotated source: n-methyl-methionine
annotated property: has_exact_synonym
annotated target: (S)-2-methylamino-4-(methylsulfanyl)butanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-methionine
annotated property: has_exact_synonym
annotated target: 2-methylamino-4-(methylthio)butanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-methionine
annotated property: has_exact_synonym
annotated target: MMT
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-methionine
annotated property: has_exact_synonym
annotated target: N-methyl-L-methionine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-methionine
annotated property: has_exact_synonym
annotated target: N-methylmethionine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-methionine
annotated property: has_exact_synonym
annotated target: [M:meth]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-methionine
annotated property: has_exact_synonym
annotated target: methylmethionine
has_synonym_type: Unique short label curated by PSI-MI

n-methyl-phenylalanine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00074.
has_exact_synonym: (S)-2-methylamino-3-phenylpropanoic acid
has_exact_synonym: FMT
has_exact_synonym: N-methyl-L-phenylalanine
has_exact_synonym: N-methylphenylalanine
has_exact_synonym: [F:meth]
has_exact_synonym: methylphenylalanine
has_obo_namespace: PSI-MI
id: MI:0169
deprecated: true

Axiom
annotated source: n-methyl-phenylalanine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00074.
database_cross_reference: PMID:14755292

Axiom
annotated source: n-methyl-phenylalanine
annotated property: has_exact_synonym
annotated target: (S)-2-methylamino-3-phenylpropanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-phenylalanine
annotated property: has_exact_synonym
annotated target: FMT
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-phenylalanine
annotated property: has_exact_synonym
annotated target: N-methyl-L-phenylalanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-phenylalanine
annotated property: has_exact_synonym
annotated target: N-methylphenylalanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-phenylalanine
annotated property: has_exact_synonym
annotated target: [F:meth]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-methyl-phenylalanine
annotated property: has_exact_synonym
annotated target: methylphenylalanine
has_synonym_type: Unique short label curated by PSI-MI

phosphorylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00696.
has_exact_synonym: phosphorylated
has_obo_namespace: PSI-MI
id: MI:0170
deprecated: true

Axiom
annotated source: phosphorylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00696.
database_cross_reference: PMID:11125103

Axiom
annotated source: phosphorylated residue
annotated property: has_exact_synonym
annotated target: phosphorylated
has_synonym_type: Unique short label curated by PSI-MI

omega-n-phospho-arginine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00227.
has_exact_synonym: (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid
has_exact_synonym: N5-[imino(phosphonoamino)methyl]-L-ornithine
has_exact_synonym: RPO
has_exact_synonym: [R:po]
has_exact_synonym: alpha-amino-delta-phosphonoguanidinovaleric acid
has_exact_synonym: omega-N-phospho-L-arginine
has_exact_synonym: phosphoarginine
has_obo_namespace: PSI-MI
id: MI:0171
deprecated: true

Axiom
annotated source: omega-n-phospho-arginine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00227.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0222

Axiom
annotated source: omega-n-phospho-arginine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-phospho-arginine
annotated property: has_exact_synonym
annotated target: N5-[imino(phosphonoamino)methyl]-L-ornithine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-phospho-arginine
annotated property: has_exact_synonym
annotated target: RPO
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-phospho-arginine
annotated property: has_exact_synonym
annotated target: [R:po]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-phospho-arginine
annotated property: has_exact_synonym
annotated target: alpha-amino-delta-phosphonoguanidinovaleric acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-phospho-arginine
annotated property: has_exact_synonym
annotated target: omega-N-phospho-L-arginine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-phospho-arginine
annotated property: has_exact_synonym
annotated target: phosphoarginine
has_synonym_type: Unique short label curated by PSI-MI

aspartic 4-phosphoric anhydride
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00042.
has_exact_synonym: (S)-2-aminobutanedioic 4-phosphoric anhydride
has_exact_synonym: DPO
has_exact_synonym: L-aspartic 4-phosphoric anhydride
has_exact_synonym: [D:po]
has_exact_synonym: beta-aspartyl phosphate
has_exact_synonym: phosphoaspartic acid
has_obo_namespace: PSI-MI
id: MI:0172
deprecated: true

Axiom
annotated source: aspartic 4-phosphoric anhydride
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00042.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0033

Axiom
annotated source: aspartic 4-phosphoric anhydride
annotated property: has_exact_synonym
annotated target: (S)-2-aminobutanedioic 4-phosphoric anhydride
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: aspartic 4-phosphoric anhydride
annotated property: has_exact_synonym
annotated target: DPO
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: aspartic 4-phosphoric anhydride
annotated property: has_exact_synonym
annotated target: L-aspartic 4-phosphoric anhydride
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: aspartic 4-phosphoric anhydride
annotated property: has_exact_synonym
annotated target: [D:po]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: aspartic 4-phosphoric anhydride
annotated property: has_exact_synonym
annotated target: beta-aspartyl phosphate
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: aspartic 4-phosphoric anhydride
annotated property: has_exact_synonym
annotated target: phosphoaspartic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: aspartic 4-phosphoric anhydride
annotated property: has_exact_synonym
annotated target: phosphoaspartic acid
has_synonym_type: Unique short label curated by PSI-MI

s-phospho-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00043.
has_exact_synonym: (R)-2-amino-3-(phosphonosulfanyl)propanoic acid
has_exact_synonym: CPO
has_exact_synonym: S-phospho-L-cysteine
has_exact_synonym: S-phosphonocysteine
has_exact_synonym: S3-phosphocysteine
has_exact_synonym: [C:po]
has_exact_synonym: cysteine phosphate thioester
has_exact_synonym: phosphocysteine
has_obo_namespace: PSI-MI
id: MI:0173
deprecated: true

Axiom
annotated source: s-phospho-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00043.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0034

Axiom
annotated source: s-phospho-cysteine
annotated property: has_exact_synonym
annotated target: (R)-2-amino-3-(phosphonosulfanyl)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-phospho-cysteine
annotated property: has_exact_synonym
annotated target: CPO
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-phospho-cysteine
annotated property: has_exact_synonym
annotated target: S-phospho-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-phospho-cysteine
annotated property: has_exact_synonym
annotated target: S-phosphonocysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-phospho-cysteine
annotated property: has_exact_synonym
annotated target: S3-phosphocysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-phospho-cysteine
annotated property: has_exact_synonym
annotated target: [C:po]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-phospho-cysteine
annotated property: has_exact_synonym
annotated target: cysteine phosphate thioester
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-phospho-cysteine
annotated property: has_exact_synonym
annotated target: phosphocysteine
has_synonym_type: Unique short label curated by PSI-MI

o-phospho-serine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00046.
has_exact_synonym: (S)-2-amino-3-(phosphonooxy)propanoic acid
has_exact_synonym: 2-amino-3-hydroxypropanoic acid 3-phosphate
has_exact_synonym: 2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine
has_exact_synonym: O-phospho-L-serine
has_exact_synonym: O-phosphonoserine
has_exact_synonym: O3-phosphoserine
has_exact_synonym: SPO
has_exact_synonym: [S:po]
has_exact_synonym: phosphoserine
has_exact_synonym: serine phosphate ester
has_obo_namespace: PSI-MI
id: MI:0176
deprecated: true

Axiom
annotated source: o-phospho-serine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00046.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0037

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-3-(phosphonooxy)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: 2-amino-3-hydroxypropanoic acid 3-phosphate
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: 2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: O-phospho-L-serine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: O-phosphonoserine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: O3-phosphoserine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: SPO
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: [S:po]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: phosphoserine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: o-phospho-serine
annotated property: has_exact_synonym
annotated target: serine phosphate ester
has_synonym_type: Alternate label curated by PSI-MI

o-phospho-threonine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00047.
has_exact_synonym: (2S,3R)-2-amino-3-phosphonooxybutanoic acid
has_exact_synonym: 2-amino-3-hydroxybutanoic acid 3-phosphate
has_exact_synonym: O-phospho-L-threonine
has_exact_synonym: O3-phosphothreonine
has_exact_synonym: TPO
has_exact_synonym: [T:po]
has_exact_synonym: phosphothreonine
has_exact_synonym: threonine phosphate ester
has_obo_namespace: PSI-MI
id: MI:0177
deprecated: true

Axiom
annotated source: o-phospho-threonine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00047.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0038

Axiom
annotated source: o-phospho-threonine
annotated property: has_exact_synonym
annotated target: (2S,3R)-2-amino-3-phosphonooxybutanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-threonine
annotated property: has_exact_synonym
annotated target: 2-amino-3-hydroxybutanoic acid 3-phosphate
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-threonine
annotated property: has_exact_synonym
annotated target: O-phospho-L-threonine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-threonine
annotated property: has_exact_synonym
annotated target: O3-phosphothreonine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-threonine
annotated property: has_exact_synonym
annotated target: TPO
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-threonine
annotated property: has_exact_synonym
annotated target: [T:po]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-phospho-threonine
annotated property: has_exact_synonym
annotated target: phosphothreonine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: o-phospho-threonine
annotated property: has_exact_synonym
annotated target: threonine phosphate ester
has_synonym_type: Alternate label curated by PSI-MI

o4'-phospho-tyrosine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00048.
has_exact_synonym: (S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid
has_exact_synonym: 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate
has_exact_synonym: O4'-phospho-L-tyrosine
has_exact_synonym: O4-phosphotyrosine
has_exact_synonym: YPO
has_exact_synonym: [Y:po]
has_exact_synonym: phosphotyrosine
has_exact_synonym: tyrosine phosphate
has_obo_namespace: PSI-MI
id: MI:0178
deprecated: true

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00048.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0039

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: has_exact_synonym
annotated target: 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: has_exact_synonym
annotated target: O4'-phospho-L-tyrosine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: has_exact_synonym
annotated target: O4-phosphotyrosine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: has_exact_synonym
annotated target: YPO
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: has_exact_synonym
annotated target: [Y:po]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: has_exact_synonym
annotated target: phosphotyrosine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: o4'-phospho-tyrosine
annotated property: has_exact_synonym
annotated target: tyrosine phosphate
has_synonym_type: Alternate label curated by PSI-MI

other modification
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00032.
has_obo_namespace: PSI-MI
id: MI:0179
deprecated: true

Axiom
annotated source: other modification
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00032.
database_cross_reference: PMID:11125103

selenocysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00031.
has_exact_synonym: 3-selenylalanine
has_exact_synonym: CSE
has_exact_synonym: L-selenocysteine
has_exact_synonym: [C:sel]
has_exact_synonym: selenium cysteine
has_obo_namespace: PSI-MI
id: MI:0180
deprecated: true

Axiom
annotated source: selenocysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00031.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0022

Axiom
annotated source: selenocysteine
annotated property: has_exact_synonym
annotated target: 3-selenylalanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: selenocysteine
annotated property: has_exact_synonym
annotated target: CSE
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: selenocysteine
annotated property: has_exact_synonym
annotated target: L-selenocysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: selenocysteine
annotated property: has_exact_synonym
annotated target: [C:sel]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: selenocysteine
annotated property: has_exact_synonym
annotated target: selenium cysteine
has_synonym_type: Alternate label curated by PSI-MI

selenomethionine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00530.
has_exact_synonym: L-selenomethionine
has_exact_synonym: MSE
has_exact_synonym: [M:sel]
has_obo_namespace: PSI-MI
id: MI:0181
deprecated: true

Axiom
annotated source: selenomethionine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00530.
database_cross_reference: PMID:11125103

Axiom
annotated source: selenomethionine
annotated property: has_exact_synonym
annotated target: L-selenomethionine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: selenomethionine
annotated property: has_exact_synonym
annotated target: MSE
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: selenomethionine
annotated property: has_exact_synonym
annotated target: [M:sel]
has_synonym_type: Alternate label curated by PSI-MI

3-oxoalanine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:01169.
has_exact_synonym: (S)-2-amino-3-oxopropanoic acid
has_exact_synonym: 2-amino-3-oxopropionic acid
has_exact_synonym: L-3-oxoalanine
has_exact_synonym: L-alpha-formylglycine
has_exact_synonym: L-amino-malonic acid semialdehyde
has_exact_synonym: L-aminomalonaldehydic acid
has_exact_synonym: L-serinesemialdehyde [misnomer]
has_exact_synonym: SOX
has_exact_synonym: [S:oxal]
has_exact_synonym: oxoalanine
has_obo_namespace: PSI-MI
id: MI:0182
deprecated: true

Axiom
annotated source: 3-oxoalanine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:01169.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0185

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-3-oxopropanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: 2-amino-3-oxopropionic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: L-3-oxoalanine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: L-alpha-formylglycine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: L-amino-malonic acid semialdehyde
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: L-aminomalonaldehydic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: L-serinesemialdehyde [misnomer]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: SOX
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: [S:oxal]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3-oxoalanine
annotated property: has_exact_synonym
annotated target: oxoalanine
has_synonym_type: Unique short label curated by PSI-MI

glutamyl 5-glycerylphosphorylethanolamine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00179.
has_exact_synonym: (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid
has_exact_synonym: EGE
has_exact_synonym: L-glutamyl 5-glycerophosphoethanolamine
has_exact_synonym: L-glutamyl 5-glycerophosphorylethanolamine
has_exact_synonym: L-glutamyl 5-glycerylphosphorylethanolamine
has_exact_synonym: [E:gpe]
has_exact_synonym: glycerylpo4etohamine
has_obo_namespace: PSI-MI
id: MI:0184
deprecated: true

Axiom
annotated source: glutamyl 5-glycerylphosphorylethanolamine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00179.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0170

Axiom
annotated source: glutamyl 5-glycerylphosphorylethanolamine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl 5-glycerylphosphorylethanolamine
annotated property: has_exact_synonym
annotated target: EGE
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl 5-glycerylphosphorylethanolamine
annotated property: has_exact_synonym
annotated target: L-glutamyl 5-glycerophosphoethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl 5-glycerylphosphorylethanolamine
annotated property: has_exact_synonym
annotated target: L-glutamyl 5-glycerophosphorylethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl 5-glycerylphosphorylethanolamine
annotated property: has_exact_synonym
annotated target: L-glutamyl 5-glycerylphosphorylethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl 5-glycerylphosphorylethanolamine
annotated property: has_exact_synonym
annotated target: [E:gpe]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl 5-glycerylphosphorylethanolamine
annotated property: has_exact_synonym
annotated target: glycerylpo4etohamine
has_synonym_type: Unique short label curated by PSI-MI

n6-biotinyl-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00126.
has_exact_synonym: (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine
has_exact_synonym: (S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid
has_exact_synonym: KBT
has_exact_synonym: N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine
has_exact_synonym: N6-biotinyl-L-lysine
has_exact_synonym: N6-biotinyllysine
has_exact_synonym: [K:biotin]
has_exact_synonym: biocytin
has_exact_synonym: biotinyllysine
has_exact_synonym: epsilon-N-biotinyllysine
has_obo_namespace: PSI-MI
id: MI:0186
deprecated: true

Axiom
annotated source: n6-biotinyl-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00126.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0117

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: KBT
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: N6-biotinyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: N6-biotinyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: [K:biotin]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: biocytin
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: biotinyllysine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: n6-biotinyl-lysine
annotated property: has_exact_synonym
annotated target: epsilon-N-biotinyllysine
has_synonym_type: Alternate label curated by PSI-MI

n6-(4-amino-2-hydroxybutyl)-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00125.
has_exact_synonym: (S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid
has_exact_synonym: KHY
has_exact_synonym: N6-(4-amino-2-hydroxybutyl)-L-lysine
has_exact_synonym: [K:hypu]
has_exact_synonym: hypusine
has_obo_namespace: PSI-MI
id: MI:0187
deprecated: true

Axiom
annotated source: n6-(4-amino-2-hydroxybutyl)-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00125.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0116

Axiom
annotated source: n6-(4-amino-2-hydroxybutyl)-lysine
annotated property: has_exact_synonym
annotated target: (S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-(4-amino-2-hydroxybutyl)-lysine
annotated property: has_exact_synonym
annotated target: KHY
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-(4-amino-2-hydroxybutyl)-lysine
annotated property: has_exact_synonym
annotated target: N6-(4-amino-2-hydroxybutyl)-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-(4-amino-2-hydroxybutyl)-lysine
annotated property: has_exact_synonym
annotated target: [K:hypu]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-(4-amino-2-hydroxybutyl)-lysine
annotated property: has_exact_synonym
annotated target: hypusine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-(4-amino-2-hydroxybutyl)-lysine
annotated property: has_exact_synonym
annotated target: hypusine
has_synonym_type: Unique short label curated by PSI-MI

n6-retinal-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00129.
has_exact_synonym: (S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid
has_exact_synonym: KRT
has_exact_synonym: N6-retinal-L-lysine
has_exact_synonym: N6-retinyl-lysine
has_exact_synonym: N6-retinylidene-L-lysine
has_exact_synonym: [K:retin]
has_exact_synonym: retinallysine
has_obo_namespace: PSI-MI
id: MI:0188
deprecated: true

Axiom
annotated source: n6-retinal-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00129.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0120

Axiom
annotated source: n6-retinal-lysine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-retinal-lysine
annotated property: has_exact_synonym
annotated target: KRT
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-retinal-lysine
annotated property: has_exact_synonym
annotated target: N6-retinal-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-retinal-lysine
annotated property: has_exact_synonym
annotated target: N6-retinyl-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-retinal-lysine
annotated property: has_exact_synonym
annotated target: N6-retinylidene-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-retinal-lysine
annotated property: has_exact_synonym
annotated target: [K:retin]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n6-retinal-lysine
annotated property: has_exact_synonym
annotated target: retinallysine
has_synonym_type: Unique short label curated by PSI-MI

ubiquitinated lysine
type: Class
definition: Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein. OBSOLETE remap to MOD:00134.
has_exact_synonym: KUB
has_exact_synonym: N6-glycyl-L-lysine
has_exact_synonym: N6-glycyllysine
has_exact_synonym: [K:ub]
has_obo_namespace: PSI-MI
id: MI:0189
deprecated: true

Axiom
annotated source: ubiquitinated lysine
annotated property: definition
annotated target: Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein. OBSOLETE remap to MOD:00134.
database_cross_reference: PMID:11125103
database_cross_reference: RESID:AA0125

Axiom
annotated source: ubiquitinated lysine
annotated property: has_exact_synonym
annotated target: KUB
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ubiquitinated lysine
annotated property: has_exact_synonym
annotated target: N6-glycyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ubiquitinated lysine
annotated property: has_exact_synonym
annotated target: N6-glycyllysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ubiquitinated lysine
annotated property: has_exact_synonym
annotated target: [K:ub]
has_synonym_type: Alternate label curated by PSI-MI

interaction type
type: Class
subclass of: molecular interaction
definition: Connection between molecule.
has_obo_namespace: PSI-MI
id: MI:0190
in_subset: PSI-MI slim

Axiom
annotated source: interaction type
annotated property: definition
annotated target: Connection between molecule.
database_cross_reference: PMID:14755292

aggregation
type: Class
definition: Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead.
has_obo_namespace: PSI-MI
id: MI:0191
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: aggregation
annotated property: definition
annotated target: Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead.
database_cross_reference: PMID:14755292

acetylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
has_exact_synonym: acetylation
has_obo_namespace: PSI-MI
id: MI:0192
in_subset: PSI-MI slim

Axiom
annotated source: acetylation reaction
annotated property: definition
annotated target: Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
database_cross_reference: GO:0006473
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0041
database_cross_reference: RESID:AA0042
database_cross_reference: RESID:AA0043
database_cross_reference: RESID:AA0044
database_cross_reference: RESID:AA0045
database_cross_reference: RESID:AA0046
database_cross_reference: RESID:AA0047
database_cross_reference: RESID:AA0048
database_cross_reference: RESID:AA0049
database_cross_reference: RESID:AA0050
database_cross_reference: RESID:AA0051
database_cross_reference: RESID:AA0052
database_cross_reference: RESID:AA0053
database_cross_reference: RESID:AA0054
database_cross_reference: RESID:AA0055
database_cross_reference: RESID:AA0056

Axiom
annotated source: acetylation reaction
annotated property: has_exact_synonym
annotated target: acetylation
has_synonym_type: Unique short label curated by PSI-MI

amidation reaction
type: Class
subclass of: enzymatic reaction
definition: Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue.
has_exact_synonym: amidation
has_obo_namespace: PSI-MI
id: MI:0193
in_subset: PSI-MI slim

Axiom
annotated source: amidation reaction
annotated property: definition
annotated target: Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue.
database_cross_reference: GO:0001519
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0081
database_cross_reference: RESID:AA0082
database_cross_reference: RESID:AA0083
database_cross_reference: RESID:AA0084
database_cross_reference: RESID:AA0085
database_cross_reference: RESID:AA0086
database_cross_reference: RESID:AA0087
database_cross_reference: RESID:AA0088
database_cross_reference: RESID:AA0089
database_cross_reference: RESID:AA0090
database_cross_reference: RESID:AA0091
database_cross_reference: RESID:AA0092
database_cross_reference: RESID:AA0093
database_cross_reference: RESID:AA0094
database_cross_reference: RESID:AA0095
database_cross_reference: RESID:AA0096
database_cross_reference: RESID:AA0097
database_cross_reference: RESID:AA0098
database_cross_reference: RESID:AA0099
database_cross_reference: RESID:AA0100

Axiom
annotated source: amidation reaction
annotated property: has_exact_synonym
annotated target: amidation
has_synonym_type: Unique short label curated by PSI-MI

cleavage reaction
type: Class
subclass of: enzymatic reaction
definition: Covalent bond breakage in a molecule leading to the formation of smaller molecules.
has_exact_synonym: cleavage
has_obo_namespace: PSI-MI
id: MI:0194
in_subset: PSI-MI slim

Axiom
annotated source: cleavage reaction
annotated property: definition
annotated target: Covalent bond breakage in a molecule leading to the formation of smaller molecules.
database_cross_reference: PMID:14755292

Axiom
annotated source: cleavage reaction
annotated property: has_exact_synonym
annotated target: cleavage
has_synonym_type: Unique short label curated by PSI-MI

covalent binding
type: Class
subclass of: direct interaction
definition: Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
has_obo_namespace: PSI-MI
id: MI:0195
in_subset: PSI-MI slim

Axiom
annotated source: covalent binding
annotated property: definition
annotated target: Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
database_cross_reference: PMID:14755292

covalent interaction
type: Class
definition: Physical interaction mediated by covalent bond rearrangement. OBSOLETE use covalent binding (MI:0195) instead.
has_obo_namespace: PSI-MI
id: MI:0196
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: covalent interaction
annotated property: definition
annotated target: Physical interaction mediated by covalent bond rearrangement. OBSOLETE use covalent binding (MI:0195) instead.
database_cross_reference: PMID:14755292

deacetylation reaction
type: Class
subclass of: enzymatic reaction
definition: N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
has_exact_synonym: deacetylation
has_obo_namespace: PSI-MI
id: MI:0197
in_subset: PSI-MI slim

Axiom
annotated source: deacetylation reaction
annotated property: definition
annotated target: N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
database_cross_reference: GO:0006476
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0055
database_cross_reference: RESID:AA0056

Axiom
annotated source: deacetylation reaction
annotated property: has_exact_synonym
annotated target: deacetylation
has_synonym_type: Unique short label curated by PSI-MI

defarnesylation reaction
type: Class
subclass of: lipoprotein cleavage reaction
definition: S-farnesyl-L-cysteined is cleaved and returns a C residue.
has_exact_synonym: defarnesylation
has_obo_namespace: PSI-MI
id: MI:0198
in_subset: PSI-MI slim

Axiom
annotated source: defarnesylation reaction
annotated property: definition
annotated target: S-farnesyl-L-cysteined is cleaved and returns a C residue.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0102

Axiom
annotated source: defarnesylation reaction
annotated property: has_exact_synonym
annotated target: defarnesylation
has_synonym_type: Unique short label curated by PSI-MI

deformylation reaction
type: Class
subclass of: enzymatic reaction
definition: N6-formyl-L-lysine is cleaved and returns a K residue.
has_exact_synonym: deformylation
has_obo_namespace: PSI-MI
id: MI:0199
in_subset: PSI-MI slim

Axiom
annotated source: deformylation reaction
annotated property: definition
annotated target: N6-formyl-L-lysine is cleaved and returns a K residue.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0211

Axiom
annotated source: deformylation reaction
annotated property: has_exact_synonym
annotated target: deformylation
has_synonym_type: Unique short label curated by PSI-MI

degeranylation reaction
type: Class
subclass of: lipoprotein cleavage reaction
definition: S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
has_exact_synonym: degeranylation
has_obo_namespace: PSI-MI
id: MI:0200
in_subset: PSI-MI slim

Axiom
annotated source: degeranylation reaction
annotated property: definition
annotated target: S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0104

Axiom
annotated source: degeranylation reaction
annotated property: has_exact_synonym
annotated target: degeranylation
has_synonym_type: Unique short label curated by PSI-MI

demyristoylation reaction
type: Class
subclass of: lipoprotein cleavage reaction
definition: N6-myristoyl-L-lysine is cleaved and returns a K residue.
has_exact_synonym: demyristoylation
has_obo_namespace: PSI-MI
id: MI:0201
in_subset: PSI-MI slim

Axiom
annotated source: demyristoylation reaction
annotated property: definition
annotated target: N6-myristoyl-L-lysine is cleaved and returns a K residue.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0078

Axiom
annotated source: demyristoylation reaction
annotated property: has_exact_synonym
annotated target: demyristoylation
has_synonym_type: Unique short label curated by PSI-MI

depalmitoylation reaction
type: Class
subclass of: lipoprotein cleavage reaction
definition: S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
has_exact_synonym: depalmitoylation
has_obo_namespace: PSI-MI
id: MI:0202
in_subset: PSI-MI slim

Axiom
annotated source: depalmitoylation reaction
annotated property: definition
annotated target: S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0060
database_cross_reference: RESID:AA0077
database_cross_reference: RESID:AA0106

Axiom
annotated source: depalmitoylation reaction
annotated property: has_exact_synonym
annotated target: depalmitoylation
has_synonym_type: Unique short label curated by PSI-MI

dephosphorylation reaction
type: Class
subclass of: enzymatic reaction
definition: Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
has_exact_synonym: dephosphorylation
has_obo_namespace: PSI-MI
id: MI:0203
in_subset: PSI-MI slim

Axiom
annotated source: dephosphorylation reaction
annotated property: definition
annotated target: Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
database_cross_reference: GO:0016311
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0033
database_cross_reference: RESID:AA0034
database_cross_reference: RESID:AA0035
database_cross_reference: RESID:AA0036
database_cross_reference: RESID:AA0037
database_cross_reference: RESID:AA0038
database_cross_reference: RESID:AA0039
database_cross_reference: RESID:AA0222

Axiom
annotated source: dephosphorylation reaction
annotated property: has_exact_synonym
annotated target: dephosphorylation
has_synonym_type: Unique short label curated by PSI-MI

deubiquitination reaction
type: Class
subclass of: enzymatic reaction
definition: Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
has_exact_synonym: deubiquitination
has_obo_namespace: PSI-MI
id: MI:0204
in_subset: PSI-MI slim

Axiom
annotated source: deubiquitination reaction
annotated property: definition
annotated target: Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
database_cross_reference: GO:0016579
database_cross_reference: PMID:11583613
database_cross_reference: RESID:AA0125

Axiom
annotated source: deubiquitination reaction
annotated property: has_exact_synonym
annotated target: deubiquitination
has_synonym_type: Unique short label curated by PSI-MI

disaggregation
type: Class
definition: Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading.
has_obo_namespace: PSI-MI
id: MI:0205
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: disaggregation
annotated property: definition
annotated target: Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading.
database_cross_reference: PMID:14755292

farnesylation reaction
type: Class
subclass of: lipid addition
definition: Reversible reaction that can affect C residue.
has_exact_synonym: farnesylation
has_obo_namespace: PSI-MI
id: MI:0206
in_subset: PSI-MI slim

Axiom
annotated source: farnesylation reaction
annotated property: definition
annotated target: Reversible reaction that can affect C residue.
database_cross_reference: GO:0018347
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0102

Axiom
annotated source: farnesylation reaction
annotated property: has_exact_synonym
annotated target: farnesylation
has_synonym_type: Unique short label curated by PSI-MI

formylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
has_exact_synonym: formylation
has_obo_namespace: PSI-MI
id: MI:0207
in_subset: PSI-MI slim

Axiom
annotated source: formylation reaction
annotated property: definition
annotated target: Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
database_cross_reference: GO:0018256
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0057
database_cross_reference: RESID:AA0211

Axiom
annotated source: formylation reaction
annotated property: has_exact_synonym
annotated target: formylation
has_synonym_type: Unique short label curated by PSI-MI

genetic interaction (sensu unexpected)
type: Class
subclass of: MI 2402
definition: An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E
is defined by: A genetic interaction refers to an unexpected phenotype not easily explained by combining the effects of individual genetic variants (7).
is defined by: A quantitative genetic interaction definition has two components: a quantitative phenotypic measure and a neutrality function that predicts the phenotype of an organism carrying two noninteracting mutations. Interaction is then defined by deviation of a double-mutant organism's phenotype from the expected neutral phenotype.
is defined by: More generally, a genetic interaction can be defined as the difference between an experimentally measured double-mutant phenotype and an expected double-mutant phenotype, the latter of which is predicted from the combination of the single-mutant effects, assuming the mutations act independently.
is defined by: Two genes A and B 'genetically interact' when the phenotype generated as the result of mutations in both genes (double mutant ab) is unexpectedly not just a combination of the phenotypes of the two single mutants a and b.
has_exact_synonym: Fisher epistasis
has_obo_namespace: PSI-MI
id: MI:0208
in_subset: PSI-MI slim

Axiom
annotated source: genetic interaction (sensu unexpected)
annotated property: definition
annotated target: An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E
database_cross_reference: PMID:16527956

Axiom
annotated source: genetic interaction (sensu unexpected)
annotated property: has_exact_synonym
annotated target: Fisher epistasis
database_cross_reference: PMID:17510664
database_cross_reference: https://doi.org/10.1017/S0080456800012163

geranylgeranylation reaction
type: Class
subclass of: lipid addition
definition: Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
has_exact_synonym: geranylgeranylation
has_obo_namespace: PSI-MI
id: MI:0209
in_subset: PSI-MI slim

Axiom
annotated source: geranylgeranylation reaction
annotated property: definition
annotated target: Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
database_cross_reference: GO:0018348
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0104

Axiom
annotated source: geranylgeranylation reaction
annotated property: has_exact_synonym
annotated target: geranylgeranylation
has_synonym_type: Unique short label curated by PSI-MI

hydroxylation reaction
type: Class
subclass of: enzymatic reaction
definition: Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
has_exact_synonym: hydroxylation
has_obo_namespace: PSI-MI
id: MI:0210
in_subset: PSI-MI slim

Axiom
annotated source: hydroxylation reaction
annotated property: definition
annotated target: Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
database_cross_reference: GO:0018126
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0028
database_cross_reference: RESID:AA0029
database_cross_reference: RESID:AA0030
database_cross_reference: RESID:AA0146
database_cross_reference: RESID:AA0215

Axiom
annotated source: hydroxylation reaction
annotated property: has_exact_synonym
annotated target: hydroxylation
has_synonym_type: Unique short label curated by PSI-MI

lipid addition
type: Class
subclass of: enzymatic reaction
definition: Covalent or non covalent binding of lipid group on a protein residue.
has_obo_namespace: PSI-MI
id: MI:0211
in_subset: PSI-MI slim

Axiom
annotated source: lipid addition
annotated property: definition
annotated target: Covalent or non covalent binding of lipid group on a protein residue.
database_cross_reference: GO:0006497
database_cross_reference: PMID:14755292

lipoprotein cleavage reaction
type: Class
subclass of: cleavage reaction
definition: Cleavage of a lipid group covalently bound to a protein residue.
has_exact_synonym: lipid cleavage
has_obo_namespace: PSI-MI
id: MI:0212
in_subset: PSI-MI slim

Axiom
annotated source: lipoprotein cleavage reaction
annotated property: definition
annotated target: Cleavage of a lipid group covalently bound to a protein residue.
database_cross_reference: PMID:14755292

Axiom
annotated source: lipoprotein cleavage reaction
annotated property: has_exact_synonym
annotated target: lipid cleavage
has_synonym_type: Unique short label curated by PSI-MI

methylation reaction
type: Class
subclass of: enzymatic reaction
definition: The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
has_exact_synonym: methylation
has_obo_namespace: PSI-MI
id: MI:0213
in_subset: PSI-MI slim

Axiom
annotated source: methylation reaction
annotated property: definition
annotated target: The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
database_cross_reference: GO:0043414
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0061
database_cross_reference: RESID:AA0062
database_cross_reference: RESID:AA0063
database_cross_reference: RESID:AA0064
database_cross_reference: RESID:AA0065
database_cross_reference: RESID:AA0066
database_cross_reference: RESID:AA0067
database_cross_reference: RESID:AA0068
database_cross_reference: RESID:AA0069
database_cross_reference: RESID:AA0070
database_cross_reference: RESID:AA0071
database_cross_reference: RESID:AA0072
database_cross_reference: RESID:AA0073
database_cross_reference: RESID:AA0074
database_cross_reference: RESID:AA0075
database_cross_reference: RESID:AA0076
database_cross_reference: RESID:AA0234
database_cross_reference: RESID:AA0272

Axiom
annotated source: methylation reaction
annotated property: has_exact_synonym
annotated target: methylation
has_synonym_type: Unique short label curated by PSI-MI

myristoylation reaction
type: Class
subclass of: lipid addition
definition: Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues.
has_exact_synonym: myristoylation
has_obo_namespace: PSI-MI
id: MI:0214
in_subset: PSI-MI slim

Axiom
annotated source: myristoylation reaction
annotated property: definition
annotated target: Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues.
database_cross_reference: GO:0018319
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0059
database_cross_reference: RESID:AA0078

Axiom
annotated source: myristoylation reaction
annotated property: has_exact_synonym
annotated target: myristoylation
has_synonym_type: Unique short label curated by PSI-MI

non covalent interaction
type: Class
definition: Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead.
has_exact_synonym: non covalent inter
has_obo_namespace: PSI-MI
id: MI:0215
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: non covalent interaction
annotated property: definition
annotated target: Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead.
database_cross_reference: PMID:14755292

Axiom
annotated source: non covalent interaction
annotated property: has_exact_synonym
annotated target: non covalent inter
has_synonym_type: Unique short label curated by PSI-MI

palmitoylation reaction
type: Class
subclass of: lipid addition
definition: Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
has_exact_synonym: palmitoylation
has_obo_namespace: PSI-MI
id: MI:0216
in_subset: PSI-MI slim

Axiom
annotated source: palmitoylation reaction
annotated property: definition
annotated target: Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
database_cross_reference: GO:0018318
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0060
database_cross_reference: RESID:AA0077
database_cross_reference: RESID:AA0079
database_cross_reference: RESID:AA0080
database_cross_reference: RESID:AA0106

Axiom
annotated source: palmitoylation reaction
annotated property: has_exact_synonym
annotated target: palmitoylation
has_synonym_type: Unique short label curated by PSI-MI

phosphorylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that can affect D,C,H,S,T,Y,R residues.
has_exact_synonym: phosphorylation
has_obo_namespace: PSI-MI
id: MI:0217
in_subset: PSI-MI slim

Axiom
annotated source: phosphorylation reaction
annotated property: definition
annotated target: Reversible reaction that can affect D,C,H,S,T,Y,R residues.
database_cross_reference: GO:0016310
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0033
database_cross_reference: RESID:AA0034
database_cross_reference: RESID:AA0035
database_cross_reference: RESID:AA0036
database_cross_reference: RESID:AA0037
database_cross_reference: RESID:AA0038
database_cross_reference: RESID:AA0039
database_cross_reference: RESID:AA0222

Axiom
annotated source: phosphorylation reaction
annotated property: has_exact_synonym
annotated target: phosphorylation
has_synonym_type: Unique short label curated by PSI-MI

physical interaction
type: Class
definition: Interaction among molecules that can be direct or indirect. OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915.
has_obo_namespace: PSI-MI
id: MI:0218
deprecated: true

Axiom
annotated source: physical interaction
annotated property: definition
annotated target: Interaction among molecules that can be direct or indirect. OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915.
database_cross_reference: PMID:14755292

synthetic lethal
type: Class
definition: Death phenotype observed on cells carrying combination of two independently silent mutations. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
has_obo_namespace: PSI-MI
id: MI:0219
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: synthetic lethal
annotated property: definition
annotated target: Death phenotype observed on cells carrying combination of two independently silent mutations. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
database_cross_reference: PMID:15608217

ubiquitination reaction
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
has_exact_synonym: ubiquitination
has_obo_namespace: PSI-MI
id: MI:0220
in_subset: PSI-MI slim

Axiom
annotated source: ubiquitination reaction
annotated property: definition
annotated target: Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
database_cross_reference: GO:0016567
database_cross_reference: PMID:11583613
database_cross_reference: RESID:AA0125

Axiom
annotated source: ubiquitination reaction
annotated property: has_exact_synonym
annotated target: ubiquitination
has_synonym_type: Unique short label curated by PSI-MI

expression level
type: Class
subclass of: experimental preparation
definition: Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell.
has_obo_namespace: PSI-MI
id: MI:0221
in_subset: PSI-MI slim

Axiom
annotated source: expression level
annotated property: definition
annotated target: Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell.
database_cross_reference: PMID:14755292

physiological level
type: Class
subclass of: expression level
definition: A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate.
has_exact_synonym: endogenous
has_exact_synonym: endogenous level
has_obo_namespace: PSI-MI
id: MI:0222
in_subset: PSI-MI slim

Axiom
annotated source: physiological level
annotated property: definition
annotated target: A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate.
database_cross_reference: PMID:14755292

Axiom
annotated source: physiological level
annotated property: has_exact_synonym
annotated target: endogenous
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: physiological level
annotated property: has_exact_synonym
annotated target: endogenous level
has_synonym_type: Alternate label curated by PSI-MI

under expressed level
type: Class
subclass of: expression level
subclass of: expression level alteration
definition: A molecule is estimated to be expressed at lower levels than in physiological condition.
has_exact_synonym: under-expressed
has_obo_namespace: PSI-MI
id: MI:0223
in_subset: PSI-MI slim

Axiom
annotated source: under expressed level
annotated property: definition
annotated target: A molecule is estimated to be expressed at lower levels than in physiological condition.
database_cross_reference: PMID:14755292

Axiom
annotated source: under expressed level
annotated property: has_exact_synonym
annotated target: under-expressed
has_synonym_type: Unique short label curated by PSI-MI

chromatin immunoprecipitation array
type: Class
subclass of: array technology
subclass of: chromatin immunoprecipitation assay
definition: The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus.
has_exact_synonym: chip-chip
has_obo_namespace: PSI-MI
id: MI:0225
in_subset: PSI-MI slim

Axiom
annotated source: chromatin immunoprecipitation array
annotated property: definition
annotated target: The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus.
database_cross_reference: PMID:11125145
database_cross_reference: PMID:11206552

Axiom
annotated source: chromatin immunoprecipitation array
annotated property: has_exact_synonym
annotated target: chip-chip
has_synonym_type: Unique short label curated by PSI-MI

ion exchange chromatography
type: Class
subclass of: chromatography technology
definition: Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns.
has_exact_synonym: IEC
has_exact_synonym: ion exchange chrom
has_obo_namespace: PSI-MI
id: MI:0226
in_subset: PSI-MI slim

Axiom
annotated source: ion exchange chromatography
annotated property: definition
annotated target: Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns.
database_cross_reference: PMID:14755292

Axiom
annotated source: ion exchange chromatography
annotated property: has_exact_synonym
annotated target: IEC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ion exchange chromatography
annotated property: has_exact_synonym
annotated target: ion exchange chrom
has_synonym_type: Unique short label curated by PSI-MI

reverse phase chromatography
type: Class
subclass of: chromatography technology
definition: Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds.
has_exact_synonym: reverse phase chrom
has_obo_namespace: PSI-MI
id: MI:0227
in_subset: PSI-MI slim

Axiom
annotated source: reverse phase chromatography
annotated property: definition
annotated target: Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds.
database_cross_reference: PMID:14755292

Axiom
annotated source: reverse phase chromatography
annotated property: has_exact_synonym
annotated target: reverse phase chrom
has_synonym_type: Unique short label curated by PSI-MI

cytoplasmic complementation assay
type: Class
definition: Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay
has_exact_synonym: cytoplasmic compl
has_obo_namespace: PSI-MI
id: MI:0228
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: cytoplasmic complementation assay
annotated property: definition
annotated target: Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay
database_cross_reference: PMID:14755292

Axiom
annotated source: cytoplasmic complementation assay
annotated property: has_exact_synonym
annotated target: cytoplasmic compl
has_synonym_type: Unique short label curated by PSI-MI

MI_0229
type: Class
IAO_0000231: IAO_0000227
IAO_0100001: bimolecular fluorescence complementation
deprecated: true

membrane bound complementation assay
type: Class
definition: OBSOLETE remap to MI:0090 protein complementation assay.
has_exact_synonym: membrane compl
has_obo_namespace: PSI-MI
id: MI:0230
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: membrane bound complementation assay
annotated property: definition
annotated target: OBSOLETE remap to MI:0090 protein complementation assay.
database_cross_reference: PMID:14755292

Axiom
annotated source: membrane bound complementation assay
annotated property: has_exact_synonym
annotated target: membrane compl
has_synonym_type: Unique short label curated by PSI-MI

mammalian protein protein interaction trap
type: Class
subclass of: protein complementation assay
definition: The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions.
has_exact_synonym: mappit
has_obo_namespace: PSI-MI
id: MI:0231
in_subset: PSI-MI slim

Axiom
annotated source: mammalian protein protein interaction trap
annotated property: definition
annotated target: The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions.
database_cross_reference: PMID:12853652

Axiom
annotated source: mammalian protein protein interaction trap
annotated property: has_exact_synonym
annotated target: mappit
has_synonym_type: Unique short label curated by PSI-MI

transcriptional complementation assay
type: Class
subclass of: protein complementation assay
definition: Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression.
has_exact_synonym: transcription compl
has_obo_namespace: PSI-MI
id: MI:0232
in_subset: PSI-MI slim

Axiom
annotated source: transcriptional complementation assay
annotated property: definition
annotated target: Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression.
database_cross_reference: PMID:14755292

Axiom
annotated source: transcriptional complementation assay
annotated property: has_exact_synonym
annotated target: transcription compl
has_synonym_type: Unique short label curated by PSI-MI

protein dna complex
type: Class
subclass of: complex composition
definition: A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
has_obo_namespace: PSI-MI
id: MI:0233
in_subset: PSI-MI slim

Axiom
annotated source: protein dna complex
annotated property: definition
annotated target: A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
database_cross_reference: PMID:14755292

131i radiolabel
type: Class
subclass of: radiolabel
definition: Molecule labelled with 131 radio isotope of iodine atoms.
has_exact_synonym: 131I
has_exact_synonym: I131
has_obo_namespace: PSI-MI
id: MI:0234
in_subset: PSI-MI slim

Axiom
annotated source: 131i radiolabel
annotated property: definition
annotated target: Molecule labelled with 131 radio isotope of iodine atoms.
database_cross_reference: PMID:14755292

Axiom
annotated source: 131i radiolabel
annotated property: has_exact_synonym
annotated target: 131I
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 131i radiolabel
annotated property: has_exact_synonym
annotated target: I131
has_synonym_type: Alternate label curated by PSI-MI

14c radiolabel
type: Class
subclass of: radiolabel
definition: Molecule labelled with the radio isotope 14 of carbon atoms.
has_exact_synonym: 14C
has_exact_synonym: C14
has_obo_namespace: PSI-MI
id: MI:0235
in_subset: PSI-MI slim

Axiom
annotated source: 14c radiolabel
annotated property: definition
annotated target: Molecule labelled with the radio isotope 14 of carbon atoms.
database_cross_reference: PMID:14755292

Axiom
annotated source: 14c radiolabel
annotated property: has_exact_synonym
annotated target: 14C
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 14c radiolabel
annotated property: has_exact_synonym
annotated target: C14
has_synonym_type: Alternate label curated by PSI-MI

32p radiolabel
type: Class
subclass of: radiolabel
definition: Molecule labelled with the radio isotope 32 of phosphorus atoms.
has_exact_synonym: 32P
has_exact_synonym: P32
has_obo_namespace: PSI-MI
id: MI:0236
in_subset: PSI-MI slim

Axiom
annotated source: 32p radiolabel
annotated property: definition
annotated target: Molecule labelled with the radio isotope 32 of phosphorus atoms.
database_cross_reference: PMID:14755292

Axiom
annotated source: 32p radiolabel
annotated property: has_exact_synonym
annotated target: 32P
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 32p radiolabel
annotated property: has_exact_synonym
annotated target: P32
has_synonym_type: Alternate label curated by PSI-MI

33p radiolabel
type: Class
subclass of: radiolabel
definition: Molecule labelled with the radio isotope 33 of phosphorus atoms.
has_exact_synonym: 33P
has_exact_synonym: P33
has_obo_namespace: PSI-MI
id: MI:0237
in_subset: PSI-MI slim

Axiom
annotated source: 33p radiolabel
annotated property: definition
annotated target: Molecule labelled with the radio isotope 33 of phosphorus atoms.
database_cross_reference: PMID:14755292

Axiom
annotated source: 33p radiolabel
annotated property: has_exact_synonym
annotated target: 33P
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 33p radiolabel
annotated property: has_exact_synonym
annotated target: P33
has_synonym_type: Alternate label curated by PSI-MI

3h radiolabel
type: Class
subclass of: radiolabel
definition: Molecules labelled with isotope 3 of hydrogen atoms.
has_exact_synonym: 3H
has_exact_synonym: H3
has_exact_synonym: tritium
has_obo_namespace: PSI-MI
id: MI:0238
in_subset: PSI-MI slim

Axiom
annotated source: 3h radiolabel
annotated property: definition
annotated target: Molecules labelled with isotope 3 of hydrogen atoms.
database_cross_reference: PMID:14755292

Axiom
annotated source: 3h radiolabel
annotated property: has_exact_synonym
annotated target: 3H
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3h radiolabel
annotated property: has_exact_synonym
annotated target: H3
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 3h radiolabel
annotated property: has_exact_synonym
annotated target: tritium
has_synonym_type: Alternate label curated by PSI-MI

biotin tag
type: Class
subclass of: tag
definition: Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation.
has_obo_namespace: PSI-MI
id: MI:0239
in_subset: PSI-MI slim

Axiom
annotated source: biotin tag
annotated property: definition
annotated target: Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation.
database_cross_reference: PMID:14755292

fusion protein
type: Class
subclass of: tag
definition: The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification.
has_obo_namespace: PSI-MI
id: MI:0240
in_subset: PSI-MI slim

Axiom
annotated source: fusion protein
annotated property: definition
annotated target: The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification.
database_cross_reference: PMID:14755292

horseradish peroxidase tag
type: Class
subclass of: enzyme tag
definition: Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
has_exact_synonym: hrp tag
has_obo_namespace: PSI-MI
id: MI:0241
in_subset: PSI-MI slim

Axiom
annotated source: horseradish peroxidase tag
annotated property: definition
annotated target: Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: horseradish peroxidase tag
annotated property: has_exact_synonym
annotated target: hrp tag
has_synonym_type: Unique short label curated by PSI-MI

gene ontology definition reference
type: Class
subclass of: cross-reference type
definition: This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference.
has_exact_synonym: go-definition-ref
has_obo_namespace: PSI-MI
id: MI:0242
in_subset: PSI-MI slim

Axiom
annotated source: gene ontology definition reference
annotated property: definition
annotated target: This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference.
database_cross_reference: PMID:14755292

Axiom
annotated source: gene ontology definition reference
annotated property: has_exact_synonym
annotated target: go-definition-ref
has_synonym_type: Unique short label curated by PSI-MI

isoform parent sequence reference
type: Class
subclass of: cross-reference type
definition: Reference to the master sequence from which this isoform has been derived.
has_exact_synonym: isoform-parent
has_obo_namespace: PSI-MI
id: MI:0243
in_subset: PSI-MI slim

Axiom
annotated source: isoform parent sequence reference
annotated property: definition
annotated target: Reference to the master sequence from which this isoform has been derived.
database_cross_reference: PMID:14755292

Axiom
annotated source: isoform parent sequence reference
annotated property: has_exact_synonym
annotated target: isoform-parent
has_synonym_type: Unique short label curated by PSI-MI

reactome complex
type: Class
definition: Collection of functional complexes within Reactome - a knowledgebase of biological processes. http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome.
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0244
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: reactome complex
annotated property: definition
annotated target: Collection of functional complexes within Reactome - a knowledgebase of biological processes. http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome.
database_cross_reference: PMID:21067998

REACT_[0-9]{1,5}\.[0-9]{1,3}|[0-9]+
type: Axiom
annotated source: reactome complex
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: reactome complex
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.reactome.org/cgi-bin/eventbrowser

reactome protein
type: Class
definition: Collection of protein within the Reactome database - a knowledgebase of biological processes. http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome.
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0245
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: reactome protein
annotated property: definition
annotated target: Collection of protein within the Reactome database - a knowledgebase of biological processes. http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome.
database_cross_reference: PMID:21067998

REACT_[0-9]{1,4}\.[0-9]{1,3}|[OPQ][0-9][A-Z0-9]{3}[0-9]|[OPQ][0-9][A-Z0-9]{3}[0-9]-[0-9]+|[A-Z]{3}[0-9]{5}|[OPQ][0-9][A-Z0-9]{3}[0-9]-PRO_[0-9]{10}
type: Axiom
annotated source: reactome protein
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: reactome protein
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.reactome.org/cgi-bin/link

cabri
type: Class
subclass of: participant database
definition: CABRI cell lines catalogue available at. http://www.cabri.org/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0246
in_subset: PSI-MI slim

Axiom
annotated source: cabri
annotated property: definition
annotated target: CABRI cell lines catalogue available at. http://www.cabri.org/
database_cross_reference: PMID:14755292

[0-9]+|ACC\s[A-Z0-9]+|ECACC\s[A-Z0-9]+|LMBP\s[A-Z0-9]+|ICLC\s[A-Z0-9]+|CIP-[0-9]+|DSMZ_MUTZ\:ACC\s[0-9]+
type: Axiom
annotated source: cabri
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: cabri
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.cabri.org/CABRI/srs-bin/wgetz

newt
type: Class
definition: New EBI Web Taxonomy. http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0247
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: newt
annotated property: definition
annotated target: New EBI Web Taxonomy. http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: newt
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: newt
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/newt/display

resid
type: Class
subclass of: feature database
definition: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. http://www.ebi.ac.uk/RESID/index.html
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0248
in_subset: PSI-MI slim

Axiom
annotated source: resid
annotated property: definition
annotated target: The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. http://www.ebi.ac.uk/RESID/index.html
database_cross_reference: PMID:14755292

AA[0-9]{4}
type: Axiom
annotated source: resid
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: resid
annotated property: database_cross_reference
annotated target: search-url:
label: http://srs.ebi.ac.uk/cgi-bin/wgetz

huge
type: Class
subclass of: sequence database
definition: A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0249
in_subset: PSI-MI slim

Axiom
annotated source: huge
annotated property: definition
annotated target: A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/
database_cross_reference: PMID:14755292

KIAA[0-9]{4}[A-Z]{0,1}
type: Axiom
annotated source: huge
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: huge
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.kazusa.or.jp/huge/gfpage/${ac}

gene
type: Class
subclass of: interactor type
definition: A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
has_obo_namespace: PSI-MI
id: MI:0250
in_subset: PSI-MI slim

Axiom
annotated source: gene
annotated property: definition
annotated target: A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
database_cross_reference: PMID:14755292
database_cross_reference: SO:0000704

gene product
type: Class
subclass of: cross-reference type
definition: Reference pointing to a protein object from its genomic or nucleic acid sequence.
has_obo_namespace: PSI-MI
id: MI:0251
in_subset: PSI-MI slim

Axiom
annotated source: gene product
annotated property: definition
annotated target: Reference pointing to a protein object from its genomic or nucleic acid sequence.
database_cross_reference: PMID:14755292

biological feature
type: Class
subclass of: feature type
definition: Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
has_obo_namespace: PSI-MI
id: MI:0252
in_subset: PSI-MI slim

Axiom
annotated source: biological feature
annotated property: definition
annotated target: Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
database_cross_reference: PMID:14755292

isotope label
type: Class
subclass of: experimental feature
definition: One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number.
has_obo_namespace: PSI-MI
id: MI:0253
in_subset: PSI-MI slim

Axiom
annotated source: isotope label
annotated property: definition
annotated target: One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number.
database_cross_reference: PMID:14755292

genetic interference
type: Class
subclass of: experimental interaction detection
definition: This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis.
has_obo_namespace: PSI-MI
id: MI:0254
in_subset: PSI-MI slim

Axiom
annotated source: genetic interference
annotated property: definition
annotated target: This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis.
database_cross_reference: PMID:14755292

post transcriptional interference
type: Class
subclass of: experimental interaction detection
definition: This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself.
has_exact_synonym: expression interfer
has_obo_namespace: PSI-MI
id: MI:0255
in_subset: PSI-MI slim

Axiom
annotated source: post transcriptional interference
annotated property: definition
annotated target: This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself.
database_cross_reference: PMID:14755292

Axiom
annotated source: post transcriptional interference
annotated property: has_exact_synonym
annotated target: expression interfer
has_synonym_type: Unique short label curated by PSI-MI

rna interference
type: Class
subclass of: post transcriptional interference
definition: RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA.
has_exact_synonym: rnai
has_obo_namespace: PSI-MI
id: MI:0256
in_subset: PSI-MI slim

Axiom
annotated source: rna interference
annotated property: definition
annotated target: RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA.
database_cross_reference: PMID:12110901
database_cross_reference: PMID:12408823

Axiom
annotated source: rna interference
annotated property: has_exact_synonym
annotated target: rnai
has_synonym_type: Unique short label curated by PSI-MI

antisense rna
type: Class
subclass of: post transcriptional interference
definition: This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
has_obo_namespace: PSI-MI
id: MI:0257
in_subset: PSI-MI slim

Axiom
annotated source: antisense rna
annotated property: definition
annotated target: This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
database_cross_reference: PMID:1340158

inhibitor antibodies
type: Class
definition: Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
has_obo_namespace: PSI-MI
id: MI:0258
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: inhibitor antibodies
annotated property: definition
annotated target: Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
database_cross_reference: PMID:10189716

perturbagens peptides
type: Class
definition: This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
has_exact_synonym: perturbagens pep
has_obo_namespace: PSI-MI
id: MI:0259
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: perturbagens peptides
annotated property: definition
annotated target: This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
database_cross_reference: PMID:11731788
database_cross_reference: PMID:8606778

Axiom
annotated source: perturbagens peptides
annotated property: has_exact_synonym
annotated target: perturbagens pep
has_synonym_type: Unique short label curated by PSI-MI

inhibitor small molecules
type: Class
definition: Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
has_exact_synonym: inhibitor small mol
has_obo_namespace: PSI-MI
id: MI:0260
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: inhibitor small molecules
annotated property: definition
annotated target: Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
database_cross_reference: PMID:10542155
database_cross_reference: PMID:10780927

Axiom
annotated source: inhibitor small molecules
annotated property: has_exact_synonym
annotated target: inhibitor small mol
has_synonym_type: Unique short label curated by PSI-MI

obsolete suppression
type: Class
definition: A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793.
has_obo_namespace: PSI-MI
id: MI:0261
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: obsolete suppression
annotated property: definition
annotated target: A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793.
database_cross_reference: PMID:15608217

suppression mutation
type: Class
definition: A given (suppressed) mutation phenotype is reverted by a supressor gene mutation. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804.
has_obo_namespace: PSI-MI
id: MI:0262
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: suppression mutation
annotated property: definition
annotated target: A given (suppressed) mutation phenotype is reverted by a supressor gene mutation. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804.
database_cross_reference: PMID:15608217

suppression knockout
type: Class
definition: Knocked out gene is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788.
has_exact_synonym: suppress knockout
has_obo_namespace: PSI-MI
id: MI:0263
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: suppression knockout
annotated property: definition
annotated target: Knocked out gene is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788.
database_cross_reference: PMID:15608217

Axiom
annotated source: suppression knockout
annotated property: has_exact_synonym
annotated target: suppress knockout
has_synonym_type: Unique short label curated by PSI-MI

suppression partial alteration
type: Class
definition: A mutation is the partial suppressor of a mutant phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789.
has_exact_synonym: suppression partial
has_obo_namespace: PSI-MI
id: MI:0264
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: suppression partial alteration
annotated property: definition
annotated target: A mutation is the partial suppressor of a mutant phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789.
database_cross_reference: PMID:15608217

Axiom
annotated source: suppression partial alteration
annotated property: has_exact_synonym
annotated target: suppression partial
has_synonym_type: Unique short label curated by PSI-MI

suppression expression alteration
type: Class
definition: An altered expression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
has_exact_synonym: suppress expression
has_obo_namespace: PSI-MI
id: MI:0265
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: suppression expression alteration
annotated property: definition
annotated target: An altered expression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
database_cross_reference: PMID:15608217

Axiom
annotated source: suppression expression alteration
annotated property: has_exact_synonym
annotated target: suppress expression
has_synonym_type: Unique short label curated by PSI-MI

suppression overexpression
type: Class
definition: Overexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506.
has_exact_synonym: suppress overexpress
has_obo_namespace: PSI-MI
id: MI:0266
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: suppression overexpression
annotated property: definition
annotated target: Overexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506.
database_cross_reference: PMID:15608217

Axiom
annotated source: suppression overexpression
annotated property: has_exact_synonym
annotated target: suppress overexpress
has_synonym_type: Unique short label curated by PSI-MI

suppression scalable
type: Class
definition: Level of over/underexpression scales the 'extend' of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
has_obo_namespace: PSI-MI
id: MI:0267
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: suppression scalable
annotated property: definition
annotated target: Level of over/underexpression scales the 'extend' of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
database_cross_reference: PMID:15608217

suppression underexpression
type: Class
definition: Underexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223.
has_exact_synonym: suppress underexpres
has_obo_namespace: PSI-MI
id: MI:0268
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: suppression underexpression
annotated property: definition
annotated target: Underexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223.
database_cross_reference: PMID:15608217

Axiom
annotated source: suppression underexpression
annotated property: has_exact_synonym
annotated target: suppress underexpres
has_synonym_type: Unique short label curated by PSI-MI

synthetic phenotype
type: Class
definition: Two silent mutations show an altered phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794.
has_obo_namespace: PSI-MI
id: MI:0269
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: synthetic phenotype
annotated property: definition
annotated target: Two silent mutations show an altered phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794.
database_cross_reference: PMID:15608217

conditional synthetic lethal
type: Class
definition: Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
has_exact_synonym: cond syntetic lethal
has_obo_namespace: PSI-MI
id: MI:0270
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: conditional synthetic lethal
annotated property: definition
annotated target: Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
database_cross_reference: PMID:15608217

Axiom
annotated source: conditional synthetic lethal
annotated property: has_exact_synonym
annotated target: cond syntetic lethal
has_synonym_type: Unique short label curated by PSI-MI

conditional synthetic lethal temperature-sensitivity
type: Class
definition: Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')
has_exact_synonym: temprtr synt lethal
has_obo_namespace: PSI-MI
id: MI:0271
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: conditional synthetic lethal temperature-sensitivity
annotated property: definition
annotated target: Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')
database_cross_reference: PMID:15608217

Axiom
annotated source: conditional synthetic lethal temperature-sensitivity
annotated property: has_exact_synonym
annotated target: temprtr synt lethal
has_synonym_type: Unique short label curated by PSI-MI

synthetic growth effect
type: Class
definition: Two silent mutations show altered growth effect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
has_exact_synonym: synt growth effect
has_obo_namespace: PSI-MI
id: MI:0273
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: synthetic growth effect
annotated property: definition
annotated target: Two silent mutations show altered growth effect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
database_cross_reference: PMID:15608217

Axiom
annotated source: synthetic growth effect
annotated property: has_exact_synonym
annotated target: synt growth effect
has_synonym_type: Unique short label curated by PSI-MI

synthetic growth defect
type: Class
definition: Two silent mutations show growth defect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
has_exact_synonym: synt growth defect
has_obo_namespace: PSI-MI
id: MI:0274
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: synthetic growth defect
annotated property: definition
annotated target: Two silent mutations show growth defect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
database_cross_reference: PMID:15608217

Axiom
annotated source: synthetic growth defect
annotated property: has_exact_synonym
annotated target: synt growth defect
has_synonym_type: Unique short label curated by PSI-MI

synthetic growth increase
type: Class
definition: Two silent mutations show growth increase when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
has_exact_synonym: synt growth increase
has_obo_namespace: PSI-MI
id: MI:0275
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: synthetic growth increase
annotated property: definition
annotated target: Two silent mutations show growth increase when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
database_cross_reference: PMID:15608217

Axiom
annotated source: synthetic growth increase
annotated property: has_exact_synonym
annotated target: synt growth increase
has_synonym_type: Unique short label curated by PSI-MI

blue native page
type: Class
subclass of: comigration in non denaturing gel electrophoresis
definition: Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE.
has_exact_synonym: bn-page
has_obo_namespace: PSI-MI
id: MI:0276
in_subset: PSI-MI slim

Axiom
annotated source: blue native page
annotated property: definition
annotated target: Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE.
database_cross_reference: PMID:14665681

Axiom
annotated source: blue native page
annotated property: has_exact_synonym
annotated target: bn-page
has_synonym_type: Unique short label curated by PSI-MI

alias type
type: Class
subclass of: molecular interaction
definition: Descriptor of type of nomenclature used to describe interactor.
has_exact_synonym: CvAliasType
has_obo_namespace: PSI-MI
id: MI:0300
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: alias type
annotated property: definition
annotated target: Descriptor of type of nomenclature used to describe interactor.
database_cross_reference: PMID:14755292

Axiom
annotated source: alias type
annotated property: has_exact_synonym
annotated target: CvAliasType
has_synonym_type: Alternate label curated by PSI-MI

gene name
type: Class
subclass of: synonym
definition: Gene name.
has_exact_synonym: gene
has_obo_namespace: PSI-MI
id: MI:0301
in_subset: PSI-MI slim

Axiom
annotated source: gene name
annotated property: definition
annotated target: Gene name.
database_cross_reference: PMID:14755292

Axiom
annotated source: gene name
annotated property: has_exact_synonym
annotated target: gene
has_synonym_type: Alternate label curated by PSI-MI

gene name synonym
type: Class
subclass of: synonym
definition: Gene name synonym.
has_obo_namespace: PSI-MI
id: MI:0302
in_subset: PSI-MI slim

Axiom
annotated source: gene name synonym
annotated property: definition
annotated target: Gene name synonym.
database_cross_reference: PMID:14755292

gene ontology synonym
type: Class
subclass of: synonym
definition: Synonym as used in Gene Ontology.
has_exact_synonym: go synonym
has_obo_namespace: PSI-MI
id: MI:0303
in_subset: PSI-MI slim

Axiom
annotated source: gene ontology synonym
annotated property: definition
annotated target: Synonym as used in Gene Ontology.
database_cross_reference: PMID:14755292

Axiom
annotated source: gene ontology synonym
annotated property: has_exact_synonym
annotated target: go synonym
has_synonym_type: Unique short label curated by PSI-MI

isoform synonym
type: Class
subclass of: synonym
definition: Isoform synonym.
has_obo_namespace: PSI-MI
id: MI:0304
in_subset: PSI-MI slim

Axiom
annotated source: isoform synonym
annotated property: definition
annotated target: Isoform synonym.
database_cross_reference: PMID:14755292

ordered locus name
type: Class
subclass of: synonym
definition: A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features.
has_exact_synonym: CDS number
has_exact_synonym: ONL
has_exact_synonym: ORF number
has_exact_synonym: Ordered locus name
has_exact_synonym: locus name
has_exact_synonym: systematic gene number
has_obo_namespace: PSI-MI
id: MI:0305
in_subset: PSI-MI slim
comment: For instance HI0934, Rv3245c, At5g34500, YER456W.

Axiom
annotated source: ordered locus name
annotated property: definition
annotated target: A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features.
database_cross_reference: PMID:14755292

Axiom
annotated source: ordered locus name
annotated property: has_exact_synonym
annotated target: CDS number
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ordered locus name
annotated property: has_exact_synonym
annotated target: ONL
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ordered locus name
annotated property: has_exact_synonym
annotated target: ORF number
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ordered locus name
annotated property: has_exact_synonym
annotated target: Ordered locus name
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ordered locus name
annotated property: has_exact_synonym
annotated target: locus name
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: ordered locus name
annotated property: has_exact_synonym
annotated target: systematic gene number
has_synonym_type: Alternate label curated by PSI-MI

open reading frame name
type: Class
subclass of: synonym
definition: A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system.
has_exact_synonym: orf name
has_obo_namespace: PSI-MI
id: MI:0306
in_subset: PSI-MI slim
comment: For instance MtCY277-28c, SYGP-ORF50, SpBC2F12-04, C06E1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames.

Axiom
annotated source: open reading frame name
annotated property: definition
annotated target: A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system.
database_cross_reference: PMID:14755292

Axiom
annotated source: open reading frame name
annotated property: has_exact_synonym
annotated target: orf name
has_synonym_type: Unique short label curated by PSI-MI

delivery method
type: Class
subclass of: experimental preparation
definition: Method by which molecule is delivered or engineered into a cell.
has_obo_namespace: PSI-MI
id: MI:0307
in_subset: PSI-MI slim

Axiom
annotated source: delivery method
annotated property: definition
annotated target: Method by which molecule is delivered or engineered into a cell.
database_cross_reference: PMID:14755292

electroporation
type: Class
subclass of: delivery method
definition: Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm.
has_obo_namespace: PSI-MI
id: MI:0308
in_subset: PSI-MI slim

Axiom
annotated source: electroporation
annotated property: definition
annotated target: Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm.
database_cross_reference: PMID:6329708

genomic tagging
type: Class
definition: A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control. OBSOLETE redundant term. Map to feature type : tag (MI:0507).
has_exact_synonym: genetic tag insertion
has_obo_namespace: PSI-MI
id: MI:0309
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: genomic tagging
annotated property: definition
annotated target: A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control. OBSOLETE redundant term. Map to feature type : tag (MI:0507).
database_cross_reference: PMID:14755292

Axiom
annotated source: genomic tagging
annotated property: has_exact_synonym
annotated target: genetic tag insertion
has_synonym_type: Alternate label curated by PSI-MI

infection
type: Class
subclass of: delivery method
definition: Molecule introduced into a cell via an external organism, usually a virus or bacteria.
has_obo_namespace: PSI-MI
id: MI:0310
in_subset: PSI-MI slim

Axiom
annotated source: infection
annotated property: definition
annotated target: Molecule introduced into a cell via an external organism, usually a virus or bacteria.
database_cross_reference: PMID:14755292

microinjection
type: Class
subclass of: delivery method
definition: The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed.
has_exact_synonym: micro-injection
has_obo_namespace: PSI-MI
id: MI:0311
in_subset: PSI-MI slim

Axiom
annotated source: microinjection
annotated property: definition
annotated target: The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed.
database_cross_reference: PMID:3016916

Axiom
annotated source: microinjection
annotated property: has_exact_synonym
annotated target: micro-injection
has_synonym_type: Alternate label curated by PSI-MI

nucleic acid transfection
type: Class
subclass of: nucleic acid delivery
definition: Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed.
has_exact_synonym: nucl transfection
has_obo_namespace: PSI-MI
id: MI:0312
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid transfection
annotated property: definition
annotated target: Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid transfection
annotated property: has_exact_synonym
annotated target: nucl transfection
has_synonym_type: Unique short label curated by PSI-MI

interactor type
type: Class
subclass of: molecular interaction
definition: Molecular species involved in the interaction.
has_exact_synonym: participant type
has_obo_namespace: PSI-MI
id: MI:0313
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: interactor type
annotated property: definition
annotated target: Molecular species involved in the interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: interactor type
annotated property: has_exact_synonym
annotated target: participant type
has_synonym_type: Alternate label curated by PSI-MI

complex
type: Class
subclass of: interactor type
definition: Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level.
has_obo_namespace: PSI-MI
id: MI:0314
in_subset: PSI-MI slim

Axiom
annotated source: complex
annotated property: definition
annotated target: Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level.
database_cross_reference: PMID:14755292

protein complex
type: Class
subclass of: complex composition
definition: A stable set of interacting proteins that can be copurified and operate as a functional unit.
has_obo_namespace: PSI-MI
id: MI:0315
in_subset: PSI-MI slim

Axiom
annotated source: protein complex
annotated property: definition
annotated target: A stable set of interacting proteins that can be copurified and operate as a functional unit.
database_cross_reference: PMID:14755292

ribonucleoprotein complex
type: Class
subclass of: complex composition
definition: A macromolecular complex containing both protein and RNA molecules.
has_exact_synonym: protein rna complex
has_exact_synonym: ribonucleoprot compl
has_obo_namespace: PSI-MI
id: MI:0316
in_subset: PSI-MI slim

Axiom
annotated source: ribonucleoprotein complex
annotated property: definition
annotated target: A macromolecular complex containing both protein and RNA molecules.
database_cross_reference: GO:0030529
database_cross_reference: PMID:14755292

Axiom
annotated source: ribonucleoprotein complex
annotated property: has_exact_synonym
annotated target: protein rna complex
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ribonucleoprotein complex
annotated property: has_exact_synonym
annotated target: ribonucleoprot compl
has_synonym_type: Unique short label curated by PSI-MI

interaction
type: Class
subclass of: interactor type
definition: Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes.
has_obo_namespace: PSI-MI
id: MI:0317
in_subset: PSI-MI slim

Axiom
annotated source: interaction
annotated property: definition
annotated target: Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes.
database_cross_reference: PMID:14755292

nucleic acid
type: Class
subclass of: biopolymer
definition: Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages.
has_obo_namespace: PSI-MI
id: MI:0318
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid
annotated property: definition
annotated target: Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages.
database_cross_reference: PMID:14755292
database_cross_reference: SO:0000348

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
definition: Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine.
has_exact_synonym: DNA
has_exact_synonym: deoxyribonucleic acid
has_exact_synonym: dna
has_obo_namespace: PSI-MI
id: MI:0319
in_subset: PSI-MI slim

Axiom
annotated source: deoxyribonucleic acid
annotated property: definition
annotated target: Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine.
database_cross_reference: PMID:14755292
database_cross_reference: SO:0000352

Axiom
annotated source: deoxyribonucleic acid
annotated property: has_exact_synonym
annotated target: DNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: deoxyribonucleic acid
annotated property: has_exact_synonym
annotated target: deoxyribonucleic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: deoxyribonucleic acid
annotated property: has_exact_synonym
annotated target: dna
has_synonym_type: Unique short label curated by PSI-MI

ribonucleic acid
type: Class
subclass of: nucleic acid
definition: Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine.
has_exact_synonym: RNA
has_exact_synonym: rna
has_obo_namespace: PSI-MI
id: MI:0320
in_subset: PSI-MI slim

Axiom
annotated source: ribonucleic acid
annotated property: definition
annotated target: Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine.
database_cross_reference: PMID:14755292
database_cross_reference: SO:0000356

Axiom
annotated source: ribonucleic acid
annotated property: has_exact_synonym
annotated target: RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ribonucleic acid
annotated property: has_exact_synonym
annotated target: rna
has_synonym_type: Unique short label curated by PSI-MI

catalytic rna
type: Class
subclass of: ribonucleic acid
definition: Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link.
has_exact_synonym: catalytic RNA
has_exact_synonym: catalytic ribonucleic acid
has_exact_synonym: crna
has_obo_namespace: PSI-MI
id: MI:0321
in_subset: PSI-MI slim

Axiom
annotated source: catalytic rna
annotated property: definition
annotated target: Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link.
database_cross_reference: PMID:14755292

Axiom
annotated source: catalytic rna
annotated property: has_exact_synonym
annotated target: catalytic RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: catalytic rna
annotated property: has_exact_synonym
annotated target: catalytic ribonucleic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: catalytic rna
annotated property: has_exact_synonym
annotated target: crna
has_synonym_type: Unique short label curated by PSI-MI

guide rna
type: Class
subclass of: ribonucleic acid
definition: Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing.
has_exact_synonym: grna
has_exact_synonym: guide RNA
has_obo_namespace: PSI-MI
id: MI:0322
in_subset: PSI-MI slim

Axiom
annotated source: guide rna
annotated property: definition
annotated target: Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing.
database_cross_reference: PMID:14755292

Axiom
annotated source: guide rna
annotated property: has_exact_synonym
annotated target: grna
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: guide rna
annotated property: has_exact_synonym
annotated target: guide RNA
has_synonym_type: Alternate label curated by PSI-MI

heterogeneous nuclear rna
type: Class
subclass of: ribonucleic acid
definition: A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein.
has_exact_synonym: heterogeneous nuclear RNA
has_exact_synonym: heterogeneous nuclear ribonucleic acid
has_exact_synonym: hnrna
has_obo_namespace: PSI-MI
id: MI:0323
in_subset: PSI-MI slim

Axiom
annotated source: heterogeneous nuclear rna
annotated property: definition
annotated target: A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: heterogeneous nuclear rna
annotated property: has_exact_synonym
annotated target: heterogeneous nuclear RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: heterogeneous nuclear rna
annotated property: has_exact_synonym
annotated target: heterogeneous nuclear ribonucleic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: heterogeneous nuclear rna
annotated property: has_exact_synonym
annotated target: hnrna
has_synonym_type: Unique short label curated by PSI-MI

messenger rna
type: Class
subclass of: ribonucleic acid
definition: Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains.
has_exact_synonym: mRNA
has_exact_synonym: mrna
has_obo_namespace: PSI-MI
id: MI:0324
in_subset: PSI-MI slim

Axiom
annotated source: messenger rna
annotated property: definition
annotated target: Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains.
database_cross_reference: PMID:14755292

Axiom
annotated source: messenger rna
annotated property: has_exact_synonym
annotated target: mRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: messenger rna
annotated property: has_exact_synonym
annotated target: mrna
has_synonym_type: Unique short label curated by PSI-MI

transfer rna
type: Class
subclass of: ribonucleic acid
definition: The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon.
has_exact_synonym: tRNA
has_exact_synonym: transfer RNA
has_exact_synonym: transfer ribonucleic acid
has_exact_synonym: trna
has_obo_namespace: PSI-MI
id: MI:0325
in_subset: PSI-MI slim

Axiom
annotated source: transfer rna
annotated property: definition
annotated target: The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon.
database_cross_reference: PMID:14755292

Axiom
annotated source: transfer rna
annotated property: has_exact_synonym
annotated target: tRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: transfer rna
annotated property: has_exact_synonym
annotated target: transfer RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: transfer rna
annotated property: has_exact_synonym
annotated target: transfer ribonucleic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: transfer rna
annotated property: has_exact_synonym
annotated target: trna
has_synonym_type: Unique short label curated by PSI-MI

protein
type: Class
subclass of: biopolymer
definition: A linear polymer of amino acids joined by peptide bonds in a specific sequence.
has_obo_namespace: PSI-MI
id: MI:0326
in_subset: PSI-MI slim

Axiom
annotated source: protein
annotated property: definition
annotated target: A linear polymer of amino acids joined by peptide bonds in a specific sequence.
database_cross_reference: PMID:14755292
database_cross_reference: SO:0000358

peptide
type: Class
subclass of: biopolymer
definition: Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
has_exact_synonym: oligopeptide
has_exact_synonym: polypeptide
has_obo_namespace: PSI-MI
id: MI:0327
in_subset: PSI-MI slim

Axiom
annotated source: peptide
annotated property: definition
annotated target: Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
database_cross_reference: PMID:14755292

Axiom
annotated source: peptide
annotated property: has_exact_synonym
annotated target: oligopeptide
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: peptide
annotated property: has_exact_synonym
annotated target: polypeptide
has_synonym_type: Alternate label curated by PSI-MI

small molecule
type: Class
subclass of: bioactive entity
definition: Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
has_obo_namespace: PSI-MI
id: MI:0328
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: small molecule
annotated property: definition
annotated target: Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
database_cross_reference: PMID:14755292

unknown participant
type: Class
subclass of: interactor type
definition: Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level.
has_obo_namespace: PSI-MI
id: MI:0329
in_subset: PSI-MI slim

Axiom
annotated source: unknown participant
annotated property: definition
annotated target: Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level.
database_cross_reference: PMID:14755292

molecular source
type: Class
subclass of: experimental preparation
definition: Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process.
has_obo_namespace: PSI-MI
id: MI:0330
in_subset: PSI-MI slim

Axiom
annotated source: molecular source
annotated property: definition
annotated target: Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process.
database_cross_reference: PMID:14755272

engineered
type: Class
subclass of: molecular source
definition: Molecule has been added into system from an external source or altered within the cell.
has_obo_namespace: PSI-MI
id: MI:0331
in_subset: PSI-MI slim

Axiom
annotated source: engineered
annotated property: definition
annotated target: Molecule has been added into system from an external source or altered within the cell.
database_cross_reference: PMID:14755292

naturally occurring
type: Class
subclass of: molecular source
definition: Unaltered endogenous molecule in its naturally occurring state.
has_exact_synonym: endogenous
has_obo_namespace: PSI-MI
id: MI:0332
in_subset: PSI-MI slim

Axiom
annotated source: naturally occurring
annotated property: definition
annotated target: Unaltered endogenous molecule in its naturally occurring state.
database_cross_reference: PMID:14755292

Axiom
annotated source: naturally occurring
annotated property: has_exact_synonym
annotated target: endogenous
has_synonym_type: Alternate label curated by PSI-MI

feature range status
type: Class
subclass of: molecular interaction
definition: Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range.
has_exact_synonym: CvFuzzyType
has_exact_synonym: endStatus
has_exact_synonym: startStatus
has_obo_namespace: PSI-MI
id: MI:0333
in_subset: PSI-MI slim

Axiom
annotated source: feature range status
annotated property: definition
annotated target: Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range.
database_cross_reference: PMID:14755292

Axiom
annotated source: feature range status
annotated property: has_exact_synonym
annotated target: CvFuzzyType
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: feature range status
annotated property: has_exact_synonym
annotated target: endStatus
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: feature range status
annotated property: has_exact_synonym
annotated target: startStatus
has_synonym_type: Alternate label curated by PSI-MI

c-terminal position
type: Class
subclass of: feature range status
definition: Term describing the last amino acid of a peptide chain.
has_exact_synonym: c-term
has_exact_synonym: c-terminal
has_exact_synonym: c-terminus
has_exact_synonym: carboxy-terminus
has_obo_namespace: PSI-MI
id: MI:0334
in_subset: PSI-MI slim
comment: Displayed as 'c'.

Axiom
annotated source: c-terminal position
annotated property: definition
annotated target: Term describing the last amino acid of a peptide chain.
database_cross_reference: PMID:14755292

Axiom
annotated source: c-terminal position
annotated property: has_exact_synonym
annotated target: c-term
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: c-terminal position
annotated property: has_exact_synonym
annotated target: c-terminal
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: c-terminal position
annotated property: has_exact_synonym
annotated target: c-terminus
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: c-terminal position
annotated property: has_exact_synonym
annotated target: carboxy-terminus
has_synonym_type: Alternate label curated by PSI-MI

certain sequence position
type: Class
subclass of: feature range status
definition: Position within the sequence clearly defined.
has_exact_synonym: certain
has_obo_namespace: PSI-MI
id: MI:0335
in_subset: PSI-MI slim

Axiom
annotated source: certain sequence position
annotated property: definition
annotated target: Position within the sequence clearly defined.
database_cross_reference: PMID:14755292

Axiom
annotated source: certain sequence position
annotated property: has_exact_synonym
annotated target: certain
has_synonym_type: Unique short label curated by PSI-MI

greater-than
type: Class
subclass of: feature range status
definition: Partially determined sequence position known to be in a location higher than a given position.
has_obo_namespace: PSI-MI
id: MI:0336
in_subset: PSI-MI slim
comment: Displayed as '>'.

Axiom
annotated source: greater-than
annotated property: definition
annotated target: Partially determined sequence position known to be in a location higher than a given position.
database_cross_reference: PMID:14755292

less-than
type: Class
subclass of: feature range status
definition: Partially determined sequence position known to be in a position lower than a given position.
has_obo_namespace: PSI-MI
id: MI:0337
in_subset: PSI-MI slim
comment: Displayed as '<'.

Axiom
annotated source: less-than
annotated property: definition
annotated target: Partially determined sequence position known to be in a position lower than a given position.
database_cross_reference: PMID:14755292

range
type: Class
subclass of: feature range status
definition: Describes a sequence position known to be in a certain range, where the exact position is unclear.
has_obo_namespace: PSI-MI
id: MI:0338
in_subset: PSI-MI slim
comment: For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'.

Axiom
annotated source: range
annotated property: definition
annotated target: Describes a sequence position known to be in a certain range, where the exact position is unclear.
database_cross_reference: PMID:14755292

undetermined sequence position
type: Class
subclass of: feature range status
definition: Term describing a completely unknown or unspecified sequence position.
has_exact_synonym: undetermined
has_obo_namespace: PSI-MI
id: MI:0339
in_subset: PSI-MI slim
comment: Displayed as '?'.

Axiom
annotated source: undetermined sequence position
annotated property: definition
annotated target: Term describing a completely unknown or unspecified sequence position.
database_cross_reference: PMID:14755292

Axiom
annotated source: undetermined sequence position
annotated property: has_exact_synonym
annotated target: undetermined
has_synonym_type: Unique short label curated by PSI-MI

n-terminal position
type: Class
subclass of: feature range status
definition: Term describing the first amino acid of a peptide chain.
has_exact_synonym: amino-terminus
has_exact_synonym: n-term
has_exact_synonym: n-terminal
has_exact_synonym: n-terminus
has_obo_namespace: PSI-MI
id: MI:0340
in_subset: PSI-MI slim
comment: Displayed as 'n'.

Axiom
annotated source: n-terminal position
annotated property: definition
annotated target: Term describing the first amino acid of a peptide chain.
database_cross_reference: PMID:14755292

Axiom
annotated source: n-terminal position
annotated property: has_exact_synonym
annotated target: amino-terminus
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-terminal position
annotated property: has_exact_synonym
annotated target: n-term
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n-terminal position
annotated property: has_exact_synonym
annotated target: n-terminal
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: n-terminal position
annotated property: has_exact_synonym
annotated target: n-terminus
has_synonym_type: Alternate label curated by PSI-MI

ragged n-terminus
type: Class
subclass of: n-terminal position
definition: Mixture of protein forms where N-terminus has been progressively truncated.
has_obo_namespace: PSI-MI
id: MI:0341
in_subset: PSI-MI slim

Axiom
annotated source: ragged n-terminus
annotated property: definition
annotated target: Mixture of protein forms where N-terminus has been progressively truncated.
database_cross_reference: PMID:14755292

sample process
type: Class
subclass of: experimental preparation
definition: Indicates the sample context in which each interacting molecule is presented to its partner.
has_obo_namespace: PSI-MI
id: MI:0342
in_subset: PSI-MI slim

Axiom
annotated source: sample process
annotated property: definition
annotated target: Indicates the sample context in which each interacting molecule is presented to its partner.
database_cross_reference: PMID:14755292

cdna library
type: Class
subclass of: sample process
definition: Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
has_obo_namespace: PSI-MI
id: MI:0343
in_subset: PSI-MI slim

Axiom
annotated source: cdna library
annotated property: definition
annotated target: Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
database_cross_reference: PMID:6110205

cell lysate
type: Class
subclass of: sample process
definition: Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components.
has_obo_namespace: PSI-MI
id: MI:0344
in_subset: PSI-MI slim

Axiom
annotated source: cell lysate
annotated property: definition
annotated target: Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components.
database_cross_reference: PMID:14755292

author assigned name
type: Class
subclass of: synonym
definition: Name assigned to a molecule by the authors within a paper that may differ from the reference database.
has_obo_namespace: PSI-MI
id: MI:0345
in_subset: PSI-MI slim

Axiom
annotated source: author assigned name
annotated property: definition
annotated target: Name assigned to a molecule by the authors within a paper that may differ from the reference database.
database_cross_reference: PMID:14755292

experimental preparation
type: Class
subclass of: molecular interaction
definition: Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list.
has_exact_synonym: experimental prep
has_obo_namespace: PSI-MI
id: MI:0346
in_subset: PSI-MI slim

Axiom
annotated source: experimental preparation
annotated property: definition
annotated target: Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list.
database_cross_reference: PMID:14755292

Axiom
annotated source: experimental preparation
annotated property: has_exact_synonym
annotated target: experimental prep
has_synonym_type: Unique short label curated by PSI-MI

fixed cell
type: Class
subclass of: sample process
definition: Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis.
has_obo_namespace: PSI-MI
id: MI:0348
in_subset: PSI-MI slim

Axiom
annotated source: fixed cell
annotated property: definition
annotated target: Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis.
database_cross_reference: PMID:14755292

living cell
type: Class
subclass of: sample process
definition: Molecule is observed within in a living cell.
has_obo_namespace: PSI-MI
id: MI:0349
in_subset: PSI-MI slim

Axiom
annotated source: living cell
annotated property: definition
annotated target: Molecule is observed within in a living cell.
database_cross_reference: PMID:14755292

purified
type: Class
subclass of: sample process
definition: Molecule has undergone one or more purification steps to isolate it from the cellular environment.
has_obo_namespace: PSI-MI
id: MI:0350
in_subset: PSI-MI slim

Axiom
annotated source: purified
annotated property: definition
annotated target: Molecule has undergone one or more purification steps to isolate it from the cellular environment.
database_cross_reference: PMID:14755292

homogeneous
type: Class
subclass of: purified
definition: The author states a molecule is completely pure, i.e. no other molecular species are present.
has_exact_synonym: pure
has_obo_namespace: PSI-MI
id: MI:0351
in_subset: PSI-MI slim

Axiom
annotated source: homogeneous
annotated property: definition
annotated target: The author states a molecule is completely pure, i.e. no other molecular species are present.
database_cross_reference: PMID:14755292

Axiom
annotated source: homogeneous
annotated property: has_exact_synonym
annotated target: pure
has_synonym_type: Alternate label curated by PSI-MI

partially purified
type: Class
subclass of: purified
definition: The author states a molecule is only partially purified, i.e. other molecular species also known to be present.
has_obo_namespace: PSI-MI
id: MI:0352
in_subset: PSI-MI slim

Axiom
annotated source: partially purified
annotated property: definition
annotated target: The author states a molecule is only partially purified, i.e. other molecular species also known to be present.
database_cross_reference: PMID:14755292

cross-reference type
type: Class
subclass of: molecular interaction
definition: Qualifier to describe the type of information a cross-reference is pointing to.
has_exact_synonym: CvXrefQualifier
has_exact_synonym: refType
has_exact_synonym: xref type
has_obo_namespace: PSI-MI
id: MI:0353
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: cross-reference type
annotated property: definition
annotated target: Qualifier to describe the type of information a cross-reference is pointing to.
database_cross_reference: PMID:14755292

Axiom
annotated source: cross-reference type
annotated property: has_exact_synonym
annotated target: CvXrefQualifier
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cross-reference type
annotated property: has_exact_synonym
annotated target: refType
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cross-reference type
annotated property: has_exact_synonym
annotated target: xref type
has_synonym_type: Unique short label curated by PSI-MI

cellular component
type: Class
subclass of: cross-reference type
definition: Cross reference pointing to a Gene Ontology -'cellular component' term.
database_cross_reference: search-url:
has_exact_synonym: component
has_exact_synonym: go component term
has_obo_namespace: PSI-MI
id: MI:0354
in_subset: PSI-MI slim

Axiom
annotated source: cellular component
annotated property: definition
annotated target: Cross reference pointing to a Gene Ontology -'cellular component' term.
database_cross_reference: PMID:14681407

Axiom
annotated source: cellular component
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.ebi.ac.uk/QuickGO/term/${ac}

Axiom
annotated source: cellular component
annotated property: has_exact_synonym
annotated target: component
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: cellular component
annotated property: has_exact_synonym
annotated target: go component term
has_synonym_type: Alternate label curated by PSI-MI

molecular function
type: Class
subclass of: cross-reference type
definition: Cross reference pointing to a Gene Ontology -'molecular function' term.
database_cross_reference: search-url:
has_exact_synonym: function
has_exact_synonym: go function term
has_obo_namespace: PSI-MI
id: MI:0355
in_subset: PSI-MI slim

Axiom
annotated source: molecular function
annotated property: definition
annotated target: Cross reference pointing to a Gene Ontology -'molecular function' term.
database_cross_reference: PMID:14681407

Axiom
annotated source: molecular function
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.ebi.ac.uk/QuickGO/term/${ac}

Axiom
annotated source: molecular function
annotated property: has_exact_synonym
annotated target: function
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: molecular function
annotated property: has_exact_synonym
annotated target: go function term
has_synonym_type: Alternate label curated by PSI-MI

identical object in an external resource
type: Class
subclass of: cross-reference type
definition: Reference to the corresponding object in another database. Correspondence may be complete or partial.
has_exact_synonym: identity
has_obo_namespace: PSI-MI
id: MI:0356
in_subset: Drugable
in_subset: PSI-MI slim
comment: For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database.

Axiom
annotated source: identical object in an external resource
annotated property: definition
annotated target: Reference to the corresponding object in another database. Correspondence may be complete or partial.
database_cross_reference: PMID:14755292

Axiom
annotated source: identical object in an external resource
annotated property: has_exact_synonym
annotated target: identity
has_synonym_type: Unique short label curated by PSI-MI

method reference
type: Class
subclass of: cross-reference type
definition: Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment.
has_obo_namespace: PSI-MI
id: MI:0357
in_subset: PSI-MI slim

Axiom
annotated source: method reference
annotated property: definition
annotated target: Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment.
database_cross_reference: PMID:14755292

primary-reference
type: Class
subclass of: cross-reference type
definition: Used to indicate the PMID from which the experimental data is extracted.
has_obo_namespace: PSI-MI
id: MI:0358
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: primary-reference
annotated property: definition
annotated target: Used to indicate the PMID from which the experimental data is extracted.
database_cross_reference: PMID:14755292

biological process
type: Class
subclass of: cross-reference type
definition: Cross reference pointing to a Gene Ontology -'cellular process' term.
database_cross_reference: search-url:
has_exact_synonym: go process term
has_exact_synonym: process
has_obo_namespace: PSI-MI
id: MI:0359
in_subset: PSI-MI slim

Axiom
annotated source: biological process
annotated property: definition
annotated target: Cross reference pointing to a Gene Ontology -'cellular process' term.
database_cross_reference: PMID:14681407

Axiom
annotated source: biological process
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.ebi.ac.uk/QuickGO/term/${ac}

Axiom
annotated source: biological process
annotated property: has_exact_synonym
annotated target: go process term
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: biological process
annotated property: has_exact_synonym
annotated target: process
has_synonym_type: Unique short label curated by PSI-MI

secondary accession number
type: Class
subclass of: cross-reference type
definition: Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number.
has_exact_synonym: secondary-ac
has_obo_namespace: PSI-MI
id: MI:0360
in_subset: PSI-MI slim

Axiom
annotated source: secondary accession number
annotated property: definition
annotated target: Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number.
database_cross_reference: PMID:14755292

Axiom
annotated source: secondary accession number
annotated property: has_exact_synonym
annotated target: secondary-ac
has_synonym_type: Unique short label curated by PSI-MI

additional information
type: Class
subclass of: cross-reference type
definition: Related object within the same database or pointing to an external database.
has_exact_synonym: see-also
has_obo_namespace: PSI-MI
id: MI:0361
in_subset: PSI-MI slim

Axiom
annotated source: additional information
annotated property: definition
annotated target: Related object within the same database or pointing to an external database.
database_cross_reference: PMID:14755292

Axiom
annotated source: additional information
annotated property: has_exact_synonym
annotated target: see-also
has_synonym_type: Unique short label curated by PSI-MI

inference
type: Class
subclass of: interaction detection method
subclass of: participant identification method
subclass of: feature detection method
definition: Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
has_exact_synonym: modeled
has_exact_synonym: modelled
has_obo_namespace: PSI-MI
id: MI:0362
in_subset: PSI-MI slim

Axiom
annotated source: inference
annotated property: definition
annotated target: Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
database_cross_reference: PMID:14755292

Axiom
annotated source: inference
annotated property: has_exact_synonym
annotated target: modeled
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: inference
annotated property: has_exact_synonym
annotated target: modelled
has_synonym_type: Alternate label curated by PSI-MI

inferred by author
type: Class
subclass of: inference
definition: Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
has_exact_synonym: modeled by author
has_exact_synonym: modelled by author
has_obo_namespace: PSI-MI
id: MI:0363
in_subset: PSI-MI slim

Axiom
annotated source: inferred by author
annotated property: definition
annotated target: Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
database_cross_reference: PMID:14755292

Axiom
annotated source: inferred by author
annotated property: has_exact_synonym
annotated target: modeled by author
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: inferred by author
annotated property: has_exact_synonym
annotated target: modelled by author
has_synonym_type: Alternate label curated by PSI-MI

inferred by curator
type: Class
subclass of: inference
definition: Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
has_exact_synonym: modeled by curator
has_exact_synonym: modelled by curator
has_obo_namespace: PSI-MI
id: MI:0364
in_subset: PSI-MI slim

Axiom
annotated source: inferred by curator
annotated property: definition
annotated target: Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
database_cross_reference: PMID:14755292

Axiom
annotated source: inferred by curator
annotated property: has_exact_synonym
annotated target: modeled by curator
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: inferred by curator
annotated property: has_exact_synonym
annotated target: modelled by curator
has_synonym_type: Alternate label curated by PSI-MI

enzyme tag
type: Class
subclass of: fusion protein
definition: Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein.
has_obo_namespace: PSI-MI
id: MI:0365
in_subset: PSI-MI slim

Axiom
annotated source: enzyme tag
annotated property: definition
annotated target: Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein.
database_cross_reference: PMID:10935637

alkaline phosphatase tag
type: Class
subclass of: enzyme tag
definition: Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
has_exact_synonym: alk phosphatase tag
has_obo_namespace: PSI-MI
id: MI:0366
in_subset: PSI-MI slim

Axiom
annotated source: alkaline phosphatase tag
annotated property: definition
annotated target: Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
database_cross_reference: PMID:10935637

Axiom
annotated source: alkaline phosphatase tag
annotated property: has_exact_synonym
annotated target: alk phosphatase tag
has_synonym_type: Unique short label curated by PSI-MI

green fluorescent protein tag
type: Class
subclass of: fluorescent protein tag
definition: The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
has_exact_synonym: GFP
has_exact_synonym: gfp tag
has_exact_synonym: green fluorescent protein
has_obo_namespace: PSI-MI
id: MI:0367
in_subset: PSI-MI slim

Axiom
annotated source: green fluorescent protein tag
annotated property: definition
annotated target: The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
database_cross_reference: PMID:7491768

Axiom
annotated source: green fluorescent protein tag
annotated property: has_exact_synonym
annotated target: GFP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: green fluorescent protein tag
annotated property: has_exact_synonym
annotated target: gfp tag
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: green fluorescent protein tag
annotated property: has_exact_synonym
annotated target: green fluorescent protein
has_synonym_type: Alternate label curated by PSI-MI

yellow fluorescent protein tag
type: Class
subclass of: fluorescent protein tag
definition: Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
has_exact_synonym: YFP
has_exact_synonym: yellow fluorescent protein
has_exact_synonym: yfp tag
has_obo_namespace: PSI-MI
id: MI:0368
in_subset: PSI-MI slim

Axiom
annotated source: yellow fluorescent protein tag
annotated property: definition
annotated target: Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
database_cross_reference: PMID:10929120

Axiom
annotated source: yellow fluorescent protein tag
annotated property: has_exact_synonym
annotated target: YFP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: yellow fluorescent protein tag
annotated property: has_exact_synonym
annotated target: yellow fluorescent protein
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: yellow fluorescent protein tag
annotated property: has_exact_synonym
annotated target: yfp tag
has_synonym_type: Unique short label curated by PSI-MI

lex-a dimerization assay
type: Class
subclass of: transcriptional complementation assay
definition: The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system.
has_exact_synonym: gallex
has_obo_namespace: PSI-MI
id: MI:0369
in_subset: PSI-MI slim

Axiom
annotated source: lex-a dimerization assay
annotated property: definition
annotated target: The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system.
database_cross_reference: PMID:12446730

Axiom
annotated source: lex-a dimerization assay
annotated property: has_exact_synonym
annotated target: gallex
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: lex-a dimerization assay
annotated property: has_exact_synonym
annotated target: gallex
has_synonym_type: Unique short label curated by PSI-MI

tox-r dimerization assay
type: Class
subclass of: protein complementation assay
definition: This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts.
has_exact_synonym: toxcat
has_obo_namespace: PSI-MI
id: MI:0370
in_subset: PSI-MI slim

Axiom
annotated source: tox-r dimerization assay
annotated property: definition
annotated target: This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts.
database_cross_reference: PMID:9927659

Axiom
annotated source: tox-r dimerization assay
annotated property: has_exact_synonym
annotated target: toxcat
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: tox-r dimerization assay
annotated property: has_exact_synonym
annotated target: toxcat
has_synonym_type: Unique short label curated by PSI-MI

35s radiolabel
type: Class
subclass of: radiolabel
definition: Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium.
has_exact_synonym: 35S
has_exact_synonym: S35
has_exact_synonym: s35 radiolabelled
has_obo_namespace: PSI-MI
id: MI:0371
in_subset: PSI-MI slim

Axiom
annotated source: 35s radiolabel
annotated property: definition
annotated target: Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium.
database_cross_reference: PMID:14755292

Axiom
annotated source: 35s radiolabel
annotated property: has_exact_synonym
annotated target: 35S
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 35s radiolabel
annotated property: has_exact_synonym
annotated target: S35
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 35s radiolabel
annotated property: has_exact_synonym
annotated target: s35 radiolabelled
has_synonym_type: Alternate label curated by PSI-MI

subcellular preparation
type: Class
subclass of: cell lysate
definition: Cell lysates are partially fractionated to isolate a specific subcellular fraction.
has_exact_synonym: subcellular prep
has_obo_namespace: PSI-MI
id: MI:0372
in_subset: PSI-MI slim

Axiom
annotated source: subcellular preparation
annotated property: definition
annotated target: Cell lysates are partially fractionated to isolate a specific subcellular fraction.
database_cross_reference: PMID:14755292

Axiom
annotated source: subcellular preparation
annotated property: has_exact_synonym
annotated target: subcellular prep
has_synonym_type: Unique short label curated by PSI-MI

dye label
type: Class
subclass of: experimental feature
definition: Dye coupled to a molecule allowing its identification isolation and monitoring.
has_exact_synonym: dye labelled
has_obo_namespace: PSI-MI
id: MI:0373
in_subset: PSI-MI slim

Axiom
annotated source: dye label
annotated property: definition
annotated target: Dye coupled to a molecule allowing its identification isolation and monitoring.
database_cross_reference: PMID:14577292

Axiom
annotated source: dye label
annotated property: has_exact_synonym
annotated target: dye labelled
has_synonym_type: Unique short label curated by PSI-MI

cyanine label
type: Class
subclass of: dye label
subclass of: fluorescent dye label
definition: The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids.
has_obo_namespace: PSI-MI
id: MI:0374
in_subset: PSI-MI slim

Axiom
annotated source: cyanine label
annotated property: definition
annotated target: The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids.
database_cross_reference: PMID:14577292

cy3 label
type: Class
subclass of: cyanine label
definition: The organic cyanine Cy3 emits maximally at 570 nm.
has_obo_namespace: PSI-MI
id: MI:0375
in_subset: PSI-MI slim

Axiom
annotated source: cy3 label
annotated property: definition
annotated target: The organic cyanine Cy3 emits maximally at 570 nm.
database_cross_reference: PMID:14577292

cy5 label
type: Class
subclass of: cyanine label
definition: The organic cyanine Cy5 emits maximally at 670 nm.
has_obo_namespace: PSI-MI
id: MI:0376
in_subset: PSI-MI slim

Axiom
annotated source: cy5 label
annotated property: definition
annotated target: The organic cyanine Cy5 emits maximally at 670 nm.
database_cross_reference: PMID:14577292

fluorescein isothiocyanate label
type: Class
subclass of: fluorescein label
definition: Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm.
has_exact_synonym: FITC labelled
has_exact_synonym: fitc labelled
has_exact_synonym: fluorescein isothiocyanate labbeled
has_obo_namespace: PSI-MI
id: MI:0377
in_subset: PSI-MI slim

Axiom
annotated source: fluorescein isothiocyanate label
annotated property: definition
annotated target: Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm.
database_cross_reference: PMID:14577292

Axiom
annotated source: fluorescein isothiocyanate label
annotated property: has_exact_synonym
annotated target: FITC labelled
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fluorescein isothiocyanate label
annotated property: has_exact_synonym
annotated target: fitc labelled
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: fluorescein isothiocyanate label
annotated property: has_exact_synonym
annotated target: fluorescein isothiocyanate labbeled
has_synonym_type: Alternate label curated by PSI-MI

rare isotope label
type: Class
subclass of: isotope label
definition: Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
has_exact_synonym: rare isotope label
has_obo_namespace: PSI-MI
id: MI:0378
in_subset: PSI-MI slim

Axiom
annotated source: rare isotope label
annotated property: definition
annotated target: Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
database_cross_reference: PMID:14577292

Axiom
annotated source: rare isotope label
annotated property: has_exact_synonym
annotated target: rare isotope label
has_synonym_type: Unique short label curated by PSI-MI

13c label
type: Class
subclass of: rare isotope label
definition: Molecules labelled with isotope 13 of carbon atoms.
has_exact_synonym: 13C
has_exact_synonym: C13
has_obo_namespace: PSI-MI
id: MI:0379
in_subset: PSI-MI slim

Axiom
annotated source: 13c label
annotated property: definition
annotated target: Molecules labelled with isotope 13 of carbon atoms.
database_cross_reference: PMID:14577292

Axiom
annotated source: 13c label
annotated property: has_exact_synonym
annotated target: 13C
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 13c label
annotated property: has_exact_synonym
annotated target: C13
has_synonym_type: Alternate label curated by PSI-MI

15n label
type: Class
subclass of: rare isotope label
definition: Molecules labelled with isotope 15 of nytrogen atoms.
has_exact_synonym: 15N
has_exact_synonym: N15
has_obo_namespace: PSI-MI
id: MI:0380
in_subset: PSI-MI slim

Axiom
annotated source: 15n label
annotated property: definition
annotated target: Molecules labelled with isotope 15 of nytrogen atoms.
database_cross_reference: PMID:14577292

Axiom
annotated source: 15n label
annotated property: has_exact_synonym
annotated target: 15N
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 15n label
annotated property: has_exact_synonym
annotated target: N15
has_synonym_type: Alternate label curated by PSI-MI

2h label
type: Class
subclass of: rare isotope label
definition: Molecules labelled with isotope 2 of hydrogen atoms.
has_exact_synonym: 2H2
has_exact_synonym: D2
has_exact_synonym: deuterium
has_obo_namespace: PSI-MI
id: MI:0381
in_subset: PSI-MI slim

Axiom
annotated source: 2h label
annotated property: definition
annotated target: Molecules labelled with isotope 2 of hydrogen atoms.
database_cross_reference: PMID:14577292

Axiom
annotated source: 2h label
annotated property: has_exact_synonym
annotated target: 2H2
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 2h label
annotated property: has_exact_synonym
annotated target: D2
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 2h label
annotated property: has_exact_synonym
annotated target: deuterium
has_synonym_type: Alternate label curated by PSI-MI

mutation increasing interaction
type: Class
subclass of: mutation
definition: Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
has_exact_synonym: mutation increasing
has_obo_namespace: PSI-MI
id: MI:0382
in_subset: PSI-MI slim

Axiom
annotated source: mutation increasing interaction
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
database_cross_reference: PMID:14577292

Axiom
annotated source: mutation increasing interaction
annotated property: has_exact_synonym
annotated target: mutation increasing
has_synonym_type: Unique short label curated by PSI-MI

biopolymer
type: Class
subclass of: interactor type
definition: Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
has_obo_namespace: PSI-MI
id: MI:0383
in_subset: PSI-MI slim

Axiom
annotated source: biopolymer
annotated property: definition
annotated target: Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
database_cross_reference: PMID:14577292

alexa label
type: Class
subclass of: fluorescent dye label
definition: All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm).
has_obo_namespace: PSI-MI
id: MI:0384
in_subset: PSI-MI slim

Axiom
annotated source: alexa label
annotated property: definition
annotated target: All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm).
database_cross_reference: PMID:10449539

alexa 350 label
type: Class
subclass of: alexa label
definition: Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm.
has_obo_namespace: PSI-MI
id: MI:0385
in_subset: PSI-MI slim

Axiom
annotated source: alexa 350 label
annotated property: definition
annotated target: Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm.
database_cross_reference: PMID:10449539

alexa 430 label
type: Class
subclass of: alexa label
definition: Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm.
has_obo_namespace: PSI-MI
id: MI:0386
in_subset: PSI-MI slim

Axiom
annotated source: alexa 430 label
annotated property: definition
annotated target: Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm.
database_cross_reference: PMID:10449539

alexa 488 label
type: Class
subclass of: alexa label
definition: Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm.
has_obo_namespace: PSI-MI
id: MI:0387
in_subset: PSI-MI slim

Axiom
annotated source: alexa 488 label
annotated property: definition
annotated target: Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm.
database_cross_reference: PMID:10449539

alexa 532 label
type: Class
subclass of: alexa label
definition: Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm.
has_obo_namespace: PSI-MI
id: MI:0388
in_subset: PSI-MI slim

Axiom
annotated source: alexa 532 label
annotated property: definition
annotated target: Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm.
database_cross_reference: PMID:10449539

alexa 546 label
type: Class
subclass of: alexa label
definition: Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm.
has_obo_namespace: PSI-MI
id: MI:0389
in_subset: PSI-MI slim

Axiom
annotated source: alexa 546 label
annotated property: definition
annotated target: Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm.
database_cross_reference: PMID:10449539

alexa 568 label
type: Class
subclass of: alexa label
definition: Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm.
has_obo_namespace: PSI-MI
id: MI:0390
in_subset: PSI-MI slim

Axiom
annotated source: alexa 568 label
annotated property: definition
annotated target: Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm.
database_cross_reference: PMID:10449539

alexa 594 label
type: Class
subclass of: alexa label
definition: Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm.
has_obo_namespace: PSI-MI
id: MI:0391
in_subset: PSI-MI slim

Axiom
annotated source: alexa 594 label
annotated property: definition
annotated target: Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm.
database_cross_reference: PMID:10449539

predetermined participant
type: Class
subclass of: experimental participant identification
definition: Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
has_exact_synonym: predetermined
has_obo_namespace: PSI-MI
id: MI:0396
in_subset: PSI-MI slim

Axiom
annotated source: predetermined participant
annotated property: definition
annotated target: Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
database_cross_reference: PMID:14755292

Axiom
annotated source: predetermined participant
annotated property: has_exact_synonym
annotated target: predetermined
has_synonym_type: Unique short label curated by PSI-MI

two hybrid array
type: Class
subclass of: two hybrid
definition: Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames.
has_obo_namespace: PSI-MI
id: MI:0397
in_subset: PSI-MI slim

Axiom
annotated source: two hybrid array
annotated property: definition
annotated target: Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames.
database_cross_reference: PMID:10688190
database_cross_reference: PMID:11827624

two hybrid pooling approach
type: Class
subclass of: two hybrid
definition: In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results.
has_exact_synonym: two hybrid pooling
has_obo_namespace: PSI-MI
id: MI:0398
in_subset: PSI-MI slim

Axiom
annotated source: two hybrid pooling approach
annotated property: definition
annotated target: In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results.
database_cross_reference: PMID:11283351
database_cross_reference: PMID:20946815

Axiom
annotated source: two hybrid pooling approach
annotated property: has_exact_synonym
annotated target: two hybrid pooling
has_synonym_type: Unique short label curated by PSI-MI

two hybrid fragment pooling approach
type: Class
subclass of: two hybrid prey pooling approach
definition: Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen.
has_exact_synonym: 2h fragment pooling
has_obo_namespace: PSI-MI
id: MI:0399
in_subset: PSI-MI slim

Axiom
annotated source: two hybrid fragment pooling approach
annotated property: definition
annotated target: Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen.
database_cross_reference: PMID:12634794

Axiom
annotated source: two hybrid fragment pooling approach
annotated property: has_exact_synonym
annotated target: 2h fragment pooling
has_synonym_type: Unique short label curated by PSI-MI

affinity technology
type: Class
subclass of: biochemical
definition: Techniques which depend upon the strength of the interaction between two entities.
has_exact_synonym: affinity techniques
has_obo_namespace: PSI-MI
id: MI:0400
in_subset: PSI-MI slim

Axiom
annotated source: affinity technology
annotated property: definition
annotated target: Techniques which depend upon the strength of the interaction between two entities.
database_cross_reference: PMID:14755292

Axiom
annotated source: affinity technology
annotated property: has_exact_synonym
annotated target: affinity techniques
has_synonym_type: Unique short label curated by PSI-MI

biochemical
type: Class
subclass of: experimental interaction detection
definition: The application of chemical principles and methods to biological experiments to demonstrate an interaction.
has_obo_namespace: PSI-MI
id: MI:0401
in_subset: PSI-MI slim

Axiom
annotated source: biochemical
annotated property: definition
annotated target: The application of chemical principles and methods to biological experiments to demonstrate an interaction.
database_cross_reference: PMID:14755292

chromatin immunoprecipitation assay
type: Class
subclass of: coimmunoprecipitation
definition: Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques
has_exact_synonym: ch-ip
has_obo_namespace: PSI-MI
id: MI:0402
in_subset: PSI-MI slim

Axiom
annotated source: chromatin immunoprecipitation assay
annotated property: definition
annotated target: Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques
database_cross_reference: PMID:12054902

Axiom
annotated source: chromatin immunoprecipitation assay
annotated property: has_exact_synonym
annotated target: ch-ip
has_synonym_type: Unique short label curated by PSI-MI

colocalization
type: Class
subclass of: interaction type
definition: Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
has_obo_namespace: PSI-MI
id: MI:0403
in_subset: PSI-MI slim

Axiom
annotated source: colocalization
annotated property: definition
annotated target: Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
database_cross_reference: PMID:14755292

comigration in non denaturing gel electrophoresis
type: Class
subclass of: comigration in gel electrophoresis
definition: A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel.
has_exact_synonym: comig non denat gel
has_obo_namespace: PSI-MI
id: MI:0404
in_subset: PSI-MI slim

Axiom
annotated source: comigration in non denaturing gel electrophoresis
annotated property: definition
annotated target: A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel.
database_cross_reference: PMID:14755292

Axiom
annotated source: comigration in non denaturing gel electrophoresis
annotated property: has_exact_synonym
annotated target: comig non denat gel
has_synonym_type: Unique short label curated by PSI-MI

competition binding
type: Class
subclass of: affinity technology
definition: Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor.
has_obo_namespace: PSI-MI
id: MI:0405
in_subset: PSI-MI slim

Axiom
annotated source: competition binding
annotated property: definition
annotated target: Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor.
database_cross_reference: PMID:14755292

deacetylase assay
type: Class
subclass of: enzymatic study
definition: Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
has_obo_namespace: PSI-MI
id: MI:0406
in_subset: PSI-MI slim

Axiom
annotated source: deacetylase assay
annotated property: definition
annotated target: Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
database_cross_reference: PMID:14755292

direct interaction
type: Class
subclass of: physical association
definition: Interaction between molecules that are in direct contact with each other.
has_obo_namespace: PSI-MI
id: MI:0407
in_subset: PSI-MI slim

Axiom
annotated source: direct interaction
annotated property: definition
annotated target: Interaction between molecules that are in direct contact with each other.
database_cross_reference: PMID:14755292

disulfide bond
type: Class
subclass of: covalent binding
definition: Covalent bond mediated by 2 sulfur atoms.
has_exact_synonym: SS-bond
has_exact_synonym: disulfide bridge
has_obo_namespace: PSI-MI
id: MI:0408
in_subset: PSI-MI slim

Axiom
annotated source: disulfide bond
annotated property: definition
annotated target: Covalent bond mediated by 2 sulfur atoms.
database_cross_reference: PMID:14755292

Axiom
annotated source: disulfide bond
annotated property: has_exact_synonym
annotated target: SS-bond
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: disulfide bond
annotated property: has_exact_synonym
annotated target: disulfide bridge
has_synonym_type: Alternate label curated by PSI-MI

dna footprinting
type: Class
definition: Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding. OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA' replace by:MI:0417
has_obo_namespace: PSI-MI
id: MI:0409
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: dna footprinting
annotated property: definition
annotated target: Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding. OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA' replace by:MI:0417
database_cross_reference: PMID:14755292

3D electron microscopy
type: Class
subclass of: transmission electron microscopy
definition: Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
has_exact_synonym: 3D-EM
has_exact_synonym: electron tomog
has_obo_namespace: PSI-MI
id: MI:0410
in_subset: PSI-MI slim

Axiom
annotated source: 3D electron microscopy
annotated property: definition
annotated target: Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
database_cross_reference: PMID:12160704

Axiom
annotated source: 3D electron microscopy
annotated property: has_exact_synonym
annotated target: 3D-EM
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: 3D electron microscopy
annotated property: has_exact_synonym
annotated target: electron tomog
has_synonym_type: Alternate label curated by PSI-MI

enzyme linked immunosorbent assay
type: Class
subclass of: identification by antibody
subclass of: solid phase assay
definition: Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein).
has_exact_synonym: ELISA
has_exact_synonym: elisa
has_obo_namespace: PSI-MI
id: MI:0411
in_subset: PSI-MI slim

Axiom
annotated source: enzyme linked immunosorbent assay
annotated property: definition
annotated target: Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein).
database_cross_reference: PMID:11906746

Axiom
annotated source: enzyme linked immunosorbent assay
annotated property: has_exact_synonym
annotated target: ELISA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: enzyme linked immunosorbent assay
annotated property: has_exact_synonym
annotated target: elisa
has_synonym_type: Unique short label curated by PSI-MI

electrophoretic mobility supershift assay
type: Class
subclass of: electrophoretic mobility shift assay
definition: The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified.
has_exact_synonym: emsa supershift
has_obo_namespace: PSI-MI
id: MI:0412
in_subset: PSI-MI slim

Axiom
annotated source: electrophoretic mobility supershift assay
annotated property: definition
annotated target: The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified.
database_cross_reference: PMID:12169687

Axiom
annotated source: electrophoretic mobility supershift assay
annotated property: has_exact_synonym
annotated target: emsa supershift
has_synonym_type: Unique short label curated by PSI-MI

electrophoretic mobility shift assay
type: Class
subclass of: comigration in gel electrophoresis
definition: This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed.
has_exact_synonym: Gel retardation assay
has_exact_synonym: band shift
has_exact_synonym: emsa
has_obo_namespace: PSI-MI
id: MI:0413
in_subset: PSI-MI slim

Axiom
annotated source: electrophoretic mobility shift assay
annotated property: definition
annotated target: This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed.
database_cross_reference: PMID:12169687

Axiom
annotated source: electrophoretic mobility shift assay
annotated property: has_exact_synonym
annotated target: Gel retardation assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: electrophoretic mobility shift assay
annotated property: has_exact_synonym
annotated target: band shift
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: electrophoretic mobility shift assay
annotated property: has_exact_synonym
annotated target: emsa
has_synonym_type: Unique short label curated by PSI-MI

enzymatic reaction
type: Class
subclass of: direct interaction
definition: terms aiming to represent biochemical reactions referring to their resulting product modifications.
has_exact_synonym: Biochemical reaction
has_obo_namespace: PSI-MI
id: MI:0414
in_subset: PSI-MI slim

Axiom
annotated source: enzymatic reaction
annotated property: definition
annotated target: terms aiming to represent biochemical reactions referring to their resulting product modifications.
database_cross_reference: PMID:14755292

Axiom
annotated source: enzymatic reaction
annotated property: has_exact_synonym
annotated target: Biochemical reaction
has_synonym_type: Alternate label curated by PSI-MI

enzymatic study
type: Class
subclass of: biochemical
definition: Participants are enzyme or substrate in a biochemical reaction.
has_obo_namespace: PSI-MI
id: MI:0415
in_subset: PSI-MI slim

Axiom
annotated source: enzymatic study
annotated property: definition
annotated target: Participants are enzyme or substrate in a biochemical reaction.
database_cross_reference: PMID:14755292

fluorescence microscopy
type: Class
subclass of: imaging technique
definition: Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample.
has_exact_synonym: fluorescence imaging
has_obo_namespace: PSI-MI
id: MI:0416
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence microscopy
annotated property: definition
annotated target: Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample.
database_cross_reference: PMID:14755292

Axiom
annotated source: fluorescence microscopy
annotated property: has_exact_synonym
annotated target: fluorescence imaging
has_synonym_type: Unique short label curated by PSI-MI

footprinting
type: Class
subclass of: biochemical
definition: Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments.
has_obo_namespace: PSI-MI
id: MI:0417
in_subset: PSI-MI slim

Axiom
annotated source: footprinting
annotated property: definition
annotated target: Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments.
database_cross_reference: PMID:14755292

genetic
type: Class
definition: methods supporting genetic interactions. OBSOLETE as too unspecific use Genetic interference instead MI:0254.
has_obo_namespace: PSI-MI
id: MI:0418
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: genetic
annotated property: definition
annotated target: methods supporting genetic interactions. OBSOLETE as too unspecific use Genetic interference instead MI:0254.
database_cross_reference: PMID:14755292

gtpase assay
type: Class
subclass of: nucleoside triphosphatase assay
definition: Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate.
has_exact_synonym: GTPase
has_exact_synonym: gtp hydrolisis
has_obo_namespace: PSI-MI
id: MI:0419
in_subset: PSI-MI slim

Axiom
annotated source: gtpase assay
annotated property: definition
annotated target: Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate.
database_cross_reference: PMID:14755292

Axiom
annotated source: gtpase assay
annotated property: has_exact_synonym
annotated target: GTPase
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gtpase assay
annotated property: has_exact_synonym
annotated target: gtp hydrolisis
has_synonym_type: Alternate label curated by PSI-MI

kinase homogeneous time resolved fluorescence
type: Class
subclass of: protein kinase assay
subclass of: homogeneous time resolved fluorescence
definition: Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase.
has_exact_synonym: homogeneous time-resolved fluorescence
has_exact_synonym: kinase HTRF
has_exact_synonym: kinase htrf
has_obo_namespace: PSI-MI
id: MI:0420
in_subset: PSI-MI slim

Axiom
annotated source: kinase homogeneous time resolved fluorescence
annotated property: definition
annotated target: Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase.
database_cross_reference: PMID:14987100

Axiom
annotated source: kinase homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: homogeneous time-resolved fluorescence
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: kinase homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: kinase HTRF
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: kinase homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: kinase htrf
has_synonym_type: Unique short label curated by PSI-MI

identification by antibody
type: Class
subclass of: experimental participant identification
definition: Antibody mediated participant identification.
has_exact_synonym: antibody detection
has_obo_namespace: PSI-MI
id: MI:0421
in_subset: PSI-MI slim

Axiom
annotated source: identification by antibody
annotated property: definition
annotated target: Antibody mediated participant identification.
database_cross_reference: PMID:14755292

Axiom
annotated source: identification by antibody
annotated property: has_exact_synonym
annotated target: antibody detection
has_synonym_type: Unique short label curated by PSI-MI

immunostaining
type: Class
subclass of: identification by antibody
definition: Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
has_obo_namespace: PSI-MI
id: MI:0422
in_subset: PSI-MI slim

Axiom
annotated source: immunostaining
annotated property: definition
annotated target: Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
database_cross_reference: PMID:14755292

in-gel kinase assay
type: Class
subclass of: protein kinase assay
definition: Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography.
has_exact_synonym: in gel kinase assay
has_obo_namespace: PSI-MI
id: MI:0423
in_subset: PSI-MI slim

Axiom
annotated source: in-gel kinase assay
annotated property: definition
annotated target: Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography.
database_cross_reference: PMID:14755292

Axiom
annotated source: in-gel kinase assay
annotated property: has_exact_synonym
annotated target: in gel kinase assay
has_synonym_type: Unique short label curated by PSI-MI

protein kinase assay
type: Class
subclass of: phosphotransferase assay
definition: Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate.
has_obo_namespace: PSI-MI
id: MI:0424
in_subset: PSI-MI slim

Axiom
annotated source: protein kinase assay
annotated property: definition
annotated target: Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate.
database_cross_reference: PMID:14755292

kinase scintillation proximity assay
type: Class
subclass of: scintillation proximity assay
subclass of: protein kinase assay
definition: Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate.
has_exact_synonym: kinase spa
has_obo_namespace: PSI-MI
id: MI:0425
in_subset: PSI-MI slim

Axiom
annotated source: kinase scintillation proximity assay
annotated property: definition
annotated target: Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: kinase scintillation proximity assay
annotated property: has_exact_synonym
annotated target: kinase spa
has_synonym_type: Unique short label curated by PSI-MI

light microscopy
type: Class
subclass of: imaging technique
definition: Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample.
has_obo_namespace: PSI-MI
id: MI:0426
in_subset: PSI-MI slim

Axiom
annotated source: light microscopy
annotated property: definition
annotated target: Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample.
database_cross_reference: PMID:14755292

Identification by mass spectrometry
type: Class
subclass of: experimental participant identification
definition: identification by mass spectrometry.
has_exact_synonym: ms participant
has_obo_namespace: PSI-MI
id: MI:0427
in_subset: PSI-MI slim

Axiom
annotated source: Identification by mass spectrometry
annotated property: definition
annotated target: identification by mass spectrometry.
database_cross_reference: PMID:14755292

Axiom
annotated source: Identification by mass spectrometry
annotated property: has_exact_synonym
annotated target: ms participant
has_synonym_type: Unique short label curated by PSI-MI

imaging technique
type: Class
subclass of: experimental interaction detection
definition: Methods that provide images of molecules at various resolution depending on the technology used.
has_exact_synonym: microscopy
has_obo_namespace: PSI-MI
id: MI:0428
in_subset: PSI-MI slim

Axiom
annotated source: imaging technique
annotated property: definition
annotated target: Methods that provide images of molecules at various resolution depending on the technology used.
database_cross_reference: PMID:14755292

Axiom
annotated source: imaging technique
annotated property: has_exact_synonym
annotated target: microscopy
has_synonym_type: Alternate label curated by PSI-MI

necessary binding region
type: Class
subclass of: binding-associated region
subclass of: mutation disrupting interaction
subclass of: mutation disrupting interaction strength
subclass of: mutation disrupting interaction rate
definition: A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner.
has_exact_synonym: deletion disrupting interaction
has_exact_synonym: necessary binding site
has_exact_synonym: required to bind
has_obo_namespace: PSI-MI
id: MI:0429
in_subset: PSI-MI slim

Axiom
annotated source: necessary binding region
annotated property: definition
annotated target: A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner.
database_cross_reference: PMID:14755292

Axiom
annotated source: necessary binding region
annotated property: has_exact_synonym
annotated target: required to bind
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid uv cross-linking assay
type: Class
subclass of: cross-linking study
definition: Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it.
has_exact_synonym: nucl ac uv crosslink
has_obo_namespace: PSI-MI
id: MI:0430
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid uv cross-linking assay
annotated property: definition
annotated target: Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid uv cross-linking assay
annotated property: has_exact_synonym
annotated target: nucl ac uv crosslink
has_synonym_type: Unique short label curated by PSI-MI

obsolete
type: Class
definition: Deprecated terms. OBSOLETE term replaced by the default OBO class 'Obsolete'.
has_obo_namespace: PSI-MI
id: MI:0431
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: obsolete
annotated property: definition
annotated target: Deprecated terms. OBSOLETE term replaced by the default OBO class 'Obsolete'.
database_cross_reference: PMID:14755292

one hybrid
type: Class
subclass of: transcriptional complementation assay
definition: Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors.
has_exact_synonym: 1 hybrid
has_exact_synonym: one-hybrid
has_exact_synonym: yeast one hybrid
has_exact_synonym: yeast one-hybrid
has_obo_namespace: PSI-MI
id: MI:0432
in_subset: PSI-MI slim

Axiom
annotated source: one hybrid
annotated property: definition
annotated target: Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors.
database_cross_reference: PMID:10589421

Axiom
annotated source: one hybrid
annotated property: has_exact_synonym
annotated target: 1 hybrid
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: one hybrid
annotated property: has_exact_synonym
annotated target: one-hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: one hybrid
annotated property: has_exact_synonym
annotated target: yeast one hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: one hybrid
annotated property: has_exact_synonym
annotated target: yeast one-hybrid
has_synonym_type: Alternate label curated by PSI-MI

partial identification of protein sequence
type: Class
subclass of: protein sequence identification
subclass of: experimental feature detection
definition: partial protein sequence identification.
has_exact_synonym: partial id prot seq
has_obo_namespace: PSI-MI
id: MI:0433
in_subset: PSI-MI slim

Axiom
annotated source: partial identification of protein sequence
annotated property: definition
annotated target: partial protein sequence identification.
database_cross_reference: PMID:14755292

Axiom
annotated source: partial identification of protein sequence
annotated property: has_exact_synonym
annotated target: partial id prot seq
has_synonym_type: Unique short label curated by PSI-MI

phosphatase assay
type: Class
subclass of: enzymatic study
definition: Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate.
has_obo_namespace: PSI-MI
id: MI:0434
in_subset: PSI-MI slim

Axiom
annotated source: phosphatase assay
annotated property: definition
annotated target: Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate.
database_cross_reference: PMID:14755292

protease assay
type: Class
subclass of: cleavage assay
definition: Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate.
has_obo_namespace: PSI-MI
id: MI:0435
in_subset: PSI-MI slim

Axiom
annotated source: protease assay
annotated property: definition
annotated target: Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate.
database_cross_reference: PMID:14755292

protein footprinting
type: Class
subclass of: experimental feature detection
definition: Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site.
has_obo_namespace: PSI-MI
id: MI:0436
in_subset: PSI-MI slim

Axiom
annotated source: protein footprinting
annotated property: definition
annotated target: Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site.
database_cross_reference: PMID:14600024
database_cross_reference: PMID:14967031
database_cross_reference: PMID:14987073

protein three hybrid
type: Class
subclass of: two hybrid
subclass of: three hybrid
definition: Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected.
has_exact_synonym: bridge assay
has_exact_synonym: protein 3-hybrid
has_exact_synonym: protein tri hybrid
has_exact_synonym: trihybrid
has_obo_namespace: PSI-MI
id: MI:0437
in_subset: PSI-MI slim

Axiom
annotated source: protein three hybrid
annotated property: definition
annotated target: Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected.
database_cross_reference: PMID:12052864
database_cross_reference: PMID:12761205
database_cross_reference: PMID:12935900

Axiom
annotated source: protein three hybrid
annotated property: has_exact_synonym
annotated target: bridge assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein three hybrid
annotated property: has_exact_synonym
annotated target: protein 3-hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein three hybrid
annotated property: has_exact_synonym
annotated target: protein tri hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein three hybrid
annotated property: has_exact_synonym
annotated target: trihybrid
has_synonym_type: Alternate label curated by PSI-MI

rna three hybrid
type: Class
subclass of: three hybrid
definition: In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated.
has_exact_synonym: Three hybrid system
has_exact_synonym: rna 3-hybrid
has_exact_synonym: rna tri hybrid
has_exact_synonym: rna-three hybrid
has_obo_namespace: PSI-MI
id: MI:0438
in_subset: PSI-MI slim

Axiom
annotated source: rna three hybrid
annotated property: definition
annotated target: In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated.
database_cross_reference: PMID:12162957
database_cross_reference: PMID:8972875

Axiom
annotated source: rna three hybrid
annotated property: has_exact_synonym
annotated target: Three hybrid system
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: rna three hybrid
annotated property: has_exact_synonym
annotated target: rna 3-hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: rna three hybrid
annotated property: has_exact_synonym
annotated target: rna tri hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: rna three hybrid
annotated property: has_exact_synonym
annotated target: rna-three hybrid
has_synonym_type: Alternate label curated by PSI-MI

random spore analysis
type: Class
subclass of: genetic interference
definition: A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability.
has_exact_synonym: RSA
has_exact_synonym: random-spore analysis
has_exact_synonym: rsa
has_exact_synonym: spore germination
has_obo_namespace: PSI-MI
id: MI:0439
in_subset: PSI-MI slim

Axiom
annotated source: random spore analysis
annotated property: definition
annotated target: A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability.
database_cross_reference: PMID:14755292

Axiom
annotated source: random spore analysis
annotated property: has_exact_synonym
annotated target: RSA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: random spore analysis
annotated property: has_exact_synonym
annotated target: random-spore analysis
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: random spore analysis
annotated property: has_exact_synonym
annotated target: rsa
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: random spore analysis
annotated property: has_exact_synonym
annotated target: spore germination
has_synonym_type: Alternate label curated by PSI-MI

saturation binding
type: Class
subclass of: affinity technology
definition: Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity.
has_obo_namespace: PSI-MI
id: MI:0440
in_subset: PSI-MI slim

Axiom
annotated source: saturation binding
annotated property: definition
annotated target: Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity.
database_cross_reference: PMID:14755292

synthetic genetic analysis
type: Class
subclass of: genetic interference
definition: Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation.
has_exact_synonym: SGA
has_exact_synonym: sga
has_obo_namespace: PSI-MI
id: MI:0441
in_subset: PSI-MI slim

Axiom
annotated source: synthetic genetic analysis
annotated property: definition
annotated target: Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation.
database_cross_reference: PMID:14755292

Axiom
annotated source: synthetic genetic analysis
annotated property: has_exact_synonym
annotated target: SGA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: synthetic genetic analysis
annotated property: has_exact_synonym
annotated target: sga
has_synonym_type: Unique short label curated by PSI-MI

sufficient binding region
type: Class
subclass of: binding-associated region
definition: Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer.
has_exact_synonym: sufficient binding site
has_exact_synonym: sufficient to bind
has_obo_namespace: PSI-MI
id: MI:0442
in_subset: PSI-MI slim

Axiom
annotated source: sufficient binding region
annotated property: definition
annotated target: Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer.
database_cross_reference: PMID:14755292

Axiom
annotated source: sufficient binding region
annotated property: has_exact_synonym
annotated target: sufficient to bind
has_synonym_type: Unique short label curated by PSI-MI

ubiquitin binding
type: Class
definition: Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner. OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type.
has_obo_namespace: PSI-MI
id: MI:0443
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: ubiquitin binding
annotated property: definition
annotated target: Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner. OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type.
database_cross_reference: PMID:14755292

database citation
type: Class
subclass of: molecular interaction
definition: Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl
has_obo_namespace: PSI-MI
id: MI:0444
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: database citation
annotated property: definition
annotated target: Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl
database_cross_reference: PMID:14755292

literature database
type: Class
subclass of: database citation
definition: Databases acting as a source of literature information.
has_exact_synonym: literature xref
has_exact_synonym: publication xref
has_obo_namespace: PSI-MI
id: MI:0445
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: literature database
annotated property: definition
annotated target: Databases acting as a source of literature information.
database_cross_reference: PMID:14755292

Axiom
annotated source: literature database
annotated property: has_exact_synonym
annotated target: literature xref
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: literature database
annotated property: has_exact_synonym
annotated target: publication xref
has_synonym_type: Alternate label curated by PSI-MI

pubmed
type: Class
subclass of: literature database
definition: PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central. http://www.ncbi.nlm.nih.gov/pubmed http://europepmc.org
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0446
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: pubmed
annotated property: definition
annotated target: PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central. http://www.ncbi.nlm.nih.gov/pubmed http://europepmc.org
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: pubmed
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: pubmed
annotated property: database_cross_reference
annotated target: search-url:
label: http://europepmc.org/abstract/MED/${ac}

feature database
type: Class
subclass of: database citation
definition: A database describing a feature on a molecule.
has_exact_synonym: feature xref
has_obo_namespace: PSI-MI
id: MI:0447
in_subset: PSI-MI slim

Axiom
annotated source: feature database
annotated property: definition
annotated target: A database describing a feature on a molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: feature database
annotated property: has_exact_synonym
annotated target: feature xref
has_synonym_type: Unique short label curated by PSI-MI

gene ontology
type: Class
subclass of: feature database
subclass of: interaction database
definition: The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. http://www.ebi.ac.uk/GO
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: go
has_obo_namespace: PSI-MI
id: MI:0448
in_subset: PSI-MI slim

Axiom
annotated source: gene ontology
annotated property: definition
annotated target: The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. http://www.ebi.ac.uk/GO
database_cross_reference: PMID:14755292

GO:[0-9]{7}
type: Axiom
annotated source: gene ontology
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: gene ontology
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.ebi.ac.uk/QuickGO/term/${ac}

Axiom
annotated source: gene ontology
annotated property: has_exact_synonym
annotated target: go
has_synonym_type: Unique short label curated by PSI-MI

interpro
type: Class
subclass of: feature database
definition: InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences. https://www.ebi.ac.uk/interpro/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: InterPro
has_obo_namespace: PSI-MI
id: MI:0449
in_subset: PSI-MI slim

Axiom
annotated source: interpro
annotated property: definition
annotated target: InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences. https://www.ebi.ac.uk/interpro/
database_cross_reference: PMID:1252001

IPR[0-9]{6}
type: Axiom
annotated source: interpro
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: interpro
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.ebi.ac.uk/interpro/entry/InterPro/${ac}

Axiom
annotated source: interpro
annotated property: has_exact_synonym
annotated target: InterPro
has_synonym_type: Alternate label curated by PSI-MI

cdd
type: Class
subclass of: feature database
definition: The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence. http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
database_cross_reference: id-validation-regexp:
has_exact_synonym: CDD
has_obo_namespace: PSI-MI
id: MI:0450
in_subset: PSI-MI slim

Axiom
annotated source: cdd
annotated property: definition
annotated target: The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence. http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: cdd
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: cdd
annotated property: has_exact_synonym
annotated target: CDD
has_synonym_type: Alternate label curated by PSI-MI

pfam
type: Class
subclass of: interpro
definition: Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. http://www.sanger.ac.uk/Software/Pfam
database_cross_reference: id-validation-regexp:
has_exact_synonym: Pfam
has_obo_namespace: PSI-MI
id: MI:0451
in_subset: PSI-MI slim

Axiom
annotated source: pfam
annotated property: definition
annotated target: Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. http://www.sanger.ac.uk/Software/Pfam
database_cross_reference: PMID:14755292

PF[0-9]{5}
type: Axiom
annotated source: pfam
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: pfam
annotated property: has_exact_synonym
annotated target: Pfam
has_synonym_type: Alternate label curated by PSI-MI

pirsf
type: Class
subclass of: interpro
definition: PIRSF is a classification system based on evolutionary relationship of whole proteins. http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
database_cross_reference: id-validation-regexp:
has_exact_synonym: PIRSF
has_obo_namespace: PSI-MI
id: MI:0452
in_subset: PSI-MI slim

Axiom
annotated source: pirsf
annotated property: definition
annotated target: PIRSF is a classification system based on evolutionary relationship of whole proteins. http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
database_cross_reference: PMID:14755292

PIRSF[0-9]{5}
type: Axiom
annotated source: pirsf
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: pirsf
annotated property: has_exact_synonym
annotated target: PIRSF
has_synonym_type: Alternate label curated by PSI-MI

prints
type: Class
subclass of: interpro
definition: PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
database_cross_reference: id-validation-regexp:
has_exact_synonym: PRINTS
has_obo_namespace: PSI-MI
id: MI:0453
in_subset: PSI-MI slim

Axiom
annotated source: prints
annotated property: definition
annotated target: PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
database_cross_reference: PMID:14755292

PR[0-9]{6}
type: Axiom
annotated source: prints
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: prints
annotated property: has_exact_synonym
annotated target: PRINTS
has_synonym_type: Alternate label curated by PSI-MI

prodom
type: Class
subclass of: interpro
definition: The ProDom protein domain database consists of an automatic compilation of homologous domains. http://protein.toulouse.inra.fr/prodom.html
database_cross_reference: id-validation-regexp:
has_exact_synonym: ProDom
has_obo_namespace: PSI-MI
id: MI:0454
in_subset: PSI-MI slim

Axiom
annotated source: prodom
annotated property: definition
annotated target: The ProDom protein domain database consists of an automatic compilation of homologous domains. http://protein.toulouse.inra.fr/prodom.html
database_cross_reference: PMID:14755292

PD[0-9]{6}
type: Axiom
annotated source: prodom
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: prodom
annotated property: has_exact_synonym
annotated target: ProDom
has_synonym_type: Alternate label curated by PSI-MI

prosite
type: Class
subclass of: interpro
definition: PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles. http://us.expasy.org/prosite/
database_cross_reference: id-validation-regexp:
has_exact_synonym: Prosite
has_obo_namespace: PSI-MI
id: MI:0455
in_subset: PSI-MI slim

Axiom
annotated source: prosite
annotated property: definition
annotated target: PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles. http://us.expasy.org/prosite/
database_cross_reference: PMID:14755292

PS[0-9]{5}
type: Axiom
annotated source: prosite
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: prosite
annotated property: has_exact_synonym
annotated target: Prosite
has_synonym_type: Alternate label curated by PSI-MI

scop superfamily
type: Class
subclass of: interpro
definition: SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain. http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
database_cross_reference: id-validation-regexp:
has_exact_synonym: SCOP superfamily
has_obo_namespace: PSI-MI
id: MI:0456
in_subset: PSI-MI slim

Axiom
annotated source: scop superfamily
annotated property: definition
annotated target: SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain. http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: scop superfamily
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: scop superfamily
annotated property: has_exact_synonym
annotated target: SCOP superfamily
has_synonym_type: Alternate label curated by PSI-MI

smart
type: Class
subclass of: interpro
definition: SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. http://smart.embl-heidelberg.de/
database_cross_reference: id-validation-regexp:
has_exact_synonym: SMART
has_obo_namespace: PSI-MI
id: MI:0457
in_subset: PSI-MI slim

Axiom
annotated source: smart
annotated property: definition
annotated target: SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. http://smart.embl-heidelberg.de/
database_cross_reference: PMID:14755292

SM[0-9]{5}
type: Axiom
annotated source: smart
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: smart
annotated property: has_exact_synonym
annotated target: SMART
has_synonym_type: Alternate label curated by PSI-MI

tigrfams
type: Class
subclass of: interpro
definition: TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation. http://www.tigr.org/TIGRFAMs
database_cross_reference: id-validation-regexp:
has_exact_synonym: TIGRFAMs
has_obo_namespace: PSI-MI
id: MI:0458
in_subset: PSI-MI slim

Axiom
annotated source: tigrfams
annotated property: definition
annotated target: TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation. http://www.tigr.org/TIGRFAMs
database_cross_reference: PMID:14755292

TIGR[0-9]+
type: Axiom
annotated source: tigrfams
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: tigrfams
annotated property: has_exact_synonym
annotated target: TIGRFAMs
has_synonym_type: Alternate label curated by PSI-MI

mmdb
type: Class
subclass of: feature database
subclass of: interaction database
definition: MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank. http://www.ncbi.nlm.nih.gov/Structure
database_cross_reference: id-validation-regexp:
has_exact_synonym: MMDB
has_obo_namespace: PSI-MI
id: MI:0459
in_subset: PSI-MI slim

Axiom
annotated source: mmdb
annotated property: definition
annotated target: MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank. http://www.ncbi.nlm.nih.gov/Structure
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: mmdb
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: mmdb
annotated property: has_exact_synonym
annotated target: MMDB
has_synonym_type: Alternate label curated by PSI-MI

rcsb pdb
type: Class
subclass of: wwpdb
definition: The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. http://www.pdb.org/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: PDB
has_obo_namespace: PSI-MI
id: MI:0460
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: rcsb pdb
annotated property: definition
annotated target: The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. http://www.pdb.org/
database_cross_reference: PMID:14634627

[0-9][a-zA-Z0-9]{3}
type: Axiom
annotated source: rcsb pdb
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: rcsb pdb
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.pdb.org/pdb/explore/explore.do

Axiom
annotated source: rcsb pdb
annotated property: has_exact_synonym
annotated target: PDB
has_synonym_type: Alternate label curated by PSI-MI

interaction database
type: Class
subclass of: database citation
definition: Databases that contain experimental or predictive molecular interaction data.
has_exact_synonym: interaction xref
has_obo_namespace: PSI-MI
id: MI:0461
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: interaction database
annotated property: definition
annotated target: Databases that contain experimental or predictive molecular interaction data.
database_cross_reference: PMID:14755292

Axiom
annotated source: interaction database
annotated property: has_exact_synonym
annotated target: interaction xref
has_synonym_type: Unique short label curated by PSI-MI

bind
type: Class
subclass of: interaction database
subclass of: source database
definition: The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. http://www.blueprint.org/bind
database_cross_reference: id-validation-regexp:
has_exact_synonym: BIND
has_obo_namespace: PSI-MI
id: MI:0462
in_subset: PSI-MI slim

Axiom
annotated source: bind
annotated property: definition
annotated target: The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. http://www.blueprint.org/bind
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: bind
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: bind
annotated property: has_exact_synonym
annotated target: BIND
has_synonym_type: Alternate label curated by PSI-MI

biogrid
type: Class
subclass of: interaction database
subclass of: source database
definition: The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions. http://thebiogrid.org
has_exact_synonym: BioGRID
has_obo_namespace: PSI-MI
id: MI:0463
in_subset: PSI-MI slim

Axiom
annotated source: biogrid
annotated property: definition
annotated target: The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions. http://thebiogrid.org
database_cross_reference: PMID:21071413

Axiom
annotated source: biogrid
annotated property: has_exact_synonym
annotated target: BioGRID
has_synonym_type: Alternate label curated by PSI-MI

cygd
type: Class
subclass of: source database
subclass of: genome databases
subclass of: pathways database
definition: The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. http://mips.gsf.de/proj/yeast/CYGD. http://mips.gsf.de/genre/proj/mpact
database_cross_reference: id-validation-regexp:
has_exact_synonym: CYGD
has_exact_synonym: CYGD (MIPS)
has_exact_synonym: MIPS
has_exact_synonym: MPact
has_obo_namespace: PSI-MI
id: MI:0464
in_subset: PSI-MI slim

Axiom
annotated source: cygd
annotated property: definition
annotated target: The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. http://mips.gsf.de/proj/yeast/CYGD. http://mips.gsf.de/genre/proj/mpact
database_cross_reference: PMID:14755292

[0-9]+|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]
type: Axiom
annotated source: cygd
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: cygd
annotated property: has_exact_synonym
annotated target: CYGD
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cygd
annotated property: has_exact_synonym
annotated target: CYGD (MIPS)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cygd
annotated property: has_exact_synonym
annotated target: MIPS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cygd
annotated property: has_exact_synonym
annotated target: MPact
has_synonym_type: Alternate label curated by PSI-MI

dip
type: Class
subclass of: interaction database
subclass of: imex source
definition: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. http://dip.doe-mbi.ucla.edu/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: DIP
has_obo_namespace: PSI-MI
id: MI:0465
in_subset: PSI-MI slim

Axiom
annotated source: dip
annotated property: definition
annotated target: The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. http://dip.doe-mbi.ucla.edu/
database_cross_reference: PMID:14755292

DIP[:-]?[0-9]+[NE]
type: Axiom
annotated source: dip
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: dip
annotated property: database_cross_reference
annotated target: search-url:
label: http://identifiers.org/dip/${ac}

Axiom
annotated source: dip
annotated property: has_exact_synonym
annotated target: DIP
has_synonym_type: Alternate label curated by PSI-MI

ecocyc
type: Class
subclass of: pathways database
definition: EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655. http://ecocyc.org/
has_exact_synonym: EcoCyc
has_obo_namespace: PSI-MI
id: MI:0466
in_subset: PSI-MI slim

Axiom
annotated source: ecocyc
annotated property: definition
annotated target: EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655. http://ecocyc.org/
database_cross_reference: PMID:14755292

Axiom
annotated source: ecocyc
annotated property: has_exact_synonym
annotated target: EcoCyc
has_synonym_type: Alternate label curated by PSI-MI

reactome
type: Class
subclass of: pathways database
definition: The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. http://www.reactome.org/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: GKB
has_exact_synonym: Genome Knowledge Base
has_exact_synonym: Reactome
has_obo_namespace: PSI-MI
id: MI:0467
in_subset: PSI-MI slim

Axiom
annotated source: reactome
annotated property: definition
annotated target: The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. http://www.reactome.org/
database_cross_reference: PMID:21067998

((R-[A-Z]{3}-\d+)|(REACT_\d+))(\.\d+)?$
type: Axiom
annotated source: reactome
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: reactome
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.reactome.org/content/detail/${ac}

Axiom
annotated source: reactome
annotated property: has_exact_synonym
annotated target: GKB
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: reactome
annotated property: has_exact_synonym
annotated target: Genome Knowledge Base
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: reactome
annotated property: has_exact_synonym
annotated target: Reactome
has_synonym_type: Alternate label curated by PSI-MI

hprd
type: Class
subclass of: interaction database
definition: The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. http://www.hprd.org/
has_exact_synonym: HPRD
has_obo_namespace: PSI-MI
id: MI:0468
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: hprd
annotated property: definition
annotated target: The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. http://www.hprd.org/
database_cross_reference: PMID:14755292

Axiom
annotated source: hprd
annotated property: has_exact_synonym
annotated target: HPRD
has_synonym_type: Alternate label curated by PSI-MI

intact
type: Class
subclass of: interaction database
subclass of: imex source
definition: INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: IntAct
has_exact_synonym: intact
has_obo_namespace: PSI-MI
id: MI:0469
in_subset: PSI-MI slim

Axiom
annotated source: intact
annotated property: definition
annotated target: INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact
database_cross_reference: PMID:14681455
database_cross_reference: PMID:19850723
database_cross_reference: PMID:22121220

EBI-[0-9]+|IA:[0-9]+
type: Axiom
annotated source: intact
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: intact
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/intact/query/${ac}

Axiom
annotated source: intact
annotated property: has_exact_synonym
annotated target: IntAct
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: intact
annotated property: has_exact_synonym
annotated target: intact
has_synonym_type: Unique short label curated by PSI-MI

kegg
type: Class
subclass of: participant database
subclass of: pathways database
definition: KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions. http://www.genome.ad.jp/kegg/
database_cross_reference: id-validation-regexp:
has_exact_synonym: KEGG
has_obo_namespace: PSI-MI
id: MI:0470
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: kegg
annotated property: definition
annotated target: KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions. http://www.genome.ad.jp/kegg/
database_cross_reference: PMID:14755292

[a-zA-Z]+:[a-zA-Z]+[0-9]+
type: Axiom
annotated source: kegg
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: kegg
annotated property: has_exact_synonym
annotated target: KEGG
has_synonym_type: Alternate label curated by PSI-MI

mint
type: Class
subclass of: interaction database
subclass of: imex source
definition: The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: MINT
has_obo_namespace: PSI-MI
id: MI:0471
in_subset: PSI-MI slim

Axiom
annotated source: mint
annotated property: definition
annotated target: The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it
database_cross_reference: PMID:14755292

MINT-[0-9]+
type: Axiom
annotated source: mint
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: mint
annotated property: database_cross_reference
annotated target: search-url:
label: https://mint.bio.uniroma2.it/index.php/results-interactions/

Axiom
annotated source: mint
annotated property: has_exact_synonym
annotated target: MINT
has_synonym_type: Unique short label curated by PSI-MI

pdbe
type: Class
subclass of: wwpdb
definition: The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB). http://www.ebi.ac.uk/pdbe/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: PQS
has_exact_synonym: e-MSD
has_obo_namespace: PSI-MI
has_related_synonym: MSD
id: MI:0472
in_subset: PSI-MI slim

Axiom
annotated source: pdbe
annotated property: definition
annotated target: The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB). http://www.ebi.ac.uk/pdbe/
database_cross_reference: PMID:16381867

[0-9][a-zA-Z0-9]{3}
type: Axiom
annotated source: pdbe
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: pdbe
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/pdbe/entry/pdb/${ac}

Axiom
annotated source: pdbe
annotated property: has_exact_synonym
annotated target: PQS
has_synonym_type: Alternate label curated by PSI-MI

participant database
type: Class
subclass of: database citation
definition: Database of molecules participating in molecular interactions.
has_exact_synonym: participant xref
has_obo_namespace: PSI-MI
id: MI:0473
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: participant database
annotated property: definition
annotated target: Database of molecules participating in molecular interactions.
database_cross_reference: PMID:14755292

Axiom
annotated source: participant database
annotated property: has_exact_synonym
annotated target: participant xref
has_synonym_type: Unique short label curated by PSI-MI

chebi
type: Class
subclass of: bioactive entity reference
definition: A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI). http://www.ebi.ac.uk/chebi/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: ChEBI
has_obo_namespace: PSI-MI
id: MI:0474
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: chebi
annotated property: definition
annotated target: A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI). http://www.ebi.ac.uk/chebi/
database_cross_reference: PMID:14755292

CHEBI:[0-9]+
type: Axiom
annotated source: chebi
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: chebi
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/chebi/searchId.do

Axiom
annotated source: chebi
annotated property: has_exact_synonym
annotated target: ChEBI
has_synonym_type: Alternate label curated by PSI-MI

ddbj/embl/genbank
type: Class
subclass of: sequence database
definition: DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation. http://www.ebi.ac.uk/embl/Contact/collaboration
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: DDBJ
has_exact_synonym: DDBJ/EMBL/GenBank
has_exact_synonym: EMBL
has_exact_synonym: GenBank
has_obo_namespace: PSI-MI
id: MI:0475
in_subset: PSI-MI slim

Axiom
annotated source: ddbj/embl/genbank
annotated property: definition
annotated target: DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation. http://www.ebi.ac.uk/embl/Contact/collaboration
database_cross_reference: PMID:14755292

[A-Z][0-9]{5}|[A-Z][0-9]{5}\.[0-9]+|[A-Z]{2}[0-9]{6}|[A-Z]{2}[0-9]{6}\.[0-9]+|[A-Z]{4}[0-9]{8}|[A-Z]{4}[0-9]{8}\.[0-9]+
type: Axiom
annotated source: ddbj/embl/genbank
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: ddbj/embl/genbank
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/cgi-bin/dbfetch

Axiom
annotated source: ddbj/embl/genbank
annotated property: has_exact_synonym
annotated target: DDBJ
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ddbj/embl/genbank
annotated property: has_exact_synonym
annotated target: DDBJ/EMBL/GenBank
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ddbj/embl/genbank
annotated property: has_exact_synonym
annotated target: EMBL
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ddbj/embl/genbank
annotated property: has_exact_synonym
annotated target: GenBank
has_synonym_type: Alternate label curated by PSI-MI

ensembl
type: Class
subclass of: genome databases
definition: Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes. http://www.ensembl.org
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: Ensembl
has_obo_namespace: PSI-MI
id: MI:0476
in_subset: PSI-MI slim

Axiom
annotated source: ensembl
annotated property: definition
annotated target: Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes. http://www.ensembl.org
database_cross_reference: PMID:15078858

ENS[A-Z]+[0-9]{11}|[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?|CG[0-9]+|[A-Z0-9]+\.[0-9]+|YM[A-Z][0-9]{3}[a-z][0-9]
type: Axiom
annotated source: ensembl
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: ensembl
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ensembl.org/Multi/Search/Results

Axiom
annotated source: ensembl
annotated property: has_exact_synonym
annotated target: Ensembl
has_synonym_type: Alternate label curated by PSI-MI

entrez gene/locuslink
type: Class
subclass of: gene database
definition: LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. http://www.ncbi.nlm.nih.gov/LocusLink/
database_cross_reference: id-validation-regexp:
has_exact_synonym: Entrez gene/locuslink
has_exact_synonym: entrezgene/locuslink
has_obo_namespace: PSI-MI
id: MI:0477
in_subset: PSI-MI slim

Axiom
annotated source: entrez gene/locuslink
annotated property: definition
annotated target: LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. http://www.ncbi.nlm.nih.gov/LocusLink/
database_cross_reference: PMID:14755292

[0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+
type: Axiom
annotated source: entrez gene/locuslink
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: entrez gene/locuslink
annotated property: has_exact_synonym
annotated target: Entrez gene/locuslink
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: entrez gene/locuslink
annotated property: has_exact_synonym
annotated target: entrezgene/locuslink
has_synonym_type: Unique short label curated by PSI-MI

flybase
type: Class
subclass of: genome databases
definition: FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. http://flybase.org
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: FlyBase
has_obo_namespace: PSI-MI
id: MI:0478
in_subset: PSI-MI slim

Axiom
annotated source: flybase
annotated property: definition
annotated target: FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. http://flybase.org
database_cross_reference: PMID:14755292

FB[a-z]{2}[0-9]{7}
type: Axiom
annotated source: flybase
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: flybase
annotated property: database_cross_reference
annotated target: search-url:
label: http://flybase.org/reports/${ac}

Axiom
annotated source: flybase
annotated property: has_exact_synonym
annotated target: FlyBase
has_synonym_type: Alternate label curated by PSI-MI

mgd/mgi
type: Class
subclass of: genome databases
definition: Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse. http://www.informatics.jax.org/
database_cross_reference: id-validation-regexp:
has_exact_synonym: MGD/MGI
has_obo_namespace: PSI-MI
id: MI:0479
in_subset: PSI-MI slim

Axiom
annotated source: mgd/mgi
annotated property: definition
annotated target: Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse. http://www.informatics.jax.org/
database_cross_reference: PMID:14755292

MGI:[0-9]+
type: Axiom
annotated source: mgd/mgi
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: mgd/mgi
annotated property: has_exact_synonym
annotated target: MGD/MGI
has_synonym_type: Alternate label curated by PSI-MI

omim
type: Class
subclass of: sequence database
definition: Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: OMIM
has_obo_namespace: PSI-MI
id: MI:0480
in_subset: PSI-MI slim

Axiom
annotated source: omim
annotated property: definition
annotated target: Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: omim
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: omim
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.omim.org/entry/${ac}

Axiom
annotated source: omim
annotated property: has_exact_synonym
annotated target: OMIM
has_synonym_type: Alternate label curated by PSI-MI

refseq
type: Class
subclass of: protein sequence databases
definition: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms. http://www.ncbi.nlm.nih.gov/RefSeq/
database_cross_reference: id-validation-regexp:
has_exact_synonym: Refseq
has_obo_namespace: PSI-MI
id: MI:0481
in_subset: PSI-MI slim

Axiom
annotated source: refseq
annotated property: definition
annotated target: The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms. http://www.ncbi.nlm.nih.gov/RefSeq/
database_cross_reference: PMID:14755292

[XNZ][A-Z]_[0-9]+|[0-9]+|[XNZ][A-Z]_[0-9]+\.[0-9]+
type: Axiom
annotated source: refseq
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: refseq
annotated property: has_exact_synonym
annotated target: Refseq
has_synonym_type: Alternate label curated by PSI-MI

rfam
type: Class
subclass of: sequence database
definition: Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. http://www.sanger.ac.uk/Software/Rfam/
database_cross_reference: id-validation-regexp:
has_exact_synonym: rfam
has_obo_namespace: PSI-MI
id: MI:0482
in_subset: PSI-MI slim

Axiom
annotated source: rfam
annotated property: definition
annotated target: Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. http://www.sanger.ac.uk/Software/Rfam/
database_cross_reference: PMID:14755292

RF[0-9]{5}
type: Axiom
annotated source: rfam
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: rfam
annotated property: has_exact_synonym
annotated target: rfam
has_synonym_type: Alternate label curated by PSI-MI

rgd
type: Class
subclass of: genome databases
definition: The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data. http://rgd.mcw.edu/
database_cross_reference: id-validation-regexp:
has_exact_synonym: RGD
has_obo_namespace: PSI-MI
id: MI:0483
in_subset: PSI-MI slim

Axiom
annotated source: rgd
annotated property: definition
annotated target: The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data. http://rgd.mcw.edu/
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: rgd
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: rgd
annotated property: has_exact_synonym
annotated target: RGD
has_synonym_type: Alternate label curated by PSI-MI

sgd
type: Class
subclass of: genome databases
definition: SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. http://www.yeastgenome.org/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: SGD
has_exact_synonym: Saccharomyces Genome Database
has_obo_namespace: PSI-MI
id: MI:0484
in_subset: PSI-MI slim

Axiom
annotated source: sgd
annotated property: definition
annotated target: SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. http://www.yeastgenome.org/
database_cross_reference: PMID:14755292

S[0-9]{9}
type: Axiom
annotated source: sgd
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: sgd
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.yeastgenome.org/locus/${ac}/overview

Axiom
annotated source: sgd
annotated property: has_exact_synonym
annotated target: SGD
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: sgd
annotated property: has_exact_synonym
annotated target: Saccharomyces Genome Database
has_synonym_type: Alternate label curated by PSI-MI

uniparc
type: Class
subclass of: uniprot
definition: UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources. http://www.ebi.ac.uk/uniparc/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: UniParc
has_obo_namespace: PSI-MI
id: MI:0485
in_subset: PSI-MI slim

Axiom
annotated source: uniparc
annotated property: definition
annotated target: UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources. http://www.ebi.ac.uk/uniparc/
database_cross_reference: PMID:14681372

UPI[A-F0-9]{10}
type: Axiom
annotated source: uniparc
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: uniparc
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.uniprot.org/uniparc/${ac}/entry

Axiom
annotated source: uniparc
annotated property: has_exact_synonym
annotated target: UniParc
has_synonym_type: Alternate label curated by PSI-MI

uniprot knowledge base
type: Class
subclass of: interaction database
subclass of: imex source
subclass of: uniprot
definition: UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. http://www.uniprot.org
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: UniProtKB
has_exact_synonym: uniprotkb
has_obo_namespace: PSI-MI
id: MI:0486
in_subset: PSI-MI slim

Axiom
annotated source: uniprot knowledge base
annotated property: definition
annotated target: UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. http://www.uniprot.org
database_cross_reference: PMID:14681372

(([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?)
type: Axiom
annotated source: uniprot knowledge base
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: uniprot knowledge base
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.uniprot.org/uniprotkb/${ac}/entry

Axiom
annotated source: uniprot knowledge base
annotated property: has_exact_synonym
annotated target: UniProtKB
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: uniprot knowledge base
annotated property: has_exact_synonym
annotated target: uniprotkb
has_synonym_type: Unique short label curated by PSI-MI

wormbase
type: Class
subclass of: genome databases
definition: WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser. http://www.wormbase.org/
database_cross_reference: id-validation-regexp:
has_exact_synonym: WormBase
has_obo_namespace: PSI-MI
id: MI:0487
in_subset: PSI-MI slim

Axiom
annotated source: wormbase
annotated property: definition
annotated target: WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser. http://www.wormbase.org/
database_cross_reference: PMID:14755292

WBGene[0-9]{8}
type: Axiom
annotated source: wormbase
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: wormbase
annotated property: has_exact_synonym
annotated target: WormBase
has_synonym_type: Alternate label curated by PSI-MI

psi-mi
type: Class
subclass of: database citation
definition: PSI-MI.
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: PSI-MI
has_obo_namespace: PSI-MI
id: MI:0488
in_subset: PSI-MI slim

Axiom
annotated source: psi-mi
annotated property: definition
annotated target: PSI-MI.
database_cross_reference: PMID:14755292

MI:[0-9]{4}
type: Axiom
annotated source: psi-mi
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: psi-mi
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/ols/ontologies/mi/terms

Axiom
annotated source: psi-mi
annotated property: has_exact_synonym
annotated target: PSI-MI
has_synonym_type: Alternate label curated by PSI-MI

source database
type: Class
subclass of: database citation
definition: Database that originally provided the interaction record for exchange purposes.
has_obo_namespace: PSI-MI
id: MI:0489
in_subset: PSI-MI slim

Axiom
annotated source: source database
annotated property: definition
annotated target: Database that originally provided the interaction record for exchange purposes.
database_cross_reference: PMID:14755292

experiment condition
type: Class
definition: Describes the location of the experiment. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
has_obo_namespace: PSI-MI
id: MI:0490
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: experiment condition
annotated property: definition
annotated target: Describes the location of the experiment. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
database_cross_reference: PMID:14755292

in silico
type: Class
definition: Results generated by predictive bioinformatics approaches rather than experimental data. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
has_exact_synonym: Predictive
has_obo_namespace: PSI-MI
id: MI:0491
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: in silico
annotated property: definition
annotated target: Results generated by predictive bioinformatics approaches rather than experimental data. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: in silico
annotated property: has_exact_synonym
annotated target: Predictive
has_synonym_type: Alternate label curated by PSI-MI

in vitro
type: Class
definition: Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
has_obo_namespace: PSI-MI
id: MI:0492
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: in vitro
annotated property: definition
annotated target: Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
database_cross_reference: PMID:14755292

in vivo
type: Class
definition: Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
has_obo_namespace: PSI-MI
id: MI:0493
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: in vivo
annotated property: definition
annotated target: Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
database_cross_reference: PMID:14755292

in situ
type: Class
definition: Literally, in place i.e. the protein is in its natural environment during the experiment. OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
has_obo_namespace: PSI-MI
id: MI:0494
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: in situ
annotated property: definition
annotated target: Literally, in place i.e. the protein is in its natural environment during the experiment. OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
database_cross_reference: PMID:14755292

experimental role
type: Class
subclass of: molecular interaction
definition: Role played by the participant within the experiment.
has_obo_namespace: PSI-MI
id: MI:0495
in_subset: PSI-MI slim

Axiom
annotated source: experimental role
annotated property: definition
annotated target: Role played by the participant within the experiment.
database_cross_reference: PMID:14755292

bait
type: Class
subclass of: experimental role
definition: Molecule experimentally treated to capture its interacting partners.
has_obo_namespace: PSI-MI
id: MI:0496
in_subset: PSI-MI slim

Axiom
annotated source: bait
annotated property: definition
annotated target: Molecule experimentally treated to capture its interacting partners.
database_cross_reference: PMID:14755292

neutral component
type: Class
subclass of: experimental role
definition: Molecule role in an experimental setting that does not have an embedded asymmetry.
has_obo_namespace: PSI-MI
id: MI:0497
in_subset: PSI-MI slim

Axiom
annotated source: neutral component
annotated property: definition
annotated target: Molecule role in an experimental setting that does not have an embedded asymmetry.
database_cross_reference: PMID:14755292

prey
type: Class
subclass of: experimental role
definition: Molecule experimentally identified as being captured by a given bait.
has_obo_namespace: PSI-MI
id: MI:0498
in_subset: PSI-MI slim

Axiom
annotated source: prey
annotated property: definition
annotated target: Molecule experimentally identified as being captured by a given bait.
database_cross_reference: PMID:14755292

unspecified role
type: Class
subclass of: experimental role
subclass of: biological role
definition: Role not specified or not applicable to the data.
has_obo_namespace: PSI-MI
id: MI:0499
in_subset: PSI-MI slim

Axiom
annotated source: unspecified role
annotated property: definition
annotated target: Role not specified or not applicable to the data.
database_cross_reference: PMID:14755292

biological role
type: Class
subclass of: molecular interaction
definition: Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment.
has_obo_namespace: PSI-MI
id: MI:0500
in_subset: PSI-MI slim

Axiom
annotated source: biological role
annotated property: definition
annotated target: Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment.
database_cross_reference: PMID:14755292

enzyme
type: Class
subclass of: biological role
definition: Molecule catalyzing a modification on its interacting partner.
has_obo_namespace: PSI-MI
id: MI:0501
in_subset: PSI-MI slim

Axiom
annotated source: enzyme
annotated property: definition
annotated target: Molecule catalyzing a modification on its interacting partner.
database_cross_reference: PMID:14755292

enzyme target
type: Class
subclass of: biological role
definition: Molecule that is the target of its binding partner catalytic activity.
has_exact_synonym: substrate
has_obo_namespace: PSI-MI
id: MI:0502
in_subset: PSI-MI slim

Axiom
annotated source: enzyme target
annotated property: definition
annotated target: Molecule that is the target of its binding partner catalytic activity.
database_cross_reference: PMID:14755292

Axiom
annotated source: enzyme target
annotated property: has_exact_synonym
annotated target: substrate
has_synonym_type: Alternate label curated by PSI-MI

self
type: Class
subclass of: experimental role
subclass of: biological role
definition: Molecule that makes intramolecular interactions.
has_obo_namespace: PSI-MI
id: MI:0503
in_subset: PSI-MI slim

Axiom
annotated source: self
annotated property: definition
annotated target: Molecule that makes intramolecular interactions.
database_cross_reference: PMID:14755292

experimental feature
type: Class
subclass of: feature type
definition: The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.
has_obo_namespace: PSI-MI
id: MI:0505
in_subset: PSI-MI slim

Axiom
annotated source: experimental feature
annotated property: definition
annotated target: The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.
database_cross_reference: PMID:14755292

over expressed level
type: Class
subclass of: expression level
subclass of: expression level alteration
definition: A molecule is estimated to be expressed at higher levels than in physiological condition.
has_exact_synonym: over-expressed
has_obo_namespace: PSI-MI
id: MI:0506
in_subset: PSI-MI slim

Axiom
annotated source: over expressed level
annotated property: definition
annotated target: A molecule is estimated to be expressed at higher levels than in physiological condition.
database_cross_reference: PMID:14755292

Axiom
annotated source: over expressed level
annotated property: has_exact_synonym
annotated target: over-expressed
has_synonym_type: Unique short label curated by PSI-MI

tag
type: Class
subclass of: experimental feature
definition: Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
has_obo_namespace: PSI-MI
id: MI:0507
in_subset: PSI-MI slim

Axiom
annotated source: tag
annotated property: definition
annotated target: Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
database_cross_reference: PMID:14755292

deacetylase radiometric assay
type: Class
subclass of: deacetylase assay
definition: Measures the release of radiolabelled acetic acid from a pre-labeled molecule.
has_exact_synonym: radiolabeled acetate
has_obo_namespace: PSI-MI
id: MI:0508
in_subset: PSI-MI slim

Axiom
annotated source: deacetylase radiometric assay
annotated property: definition
annotated target: Measures the release of radiolabelled acetic acid from a pre-labeled molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: deacetylase radiometric assay
annotated property: has_exact_synonym
annotated target: radiolabeled acetate
has_synonym_type: Unique short label curated by PSI-MI

phosphatase homogeneous time resolved fluorescence
type: Class
subclass of: phosphatase assay
subclass of: homogeneous time resolved fluorescence
definition: Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase.
has_exact_synonym: homogeneous time-resolved fluorescence
has_exact_synonym: phosphatase HTRF
has_exact_synonym: phosphatase htrf
has_obo_namespace: PSI-MI
id: MI:0509
in_subset: PSI-MI slim

Axiom
annotated source: phosphatase homogeneous time resolved fluorescence
annotated property: definition
annotated target: Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase.
database_cross_reference: PMID:14987100

Axiom
annotated source: phosphatase homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: homogeneous time-resolved fluorescence
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: phosphatase homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: phosphatase HTRF
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: phosphatase homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: phosphatase htrf
has_synonym_type: Unique short label curated by PSI-MI

homogeneous time resolved fluorescence
type: Class
subclass of: fluorescence technology
definition: Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates.
has_exact_synonym: homogeneous time-resolved fluorescence
has_exact_synonym: htrf
has_obo_namespace: PSI-MI
id: MI:0510
in_subset: PSI-MI slim

Axiom
annotated source: homogeneous time resolved fluorescence
annotated property: definition
annotated target: Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates.
database_cross_reference: PMID:14987100

Axiom
annotated source: homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: homogeneous time-resolved fluorescence
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: htrf
has_synonym_type: Unique short label curated by PSI-MI

protease homogeneous time resolved fluorescence
type: Class
subclass of: protease assay
subclass of: homogeneous time resolved fluorescence
definition: Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease.
has_exact_synonym: Protease HTRF
has_exact_synonym: protease htrf
has_obo_namespace: PSI-MI
id: MI:0511
in_subset: PSI-MI slim

Axiom
annotated source: protease homogeneous time resolved fluorescence
annotated property: definition
annotated target: Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease.
database_cross_reference: PMID:14987100

Axiom
annotated source: protease homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: Protease HTRF
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protease homogeneous time resolved fluorescence
annotated property: has_exact_synonym
annotated target: protease htrf
has_synonym_type: Unique short label curated by PSI-MI

zymography
type: Class
subclass of: protease assay
definition: Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity.
has_obo_namespace: PSI-MI
id: MI:0512
in_subset: PSI-MI slim

Axiom
annotated source: zymography
annotated property: definition
annotated target: Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity.
database_cross_reference: PMID:2071592

collagen film assay
type: Class
subclass of: protease assay
definition: Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen.
has_obo_namespace: PSI-MI
id: MI:0513
in_subset: PSI-MI slim

Axiom
annotated source: collagen film assay
annotated property: definition
annotated target: Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen.
database_cross_reference: PMID:6247938

in gel phosphatase assay
type: Class
subclass of: phosphatase assay
definition: Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography.
has_exact_synonym: in gel phosphatase
has_obo_namespace: PSI-MI
id: MI:0514
in_subset: PSI-MI slim

Axiom
annotated source: in gel phosphatase assay
annotated property: definition
annotated target: Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography.
database_cross_reference: PMID:14755292

Axiom
annotated source: in gel phosphatase assay
annotated property: has_exact_synonym
annotated target: in gel phosphatase
has_synonym_type: Unique short label curated by PSI-MI

methyltransferase assay
type: Class
subclass of: enzymatic study
definition: Measures the catalysis of the transfer of a methyl group to an acceptor molecule.
has_exact_synonym: methyltransferase as
has_obo_namespace: PSI-MI
id: MI:0515
in_subset: PSI-MI slim

Axiom
annotated source: methyltransferase assay
annotated property: definition
annotated target: Measures the catalysis of the transfer of a methyl group to an acceptor molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: methyltransferase assay
annotated property: has_exact_synonym
annotated target: methyltransferase as
has_synonym_type: Unique short label curated by PSI-MI

methyltransferase radiometric assay
type: Class
subclass of: methyltransferase assay
definition: Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor.
has_exact_synonym: radiolabeled methyl
has_obo_namespace: PSI-MI
id: MI:0516
in_subset: PSI-MI slim

Axiom
annotated source: methyltransferase radiometric assay
annotated property: definition
annotated target: Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor.
database_cross_reference: PMID:14755292

Axiom
annotated source: methyltransferase radiometric assay
annotated property: has_exact_synonym
annotated target: radiolabeled methyl
has_synonym_type: Unique short label curated by PSI-MI

radiolabel
type: Class
subclass of: isotope label
definition: A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
has_exact_synonym: radiolabeled
has_exact_synonym: radiolabelled
has_obo_namespace: PSI-MI
id: MI:0517
in_subset: PSI-MI slim

Axiom
annotated source: radiolabel
annotated property: definition
annotated target: A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: radiolabel
annotated property: has_exact_synonym
annotated target: radiolabeled
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: radiolabel
annotated property: has_exact_synonym
annotated target: radiolabelled
has_synonym_type: Unique short label curated by PSI-MI

flag tag
type: Class
subclass of: tag
definition: The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
has_exact_synonym: DYKDDDDKV epitope tag
has_exact_synonym: FLAG
has_exact_synonym: FLAG-tagged
has_obo_namespace: PSI-MI
id: MI:0518
in_subset: PSI-MI slim

Axiom
annotated source: flag tag
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
database_cross_reference: PMID:14755292

Axiom
annotated source: flag tag
annotated property: has_exact_synonym
annotated target: DYKDDDDKV epitope tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: flag tag
annotated property: has_exact_synonym
annotated target: FLAG
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: flag tag
annotated property: has_exact_synonym
annotated target: FLAG-tagged
has_synonym_type: Alternate label curated by PSI-MI

glutathione s tranferase tag
type: Class
subclass of: enzyme tag
definition: The protein is expressed and purified as a fusion to the glutathione S-tranferase protein.
has_exact_synonym: glutathione S-tranferase tag
has_exact_synonym: gst tag
has_obo_namespace: PSI-MI
id: MI:0519
in_subset: PSI-MI slim

Axiom
annotated source: glutathione s tranferase tag
annotated property: definition
annotated target: The protein is expressed and purified as a fusion to the glutathione S-tranferase protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: glutathione s tranferase tag
annotated property: has_exact_synonym
annotated target: glutathione S-tranferase tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutathione s tranferase tag
annotated property: has_exact_synonym
annotated target: gst tag
has_synonym_type: Unique short label curated by PSI-MI

ha tag
type: Class
subclass of: tag
definition: The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available.
has_exact_synonym: YPYDVPDYA epitope tag
has_obo_namespace: PSI-MI
id: MI:0520
in_subset: PSI-MI slim

Axiom
annotated source: ha tag
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available.
database_cross_reference: PMID:14755292

Axiom
annotated source: ha tag
annotated property: has_exact_synonym
annotated target: YPYDVPDYA epitope tag
has_synonym_type: Alternate label curated by PSI-MI

his tag
type: Class
subclass of: tag
definition: The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
has_exact_synonym: 6-His-tag
has_exact_synonym: Hexa-His-tag
has_exact_synonym: Histidine-tag
has_obo_namespace: PSI-MI
id: MI:0521
in_subset: PSI-MI slim

Axiom
annotated source: his tag
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
database_cross_reference: PMID:14755292

Axiom
annotated source: his tag
annotated property: has_exact_synonym
annotated target: 6-His-tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: his tag
annotated property: has_exact_synonym
annotated target: Hexa-His-tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: his tag
annotated property: has_exact_synonym
annotated target: Histidine-tag
has_synonym_type: Alternate label curated by PSI-MI

myc tag
type: Class
subclass of: tag
definition: The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
has_exact_synonym: EUKLISEED epitope tag
has_obo_namespace: PSI-MI
id: MI:0522
in_subset: PSI-MI slim

Axiom
annotated source: myc tag
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
database_cross_reference: PMID:14755292

Axiom
annotated source: myc tag
annotated property: has_exact_synonym
annotated target: EUKLISEED epitope tag
has_synonym_type: Alternate label curated by PSI-MI

t7 tag
type: Class
subclass of: tag
definition: The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available.
has_exact_synonym: MASMTGGQQMG epitope tag
has_obo_namespace: PSI-MI
id: MI:0523
in_subset: PSI-MI slim

Axiom
annotated source: t7 tag
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available.
database_cross_reference: PMID:14755292

Axiom
annotated source: t7 tag
annotated property: has_exact_synonym
annotated target: MASMTGGQQMG epitope tag
has_synonym_type: Alternate label curated by PSI-MI

calmodulin binding peptide plus protein a tag
type: Class
subclass of: tandem tag
definition: Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein.
has_exact_synonym: CBP-ProtA tagged
has_exact_synonym: tap tagged
has_obo_namespace: PSI-MI
id: MI:0524
in_subset: PSI-MI slim

Axiom
annotated source: calmodulin binding peptide plus protein a tag
annotated property: definition
annotated target: Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: calmodulin binding peptide plus protein a tag
annotated property: has_exact_synonym
annotated target: CBP-ProtA tagged
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: calmodulin binding peptide plus protein a tag
annotated property: has_exact_synonym
annotated target: tap tagged
has_synonym_type: Unique short label curated by PSI-MI

v5 tag
type: Class
subclass of: tag
definition: The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available.
has_exact_synonym: GKPIPNPLLGLDST epitope tag
has_obo_namespace: PSI-MI
id: MI:0525
in_subset: PSI-MI slim

Axiom
annotated source: v5 tag
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available.
database_cross_reference: PMID:14755292

Axiom
annotated source: v5 tag
annotated property: has_exact_synonym
annotated target: GKPIPNPLLGLDST epitope tag
has_synonym_type: Alternate label curated by PSI-MI

n-acetyl-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00723.
has_exact_synonym: acetyllysine
has_obo_namespace: PSI-MI
id: MI:0526
deprecated: true

Axiom
annotated source: n-acetyl-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00723.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0048
database_cross_reference: RESID:AA0055

Axiom
annotated source: n-acetyl-lysine
annotated property: has_exact_synonym
annotated target: acetyllysine
has_synonym_type: Unique short label curated by PSI-MI

adp ribosylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00752.
has_exact_synonym: adp-ribosylated
has_obo_namespace: PSI-MI
id: MI:0527
deprecated: true

Axiom
annotated source: adp ribosylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00752.
database_cross_reference: PMID:14755292

Axiom
annotated source: adp ribosylated residue
annotated property: has_exact_synonym
annotated target: adp-ribosylated
has_synonym_type: Unique short label curated by PSI-MI

omega-n-(adp-ribosyl)-arginine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00177.
has_exact_synonym: (S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid
has_exact_synonym: N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine
has_exact_synonym: N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_exact_synonym: adp-ribosylarginine
has_exact_synonym: omega-N-(ADP-ribosyl)-L-arginine
has_obo_namespace: PSI-MI
id: MI:0528
deprecated: true

Axiom
annotated source: omega-n-(adp-ribosyl)-arginine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00177.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0168

Axiom
annotated source: omega-n-(adp-ribosyl)-arginine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-(adp-ribosyl)-arginine
annotated property: has_exact_synonym
annotated target: N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-(adp-ribosyl)-arginine
annotated property: has_exact_synonym
annotated target: N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-(adp-ribosyl)-arginine
annotated property: has_exact_synonym
annotated target: adp-ribosylarginine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: omega-n-(adp-ribosyl)-arginine
annotated property: has_exact_synonym
annotated target: omega-N-(ADP-ribosyl)-L-arginine
has_synonym_type: Alternate label curated by PSI-MI

s-(adp-ribosyl)-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00178.
has_exact_synonym: (R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid
has_exact_synonym: S-(ADP-ribosyl)-L-cysteine
has_exact_synonym: S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_exact_synonym: S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_exact_synonym: adp-ribosylcysteine
has_obo_namespace: PSI-MI
id: MI:0529
deprecated: true

Axiom
annotated source: s-(adp-ribosyl)-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00178.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0169

Axiom
annotated source: s-(adp-ribosyl)-cysteine
annotated property: has_exact_synonym
annotated target: (R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-(adp-ribosyl)-cysteine
annotated property: has_exact_synonym
annotated target: S-(ADP-ribosyl)-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-(adp-ribosyl)-cysteine
annotated property: has_exact_synonym
annotated target: S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-(adp-ribosyl)-cysteine
annotated property: has_exact_synonym
annotated target: S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-(adp-ribosyl)-cysteine
annotated property: has_exact_synonym
annotated target: adp-ribosylcysteine
has_synonym_type: Unique short label curated by PSI-MI

glutamyl-5-poly(adp-ribose)
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00300.
has_exact_synonym: (S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid
has_exact_synonym: L-glutamyl-5-poly(ADP-ribose)
has_exact_synonym: L-isoglutamyl-poly(ADP-ribose)
has_exact_synonym: adp-ribosylglutamate
has_obo_namespace: PSI-MI
id: MI:0530
deprecated: true

Axiom
annotated source: glutamyl-5-poly(adp-ribose)
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00300.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0295

Axiom
annotated source: glutamyl-5-poly(adp-ribose)
annotated property: has_exact_synonym
annotated target: (S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl-5-poly(adp-ribose)
annotated property: has_exact_synonym
annotated target: L-glutamyl-5-poly(ADP-ribose)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl-5-poly(adp-ribose)
annotated property: has_exact_synonym
annotated target: L-isoglutamyl-poly(ADP-ribose)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glutamyl-5-poly(adp-ribose)
annotated property: has_exact_synonym
annotated target: adp-ribosylglutamate
has_synonym_type: Unique short label curated by PSI-MI

o-(adp-ribosyl)-serine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00242.
has_exact_synonym: (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula
has_exact_synonym: O-(ADP-ribosyl)-L-serine
has_exact_synonym: O3-(ADP-ribosyl)-L-serine
has_exact_synonym: O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine
has_exact_synonym: O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_exact_synonym: adp-ribosylserine
has_obo_namespace: PSI-MI
id: MI:0531
deprecated: true

Axiom
annotated source: o-(adp-ribosyl)-serine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00242.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0237

Axiom
annotated source: o-(adp-ribosyl)-serine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-(adp-ribosyl)-serine
annotated property: has_exact_synonym
annotated target: O-(ADP-ribosyl)-L-serine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-(adp-ribosyl)-serine
annotated property: has_exact_synonym
annotated target: O3-(ADP-ribosyl)-L-serine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-(adp-ribosyl)-serine
annotated property: has_exact_synonym
annotated target: O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-(adp-ribosyl)-serine
annotated property: has_exact_synonym
annotated target: O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o-(adp-ribosyl)-serine
annotated property: has_exact_synonym
annotated target: adp-ribosylserine
has_synonym_type: Unique short label curated by PSI-MI

n4-(adp-ribosyl)-asparagine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00236.
has_exact_synonym: (S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid
has_exact_synonym: N4-(ADP-ribosyl)-L-asparagine
has_exact_synonym: N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine
has_exact_synonym: N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_exact_synonym: adpribosylasparagine
has_obo_namespace: PSI-MI
id: MI:0532
deprecated: true

Axiom
annotated source: n4-(adp-ribosyl)-asparagine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00236.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0231

Axiom
annotated source: n4-(adp-ribosyl)-asparagine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n4-(adp-ribosyl)-asparagine
annotated property: has_exact_synonym
annotated target: N4-(ADP-ribosyl)-L-asparagine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n4-(adp-ribosyl)-asparagine
annotated property: has_exact_synonym
annotated target: N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n4-(adp-ribosyl)-asparagine
annotated property: has_exact_synonym
annotated target: N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n4-(adp-ribosyl)-asparagine
annotated property: has_exact_synonym
annotated target: adpribosylasparagine
has_synonym_type: Unique short label curated by PSI-MI

glycosylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00693.
has_obo_namespace: PSI-MI
id: MI:0533
deprecated: true

Axiom
annotated source: glycosylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00693.
database_cross_reference: PMID:14755292

glycosyl-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00131.
has_exact_synonym: S-glycosyl-L-cysteine
has_obo_namespace: PSI-MI
id: MI:0534
deprecated: true

Axiom
annotated source: glycosyl-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00131.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0122

Axiom
annotated source: glycosyl-cysteine
annotated property: has_exact_synonym
annotated target: S-glycosyl-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

glycosyl-serine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00163.
has_exact_synonym: O-glycosyl-L-serine
has_exact_synonym: O3-glycosyl-L-serine
has_obo_namespace: PSI-MI
id: MI:0535
deprecated: true

Axiom
annotated source: glycosyl-serine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00163.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0154

Axiom
annotated source: glycosyl-serine
annotated property: has_exact_synonym
annotated target: O-glycosyl-L-serine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glycosyl-serine
annotated property: has_exact_synonym
annotated target: O3-glycosyl-L-serine
has_synonym_type: Alternate label curated by PSI-MI

glycosyl-threonine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00164.
has_exact_synonym: O-glycosyl-L-threonine
has_exact_synonym: O3-glycosyl-L-threonine
has_obo_namespace: PSI-MI
id: MI:0536
deprecated: true

Axiom
annotated source: glycosyl-threonine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00164.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0155

Axiom
annotated source: glycosyl-threonine
annotated property: has_exact_synonym
annotated target: O-glycosyl-L-threonine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: glycosyl-threonine
annotated property: has_exact_synonym
annotated target: O3-glycosyl-L-threonine
has_synonym_type: Alternate label curated by PSI-MI

omega-n-glycosyl-arginine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00332.
has_exact_synonym: glycosylarginine
has_exact_synonym: omega-N-glycosyl-L-arginine
has_obo_namespace: PSI-MI
id: MI:0537
deprecated: true

Axiom
annotated source: omega-n-glycosyl-arginine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00332.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0327

Axiom
annotated source: omega-n-glycosyl-arginine
annotated property: has_exact_synonym
annotated target: glycosylarginine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: omega-n-glycosyl-arginine
annotated property: has_exact_synonym
annotated target: omega-N-glycosyl-L-arginine
has_synonym_type: Alternate label curated by PSI-MI

n4-glycosyl-asparagine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00160.
has_exact_synonym: N4-glycosyl-L-asparagine
has_exact_synonym: glycosylasparagine
has_obo_namespace: PSI-MI
id: MI:0538
deprecated: true

Axiom
annotated source: n4-glycosyl-asparagine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00160.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0151

Axiom
annotated source: n4-glycosyl-asparagine
annotated property: has_exact_synonym
annotated target: N4-glycosyl-L-asparagine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: n4-glycosyl-asparagine
annotated property: has_exact_synonym
annotated target: glycosylasparagine
has_synonym_type: Unique short label curated by PSI-MI

gpi anchor residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00818.
has_obo_namespace: PSI-MI
id: MI:0539
deprecated: true

Axiom
annotated source: gpi anchor residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00818.
database_cross_reference: PMID:14755292

gpi-anchor amidated alanine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00172.
has_exact_synonym: N-alanyl-glycosylphosphatidylinositolethanolamine
has_exact_synonym: gpi-alanine
has_obo_namespace: PSI-MI
id: MI:0540
deprecated: true

Axiom
annotated source: gpi-anchor amidated alanine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00172.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0163

Axiom
annotated source: gpi-anchor amidated alanine
annotated property: has_exact_synonym
annotated target: N-alanyl-glycosylphosphatidylinositolethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gpi-anchor amidated alanine
annotated property: has_exact_synonym
annotated target: gpi-alanine
has_synonym_type: Unique short label curated by PSI-MI

gpi-anchor amidated asparagine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00167.
has_exact_synonym: N-asparaginyl-glycosylphosphatidylinositolethanolamine
has_exact_synonym: gpi-asparagine
has_obo_namespace: PSI-MI
id: MI:0541
deprecated: true

Axiom
annotated source: gpi-anchor amidated asparagine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00167.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0158

Axiom
annotated source: gpi-anchor amidated asparagine
annotated property: has_exact_synonym
annotated target: N-asparaginyl-glycosylphosphatidylinositolethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gpi-anchor amidated asparagine
annotated property: has_exact_synonym
annotated target: gpi-asparagine
has_synonym_type: Unique short label curated by PSI-MI

gpi-anchor amidated aspartate
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00168.
has_exact_synonym: N-aspartyl-glycosylphosphatidylinositolethanolamine
has_exact_synonym: gpi-aspartate
has_obo_namespace: PSI-MI
id: MI:0542
deprecated: true

Axiom
annotated source: gpi-anchor amidated aspartate
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00168.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0159

Axiom
annotated source: gpi-anchor amidated aspartate
annotated property: has_exact_synonym
annotated target: N-aspartyl-glycosylphosphatidylinositolethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gpi-anchor amidated aspartate
annotated property: has_exact_synonym
annotated target: gpi-aspartate
has_synonym_type: Unique short label curated by PSI-MI

gpi-anchor amidated cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00169.
has_exact_synonym: N-cysteinyl-glycosylphosphatidylinositolethanolamine
has_exact_synonym: gpi-cysteine
has_obo_namespace: PSI-MI
id: MI:0543
deprecated: true

Axiom
annotated source: gpi-anchor amidated cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00169.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0160

Axiom
annotated source: gpi-anchor amidated cysteine
annotated property: has_exact_synonym
annotated target: N-cysteinyl-glycosylphosphatidylinositolethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gpi-anchor amidated cysteine
annotated property: has_exact_synonym
annotated target: gpi-cysteine
has_synonym_type: Unique short label curated by PSI-MI

gpi-anchor amidated glycine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00170.
has_exact_synonym: N-glycyl-glycosylphosphatidylinositolethanolamine
has_exact_synonym: gpi-glycine
has_obo_namespace: PSI-MI
id: MI:0544
deprecated: true

Axiom
annotated source: gpi-anchor amidated glycine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00170.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0161

Axiom
annotated source: gpi-anchor amidated glycine
annotated property: has_exact_synonym
annotated target: N-glycyl-glycosylphosphatidylinositolethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gpi-anchor amidated glycine
annotated property: has_exact_synonym
annotated target: gpi-glycine
has_synonym_type: Unique short label curated by PSI-MI

gpi-anchor amidated serine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00171.
has_exact_synonym: N-seryl-glycosylphosphatidylinositolethanolamine
has_exact_synonym: gpi-serine
has_obo_namespace: PSI-MI
id: MI:0545
deprecated: true

Axiom
annotated source: gpi-anchor amidated serine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00171.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0162

Axiom
annotated source: gpi-anchor amidated serine
annotated property: has_exact_synonym
annotated target: N-seryl-glycosylphosphatidylinositolethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gpi-anchor amidated serine
annotated property: has_exact_synonym
annotated target: gpi-serine
has_synonym_type: Unique short label curated by PSI-MI

gpi-anchor amidated threonine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00173.
has_exact_synonym: N-threonyl-glycosylphosphatidylinositolethanolamine
has_exact_synonym: gpi-threonine
has_obo_namespace: PSI-MI
id: MI:0546
deprecated: true

Axiom
annotated source: gpi-anchor amidated threonine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00173.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0164

Axiom
annotated source: gpi-anchor amidated threonine
annotated property: has_exact_synonym
annotated target: N-threonyl-glycosylphosphatidylinositolethanolamine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gpi-anchor amidated threonine
annotated property: has_exact_synonym
annotated target: gpi-threonine
has_synonym_type: Unique short label curated by PSI-MI

s-prenyl-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:01110.
has_exact_synonym: prenylcysteine
has_obo_namespace: PSI-MI
id: MI:0547
deprecated: true

Axiom
annotated source: s-prenyl-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:01110.
database_cross_reference: PMID:14755292

Axiom
annotated source: s-prenyl-cysteine
annotated property: has_exact_synonym
annotated target: prenylcysteine
has_synonym_type: Unique short label curated by PSI-MI

methylated-lysine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00663.
has_exact_synonym: methylatedlysine
has_obo_namespace: PSI-MI
id: MI:0548
deprecated: true

Axiom
annotated source: methylated-lysine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00663.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0074
database_cross_reference: RESID:AA0075
database_cross_reference: RESID:AA0076

Axiom
annotated source: methylated-lysine
annotated property: has_exact_synonym
annotated target: methylatedlysine
has_synonym_type: Unique short label curated by PSI-MI

alkylated cysteine
type: Class
definition: Artificial residue modification enabling studies of cysteine binding status. OBSOLETE remap to MOD:00660.
has_obo_namespace: PSI-MI
id: MI:0549
deprecated: true

Axiom
annotated source: alkylated cysteine
annotated property: definition
annotated target: Artificial residue modification enabling studies of cysteine binding status. OBSOLETE remap to MOD:00660.
database_cross_reference: PMID:15325307

gamma-carboxyglutamic acid
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00041.
has_exact_synonym: (S)-3-amino-1,1,3-propanetricarboxylic acid
has_exact_synonym: 1-carboxyglutamic acid [misnomer]
has_exact_synonym: 4-carboxyglutamic acid
has_exact_synonym: L-gamma-carboxyglutamic acid
has_exact_synonym: carboxyglutamic acid
has_obo_namespace: PSI-MI
id: MI:0550
deprecated: true

Axiom
annotated source: gamma-carboxyglutamic acid
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00041.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0032

Axiom
annotated source: gamma-carboxyglutamic acid
annotated property: has_exact_synonym
annotated target: (S)-3-amino-1,1,3-propanetricarboxylic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gamma-carboxyglutamic acid
annotated property: has_exact_synonym
annotated target: 1-carboxyglutamic acid [misnomer]
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gamma-carboxyglutamic acid
annotated property: has_exact_synonym
annotated target: 4-carboxyglutamic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gamma-carboxyglutamic acid
annotated property: has_exact_synonym
annotated target: L-gamma-carboxyglutamic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gamma-carboxyglutamic acid
annotated property: has_exact_synonym
annotated target: carboxyglutamic acid
has_synonym_type: Unique short label curated by PSI-MI

nitro-tyrosine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00461.
has_exact_synonym: nitrated tyrosine
has_obo_namespace: PSI-MI
id: MI:0551
deprecated: true

Axiom
annotated source: nitro-tyrosine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00461.
database_cross_reference: PMID:15657065
database_cross_reference: PMID:9636206

Axiom
annotated source: nitro-tyrosine
annotated property: has_exact_synonym
annotated target: nitrated tyrosine
has_synonym_type: Alternate label curated by PSI-MI

s-nitrosyl-cysteine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00235.
has_exact_synonym: (R)-2-amino-3-nitrososulfanyl-propanoic acid
has_exact_synonym: L-cysteine nitrite ester
has_exact_synonym: S-nitrosocysteine
has_exact_synonym: S-nitrosyl-L-cysteine
has_exact_synonym: nitrosylcysteine
has_obo_namespace: PSI-MI
id: MI:0552
deprecated: true

Axiom
annotated source: s-nitrosyl-cysteine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00235.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0230

Axiom
annotated source: s-nitrosyl-cysteine
annotated property: has_exact_synonym
annotated target: (R)-2-amino-3-nitrososulfanyl-propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-nitrosyl-cysteine
annotated property: has_exact_synonym
annotated target: L-cysteine nitrite ester
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-nitrosyl-cysteine
annotated property: has_exact_synonym
annotated target: S-nitrosocysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-nitrosyl-cysteine
annotated property: has_exact_synonym
annotated target: S-nitrosyl-L-cysteine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: s-nitrosyl-cysteine
annotated property: has_exact_synonym
annotated target: nitrosylcysteine
has_synonym_type: Unique short label curated by PSI-MI

o4'-sulfo-tyrosine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00181.
has_exact_synonym: (S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid
has_exact_synonym: 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate
has_exact_synonym: O4'-sulfo-L-tyrosine
has_exact_synonym: O4-sulfotyrosine
has_exact_synonym: sulfotyrosine
has_exact_synonym: tyrosine sulfate
has_obo_namespace: PSI-MI
id: MI:0553
deprecated: true

Axiom
annotated source: o4'-sulfo-tyrosine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00181.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0172

Axiom
annotated source: o4'-sulfo-tyrosine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-sulfo-tyrosine
annotated property: has_exact_synonym
annotated target: 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-sulfo-tyrosine
annotated property: has_exact_synonym
annotated target: O4'-sulfo-L-tyrosine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-sulfo-tyrosine
annotated property: has_exact_synonym
annotated target: O4-sulfotyrosine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: o4'-sulfo-tyrosine
annotated property: has_exact_synonym
annotated target: sulfotyrosine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: o4'-sulfo-tyrosine
annotated property: has_exact_synonym
annotated target: tyrosine sulfate
has_synonym_type: Alternate label curated by PSI-MI

sumoylated lysine
type: Class
definition: Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein. OBSOLETE remap to MOD:01149.
has_exact_synonym: (S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid
has_exact_synonym: N6-glycyl-L-lysine
has_exact_synonym: N6-glycyllysine
has_obo_namespace: PSI-MI
id: MI:0554
deprecated: true

Axiom
annotated source: sumoylated lysine
annotated property: definition
annotated target: Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein. OBSOLETE remap to MOD:01149.
database_cross_reference: PMID:12612601
database_cross_reference: RESID:AA0125

Axiom
annotated source: sumoylated lysine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: sumoylated lysine
annotated property: has_exact_synonym
annotated target: N6-glycyl-L-lysine
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: sumoylated lysine
annotated property: has_exact_synonym
annotated target: N6-glycyllysine
has_synonym_type: Alternate label curated by PSI-MI

phospho-histidine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00890.
has_exact_synonym: phosphoshistidine
has_obo_namespace: PSI-MI
id: MI:0555
deprecated: true

Axiom
annotated source: phospho-histidine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00890.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0035
database_cross_reference: RESID:AA0036

Axiom
annotated source: phospho-histidine
annotated property: has_exact_synonym
annotated target: phosphoshistidine
has_synonym_type: Unique short label curated by PSI-MI

transglutamination reaction
type: Class
subclass of: covalent binding
definition: Gln-Lys cross-link catalyzed by a transglutaminase.
has_exact_synonym: transglutamination
has_obo_namespace: PSI-MI
id: MI:0556
in_subset: PSI-MI slim

Axiom
annotated source: transglutamination reaction
annotated property: definition
annotated target: Gln-Lys cross-link catalyzed by a transglutaminase.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0124

Axiom
annotated source: transglutamination reaction
annotated property: has_exact_synonym
annotated target: transglutamination
has_synonym_type: Unique short label curated by PSI-MI

adp ribosylation reaction
type: Class
subclass of: enzymatic reaction
definition: Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
has_exact_synonym: adp ribosylation
has_obo_namespace: PSI-MI
id: MI:0557
in_subset: PSI-MI slim

Axiom
annotated source: adp ribosylation reaction
annotated property: definition
annotated target: Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
database_cross_reference: GO:0006471
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0168
database_cross_reference: RESID:AA0169
database_cross_reference: RESID:AA0231
database_cross_reference: RESID:AA0237
database_cross_reference: RESID:AA0295

Axiom
annotated source: adp ribosylation reaction
annotated property: has_exact_synonym
annotated target: adp ribosylation
has_synonym_type: Unique short label curated by PSI-MI

deglycosylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins.
has_exact_synonym: deglycosylation
has_obo_namespace: PSI-MI
id: MI:0558
in_subset: PSI-MI slim

Axiom
annotated source: deglycosylation reaction
annotated property: definition
annotated target: Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins.
database_cross_reference: GO:0006517
database_cross_reference: PMID:15670854

Axiom
annotated source: deglycosylation reaction
annotated property: has_exact_synonym
annotated target: deglycosylation
has_synonym_type: Unique short label curated by PSI-MI

glycosylation reaction
type: Class
subclass of: enzymatic reaction
definition: The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate.
has_exact_synonym: glycosylation
has_obo_namespace: PSI-MI
id: MI:0559
in_subset: PSI-MI slim

Axiom
annotated source: glycosylation reaction
annotated property: definition
annotated target: The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate.
database_cross_reference: GO:0043413
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0122
database_cross_reference: RESID:AA0151
database_cross_reference: RESID:AA0154
database_cross_reference: RESID:AA0155
database_cross_reference: RESID:AA0327

Axiom
annotated source: glycosylation reaction
annotated property: has_exact_synonym
annotated target: glycosylation
has_synonym_type: Unique short label curated by PSI-MI

myristoylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00438.
has_exact_synonym: myristoylated aa
has_obo_namespace: PSI-MI
id: MI:0560
deprecated: true

Axiom
annotated source: myristoylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00438.
database_cross_reference: PMID:14755292

Axiom
annotated source: myristoylated residue
annotated property: has_exact_synonym
annotated target: myristoylated aa
has_synonym_type: Unique short label curated by PSI-MI

palmitoylated residue
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00440.
has_exact_synonym: palmitoylated aa
has_obo_namespace: PSI-MI
id: MI:0561
deprecated: true

Axiom
annotated source: palmitoylated residue
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00440.
database_cross_reference: PMID:14755292

Axiom
annotated source: palmitoylated residue
annotated property: has_exact_synonym
annotated target: palmitoylated aa
has_synonym_type: Unique short label curated by PSI-MI

methylated alanine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00665.
has_obo_namespace: PSI-MI
id: MI:0562
deprecated: true

Axiom
annotated source: methylated alanine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00665.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0061
database_cross_reference: RESID:AA0062

methylated arginine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00658.
has_obo_namespace: PSI-MI
id: MI:0563
deprecated: true

Axiom
annotated source: methylated arginine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00658.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0068
database_cross_reference: RESID:AA0069

omega-n-methyl-arginine
type: Class
definition: Residue modification. OBSOLETE remap to MOD:00078.
has_exact_synonym: (S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid
has_exact_synonym: NG-methylarginine;
has_exact_synonym: methylarginine
has_exact_synonym: omega-N-methyl-L-arginine
has_obo_namespace: PSI-MI
id: MI:0564
deprecated: true

Axiom
annotated source: omega-n-methyl-arginine
annotated property: definition
annotated target: Residue modification. OBSOLETE remap to MOD:00078.
database_cross_reference: PMID:14755292
database_cross_reference: RESID:AA0069

Axiom
annotated source: omega-n-methyl-arginine
annotated property: has_exact_synonym
annotated target: (S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-methyl-arginine
annotated property: has_exact_synonym
annotated target: NG-methylarginine;
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: omega-n-methyl-arginine
annotated property: has_exact_synonym
annotated target: methylarginine
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: omega-n-methyl-arginine
annotated property: has_exact_synonym
annotated target: omega-N-methyl-L-arginine
has_synonym_type: Alternate label curated by PSI-MI

neddylated lysine
type: Class
definition: Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family. OBSOLETE remap to MOD:01150.
has_obo_namespace: PSI-MI
id: MI:0565
deprecated: true

Axiom
annotated source: neddylated lysine
annotated property: definition
annotated target: Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family. OBSOLETE remap to MOD:01150.
database_cross_reference: PMID:111

sumoylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
has_exact_synonym: sumoylation
has_obo_namespace: PSI-MI
id: MI:0566
in_subset: PSI-MI slim

Axiom
annotated source: sumoylation reaction
annotated property: definition
annotated target: Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
database_cross_reference: GO:0016925
database_cross_reference: PMID:15985640

Axiom
annotated source: sumoylation reaction
annotated property: has_exact_synonym
annotated target: sumoylation
has_synonym_type: Unique short label curated by PSI-MI

neddylation reaction
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
has_exact_synonym: neddylation
has_obo_namespace: PSI-MI
id: MI:0567
in_subset: PSI-MI slim

Axiom
annotated source: neddylation reaction
annotated property: definition
annotated target: Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
database_cross_reference: GO:0045116
database_cross_reference: PMID:16127432

Axiom
annotated source: neddylation reaction
annotated property: has_exact_synonym
annotated target: neddylation
has_synonym_type: Unique short label curated by PSI-MI

desumoylation reaction
type: Class
subclass of: enzymatic reaction
definition: Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins.
has_exact_synonym: desumoylation
has_obo_namespace: PSI-MI
id: MI:0568
in_subset: PSI-MI slim

Axiom
annotated source: desumoylation reaction
annotated property: definition
annotated target: Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins.
database_cross_reference: GO:0016926
database_cross_reference: PMID:15985640

Axiom
annotated source: desumoylation reaction
annotated property: has_exact_synonym
annotated target: desumoylation
has_synonym_type: Unique short label curated by PSI-MI

deneddylation reaction
type: Class
subclass of: enzymatic reaction
definition: Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome.
has_exact_synonym: deneddylation
has_obo_namespace: PSI-MI
id: MI:0569
in_subset: PSI-MI slim

Axiom
annotated source: deneddylation reaction
annotated property: definition
annotated target: Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome.
database_cross_reference: GO:0000338
database_cross_reference: PMID:16127432

Axiom
annotated source: deneddylation reaction
annotated property: has_exact_synonym
annotated target: deneddylation
has_synonym_type: Unique short label curated by PSI-MI

protein cleavage
type: Class
subclass of: cleavage reaction
definition: Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation.
has_obo_namespace: PSI-MI
id: MI:0570
in_subset: PSI-MI slim

Axiom
annotated source: protein cleavage
annotated property: definition
annotated target: Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation.
database_cross_reference: PMID:14744292

mrna cleavage
type: Class
subclass of: rna cleavage
definition: Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
has_obo_namespace: PSI-MI
id: MI:0571
in_subset: PSI-MI slim

Axiom
annotated source: mrna cleavage
annotated property: definition
annotated target: Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
database_cross_reference: GO:0006379
database_cross_reference: PMID:14681407

dna cleavage
type: Class
subclass of: nucleic acid cleavage
definition: Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments.
has_obo_namespace: PSI-MI
id: MI:0572
in_subset: PSI-MI slim

Axiom
annotated source: dna cleavage
annotated property: definition
annotated target: Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments.
database_cross_reference: PMID:14755292

mutation disrupting interaction
type: Class
subclass of: mutation decreasing interaction
definition: Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction)..
has_exact_synonym: mutation disrupting
has_obo_namespace: PSI-MI
id: MI:0573
in_subset: PSI-MI slim

Axiom
annotated source: mutation disrupting interaction
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction)..
database_cross_reference: PMID:14755292

Axiom
annotated source: mutation disrupting interaction
annotated property: has_exact_synonym
annotated target: mutation disrupting
has_synonym_type: Unique short label curated by PSI-MI

digital object identifier
type: Class
subclass of: literature database
definition: Identifier of a publication prior to pubmed indexing.
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: doi
has_obo_namespace: PSI-MI
id: MI:0574
in_subset: PSI-MI slim

Axiom
annotated source: digital object identifier
annotated property: definition
annotated target: Identifier of a publication prior to pubmed indexing.
database_cross_reference: PMID:14755292

\d+.\d+/[a-zA-Z0-9\.\:]+
type: Axiom
annotated source: digital object identifier
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: digital object identifier
annotated property: database_cross_reference
annotated target: search-url:
label: http://dx.doi.org/${ac}

Axiom
annotated source: digital object identifier
annotated property: has_exact_synonym
annotated target: doi
has_synonym_type: Unique short label curated by PSI-MI

alliance for cellular signaling
type: Class
subclass of: interaction database
subclass of: source database
definition: Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all. http://www.signaling-gateway.org
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: AfCS
has_exact_synonym: afcs
has_obo_namespace: PSI-MI
id: MI:0575
in_subset: PSI-MI slim

Axiom
annotated source: alliance for cellular signaling
annotated property: definition
annotated target: Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all. http://www.signaling-gateway.org
database_cross_reference: PMID:14755292

[0-9]+
type: Axiom
annotated source: alliance for cellular signaling
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: alliance for cellular signaling
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.signaling-gateway.org/data/Y2H/cgi-bin/y2h_int.cgi

Axiom
annotated source: alliance for cellular signaling
annotated property: has_exact_synonym
annotated target: AfCS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: alliance for cellular signaling
annotated property: has_exact_synonym
annotated target: afcs
has_synonym_type: Unique short label curated by PSI-MI

structural proximity
type: Class
subclass of: feature prediction from structure
definition: Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact.
has_obo_namespace: PSI-MI
id: MI:0576
in_subset: PSI-MI slim

Axiom
annotated source: structural proximity
annotated property: definition
annotated target: Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact.
database_cross_reference: PMID:15353450

feature prediction from structure
type: Class
subclass of: feature prediction
definition: Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules.
has_exact_synonym: feature struct pred
has_obo_namespace: PSI-MI
id: MI:0577
in_subset: PSI-MI slim

Axiom
annotated source: feature prediction from structure
annotated property: definition
annotated target: Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules.
database_cross_reference: PMID:14755292

Axiom
annotated source: feature prediction from structure
annotated property: has_exact_synonym
annotated target: feature struct pred
has_synonym_type: Unique short label curated by PSI-MI

maltose binding protein tag
type: Class
subclass of: fusion protein
definition: The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin.
has_exact_synonym: maltose binding protein tag
has_exact_synonym: mbp tag
has_obo_namespace: PSI-MI
id: MI:0578
in_subset: PSI-MI slim

Axiom
annotated source: maltose binding protein tag
annotated property: definition
annotated target: The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin.
database_cross_reference: PMID:14755292

Axiom
annotated source: maltose binding protein tag
annotated property: has_exact_synonym
annotated target: maltose binding protein tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: maltose binding protein tag
annotated property: has_exact_synonym
annotated target: mbp tag
has_synonym_type: Unique short label curated by PSI-MI

electron donor
type: Class
subclass of: donor
definition: Any molecule that is able to transfer an electron to another chemical species.
has_obo_namespace: PSI-MI
id: MI:0579
in_subset: PSI-MI slim

Axiom
annotated source: electron donor
annotated property: definition
annotated target: Any molecule that is able to transfer an electron to another chemical species.
database_cross_reference: PMID:14755292

electron acceptor
type: Class
subclass of: acceptor
definition: Molecule to which an electron may be transferred from an electron donor.
has_obo_namespace: PSI-MI
id: MI:0580
in_subset: PSI-MI slim

Axiom
annotated source: electron acceptor
annotated property: definition
annotated target: Molecule to which an electron may be transferred from an electron donor.
database_cross_reference: PMID:14755292

suppressor gene
type: Class
subclass of: experimental role
definition: A gene whose genetic perturbation suppresses the phenotype resulting from a different genetic perturbation.
has_exact_synonym: suppressor
has_obo_namespace: PSI-MI
id: MI:0581
in_subset: PSI-MI slim

Axiom
annotated source: suppressor gene
annotated property: definition
annotated target: A gene whose genetic perturbation suppresses the phenotype resulting from a different genetic perturbation.
database_cross_reference: PMID:14755292

Axiom
annotated source: suppressor gene
annotated property: has_exact_synonym
annotated target: suppressor
has_synonym_type: Unique short label curated by PSI-MI

suppressed gene
type: Class
subclass of: experimental role
definition: A gene whose genetic perturbation phenotype is suppressed by a different genetic perturbation.
has_exact_synonym: suppressed
has_obo_namespace: PSI-MI
id: MI:0582
in_subset: PSI-MI slim

Axiom
annotated source: suppressed gene
annotated property: definition
annotated target: A gene whose genetic perturbation phenotype is suppressed by a different genetic perturbation.
database_cross_reference: PMID:14755292

Axiom
annotated source: suppressed gene
annotated property: has_exact_synonym
annotated target: suppressed
has_synonym_type: Unique short label curated by PSI-MI

fluorescence donor
type: Class
subclass of: luminescence donor
definition: Fluorophore which emits electromagnetic radiation of given wavelength.
has_obo_namespace: PSI-MI
id: MI:0583
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence donor
annotated property: definition
annotated target: Fluorophore which emits electromagnetic radiation of given wavelength.
database_cross_reference: PMID:14755292

fluorescence acceptor
type: Class
subclass of: luminescence acceptor
definition: Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, then re-emiting its own characteristic fluorescence.
has_exact_synonym: fluorescence accept
has_obo_namespace: PSI-MI
id: MI:0584
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence acceptor
annotated property: definition
annotated target: Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, then re-emiting its own characteristic fluorescence.
database_cross_reference: PMID:14755292

Axiom
annotated source: fluorescence acceptor
annotated property: has_exact_synonym
annotated target: fluorescence accept
has_synonym_type: Unique short label curated by PSI-MI

intenz
type: Class
subclass of: interaction database
definition: IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at. http://www.ebi.ac.uk/intenz
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0585
in_subset: PSI-MI slim

Axiom
annotated source: intenz
annotated property: definition
annotated target: IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at. http://www.ebi.ac.uk/intenz
database_cross_reference: PMID:14681451

[0-6]{1}\.(\d+|-)\.(\d+|-)\.(\d+|-)
type: Axiom
annotated source: intenz
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: intenz
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/intenz/query

inhibitor
type: Class
subclass of: regulator
definition: Molecule inhibiting an interaction by interacting with one or more of its participants.
has_obo_namespace: PSI-MI
id: MI:0586
in_subset: PSI-MI slim

Axiom
annotated source: inhibitor
annotated property: definition
annotated target: Molecule inhibiting an interaction by interacting with one or more of its participants.
database_cross_reference: PMID:14755292

inhibited
type: Class
definition: Molecule being identified as target of an inhibitor. OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role.
has_obo_namespace: PSI-MI
id: MI:0587
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: inhibited
annotated property: definition
annotated target: Molecule being identified as target of an inhibitor. OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role.
database_cross_reference: PMID:14755292

three hybrid
type: Class
subclass of: transcriptional complementation assay
definition: Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey.
has_exact_synonym: 3 hybrid
has_exact_synonym: 3-hybrid
has_exact_synonym: tri hybrid
has_exact_synonym: tri-hybrid assay
has_obo_namespace: PSI-MI
id: MI:0588
in_subset: PSI-MI slim

Axiom
annotated source: three hybrid
annotated property: definition
annotated target: Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey.
database_cross_reference: PMID:14755292

Axiom
annotated source: three hybrid
annotated property: has_exact_synonym
annotated target: 3 hybrid
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: three hybrid
annotated property: has_exact_synonym
annotated target: 3-hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: three hybrid
annotated property: has_exact_synonym
annotated target: tri hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: three hybrid
annotated property: has_exact_synonym
annotated target: tri-hybrid assay
has_synonym_type: Alternate label curated by PSI-MI

in vitro translated protein
type: Class
subclass of: sample process
definition: Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery.
has_exact_synonym: in vitro translated
has_obo_namespace: PSI-MI
id: MI:0589
in_subset: PSI-MI slim

Axiom
annotated source: in vitro translated protein
annotated property: definition
annotated target: Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery.
database_cross_reference: PMID:14755292

Axiom
annotated source: in vitro translated protein
annotated property: has_exact_synonym
annotated target: in vitro translated
has_synonym_type: Unique short label curated by PSI-MI

attribute name
type: Class
subclass of: molecular interaction
definition: Collection of topics describing the free text stored as an attribute value.
has_exact_synonym: CvTopic
has_obo_namespace: PSI-MI
id: MI:0590
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: attribute name
annotated property: definition
annotated target: Collection of topics describing the free text stored as an attribute value.
database_cross_reference: PMID:14755292

Axiom
annotated source: attribute name
annotated property: has_exact_synonym
annotated target: CvTopic
has_synonym_type: Alternate label curated by PSI-MI

experiment description
type: Class
subclass of: experiment attribute name
definition: The experimental condition text description, should contain information about the organisms hosting the interaction.
has_exact_synonym: experiment descripti
has_obo_namespace: PSI-MI
id: MI:0591
in_subset: PSI-MI slim

Axiom
annotated source: experiment description
annotated property: definition
annotated target: The experimental condition text description, should contain information about the organisms hosting the interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: experiment description
annotated property: has_exact_synonym
annotated target: experiment descripti
has_synonym_type: Unique short label curated by PSI-MI

ipfam
type: Class
subclass of: feature database
definition: Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at. http://www.sanger.ac.uk/Software/Pfam/iPfam/
has_obo_namespace: PSI-MI
id: MI:0592
in_subset: PSI-MI slim

Axiom
annotated source: ipfam
annotated property: definition
annotated target: Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at. http://www.sanger.ac.uk/Software/Pfam/iPfam/
database_cross_reference: PMID:15353450

translocation
type: Class
subclass of: cross-reference type
definition: Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'.
has_obo_namespace: PSI-MI
id: MI:0593
in_subset: PSI-MI slim

Axiom
annotated source: translocation
annotated property: definition
annotated target: Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'.
database_cross_reference: PMID:14681407

translocation start
type: Class
subclass of: translocation
definition: Xref pointing to a GO compartment term describing the start location of a migrating molecule.
has_obo_namespace: PSI-MI
id: MI:0594
in_subset: PSI-MI slim

Axiom
annotated source: translocation start
annotated property: definition
annotated target: Xref pointing to a GO compartment term describing the start location of a migrating molecule.
database_cross_reference: PMID:14681407

translocation end
type: Class
subclass of: translocation
definition: Xref pointing to a GO compartment term describing the end location of a migrating molecule.
has_obo_namespace: PSI-MI
id: MI:0595
in_subset: PSI-MI slim

Axiom
annotated source: translocation end
annotated property: definition
annotated target: Xref pointing to a GO compartment term describing the end location of a migrating molecule.
database_cross_reference: PMID:14755292

experimental form description
type: Class
subclass of: participant attribute name
definition: Free text description of all the tags and artificial process undergone by a molecule during an experiment.
has_exact_synonym: experimental form de
has_obo_namespace: PSI-MI
id: MI:0596
in_subset: PSI-MI slim

Axiom
annotated source: experimental form description
annotated property: definition
annotated target: Free text description of all the tags and artificial process undergone by a molecule during an experiment.
database_cross_reference: PMID:14755292

Axiom
annotated source: experimental form description
annotated property: has_exact_synonym
annotated target: experimental form de
has_synonym_type: Unique short label curated by PSI-MI

feature description
type: Class
subclass of: feature attribute name
definition: The feature text description may include information about the feature detection method.
has_obo_namespace: PSI-MI
id: MI:0597
in_subset: PSI-MI slim

Axiom
annotated source: feature description
annotated property: definition
annotated target: The feature text description may include information about the feature detection method.
database_cross_reference: PMID:14755292

feature constraint
type: Class
subclass of: feature attribute name
definition: The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction).
has_obo_namespace: PSI-MI
id: MI:0598
in_subset: PSI-MI slim

Axiom
annotated source: feature constraint
annotated property: definition
annotated target: The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction).
database_cross_reference: PMID:14755292

figure legend
type: Class
subclass of: interaction attribute name
subclass of: experiment attribute name
definition: Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found.
has_obo_namespace: PSI-MI
id: MI:0599
in_subset: PSI-MI slim

Axiom
annotated source: figure legend
annotated property: definition
annotated target: Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found.
database_cross_reference: PMID:14755292

conditional synthetic lethal nutrition-sensitivity
type: Class
definition: Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description.
has_exact_synonym: nutrition synt letal
has_obo_namespace: PSI-MI
id: MI:0600
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: conditional synthetic lethal nutrition-sensitivity
annotated property: definition
annotated target: Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description.
database_cross_reference: PMID:15608217

Axiom
annotated source: conditional synthetic lethal nutrition-sensitivity
annotated property: has_exact_synonym
annotated target: nutrition synt letal
has_synonym_type: Unique short label curated by PSI-MI

sequence ontology
type: Class
subclass of: feature database
subclass of: participant database
definition: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data.
database_cross_reference: id-validation-regexp:
has_exact_synonym: so
has_obo_namespace: PSI-MI
id: MI:0601
in_subset: PSI-MI slim

Axiom
annotated source: sequence ontology
annotated property: definition
annotated target: The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data.
database_cross_reference: PMID:15892872

SO:[0-9]{7}
type: Axiom
annotated source: sequence ontology
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: sequence ontology
annotated property: has_exact_synonym
annotated target: so
has_synonym_type: Unique short label curated by PSI-MI

chemical footprinting
type: Class
subclass of: footprinting
definition: Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
has_exact_synonym: chemical footprint
has_obo_namespace: PSI-MI
id: MI:0602
in_subset: PSI-MI slim

Axiom
annotated source: chemical footprinting
annotated property: definition
annotated target: Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
database_cross_reference: PMID:8238889

Axiom
annotated source: chemical footprinting
annotated property: has_exact_synonym
annotated target: chemical footprint
has_synonym_type: Unique short label curated by PSI-MI

dimethylsulphate footprinting
type: Class
subclass of: chemical footprinting
definition: Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction.
has_exact_synonym: dms footprinting
has_obo_namespace: PSI-MI
id: MI:0603
in_subset: PSI-MI slim

Axiom
annotated source: dimethylsulphate footprinting
annotated property: definition
annotated target: Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction.
database_cross_reference: PMID:8238889

Axiom
annotated source: dimethylsulphate footprinting
annotated property: has_exact_synonym
annotated target: dms footprinting
has_synonym_type: Unique short label curated by PSI-MI

potassium permanganate footprinting
type: Class
subclass of: chemical footprinting
definition: Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control.
has_exact_synonym: k-mn-04 footprinting
has_obo_namespace: PSI-MI
id: MI:0604
in_subset: PSI-MI slim

Axiom
annotated source: potassium permanganate footprinting
annotated property: definition
annotated target: Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control.
database_cross_reference: PMID:8238889

Axiom
annotated source: potassium permanganate footprinting
annotated property: has_exact_synonym
annotated target: k-mn-04 footprinting
has_synonym_type: Unique short label curated by PSI-MI

enzymatic footprinting
type: Class
subclass of: footprinting
definition: Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
has_exact_synonym: enzymatic footprint
has_obo_namespace: PSI-MI
id: MI:0605
in_subset: PSI-MI slim

Axiom
annotated source: enzymatic footprinting
annotated property: definition
annotated target: Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
database_cross_reference: PMID:8238889

Axiom
annotated source: enzymatic footprinting
annotated property: has_exact_synonym
annotated target: enzymatic footprint
has_synonym_type: Unique short label curated by PSI-MI

DNase I footprinting
type: Class
subclass of: nuclease footprinting
definition: Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA.
has_exact_synonym: dnase 1 footprinting
has_obo_namespace: PSI-MI
has_related_synonym: DNase I protection
id: MI:0606
in_subset: PSI-MI slim

Axiom
annotated source: DNase I footprinting
annotated property: definition
annotated target: Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA.
database_cross_reference: PMID:8238889

Axiom
annotated source: DNase I footprinting
annotated property: has_exact_synonym
annotated target: dnase 1 footprinting
has_synonym_type: Unique short label curated by PSI-MI

small nuclear rna
type: Class
subclass of: ribonucleic acid
definition: These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome.
has_exact_synonym: snRNA
has_exact_synonym: snrna
has_obo_namespace: PSI-MI
id: MI:0607
in_subset: PSI-MI slim

Axiom
annotated source: small nuclear rna
annotated property: definition
annotated target: These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome.
database_cross_reference: PMID:14755292

Axiom
annotated source: small nuclear rna
annotated property: has_exact_synonym
annotated target: snRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: small nuclear rna
annotated property: has_exact_synonym
annotated target: snrna
has_synonym_type: Unique short label curated by PSI-MI

ribosomal rna
type: Class
subclass of: ribonucleic acid
definition: RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes.
has_exact_synonym: rRNA
has_exact_synonym: rrna
has_obo_namespace: PSI-MI
id: MI:0608
in_subset: PSI-MI slim

Axiom
annotated source: ribosomal rna
annotated property: definition
annotated target: RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes.
database_cross_reference: PMID:14755292

Axiom
annotated source: ribosomal rna
annotated property: has_exact_synonym
annotated target: rRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ribosomal rna
annotated property: has_exact_synonym
annotated target: rrna
has_synonym_type: Unique short label curated by PSI-MI

small nucleolar rna
type: Class
subclass of: ribonucleic acid
definition: The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA.
has_exact_synonym: snoRNA
has_exact_synonym: snorna
has_obo_namespace: PSI-MI
id: MI:0609
in_subset: PSI-MI slim

Axiom
annotated source: small nucleolar rna
annotated property: definition
annotated target: The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA.
database_cross_reference: PMID:14755292

Axiom
annotated source: small nucleolar rna
annotated property: has_exact_synonym
annotated target: snoRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: small nucleolar rna
annotated property: has_exact_synonym
annotated target: snorna
has_synonym_type: Unique short label curated by PSI-MI

small interfering rna
type: Class
subclass of: ribonucleic acid
definition: Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression.
has_exact_synonym: dicer RNA
has_exact_synonym: micro RNA
has_exact_synonym: siRNA
has_exact_synonym: sirna
has_obo_namespace: PSI-MI
id: MI:0610
in_subset: PSI-MI slim

Axiom
annotated source: small interfering rna
annotated property: definition
annotated target: Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression.
database_cross_reference: PMID:10542148

Axiom
annotated source: small interfering rna
annotated property: has_exact_synonym
annotated target: dicer RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: small interfering rna
annotated property: has_exact_synonym
annotated target: micro RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: small interfering rna
annotated property: has_exact_synonym
annotated target: siRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: small interfering rna
annotated property: has_exact_synonym
annotated target: sirna
has_synonym_type: Unique short label curated by PSI-MI

signal recognition particle rna
type: Class
subclass of: ribonucleic acid
definition: Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
has_exact_synonym: srpRNA
has_exact_synonym: srprna
has_obo_namespace: PSI-MI
id: MI:0611
in_subset: PSI-MI slim

Axiom
annotated source: signal recognition particle rna
annotated property: definition
annotated target: Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
database_cross_reference: PMID:14755292

Axiom
annotated source: signal recognition particle rna
annotated property: has_exact_synonym
annotated target: srpRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: signal recognition particle rna
annotated property: has_exact_synonym
annotated target: srprna
has_synonym_type: Unique short label curated by PSI-MI

comment
type: Class
subclass of: interaction attribute name
subclass of: experiment attribute name
subclass of: participant attribute name
subclass of: controlled vocabulary attribute name
subclass of: feature attribute name
subclass of: organism attribute name
definition: Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant.
has_obo_namespace: PSI-MI
id: MI:0612
in_subset: PSI-MI slim

Axiom
annotated source: comment
annotated property: definition
annotated target: Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant.
database_cross_reference: PMID:14755292

function
type: Class
subclass of: interaction attribute name
subclass of: participant attribute name
definition: Biological function of a participant or of an interaction.
has_obo_namespace: PSI-MI
id: MI:0613
in_subset: PSI-MI slim

Axiom
annotated source: function
annotated property: definition
annotated target: Biological function of a participant or of an interaction.
database_cross_reference: PMID:14755292

url
type: Class
subclass of: interaction attribute name
subclass of: experiment attribute name
subclass of: controlled vocabulary attribute name
subclass of: organism attribute name
definition: URL/Web address describing an experiment, an interaction, a Cv term or an organism.
has_obo_namespace: PSI-MI
id: MI:0614
in_subset: PSI-MI slim

Axiom
annotated source: url
annotated property: definition
annotated target: URL/Web address describing an experiment, an interaction, a Cv term or an organism.
database_cross_reference: PMID:14755292

search-url
type: Class
subclass of: controlled vocabulary attribute name
definition: Search engine URL associated to Cv Database terms.
has_obo_namespace: PSI-MI
id: MI:0615
in_subset: PSI-MI slim

Axiom
annotated source: search-url
annotated property: definition
annotated target: Search engine URL associated to Cv Database terms.
database_cross_reference: PMID:14755292

example
type: Class
subclass of: controlled vocabulary attribute name
subclass of: synonym
definition: Example generally associated to Cv terms. Test.
has_obo_namespace: PSI-MI
id: MI:0616
in_subset: PSI-MI slim

Axiom
annotated source: example
annotated property: definition
annotated target: Example generally associated to Cv terms. Test.
database_cross_reference: PMID:14755292

disease
type: Class
subclass of: interaction attribute name
definition: The interaction has a known or demonstrated disease association.
has_obo_namespace: PSI-MI
id: MI:0617
in_subset: PSI-MI slim

Axiom
annotated source: disease
annotated property: definition
annotated target: The interaction has a known or demonstrated disease association.
database_cross_reference: PMID:14755292

caution
type: Class
subclass of: interaction attribute name
subclass of: experiment attribute name
subclass of: participant attribute name
subclass of: controlled vocabulary attribute name
subclass of: feature attribute name
subclass of: organism attribute name
definition: Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant.
has_obo_namespace: PSI-MI
id: MI:0618
in_subset: PSI-MI slim

Axiom
annotated source: caution
annotated property: definition
annotated target: Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant.
database_cross_reference: PMID:14755292

pathway
type: Class
subclass of: interaction attribute name
definition: Refers to the metabolic or signalling pathway involving an interaction or a complex.
has_obo_namespace: PSI-MI
id: MI:0619
in_subset: PSI-MI slim

Axiom
annotated source: pathway
annotated property: definition
annotated target: Refers to the metabolic or signalling pathway involving an interaction or a complex.
database_cross_reference: PMID:14755292

search-url-ascii
type: Class
subclass of: controlled vocabulary attribute name
definition: Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms.
has_obo_namespace: PSI-MI
id: MI:0620
in_subset: PSI-MI slim

Axiom
annotated source: search-url-ascii
annotated property: definition
annotated target: Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms.
database_cross_reference: PMID:14755292

author-confidence
type: Class
subclass of: interaction attribute name
definition: Confidence classification assigned by the author of the publication to a specific interaction.
has_obo_namespace: PSI-MI
id: MI:0621
in_subset: PSI-MI slim

Axiom
annotated source: author-confidence
annotated property: definition
annotated target: Confidence classification assigned by the author of the publication to a specific interaction.
database_cross_reference: PMID:14755292

confidence-mapping
type: Class
subclass of: experiment attribute name
definition: Description of confidence assessment method generally associated to the experiment.
has_obo_namespace: PSI-MI
id: MI:0622
in_subset: PSI-MI slim

Axiom
annotated source: confidence-mapping
annotated property: definition
annotated target: Description of confidence assessment method generally associated to the experiment.
database_cross_reference: PMID:14755292

inhibition
type: Class
subclass of: interaction attribute name
definition: The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors.
has_obo_namespace: PSI-MI
id: MI:0623
in_subset: PSI-MI slim

Axiom
annotated source: inhibition
annotated property: definition
annotated target: The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors.
database_cross_reference: PMID:14755292

stimulant
type: Class
subclass of: interaction attribute name
definition: Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule.
has_obo_namespace: PSI-MI
id: MI:0624
in_subset: PSI-MI slim

Axiom
annotated source: stimulant
annotated property: definition
annotated target: Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule.
database_cross_reference: PMID:14755292

agonist
type: Class
subclass of: interaction attribute name
definition: Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors.
has_obo_namespace: PSI-MI
id: MI:0625
in_subset: PSI-MI slim

Axiom
annotated source: agonist
annotated property: definition
annotated target: Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors.
database_cross_reference: PMID:14755292

antagonist
type: Class
subclass of: interaction attribute name
definition: Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors.
has_obo_namespace: PSI-MI
id: MI:0626
in_subset: PSI-MI slim

Axiom
annotated source: antagonist
annotated property: definition
annotated target: Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors.
database_cross_reference: PMID:14755292

experiment modification
type: Class
subclass of: experiment attribute name
definition: Modifications of the standard experimental method described in the CV.
has_exact_synonym: exp-modification
has_obo_namespace: PSI-MI
id: MI:0627
in_subset: PSI-MI slim

Axiom
annotated source: experiment modification
annotated property: definition
annotated target: Modifications of the standard experimental method described in the CV.
database_cross_reference: PMID:14755292

Axiom
annotated source: experiment modification
annotated property: has_exact_synonym
annotated target: exp-modification
has_synonym_type: Unique short label curated by PSI-MI

validation regular expression
type: Class
subclass of: controlled vocabulary attribute name
definition: Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database.
has_exact_synonym: id-validation-regexp
has_obo_namespace: PSI-MI
id: MI:0628
in_subset: PSI-MI slim

Axiom
annotated source: validation regular expression
annotated property: definition
annotated target: Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database.
database_cross_reference: PMID:14755292

Axiom
annotated source: validation regular expression
annotated property: has_exact_synonym
annotated target: id-validation-regexp
has_synonym_type: Unique short label curated by PSI-MI

complex-properties
type: Class
subclass of: interaction attribute name
subclass of: experiment attribute name
definition: Information on the complex being annotated. Attribute generally associated to an interaction.
has_obo_namespace: PSI-MI
id: MI:0629
in_subset: PSI-MI slim

Axiom
annotated source: complex-properties
annotated property: definition
annotated target: Information on the complex being annotated. Attribute generally associated to an interaction.
database_cross_reference: PMID:14755292

3d-structure
type: Class
subclass of: interaction attribute name
definition: Comments on the 3D structure. This attribute is generally associated to an interaction.
has_obo_namespace: PSI-MI
id: MI:0630
in_subset: PSI-MI slim

Axiom
annotated source: 3d-structure
annotated property: definition
annotated target: Comments on the 3D structure. This attribute is generally associated to an interaction.
database_cross_reference: PMID:14755292

3d-r-factors
type: Class
subclass of: interaction attribute name
definition: Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction.
has_obo_namespace: PSI-MI
id: MI:0631
in_subset: PSI-MI slim

Axiom
annotated source: 3d-r-factors
annotated property: definition
annotated target: Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction.
database_cross_reference: PMID:14755292

3d-resolution
type: Class
subclass of: interaction attribute name
definition: Resolution of the 3D structure. This attribute is generally associated to an interaction.
has_obo_namespace: PSI-MI
id: MI:0632
in_subset: PSI-MI slim

Axiom
annotated source: 3d-resolution
annotated property: definition
annotated target: Resolution of the 3D structure. This attribute is generally associated to an interaction.
database_cross_reference: PMID:14755292

data-processing
type: Class
subclass of: experiment attribute name
definition: Information about how the data was processed. This attribute is used mainly for large scale experiment.
has_obo_namespace: PSI-MI
id: MI:0633
in_subset: PSI-MI slim

Axiom
annotated source: data-processing
annotated property: definition
annotated target: Information about how the data was processed. This attribute is used mainly for large scale experiment.
database_cross_reference: PMID:14755292

contact-email
type: Class
subclass of: bibliographic attribute name
definition: E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment.
has_obo_namespace: PSI-MI
id: MI:0634
in_subset: PSI-MI slim

Axiom
annotated source: contact-email
annotated property: definition
annotated target: E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment.
database_cross_reference: PMID:14755292

contact-comment
type: Class
subclass of: bibliographic attribute name
definition: Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment.
has_obo_namespace: PSI-MI
id: MI:0635
in_subset: PSI-MI slim

Axiom
annotated source: contact-comment
annotated property: definition
annotated target: Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment.
database_cross_reference: PMID:14755292

author-list
type: Class
subclass of: bibliographic attribute name
definition: List of authors associated to a publication. This attribute is generally associated to an experiment.
has_obo_namespace: PSI-MI
id: MI:0636
in_subset: PSI-MI slim

Axiom
annotated source: author-list
annotated property: definition
annotated target: List of authors associated to a publication. This attribute is generally associated to an experiment.
database_cross_reference: PMID:14755292

isoform-comment
type: Class
subclass of: interaction attribute name
subclass of: participant attribute name
definition: Participant isoform's comment. This attribute can be attached to interactions or participants.
has_obo_namespace: PSI-MI
id: MI:0637
in_subset: PSI-MI slim

Axiom
annotated source: isoform-comment
annotated property: definition
annotated target: Participant isoform's comment. This attribute can be attached to interactions or participants.
database_cross_reference: PMID:14755292

prerequisite-ptm
type: Class
subclass of: observed-ptm
definition: Post translational modification required for an interaction to occur.
has_exact_synonym: prerequisite ptm
has_exact_synonym: prerequisite-ptm
has_exact_synonym: required ptm
has_exact_synonym: required-ptm
has_obo_namespace: PSI-MI
id: MI:0638
in_subset: PSI-MI slim

Axiom
annotated source: prerequisite-ptm
annotated property: definition
annotated target: Post translational modification required for an interaction to occur.
database_cross_reference: PMID:14755292

Axiom
annotated source: prerequisite-ptm
annotated property: has_exact_synonym
annotated target: prerequisite ptm
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: prerequisite-ptm
annotated property: has_exact_synonym
annotated target: prerequisite-ptm
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: prerequisite-ptm
annotated property: has_exact_synonym
annotated target: required ptm
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: prerequisite-ptm
annotated property: has_exact_synonym
annotated target: required-ptm
has_synonym_type: Alternate label curated by PSI-MI

resulting-ptm
type: Class
subclass of: observed-ptm
definition: Post translational modification occurs subsequently to an interaction.
has_exact_synonym: resulting ptm
has_exact_synonym: resulting-ptm
has_obo_namespace: PSI-MI
id: MI:0639
in_subset: PSI-MI slim

Axiom
annotated source: resulting-ptm
annotated property: definition
annotated target: Post translational modification occurs subsequently to an interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: resulting-ptm
annotated property: has_exact_synonym
annotated target: resulting ptm
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: resulting-ptm
annotated property: has_exact_synonym
annotated target: resulting-ptm
has_synonym_type: Unique short label curated by PSI-MI

parameter type
type: Class
subclass of: molecular interaction
definition: Parameter for enzymatic or binding kinetic studies.
has_obo_namespace: PSI-MI
id: MI:0640
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: parameter type
annotated property: definition
annotated target: Parameter for enzymatic or binding kinetic studies.
database_cross_reference: PMID:14755292

ic50
type: Class
subclass of: parameter type
definition: Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
has_exact_synonym: IC50
has_obo_namespace: PSI-MI
id: MI:0641
in_subset: PSI-MI slim

Axiom
annotated source: ic50
annotated property: definition
annotated target: Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
database_cross_reference: PMID:14755292

Axiom
annotated source: ic50
annotated property: has_exact_synonym
annotated target: IC50
has_synonym_type: Alternate label curated by PSI-MI

ec50
type: Class
subclass of: parameter type
definition: Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
has_exact_synonym: EC50
has_obo_namespace: PSI-MI
id: MI:0642
in_subset: PSI-MI slim

Axiom
annotated source: ec50
annotated property: definition
annotated target: Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
database_cross_reference: PMID:14755292

Axiom
annotated source: ec50
annotated property: has_exact_synonym
annotated target: EC50
has_synonym_type: Alternate label curated by PSI-MI

ki
type: Class
subclass of: parameter type
definition: Equilibrium constant for dissociation of an inhibitor. Unit Molar.
has_exact_synonym: Ki
has_obo_namespace: PSI-MI
id: MI:0643
in_subset: PSI-MI slim

Axiom
annotated source: ki
annotated property: definition
annotated target: Equilibrium constant for dissociation of an inhibitor. Unit Molar.
database_cross_reference: PMID:14755292

Axiom
annotated source: ki
annotated property: has_exact_synonym
annotated target: Ki
has_synonym_type: Alternate label curated by PSI-MI

km
type: Class
subclass of: parameter type
definition: Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar.
has_exact_synonym: Km
has_obo_namespace: PSI-MI
id: MI:0644
in_subset: PSI-MI slim

Axiom
annotated source: km
annotated property: definition
annotated target: Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar.
database_cross_reference: PMID:14755292

Axiom
annotated source: km
annotated property: has_exact_synonym
annotated target: Km
has_synonym_type: Alternate label curated by PSI-MI

kcat
type: Class
subclass of: parameter type
definition: The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1.
has_exact_synonym: turnover number
has_obo_namespace: PSI-MI
id: MI:0645
in_subset: PSI-MI slim

Axiom
annotated source: kcat
annotated property: definition
annotated target: The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1.
database_cross_reference: PMID:14755292

Axiom
annotated source: kcat
annotated property: has_exact_synonym
annotated target: turnover number
has_synonym_type: Alternate label curated by PSI-MI

Kd
type: Class
subclass of: parameter type
definition: The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1).
has_exact_synonym: Kd
has_obo_namespace: PSI-MI
id: MI:0646
in_subset: PSI-MI slim

Axiom
annotated source: Kd
annotated property: definition
annotated target: The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1).
database_cross_reference: PMID:14755292

Axiom
annotated source: Kd
annotated property: has_exact_synonym
annotated target: Kd
has_synonym_type: Alternate label curated by PSI-MI

parameter unit
type: Class
subclass of: molecular interaction
definition: Controlled vocabulary for kinetic constant units.
has_obo_namespace: PSI-MI
id: MI:0647
in_subset: PSI-MI slim

Axiom
annotated source: parameter unit
annotated property: definition
annotated target: Controlled vocabulary for kinetic constant units.
database_cross_reference: PMID:14755292

molar
type: Class
subclass of: parameter unit
definition: Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles).
has_exact_synonym: M
has_obo_namespace: PSI-MI
id: MI:0648
in_subset: PSI-MI slim

Axiom
annotated source: molar
annotated property: definition
annotated target: Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles).
database_cross_reference: PMID:14755292

Axiom
annotated source: molar
annotated property: has_exact_synonym
annotated target: M
has_synonym_type: Alternate label curated by PSI-MI

second
type: Class
subclass of: parameter unit
definition: The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant.
has_exact_synonym: s
has_exact_synonym: sec
has_obo_namespace: PSI-MI
id: MI:0649
in_subset: PSI-MI slim

Axiom
annotated source: second
annotated property: definition
annotated target: The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant.
database_cross_reference: PMID:14755292

Axiom
annotated source: second
annotated property: has_exact_synonym
annotated target: s
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: second
annotated property: has_exact_synonym
annotated target: sec
has_synonym_type: Alternate label curated by PSI-MI

millimolar
type: Class
definition: 10E-3 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
has_exact_synonym: mM
has_obo_namespace: PSI-MI
id: MI:0650
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: millimolar
annotated property: definition
annotated target: 10E-3 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
database_cross_reference: PMID:14755292

Axiom
annotated source: millimolar
annotated property: has_exact_synonym
annotated target: mM
has_synonym_type: Alternate label curated by PSI-MI

micromolar
type: Class
definition: 10E-6 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
has_exact_synonym: uM
has_obo_namespace: PSI-MI
id: MI:0651
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: micromolar
annotated property: definition
annotated target: 10E-6 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
database_cross_reference: PMID:14755292

Axiom
annotated source: micromolar
annotated property: has_exact_synonym
annotated target: uM
has_synonym_type: Alternate label curated by PSI-MI

nanomolar
type: Class
definition: 10E-9 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
has_exact_synonym: nM
has_obo_namespace: PSI-MI
id: MI:0652
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: nanomolar
annotated property: definition
annotated target: 10E-9 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
database_cross_reference: PMID:14755292

Axiom
annotated source: nanomolar
annotated property: has_exact_synonym
annotated target: nM
has_synonym_type: Alternate label curated by PSI-MI

picomolar
type: Class
definition: 10E-12 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
has_exact_synonym: pM
has_obo_namespace: PSI-MI
id: MI:0653
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: picomolar
annotated property: definition
annotated target: 10E-12 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
database_cross_reference: PMID:14755292

Axiom
annotated source: picomolar
annotated property: has_exact_synonym
annotated target: pM
has_synonym_type: Alternate label curated by PSI-MI

fentomolar
type: Class
definition: 10E-15 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
has_exact_synonym: fM
has_obo_namespace: PSI-MI
id: MI:0654
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: fentomolar
annotated property: definition
annotated target: 10E-15 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
database_cross_reference: PMID:14755292

Axiom
annotated source: fentomolar
annotated property: has_exact_synonym
annotated target: fM
has_synonym_type: Alternate label curated by PSI-MI

lambda repressor two hybrid
type: Class
subclass of: transcriptional complementation assay
definition: A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization.
has_exact_synonym: BacterioMatch
has_exact_synonym: lambda two hybrid
has_obo_namespace: PSI-MI
id: MI:0655
in_subset: PSI-MI slim

Axiom
annotated source: lambda repressor two hybrid
annotated property: definition
annotated target: A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization.
database_cross_reference: PMID:15792953

Axiom
annotated source: lambda repressor two hybrid
annotated property: has_exact_synonym
annotated target: BacterioMatch
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: lambda repressor two hybrid
annotated property: has_exact_synonym
annotated target: lambda two hybrid
has_synonym_type: Unique short label curated by PSI-MI

identified peptide
type: Class
subclass of: experimental feature
definition: Peptide whose sequence is experimentally identified and can lead to a full protein identification.
has_obo_namespace: PSI-MI
id: MI:0656
in_subset: PSI-MI slim

Axiom
annotated source: identified peptide
annotated property: definition
annotated target: Peptide whose sequence is experimentally identified and can lead to a full protein identification.
database_cross_reference: PMID:14755292

systematic evolution of ligands by exponential enrichment
type: Class
subclass of: affinity technology
definition: RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing.
has_exact_synonym: in vitro evolution of nucleic acids
has_exact_synonym: selex
has_obo_namespace: PSI-MI
id: MI:0657
in_subset: PSI-MI slim

Axiom
annotated source: systematic evolution of ligands by exponential enrichment
annotated property: definition
annotated target: RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing.
database_cross_reference: PMID:11539574

Axiom
annotated source: systematic evolution of ligands by exponential enrichment
annotated property: has_exact_synonym
annotated target: in vitro evolution of nucleic acids
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: systematic evolution of ligands by exponential enrichment
annotated property: has_exact_synonym
annotated target: selex
has_synonym_type: Unique short label curated by PSI-MI

multidimensional protein identification technology
type: Class
subclass of: protein sequence identification
subclass of: Identification by mass spectrometry
subclass of: confirmation by molecular weight
definition: MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified.
has_exact_synonym: mudpit
has_obo_namespace: PSI-MI
id: MI:0658
in_subset: PSI-MI slim

Axiom
annotated source: multidimensional protein identification technology
annotated property: definition
annotated target: MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified.
database_cross_reference: PMID:11231557

Axiom
annotated source: multidimensional protein identification technology
annotated property: has_exact_synonym
annotated target: mudpit
has_synonym_type: Unique short label curated by PSI-MI

experimental feature detection
type: Class
subclass of: feature detection method
definition: Experimental method by which a feature is detected or identified.
has_exact_synonym: exp feature detect
has_obo_namespace: PSI-MI
id: MI:0659
in_subset: PSI-MI slim

Axiom
annotated source: experimental feature detection
annotated property: definition
annotated target: Experimental method by which a feature is detected or identified.
database_cross_reference: PMID:14755292

Axiom
annotated source: experimental feature detection
annotated property: has_exact_synonym
annotated target: exp feature detect
has_synonym_type: Unique short label curated by PSI-MI

feature prediction
type: Class
subclass of: feature detection method
definition: Feature detection based on computational analysis.
has_obo_namespace: PSI-MI
id: MI:0660
in_subset: PSI-MI slim

Axiom
annotated source: feature prediction
annotated property: definition
annotated target: Feature detection based on computational analysis.
database_cross_reference: PMID:14755292

experimental participant identification
type: Class
subclass of: participant identification method
definition: experimental participant identification.
has_exact_synonym: experimental particp
has_obo_namespace: PSI-MI
id: MI:0661
in_subset: PSI-MI slim

Axiom
annotated source: experimental participant identification
annotated property: definition
annotated target: experimental participant identification.
database_cross_reference: PMID:14755292

Axiom
annotated source: experimental participant identification
annotated property: has_exact_synonym
annotated target: experimental particp
has_synonym_type: Unique short label curated by PSI-MI

imex-primary
type: Class
subclass of: cross-reference type
definition: IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner. http://imex.sourceforge.net/
has_obo_namespace: PSI-MI
id: MI:0662
in_subset: PSI-MI slim

Axiom
annotated source: imex-primary
annotated property: definition
annotated target: IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner. http://imex.sourceforge.net/
database_cross_reference: PMID:14755292

confocal microscopy
type: Class
subclass of: imaging technique
definition: A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen.
has_obo_namespace: PSI-MI
id: MI:0663
in_subset: PSI-MI slim

Axiom
annotated source: confocal microscopy
annotated property: definition
annotated target: A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen.
database_cross_reference: PMID:14755292

interaction attribute name
type: Class
subclass of: attribute name
definition: Attribute name of annotation associated to an interaction element.
has_exact_synonym: interaction att name
has_obo_namespace: PSI-MI
id: MI:0664
in_subset: PSI-MI slim

Axiom
annotated source: interaction attribute name
annotated property: definition
annotated target: Attribute name of annotation associated to an interaction element.
database_cross_reference: PMID:14755292

Axiom
annotated source: interaction attribute name
annotated property: has_exact_synonym
annotated target: interaction att name
has_synonym_type: Unique short label curated by PSI-MI

experiment attribute name
type: Class
subclass of: attribute name
definition: Attribute name of annotation associated to an experiment element.
has_exact_synonym: experiment att name
has_obo_namespace: PSI-MI
id: MI:0665
in_subset: PSI-MI slim

Axiom
annotated source: experiment attribute name
annotated property: definition
annotated target: Attribute name of annotation associated to an experiment element.
database_cross_reference: PMID:14755292

Axiom
annotated source: experiment attribute name
annotated property: has_exact_synonym
annotated target: experiment att name
has_synonym_type: Unique short label curated by PSI-MI

participant attribute name
type: Class
subclass of: attribute name
definition: Attribute name of annotation associated to a participant element.
has_exact_synonym: participant att name
has_obo_namespace: PSI-MI
id: MI:0666
in_subset: PSI-MI slim

Axiom
annotated source: participant attribute name
annotated property: definition
annotated target: Attribute name of annotation associated to a participant element.
database_cross_reference: PMID:14755292

Axiom
annotated source: participant attribute name
annotated property: has_exact_synonym
annotated target: participant att name
has_synonym_type: Unique short label curated by PSI-MI

controlled vocabulary attribute name
type: Class
subclass of: attribute name
definition: Attribute name of annotation associated to a CV term.
has_exact_synonym: cv att name
has_obo_namespace: PSI-MI
id: MI:0667
in_subset: PSI-MI slim

Axiom
annotated source: controlled vocabulary attribute name
annotated property: definition
annotated target: Attribute name of annotation associated to a CV term.
database_cross_reference: PMID:14755292

Axiom
annotated source: controlled vocabulary attribute name
annotated property: has_exact_synonym
annotated target: cv att name
has_synonym_type: Unique short label curated by PSI-MI

feature attribute name
type: Class
subclass of: attribute name
definition: Attribute name of annotation associated to a feature element.
has_exact_synonym: feature att name
has_obo_namespace: PSI-MI
id: MI:0668
in_subset: PSI-MI slim

Axiom
annotated source: feature attribute name
annotated property: definition
annotated target: Attribute name of annotation associated to a feature element.
database_cross_reference: PMID:14755292

Axiom
annotated source: feature attribute name
annotated property: has_exact_synonym
annotated target: feature att name
has_synonym_type: Unique short label curated by PSI-MI

organism attribute name
type: Class
subclass of: attribute name
definition: Attribute name of annotation associated to an organism element.
has_exact_synonym: organism att name
has_obo_namespace: PSI-MI
id: MI:0669
in_subset: PSI-MI slim

Axiom
annotated source: organism attribute name
annotated property: definition
annotated target: Attribute name of annotation associated to an organism element.
database_cross_reference: PMID:14755292

Axiom
annotated source: organism attribute name
annotated property: has_exact_synonym
annotated target: organism att name
has_synonym_type: Unique short label curated by PSI-MI

imex
type: Class
subclass of: interaction database
definition: International Molecular Interaction Exchange.
database_cross_reference: search-url:
has_exact_synonym: IMEx
has_obo_namespace: PSI-MI
id: MI:0670
in_subset: PSI-MI slim

Axiom
annotated source: imex
annotated property: definition
annotated target: International Molecular Interaction Exchange.
database_cross_reference: PMID:22453911

Axiom
annotated source: imex
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/intact/imex/main.xhtml

Axiom
annotated source: imex
annotated property: has_exact_synonym
annotated target: IMEx
has_synonym_type: Alternate label curated by PSI-MI

antibodies
type: Class
subclass of: experiment attribute name
definition: This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used.
has_obo_namespace: PSI-MI
id: MI:0671
in_subset: PSI-MI slim

Axiom
annotated source: antibodies
annotated property: definition
annotated target: This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used.
database_cross_reference: PMID:14755292

library-used
type: Class
subclass of: experiment attribute name
definition: This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library.
has_obo_namespace: PSI-MI
id: MI:0672
in_subset: PSI-MI slim

Axiom
annotated source: library-used
annotated property: definition
annotated target: This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library.
database_cross_reference: PMID:14755292

complex synonym
type: Class
subclass of: synonym
definition: Alternative names to describe a complex.
has_exact_synonym: complex-synonym
has_obo_namespace: PSI-MI
id: MI:0673
in_subset: PSI-MI slim

Axiom
annotated source: complex synonym
annotated property: definition
annotated target: Alternative names to describe a complex.
database_cross_reference: PMID:14755292

peptide parent sequence reference
type: Class
subclass of: cross-reference type
definition: Describe a cross reference pointing to a peptide parent sequence.
has_exact_synonym: peptide-parent
has_obo_namespace: PSI-MI
id: MI:0674
in_subset: PSI-MI slim

Axiom
annotated source: peptide parent sequence reference
annotated property: definition
annotated target: Describe a cross reference pointing to a peptide parent sequence.
database_cross_reference: PMID:14755292

Axiom
annotated source: peptide parent sequence reference
annotated property: has_exact_synonym
annotated target: peptide-parent
has_synonym_type: Unique short label curated by PSI-MI

international protein index
type: Class
subclass of: protein sequence databases
definition: IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources.
database_cross_reference: id-validation-regexp:
has_exact_synonym: ipi
has_obo_namespace: PSI-MI
id: MI:0675
in_subset: PSI-MI slim

Axiom
annotated source: international protein index
annotated property: definition
annotated target: IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources.
database_cross_reference: PMID:15221759

IPI[0-9]+.[0-9]+|IPI[0-9]+
type: Axiom
annotated source: international protein index
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: international protein index
annotated property: has_exact_synonym
annotated target: ipi
has_synonym_type: Unique short label curated by PSI-MI

tandem affinity purification
type: Class
subclass of: affinity chromatography technology
definition: Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification.
has_exact_synonym: TAP
has_exact_synonym: tap
has_obo_namespace: PSI-MI
id: MI:0676
in_subset: PSI-MI slim

Axiom
annotated source: tandem affinity purification
annotated property: definition
annotated target: Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification.
database_cross_reference: PMID:11403571

Axiom
annotated source: tandem affinity purification
annotated property: has_exact_synonym
annotated target: TAP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: tandem affinity purification
annotated property: has_exact_synonym
annotated target: tap
has_synonym_type: Unique short label curated by PSI-MI

tandem tag
type: Class
subclass of: tag
definition: A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features.
has_obo_namespace: PSI-MI
id: MI:0677
in_subset: PSI-MI slim

Axiom
annotated source: tandem tag
annotated property: definition
annotated target: A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features.
database_cross_reference: PMID:14755292

antibody array
type: Class
subclass of: protein array
definition: A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others).
has_exact_synonym: antigen capture assay
has_exact_synonym: sandwich immunoassay
has_obo_namespace: PSI-MI
id: MI:0678
in_subset: PSI-MI slim

Axiom
annotated source: antibody array
annotated property: definition
annotated target: A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others).
database_cross_reference: PMID:12454649

Axiom
annotated source: antibody array
annotated property: has_exact_synonym
annotated target: antigen capture assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: antibody array
annotated property: has_exact_synonym
annotated target: sandwich immunoassay
has_synonym_type: Alternate label curated by PSI-MI

poly adenine
type: Class
subclass of: ribonucleic acid
definition: A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule.
has_exact_synonym: poly A
has_exact_synonym: poly a
has_obo_namespace: PSI-MI
id: MI:0679
in_subset: PSI-MI slim

Axiom
annotated source: poly adenine
annotated property: definition
annotated target: A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: poly adenine
annotated property: has_exact_synonym
annotated target: poly A
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: poly adenine
annotated property: has_exact_synonym
annotated target: poly a
has_synonym_type: Unique short label curated by PSI-MI

single stranded deoxyribonucleic acid
type: Class
subclass of: deoxyribonucleic acid
definition: DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form.
has_exact_synonym: ss DNA
has_exact_synonym: ss dna
has_obo_namespace: PSI-MI
id: MI:0680
in_subset: PSI-MI slim

Axiom
annotated source: single stranded deoxyribonucleic acid
annotated property: definition
annotated target: DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form.
database_cross_reference: PMID:14755292

Axiom
annotated source: single stranded deoxyribonucleic acid
annotated property: has_exact_synonym
annotated target: ss DNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: single stranded deoxyribonucleic acid
annotated property: has_exact_synonym
annotated target: ss dna
has_synonym_type: Unique short label curated by PSI-MI

double stranded deoxyribonucleic acid
type: Class
subclass of: deoxyribonucleic acid
definition: DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
has_exact_synonym: ds DNA
has_exact_synonym: ds dna
has_obo_namespace: PSI-MI
id: MI:0681
in_subset: PSI-MI slim

Axiom
annotated source: double stranded deoxyribonucleic acid
annotated property: definition
annotated target: DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
database_cross_reference: PMID:14755292

Axiom
annotated source: double stranded deoxyribonucleic acid
annotated property: has_exact_synonym
annotated target: ds DNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: double stranded deoxyribonucleic acid
annotated property: has_exact_synonym
annotated target: ds dna
has_synonym_type: Unique short label curated by PSI-MI

cofactor
type: Class
subclass of: biological role
definition: A cofactor is a small molecule required for the catalysis of an enzyme.
has_exact_synonym: coenzyme
has_obo_namespace: PSI-MI
id: MI:0682
in_subset: PSI-MI slim

Axiom
annotated source: cofactor
annotated property: definition
annotated target: A cofactor is a small molecule required for the catalysis of an enzyme.
database_cross_reference: PMID:14755292

Axiom
annotated source: cofactor
annotated property: has_exact_synonym
annotated target: coenzyme
has_synonym_type: Alternate label curated by PSI-MI

sequence database
type: Class
subclass of: participant database
definition: Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing.
has_obo_namespace: PSI-MI
id: MI:0683
in_subset: PSI-MI slim

Axiom
annotated source: sequence database
annotated property: definition
annotated target: Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing.
database_cross_reference: PMID:14755292

ancillary
type: Class
subclass of: experimental role
subclass of: biological role
definition: Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc).
has_obo_namespace: PSI-MI
id: MI:0684
in_subset: PSI-MI slim

Axiom
annotated source: ancillary
annotated property: definition
annotated target: Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc).
database_cross_reference: PMID:14755292

source reference
type: Class
subclass of: cross-reference type
definition: Publication or document describing the originating resource where an interaction, or other curated information, was first described.
has_obo_namespace: PSI-MI
id: MI:0685
in_subset: PSI-MI slim

Axiom
annotated source: source reference
annotated property: definition
annotated target: Publication or document describing the originating resource where an interaction, or other curated information, was first described.
database_cross_reference: PMID:14755292

unspecified method
type: Class
subclass of: interaction detection method
definition: Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation.
has_obo_namespace: PSI-MI
id: MI:0686
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: unspecified method
annotated property: definition
annotated target: Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation.
database_cross_reference: PMID:14755292

fluorescent protein tag
type: Class
subclass of: fusion protein
definition: Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification.
has_exact_synonym: fluorescent prot tag
has_obo_namespace: PSI-MI
id: MI:0687
in_subset: PSI-MI slim

Axiom
annotated source: fluorescent protein tag
annotated property: definition
annotated target: Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification.
database_cross_reference: PMID:14755292

Axiom
annotated source: fluorescent protein tag
annotated property: has_exact_synonym
annotated target: fluorescent prot tag
has_synonym_type: Unique short label curated by PSI-MI

dna binding domain tag
type: Class
subclass of: fusion protein
definition: Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag.
has_exact_synonym: dna binding domain
has_obo_namespace: PSI-MI
id: MI:0688
in_subset: PSI-MI slim

Axiom
annotated source: dna binding domain tag
annotated property: definition
annotated target: Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag.
database_cross_reference: PMID:14755292

Axiom
annotated source: dna binding domain tag
annotated property: has_exact_synonym
annotated target: dna binding domain
has_synonym_type: Unique short label curated by PSI-MI

activation domain tag
type: Class
subclass of: fusion protein
definition: Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag.
has_exact_synonym: activation domain
has_obo_namespace: PSI-MI
id: MI:0689
in_subset: PSI-MI slim

Axiom
annotated source: activation domain tag
annotated property: definition
annotated target: Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag.
database_cross_reference: PMID:14755292

Axiom
annotated source: activation domain tag
annotated property: has_exact_synonym
annotated target: activation domain
has_synonym_type: Unique short label curated by PSI-MI

gal4 activation domain
type: Class
subclass of: activation domain tag
definition: Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation.
has_exact_synonym: gal4 ad
has_obo_namespace: PSI-MI
id: MI:0690
in_subset: PSI-MI slim

Axiom
annotated source: gal4 activation domain
annotated property: definition
annotated target: Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation.
database_cross_reference: PMID:14755292

Axiom
annotated source: gal4 activation domain
annotated property: has_exact_synonym
annotated target: gal4 ad
has_synonym_type: Unique short label curated by PSI-MI

vp16 activation domain
type: Class
subclass of: activation domain tag
definition: Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor.
has_exact_synonym: vp16 ad
has_obo_namespace: PSI-MI
id: MI:0691
in_subset: PSI-MI slim

Axiom
annotated source: vp16 activation domain
annotated property: definition
annotated target: Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor.
database_cross_reference: PMID:14755292

Axiom
annotated source: vp16 activation domain
annotated property: has_exact_synonym
annotated target: vp16 ad
has_synonym_type: Unique short label curated by PSI-MI

b42 activation domain
type: Class
subclass of: activation domain tag
definition: B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection.
has_exact_synonym: b42 ad
has_obo_namespace: PSI-MI
id: MI:0692
in_subset: PSI-MI slim

Axiom
annotated source: b42 activation domain
annotated property: definition
annotated target: B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection.
database_cross_reference: PMID:14613974

Axiom
annotated source: b42 activation domain
annotated property: has_exact_synonym
annotated target: b42 ad
has_synonym_type: Unique short label curated by PSI-MI

gal4 dna binding domain
type: Class
subclass of: dna binding domain tag
definition: Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.
has_exact_synonym: gal4 dna bd
has_obo_namespace: PSI-MI
id: MI:0693
in_subset: PSI-MI slim

Axiom
annotated source: gal4 dna binding domain
annotated property: definition
annotated target: Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.
database_cross_reference: PMID:14755292

Axiom
annotated source: gal4 dna binding domain
annotated property: has_exact_synonym
annotated target: gal4 dna bd
has_synonym_type: Unique short label curated by PSI-MI

lexa dna binding domain
type: Class
subclass of: dna binding domain tag
definition: Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences.
has_exact_synonym: lexa dna bd
has_obo_namespace: PSI-MI
id: MI:0694
in_subset: PSI-MI slim

Axiom
annotated source: lexa dna binding domain
annotated property: definition
annotated target: Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences.
database_cross_reference: PMID:14755292

Axiom
annotated source: lexa dna binding domain
annotated property: has_exact_synonym
annotated target: lexa dna bd
has_synonym_type: Unique short label curated by PSI-MI

sandwich immunoassay
type: Class
subclass of: antibody array
definition: Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin.
has_obo_namespace: PSI-MI
id: MI:0695
in_subset: PSI-MI slim

Axiom
annotated source: sandwich immunoassay
annotated property: definition
annotated target: Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin.
database_cross_reference: PMID:12454649

polymerase assay
type: Class
subclass of: enzymatic study
definition: Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain.
has_exact_synonym: nucleotidyltransferase assay
has_obo_namespace: PSI-MI
id: MI:0696
in_subset: PSI-MI slim

Axiom
annotated source: polymerase assay
annotated property: definition
annotated target: Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain.
database_cross_reference: PMID:14755292

Axiom
annotated source: polymerase assay
annotated property: has_exact_synonym
annotated target: nucleotidyltransferase assay
has_synonym_type: Alternate label curated by PSI-MI

dna directed dna polymerase assay
type: Class
subclass of: polymerase assay
definition: Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer.
has_exact_synonym: dna dna pol assay
has_obo_namespace: PSI-MI
id: MI:0697
in_subset: PSI-MI slim

Axiom
annotated source: dna directed dna polymerase assay
annotated property: definition
annotated target: Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer.
database_cross_reference: PMID:14755292

Axiom
annotated source: dna directed dna polymerase assay
annotated property: has_exact_synonym
annotated target: dna dna pol assay
has_synonym_type: Unique short label curated by PSI-MI

dna directed rna polymerase assay
type: Class
subclass of: polymerase assay
definition: Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
has_exact_synonym: dna rna pol assay
has_obo_namespace: PSI-MI
id: MI:0698
in_subset: PSI-MI slim

Axiom
annotated source: dna directed rna polymerase assay
annotated property: definition
annotated target: Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
database_cross_reference: PMID:14755292

Axiom
annotated source: dna directed rna polymerase assay
annotated property: has_exact_synonym
annotated target: dna rna pol assay
has_synonym_type: Unique short label curated by PSI-MI

rna directed dna polymerase assay
type: Class
subclass of: polymerase assay
definition: Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
has_exact_synonym: rna dna pol assay
has_obo_namespace: PSI-MI
id: MI:0699
in_subset: PSI-MI slim

Axiom
annotated source: rna directed dna polymerase assay
annotated property: definition
annotated target: Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
database_cross_reference: PMID:14755292

Axiom
annotated source: rna directed dna polymerase assay
annotated property: has_exact_synonym
annotated target: rna dna pol assay
has_synonym_type: Unique short label curated by PSI-MI

rna directed rna polymerase assay
type: Class
subclass of: polymerase assay
definition: Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template.
has_exact_synonym: rna rna pol assay
has_obo_namespace: PSI-MI
id: MI:0700
in_subset: PSI-MI slim

Axiom
annotated source: rna directed rna polymerase assay
annotated property: definition
annotated target: Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template.
database_cross_reference: PMID:14755292

Axiom
annotated source: rna directed rna polymerase assay
annotated property: has_exact_synonym
annotated target: rna rna pol assay
has_synonym_type: Unique short label curated by PSI-MI

dna strand elongation
type: Class
subclass of: nucleic acid strand elongation reaction
definition: The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
has_exact_synonym: DNA replication elongation
has_exact_synonym: dna elongation
has_obo_namespace: PSI-MI
id: MI:0701
in_subset: PSI-MI slim

Axiom
annotated source: dna strand elongation
annotated property: definition
annotated target: The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
database_cross_reference: GO:0006271
database_cross_reference: PMID:14755292

Axiom
annotated source: dna strand elongation
annotated property: has_exact_synonym
annotated target: DNA replication elongation
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: dna strand elongation
annotated property: has_exact_synonym
annotated target: dna elongation
has_synonym_type: Unique short label curated by PSI-MI

panther
type: Class
subclass of: interpro
definition: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. www.pantherdb.org/
has_exact_synonym: PANTHER
has_obo_namespace: PSI-MI
id: MI:0702
in_subset: PSI-MI slim

Axiom
annotated source: panther
annotated property: definition
annotated target: The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. www.pantherdb.org/
database_cross_reference: PMID:14755292

Axiom
annotated source: panther
annotated property: has_exact_synonym
annotated target: PANTHER
has_synonym_type: Alternate label curated by PSI-MI

gene3d
type: Class
subclass of: interpro
definition: The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
has_exact_synonym: Gene3D
has_obo_namespace: PSI-MI
id: MI:0703
in_subset: PSI-MI slim

Axiom
annotated source: gene3d
annotated property: definition
annotated target: The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
database_cross_reference: PMID:14755292

Axiom
annotated source: gene3d
annotated property: has_exact_synonym
annotated target: Gene3D
has_synonym_type: Alternate label curated by PSI-MI

nucleic acid delivery
type: Class
subclass of: delivery method
definition: Method by which nucleic acids are delivered or engineered into a cell.
has_exact_synonym: nucl delivery
has_obo_namespace: PSI-MI
id: MI:0704
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid delivery
annotated property: definition
annotated target: Method by which nucleic acids are delivered or engineered into a cell.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid delivery
annotated property: has_exact_synonym
annotated target: nucl delivery
has_synonym_type: Unique short label curated by PSI-MI

anti tag western blot
type: Class
subclass of: western blot
subclass of: tag visualisation
definition: Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal.
has_exact_synonym: anti tag western
has_obo_namespace: PSI-MI
id: MI:0705
in_subset: PSI-MI slim

Axiom
annotated source: anti tag western blot
annotated property: definition
annotated target: Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal.
database_cross_reference: PMID:14755292

Axiom
annotated source: anti tag western blot
annotated property: has_exact_synonym
annotated target: anti tag western
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid transformation
type: Class
subclass of: nucleic acid delivery
definition: Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA).
has_exact_synonym: nucl transformation
has_obo_namespace: PSI-MI
id: MI:0706
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid transformation
annotated property: definition
annotated target: Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA).
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid transformation
annotated property: has_exact_synonym
annotated target: nucl transformation
has_synonym_type: Unique short label curated by PSI-MI

anti tag immunostaining
type: Class
subclass of: immunostaining
definition: Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal.
has_exact_synonym: anti tag immunost
has_obo_namespace: PSI-MI
id: MI:0707
in_subset: PSI-MI slim

Axiom
annotated source: anti tag immunostaining
annotated property: definition
annotated target: Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal.
database_cross_reference: PMID:14755292

Axiom
annotated source: anti tag immunostaining
annotated property: has_exact_synonym
annotated target: anti tag immunost
has_synonym_type: Unique short label curated by PSI-MI

monoclonal antibody immunostaining
type: Class
subclass of: immunostaining
definition: A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample.
has_exact_synonym: monoclonal immunost
has_obo_namespace: PSI-MI
id: MI:0708
in_subset: PSI-MI slim

Axiom
annotated source: monoclonal antibody immunostaining
annotated property: definition
annotated target: A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample.
database_cross_reference: PMID:14755292

Axiom
annotated source: monoclonal antibody immunostaining
annotated property: has_exact_synonym
annotated target: monoclonal immunost
has_synonym_type: Unique short label curated by PSI-MI

polyclonal antibody immunostaining
type: Class
subclass of: immunostaining
definition: Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample.
has_exact_synonym: polyclonal immunost
has_obo_namespace: PSI-MI
id: MI:0709
in_subset: PSI-MI slim

Axiom
annotated source: polyclonal antibody immunostaining
annotated property: definition
annotated target: Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample.
database_cross_reference: PMID:14755292

Axiom
annotated source: polyclonal antibody immunostaining
annotated property: has_exact_synonym
annotated target: polyclonal immunost
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid transformation by treatment with divalent cation
type: Class
subclass of: nucleic acid transformation
definition: Stable introduction and expression of nucleic acid carried out by treatment with divalent cation.
has_exact_synonym: n transformat cation
has_obo_namespace: PSI-MI
id: MI:0710
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid transformation by treatment with divalent cation
annotated property: definition
annotated target: Stable introduction and expression of nucleic acid carried out by treatment with divalent cation.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid transformation by treatment with divalent cation
annotated property: has_exact_synonym
annotated target: n transformat cation
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid electroporation
type: Class
subclass of: electroporation
subclass of: nucleic acid delivery
definition: Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA.
has_exact_synonym: nucl electroporation
has_obo_namespace: PSI-MI
id: MI:0711
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid electroporation
annotated property: definition
annotated target: Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid electroporation
annotated property: has_exact_synonym
annotated target: nucl electroporation
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid microinjection
type: Class
subclass of: microinjection
subclass of: nucleic acid delivery
definition: Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids.
has_exact_synonym: nucl microinjection
has_obo_namespace: PSI-MI
id: MI:0712
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid microinjection
annotated property: definition
annotated target: Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid microinjection
annotated property: has_exact_synonym
annotated target: nucl microinjection
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid passive uptake
type: Class
subclass of: nucleic acid delivery
subclass of: passive uptake
definition: Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes.
has_exact_synonym: nucl passive uptake
has_obo_namespace: PSI-MI
id: MI:0713
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid passive uptake
annotated property: definition
annotated target: Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid passive uptake
annotated property: has_exact_synonym
annotated target: nucl passive uptake
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid transduction
type: Class
subclass of: nucleic acid delivery
definition: Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus.
has_exact_synonym: nucl transduction
has_obo_namespace: PSI-MI
id: MI:0714
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid transduction
annotated property: definition
annotated target: Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid transduction
annotated property: has_exact_synonym
annotated target: nucl transduction
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid conjugation
type: Class
subclass of: nucleic acid delivery
definition: Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient
has_exact_synonym: nucl conjugation
has_obo_namespace: PSI-MI
id: MI:0715
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid conjugation
annotated property: definition
annotated target: Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid conjugation
annotated property: has_exact_synonym
annotated target: nucl conjugation
has_synonym_type: Unique short label curated by PSI-MI

passive uptake
type: Class
subclass of: delivery method
definition: Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes.
has_obo_namespace: PSI-MI
id: MI:0716
in_subset: PSI-MI slim

Axiom
annotated source: passive uptake
annotated property: definition
annotated target: Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes.
database_cross_reference: PMID:14755292

nucleic acid transfection with liposome
type: Class
subclass of: nucleic acid transfection
definition: Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer.
has_exact_synonym: nucl lipotransfect
has_obo_namespace: PSI-MI
id: MI:0717
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid transfection with liposome
annotated property: definition
annotated target: Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid transfection with liposome
annotated property: has_exact_synonym
annotated target: nucl lipotransfect
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid transfection by treatment
type: Class
subclass of: nucleic acid transfection
definition: Transient introduction and expression of nucleic acid carried out by treatment with chemicals.
has_exact_synonym: n transfection treat
has_obo_namespace: PSI-MI
id: MI:0718
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid transfection by treatment
annotated property: definition
annotated target: Transient introduction and expression of nucleic acid carried out by treatment with chemicals.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid transfection by treatment
annotated property: has_exact_synonym
annotated target: n transfection treat
has_synonym_type: Unique short label curated by PSI-MI

calcium phosphate nucleic acid transfection
type: Class
subclass of: nucleic acid transfection by treatment
definition: Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate.
has_exact_synonym: ca po nuc transfect
has_obo_namespace: PSI-MI
id: MI:0719
in_subset: PSI-MI slim

Axiom
annotated source: calcium phosphate nucleic acid transfection
annotated property: definition
annotated target: Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate.
database_cross_reference: PMID:14755292

Axiom
annotated source: calcium phosphate nucleic acid transfection
annotated property: has_exact_synonym
annotated target: ca po nuc transfect
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid delivery by infection
type: Class
subclass of: infection
subclass of: nucleic acid delivery
definition: Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria..
has_exact_synonym: nucl infection
has_obo_namespace: PSI-MI
id: MI:0720
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid delivery by infection
annotated property: definition
annotated target: Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria..
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid delivery by infection
annotated property: has_exact_synonym
annotated target: nucl infection
has_synonym_type: Unique short label curated by PSI-MI

protein delivery
type: Class
subclass of: delivery method
definition: Method by which proteins are delivered into a cell.
has_obo_namespace: PSI-MI
id: MI:0721
in_subset: PSI-MI slim

Axiom
annotated source: protein delivery
annotated property: definition
annotated target: Method by which proteins are delivered into a cell.
database_cross_reference: PMID:14755292

protein electroporation
type: Class
subclass of: electroporation
subclass of: protein delivery
definition: Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein.
has_exact_synonym: prot electroporation
has_obo_namespace: PSI-MI
id: MI:0722
in_subset: PSI-MI slim

Axiom
annotated source: protein electroporation
annotated property: definition
annotated target: Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein electroporation
annotated property: has_exact_synonym
annotated target: prot electroporation
has_synonym_type: Unique short label curated by PSI-MI

protein microinjection
type: Class
subclass of: microinjection
subclass of: protein delivery
definition: Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins.
has_exact_synonym: prot microinjection
has_obo_namespace: PSI-MI
id: MI:0723
in_subset: PSI-MI slim

Axiom
annotated source: protein microinjection
annotated property: definition
annotated target: Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein microinjection
annotated property: has_exact_synonym
annotated target: prot microinjection
has_synonym_type: Unique short label curated by PSI-MI

protein delivery by cationic lipid treatment
type: Class
subclass of: protein delivery
definition: Proteins are delivered into cells by treatment with cationic lipids.
has_exact_synonym: prot cationic lipid
has_obo_namespace: PSI-MI
id: MI:0724
in_subset: PSI-MI slim

Axiom
annotated source: protein delivery by cationic lipid treatment
annotated property: definition
annotated target: Proteins are delivered into cells by treatment with cationic lipids.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein delivery by cationic lipid treatment
annotated property: has_exact_synonym
annotated target: prot cationic lipid
has_synonym_type: Unique short label curated by PSI-MI

protein delivery by infection
type: Class
subclass of: infection
subclass of: protein delivery
definition: Protein introduced into a cell via an external organism, usually a virus or bacteria.
has_exact_synonym: prot infection
has_obo_namespace: PSI-MI
id: MI:0725
in_subset: PSI-MI slim

Axiom
annotated source: protein delivery by infection
annotated property: definition
annotated target: Protein introduced into a cell via an external organism, usually a virus or bacteria.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein delivery by infection
annotated property: has_exact_synonym
annotated target: prot infection
has_synonym_type: Unique short label curated by PSI-MI

reverse two hybrid
type: Class
subclass of: feature detection method
subclass of: transcriptional complementation assay
definition: Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site.
has_obo_namespace: PSI-MI
id: MI:0726
in_subset: PSI-MI slim

Axiom
annotated source: reverse two hybrid
annotated property: definition
annotated target: Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site.
database_cross_reference: PMID:8816797

lexa b52 complementation
type: Class
subclass of: two hybrid
definition: Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements.
has_exact_synonym: LexA B52 transcription complementation
has_exact_synonym: lexa b52 complement
has_obo_namespace: PSI-MI
id: MI:0727
in_subset: PSI-MI slim

Axiom
annotated source: lexa b52 complementation
annotated property: definition
annotated target: Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements.
database_cross_reference: PMID:14613974

Axiom
annotated source: lexa b52 complementation
annotated property: has_exact_synonym
annotated target: LexA B52 transcription complementation
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: lexa b52 complementation
annotated property: has_exact_synonym
annotated target: lexa b52 complement
has_synonym_type: Unique short label curated by PSI-MI

gal4 vp16 complementation
type: Class
subclass of: two hybrid
definition: A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated.
has_exact_synonym: KISS
has_exact_synonym: gal4 vp16 complement
has_exact_synonym: karyoplasmic interaction ion strategy
has_exact_synonym: mammalian two hybrid
has_obo_namespace: PSI-MI
id: MI:0728
in_subset: PSI-MI slim

Axiom
annotated source: gal4 vp16 complementation
annotated property: definition
annotated target: A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated.
database_cross_reference: PMID:1387709

Axiom
annotated source: gal4 vp16 complementation
annotated property: has_exact_synonym
annotated target: KISS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gal4 vp16 complementation
annotated property: has_exact_synonym
annotated target: gal4 vp16 complement
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: gal4 vp16 complementation
annotated property: has_exact_synonym
annotated target: karyoplasmic interaction ion strategy
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gal4 vp16 complementation
annotated property: has_exact_synonym
annotated target: mammalian two hybrid
has_synonym_type: Alternate label curated by PSI-MI

luminescence based mammalian interactome mapping
type: Class
subclass of: affinity chromatography technology
definition: This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates.
has_exact_synonym: lumier
has_obo_namespace: PSI-MI
id: MI:0729
in_subset: PSI-MI slim

Axiom
annotated source: luminescence based mammalian interactome mapping
annotated property: definition
annotated target: This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates.
database_cross_reference: PMID:15761153

Axiom
annotated source: luminescence based mammalian interactome mapping
annotated property: has_exact_synonym
annotated target: lumier
has_synonym_type: Unique short label curated by PSI-MI

pubchem
type: Class
subclass of: bioactive entity reference
definition: PubChem provides information on the biological activities of small molecules. http://pubchem.ncbi.nlm.nih.gov/
has_exact_synonym: PubChem
has_obo_namespace: PSI-MI
id: MI:0730
in_subset: PSI-MI slim

Axiom
annotated source: pubchem
annotated property: definition
annotated target: PubChem provides information on the biological activities of small molecules. http://pubchem.ncbi.nlm.nih.gov/
database_cross_reference: PMID:16381840

Axiom
annotated source: pubchem
annotated property: has_exact_synonym
annotated target: PubChem
has_synonym_type: Alternate label curated by PSI-MI

3d repertoire
type: Class
subclass of: source database
definition: The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository.
has_exact_synonym: 3D Repertoire
has_obo_namespace: PSI-MI
id: MI:0731
in_subset: PSI-MI slim

Axiom
annotated source: 3d repertoire
annotated property: definition
annotated target: The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository.
database_cross_reference: PMID:14755292

Axiom
annotated source: 3d repertoire
annotated property: has_exact_synonym
annotated target: 3D Repertoire
has_synonym_type: Alternate label curated by PSI-MI

red fluorescent protein tag
type: Class
subclass of: fluorescent protein tag
definition: The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
has_exact_synonym: RFP
has_exact_synonym: red fluorescent protein
has_exact_synonym: rfp tag
has_obo_namespace: PSI-MI
id: MI:0732
in_subset: PSI-MI slim

Axiom
annotated source: red fluorescent protein tag
annotated property: definition
annotated target: The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
database_cross_reference: PMID:14755292

Axiom
annotated source: red fluorescent protein tag
annotated property: has_exact_synonym
annotated target: RFP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: red fluorescent protein tag
annotated property: has_exact_synonym
annotated target: red fluorescent protein
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: red fluorescent protein tag
annotated property: has_exact_synonym
annotated target: rfp tag
has_synonym_type: Unique short label curated by PSI-MI

cyan fluorescent protein tag
type: Class
subclass of: fluorescent protein tag
definition: The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
has_exact_synonym: CFP
has_exact_synonym: cfp tag
has_exact_synonym: cyan fluorescent protein
has_obo_namespace: PSI-MI
id: MI:0733
in_subset: PSI-MI slim

Axiom
annotated source: cyan fluorescent protein tag
annotated property: definition
annotated target: The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
database_cross_reference: PMID:14755292

Axiom
annotated source: cyan fluorescent protein tag
annotated property: has_exact_synonym
annotated target: CFP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cyan fluorescent protein tag
annotated property: has_exact_synonym
annotated target: cfp tag
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: cyan fluorescent protein tag
annotated property: has_exact_synonym
annotated target: cyan fluorescent protein
has_synonym_type: Alternate label curated by PSI-MI

enhanced green fluorescent protein tag
type: Class
subclass of: green fluorescent protein tag
definition: Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
has_exact_synonym: EGFP
has_exact_synonym: egfp tag
has_exact_synonym: enhanced green fluorescent protein
has_obo_namespace: PSI-MI
id: MI:0734
in_subset: PSI-MI slim

Axiom
annotated source: enhanced green fluorescent protein tag
annotated property: definition
annotated target: Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
database_cross_reference: PMID:14755292

Axiom
annotated source: enhanced green fluorescent protein tag
annotated property: has_exact_synonym
annotated target: EGFP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: enhanced green fluorescent protein tag
annotated property: has_exact_synonym
annotated target: egfp tag
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: enhanced green fluorescent protein tag
annotated property: has_exact_synonym
annotated target: enhanced green fluorescent protein
has_synonym_type: Alternate label curated by PSI-MI

transactivating tag
type: Class
subclass of: cell penetrating peptide tag
definition: Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells.
has_exact_synonym: Tat tag
has_exact_synonym: tat tag
has_obo_namespace: PSI-MI
id: MI:0735
in_subset: PSI-MI slim

Axiom
annotated source: transactivating tag
annotated property: definition
annotated target: Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells.
database_cross_reference: PMID:8290579

Axiom
annotated source: transactivating tag
annotated property: has_exact_synonym
annotated target: Tat tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: transactivating tag
annotated property: has_exact_synonym
annotated target: tat tag
has_synonym_type: Unique short label curated by PSI-MI

protein passive uptake
type: Class
subclass of: passive uptake
subclass of: protein delivery
definition: Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes.
has_exact_synonym: prot passive uptake
has_obo_namespace: PSI-MI
id: MI:0736
in_subset: PSI-MI slim

Axiom
annotated source: protein passive uptake
annotated property: definition
annotated target: Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein passive uptake
annotated property: has_exact_synonym
annotated target: prot passive uptake
has_synonym_type: Unique short label curated by PSI-MI

peptide sequence database
type: Class
subclass of: sequence database
definition: database storing sequences detected by peptide identification methods.
has_exact_synonym: pep seq db
has_obo_namespace: PSI-MI
id: MI:0737
in_subset: PSI-MI slim

Axiom
annotated source: peptide sequence database
annotated property: definition
annotated target: database storing sequences detected by peptide identification methods.
database_cross_reference: PMID:14755292

Axiom
annotated source: peptide sequence database
annotated property: has_exact_synonym
annotated target: pep seq db
has_synonym_type: Unique short label curated by PSI-MI

pride
type: Class
subclass of: peptide sequence database
definition: PRIDE is a public repository of protein and peptide identifications for the proteomics community. http://www.ebi.ac.uk/pride/
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0738
in_subset: PSI-MI slim

Axiom
annotated source: pride
annotated property: definition
annotated target: PRIDE is a public repository of protein and peptide identifications for the proteomics community. http://www.ebi.ac.uk/pride/
database_cross_reference: PMID:16381953

Axiom
annotated source: pride
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/pride/archive/projects/${ac}

penetrating tag
type: Class
subclass of: cell penetrating peptide tag
definition: Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK
has_obo_namespace: PSI-MI
id: MI:0739
in_subset: PSI-MI slim

Axiom
annotated source: penetrating tag
annotated property: definition
annotated target: Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK
database_cross_reference: PMID:16574060

cell penetrating peptide tag
type: Class
subclass of: tag
definition: The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus.
has_exact_synonym: CPPs
has_exact_synonym: MTS
has_exact_synonym: PTDs
has_exact_synonym: Trojan peptides
has_exact_synonym: cell penetrating pep
has_exact_synonym: cell-penetrating peptides
has_exact_synonym: membrane translocating sequences
has_exact_synonym: protein transduction domains
has_obo_namespace: PSI-MI
id: MI:0740
in_subset: PSI-MI slim

Axiom
annotated source: cell penetrating peptide tag
annotated property: definition
annotated target: The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus.
database_cross_reference: PMID:16574060

Axiom
annotated source: cell penetrating peptide tag
annotated property: has_exact_synonym
annotated target: CPPs
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cell penetrating peptide tag
annotated property: has_exact_synonym
annotated target: MTS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cell penetrating peptide tag
annotated property: has_exact_synonym
annotated target: PTDs
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cell penetrating peptide tag
annotated property: has_exact_synonym
annotated target: Trojan peptides
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cell penetrating peptide tag
annotated property: has_exact_synonym
annotated target: cell penetrating pep
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: cell penetrating peptide tag
annotated property: has_exact_synonym
annotated target: cell-penetrating peptides
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cell penetrating peptide tag
annotated property: has_exact_synonym
annotated target: membrane translocating sequences
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cell penetrating peptide tag
annotated property: has_exact_synonym
annotated target: protein transduction domains
has_synonym_type: Alternate label curated by PSI-MI

peptide atlas
type: Class
subclass of: peptide sequence database
definition: PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. http://www.peptideatlas.org/
has_exact_synonym: PeptideAtlas
has_obo_namespace: PSI-MI
id: MI:0741
in_subset: PSI-MI slim

Axiom
annotated source: peptide atlas
annotated property: definition
annotated target: PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. http://www.peptideatlas.org/
database_cross_reference: PMID:15642101
database_cross_reference: PMID:16381952

Axiom
annotated source: peptide atlas
annotated property: has_exact_synonym
annotated target: PeptideAtlas
has_synonym_type: Alternate label curated by PSI-MI

gpm
type: Class
subclass of: peptide sequence database
definition: Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. http://www.thegpm.org
has_exact_synonym: Global Proteome Machine
has_obo_namespace: PSI-MI
id: MI:0742
in_subset: PSI-MI slim

Axiom
annotated source: gpm
annotated property: definition
annotated target: Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. http://www.thegpm.org
database_cross_reference: PMID:15595733

Axiom
annotated source: gpm
annotated property: has_exact_synonym
annotated target: Global Proteome Machine
has_synonym_type: Alternate label curated by PSI-MI

genetic experimental form
type: Class
subclass of: experimental preparation
definition: Descriptor of an experimental form involved in a genetic interaction
has_exact_synonym: genetic exp form
has_obo_namespace: PSI-MI
id: MI:0787
in_subset: PSI-MI slim

Axiom
annotated source: genetic experimental form
annotated property: definition
annotated target: Descriptor of an experimental form involved in a genetic interaction
database_cross_reference: PMID:14755292

Axiom
annotated source: genetic experimental form
annotated property: has_exact_synonym
annotated target: genetic exp form
has_synonym_type: Unique short label curated by PSI-MI

knock out
type: Class
subclass of: mutated gene
definition: The gene has been completely removed e.g. by genetic engineering
has_exact_synonym: knock-out
has_obo_namespace: PSI-MI
id: MI:0788
in_subset: PSI-MI slim

Axiom
annotated source: knock out
annotated property: definition
annotated target: The gene has been completely removed e.g. by genetic engineering
database_cross_reference: PMID:14755292

Axiom
annotated source: knock out
annotated property: has_exact_synonym
annotated target: knock-out
has_synonym_type: Unique short label curated by PSI-MI

knock down
type: Class
subclass of: mutated gene
definition: The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference.
has_exact_synonym: knock-down
has_obo_namespace: PSI-MI
id: MI:0789
in_subset: PSI-MI slim

Axiom
annotated source: knock down
annotated property: definition
annotated target: The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference.
database_cross_reference: PMID:14755292

Axiom
annotated source: knock down
annotated property: has_exact_synonym
annotated target: knock-down
has_synonym_type: Unique short label curated by PSI-MI

hypermorph
type: Class
subclass of: genetic experimental form
definition: The gene function has been partially improved compared to wild-type by altering its sequence.
has_obo_namespace: PSI-MI
id: MI:0790
in_subset: PSI-MI slim

Axiom
annotated source: hypermorph
annotated property: definition
annotated target: The gene function has been partially improved compared to wild-type by altering its sequence.
database_cross_reference: PMID:14755292

hypomorph
type: Class
subclass of: genetic experimental form
definition: The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant.
has_obo_namespace: PSI-MI
id: MI:0791
in_subset: PSI-MI slim

Axiom
annotated source: hypomorph
annotated property: definition
annotated target: The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant.
database_cross_reference: PMID:14755292

antimorph
type: Class
subclass of: genetic experimental form
definition: The gene function has been antagonized by a mutation in another copy of the gene.
has_obo_namespace: PSI-MI
id: MI:0792
in_subset: PSI-MI slim

Axiom
annotated source: antimorph
annotated property: definition
annotated target: The gene function has been antagonized by a mutation in another copy of the gene.
database_cross_reference: PMID:14755292

amorph
type: Class
subclass of: genetic experimental form
definition: The gene function has been abolished by mutation, though the type of mutation is not known.
has_obo_namespace: PSI-MI
id: MI:0793
in_subset: PSI-MI slim

Axiom
annotated source: amorph
annotated property: definition
annotated target: The gene function has been abolished by mutation, though the type of mutation is not known.
database_cross_reference: PMID:14755292

synthetic genetic interaction
type: Class
subclass of: diverging genetic interaction
subclass of: MI 2381
definition: An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (or minimally observed) as a result of any of the individual perturbations. wt = a = b = E (not=) ab
has_exact_synonym: aphenotypic diverging genetic interaction
has_exact_synonym: synthetic genetic interaction (sensu inequality)
has_exact_synonym: synthetic genetic interaction defined by inequality
has_obo_namespace: PSI-MI
id: MI:0794
in_subset: PSI-MI slim

Axiom
annotated source: synthetic genetic interaction
annotated property: definition
annotated target: An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (or minimally observed) as a result of any of the individual perturbations. wt = a = b = E (not=) ab
database_cross_reference: PMID:15833125

asynthetic genetic interaction
type: Class
subclass of: converging genetic interaction
subclass of: MI 2386
definition: An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a = b = ab != wt where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
is defined by: A, B, and the AB combination all have the same effect on the WT background (2 inequalities).
is defined by: Another subtype of alleviating interaction, 'coequal' interaction, is defined by single- and double-mutant strains that exhibit fitness values that are indistinguishable from one another (19).
is defined by: Lastly, we observed ten gene pairs for which the MMS sensitivity of the single- and double-deletion strains was statistically indistinguishable (Sxy = Sx = Sy). These interactions, which we call ‘coequal’, are related to‘complementary gene action’, ‘complementary epistasis’ or ‘asynthetic’ relationship types that have been previously described18,30,31.
has_exact_synonym: asynthetic
has_exact_synonym: asynthetic genetic interaction (sensu inequality)
has_exact_synonym: coequal genetic interaction
has_exact_synonym: isophenotypic masking genetic interaction
has_obo_namespace: PSI-MI
id: MI:0795
in_subset: PSI-MI slim

Axiom
annotated source: asynthetic genetic interaction
annotated property: definition
annotated target: An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a = b = ab != wt where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

Axiom
annotated source: asynthetic genetic interaction
annotated property: has_exact_synonym
annotated target: asynthetic
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: asynthetic genetic interaction
annotated property: has_exact_synonym
annotated target: asynthetic genetic interaction (sensu inequality)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: asynthetic genetic interaction
annotated property: has_exact_synonym
annotated target: coequal genetic interaction
database_cross_reference: PMID:18305163

genetic suppression (sensu unexpected)
type: Class
subclass of: converging genetic interaction
subclass of: MI 2379
definition: An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab <= wt [E = a*] OR wt <= ab < a* [E = a*] where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
has_exact_synonym: suppression
has_exact_synonym: suppressive genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
has_related_synonym: Alleviating interaction
id: MI:0796
in_subset: PSI-MI slim

Axiom
annotated source: genetic suppression (sensu unexpected)
annotated property: definition
annotated target: An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab <= wt [E = a*] OR wt <= ab < a* [E = a*] where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

Axiom
annotated source: genetic suppression (sensu unexpected)
annotated property: has_exact_synonym
annotated target: suppression
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: genetic suppression (sensu unexpected)
annotated property: has_exact_synonym
annotated target: suppressive genetic interaction (sensu inequality)
has_synonym_type: Alternate label curated by PSI-MI

genetic epistasis (sensu Bateson)
type: Class
subclass of: genetic interaction (sensu unexpected)
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
has_broad_synonym: masking genetic interaction
has_exact_synonym: Bateson genetic epistasis
has_exact_synonym: epistatic
has_exact_synonym: epistatic genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
id: MI:0797
in_subset: PSI-MI slim

Axiom
annotated source: genetic epistasis (sensu Bateson)
annotated property: definition
annotated target: An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
database_cross_reference: PMID:15833125

Axiom
annotated source: genetic epistasis (sensu Bateson)
annotated property: has_exact_synonym
annotated target: Bateson genetic epistasis
database_cross_reference: PMID:17510664
database_cross_reference: https://archive.org/details/mendelsprinciple00bate/page/n8

Axiom
annotated source: genetic epistasis (sensu Bateson)
annotated property: has_exact_synonym
annotated target: epistatic
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: genetic epistasis (sensu Bateson)
annotated property: has_exact_synonym
annotated target: epistatic genetic interaction (sensu inequality)
has_synonym_type: Alternate label curated by PSI-MI

conditional genetic interaction defined by inequality
type: Class
definition: The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
has_exact_synonym: conditional
has_exact_synonym: conditional genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
id: MI:0798
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: conditional genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
database_cross_reference: PMID:15833125

Axiom
annotated source: conditional genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: conditional
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: conditional genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: conditional genetic interaction (sensu inequality)
has_synonym_type: Alternate label curated by PSI-MI

additive genetic interaction defined by inequality
type: Class
definition: Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
has_exact_synonym: additive
has_exact_synonym: additive genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
id: MI:0799
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: additive genetic interaction defined by inequality
annotated property: definition
annotated target: Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
database_cross_reference: PMID:15833125

Axiom
annotated source: additive genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: additive
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: additive genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: additive genetic interaction (sensu inequality)
has_synonym_type: Alternate label curated by PSI-MI

single nonmonotonic genetic interaction defined by inequality
type: Class
definition: The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b.
has_exact_synonym: single nonmonotonic
has_exact_synonym: single nonmonotonic genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
id: MI:0800
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: single nonmonotonic genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b.
database_cross_reference: PMID:15833125

Axiom
annotated source: single nonmonotonic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: single nonmonotonic
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: single nonmonotonic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: single nonmonotonic genetic interaction (sensu inequality)
has_synonym_type: Alternate label curated by PSI-MI

double nonmonotonic genetic interaction defined by inequality
type: Class
definition: The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b
has_exact_synonym: double nonmonotonic
has_exact_synonym: double nonmonotonic genetic interaction (sensu inequality)
has_obo_namespace: PSI-MI
id: MI:0801
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: double nonmonotonic genetic interaction defined by inequality
annotated property: definition
annotated target: The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b
database_cross_reference: PMID:15833125

Axiom
annotated source: double nonmonotonic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: double nonmonotonic
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: double nonmonotonic genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: double nonmonotonic genetic interaction (sensu inequality)
has_synonym_type: Alternate label curated by PSI-MI

enhancement interaction
type: Class
definition: The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme. OBSOLETE: remap to MI:0933 'negative genetic interaction'
has_exact_synonym: enhancement
has_obo_namespace: PSI-MI
id: MI:0802
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: enhancement interaction
annotated property: definition
annotated target: The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme. OBSOLETE: remap to MI:0933 'negative genetic interaction'
database_cross_reference: PMID:15833125

Axiom
annotated source: enhancement interaction
annotated property: has_exact_synonym
annotated target: enhancement
has_synonym_type: Unique short label curated by PSI-MI

expression level alteration
type: Class
subclass of: genetic experimental form
definition: Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell.
has_exact_synonym: expression modif
has_obo_namespace: PSI-MI
id: MI:0803
in_subset: PSI-MI slim

Axiom
annotated source: expression level alteration
annotated property: definition
annotated target: Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell.
database_cross_reference: PMID:14755292

Axiom
annotated source: expression level alteration
annotated property: has_exact_synonym
annotated target: expression modif
has_synonym_type: Unique short label curated by PSI-MI

mutated gene
type: Class
subclass of: genetic experimental form
definition: The gene is mutated in some unknown manner
has_obo_namespace: PSI-MI
id: MI:0804
in_subset: PSI-MI slim

Axiom
annotated source: mutated gene
annotated property: definition
annotated target: The gene is mutated in some unknown manner
database_cross_reference: PMID:14755292

wwpdb
type: Class
subclass of: feature database
subclass of: interaction database
subclass of: source database
definition: The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. http://www.wwpdb.org/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: wwPDB
has_obo_namespace: PSI-MI
id: MI:0805
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: wwpdb
annotated property: definition
annotated target: The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. http://www.wwpdb.org/
database_cross_reference: PMID:14634627

[0-9][a-zA-Z0-9]{3}
type: Axiom
annotated source: wwpdb
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: wwpdb
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.pdbe.org/${ac}

Axiom
annotated source: wwpdb
annotated property: has_exact_synonym
annotated target: wwPDB
has_synonym_type: Alternate label curated by PSI-MI

pdbj
type: Class
subclass of: wwpdb
definition: PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites. http://www.pdbj.org/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: PDBj
has_obo_namespace: PSI-MI
id: MI:0806
in_subset: PSI-MI slim

Axiom
annotated source: pdbj
annotated property: definition
annotated target: PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites. http://www.pdbj.org/
database_cross_reference: PMID:12099029

[0-9][a-zA-Z0-9]{3}
type: Axiom
annotated source: pdbj
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: pdbj
annotated property: database_cross_reference
annotated target: search-url:
label: http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet

Axiom
annotated source: pdbj
annotated property: has_exact_synonym
annotated target: PDBj
has_synonym_type: Alternate label curated by PSI-MI

comigration in gel electrophoresis
type: Class
subclass of: electrophoretic mobility-based method
definition: The interaction of two or more molecules is determined by their very close proximity or the overlap of their respective bands in a gel.
has_exact_synonym: comigration in gel
has_obo_namespace: PSI-MI
id: MI:0807
in_subset: PSI-MI slim

Axiom
annotated source: comigration in gel electrophoresis
annotated property: definition
annotated target: The interaction of two or more molecules is determined by their very close proximity or the overlap of their respective bands in a gel.
database_cross_reference: PMID:14755292

Axiom
annotated source: comigration in gel electrophoresis
annotated property: has_exact_synonym
annotated target: comigration in gel
has_synonym_type: Unique short label curated by PSI-MI

comigration in sds page
type: Class
subclass of: comigration in gel electrophoresis
definition: A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a denaturing gel.
has_exact_synonym: comigration in sds
has_obo_namespace: PSI-MI
id: MI:0808
in_subset: PSI-MI slim

Axiom
annotated source: comigration in sds page
annotated property: definition
annotated target: A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a denaturing gel.
database_cross_reference: PMID:14755292
database_cross_reference: PMID:16732283

Axiom
annotated source: comigration in sds page
annotated property: has_exact_synonym
annotated target: comigration in sds
has_synonym_type: Unique short label curated by PSI-MI

bimolecular fluorescence complementation
type: Class
subclass of: fluorescence technology
subclass of: protein complementation assay
definition: The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy.
has_alternative_id: MI:0229
has_exact_synonym: bifc
has_exact_synonym: gfp complementation
has_exact_synonym: green fluorescence protein complementation assay
has_obo_namespace: PSI-MI
id: MI:0809
in_subset: PSI-MI slim

Axiom
annotated source: bimolecular fluorescence complementation
annotated property: definition
annotated target: The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy.
database_cross_reference: PMID:11983170

Axiom
annotated source: bimolecular fluorescence complementation
annotated property: has_exact_synonym
annotated target: bifc
has_synonym_type: Unique short label curated by PSI-MI

substitution analysis
type: Class
subclass of: mutation analysis
definition: In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction.
has_exact_synonym: substitut analysis
has_obo_namespace: PSI-MI
id: MI:0810
in_subset: PSI-MI slim

Axiom
annotated source: substitution analysis
annotated property: definition
annotated target: In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: substitution analysis
annotated property: has_exact_synonym
annotated target: substitut analysis
has_synonym_type: Unique short label curated by PSI-MI

insertion analysis
type: Class
subclass of: mutation analysis
definition: In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction.
has_obo_namespace: PSI-MI
id: MI:0811
in_subset: PSI-MI slim

Axiom
annotated source: insertion analysis
annotated property: definition
annotated target: In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction.
database_cross_reference: PMID:14755292

calmodulin binding protein tag
type: Class
subclass of: fusion protein
definition: The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin.
has_exact_synonym: cam tag
has_obo_namespace: PSI-MI
id: MI:0812
in_subset: PSI-MI slim

Axiom
annotated source: calmodulin binding protein tag
annotated property: definition
annotated target: The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin.
database_cross_reference: PMID:14755292

Axiom
annotated source: calmodulin binding protein tag
annotated property: has_exact_synonym
annotated target: cam tag
has_synonym_type: Unique short label curated by PSI-MI

proximity ligation assay
type: Class
subclass of: affinity technology
subclass of: identification by antibody
definition: Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides.
has_exact_synonym: PLA
has_exact_synonym: p elisa
has_exact_synonym: pELISA
has_obo_namespace: PSI-MI
has_related_synonym: in situ proximity ligation assay
has_related_synonym: pLISA
has_related_synonym: proximity ligation
id: MI:0813
in_subset: PSI-MI slim

Axiom
annotated source: proximity ligation assay
annotated property: definition
annotated target: Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides.
database_cross_reference: PMID:15155907
database_cross_reference: PMID::17072308

Axiom
annotated source: proximity ligation assay
annotated property: has_exact_synonym
annotated target: PLA
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: proximity ligation assay
annotated property: has_exact_synonym
annotated target: pELISA
has_synonym_type: Alternate label curated by PSI-MI

protease accessibility laddering
type: Class
subclass of: enzymatic footprinting
definition: In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis).
has_exact_synonym: pal
has_exact_synonym: protease access
has_obo_namespace: PSI-MI
id: MI:0814
in_subset: PSI-MI slim

Axiom
annotated source: protease accessibility laddering
annotated property: definition
annotated target: In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis).
database_cross_reference: PMID:16615907

Axiom
annotated source: protease accessibility laddering
annotated property: has_exact_synonym
annotated target: pal
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protease accessibility laddering
annotated property: has_exact_synonym
annotated target: protease access
has_synonym_type: Unique short label curated by PSI-MI

confirmation by molecular weight
type: Class
subclass of: predetermined participant
definition: Molecule whose sequence identity is derived from their molecular weight
has_exact_synonym: weight identificat
has_obo_namespace: PSI-MI
id: MI:0815
in_subset: PSI-MI slim

Axiom
annotated source: confirmation by molecular weight
annotated property: definition
annotated target: Molecule whose sequence identity is derived from their molecular weight
database_cross_reference: PMID:14755292

Axiom
annotated source: confirmation by molecular weight
annotated property: has_exact_synonym
annotated target: weight identificat
has_synonym_type: Unique short label curated by PSI-MI

molecular weight estimation by staining
type: Class
subclass of: confirmation by molecular weight
definition: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker.
has_exact_synonym: weight by staining
has_obo_namespace: PSI-MI
id: MI:0816
in_subset: PSI-MI slim

Axiom
annotated source: molecular weight estimation by staining
annotated property: definition
annotated target: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker.
database_cross_reference: PMID:14755292

Axiom
annotated source: molecular weight estimation by staining
annotated property: has_exact_synonym
annotated target: weight by staining
has_synonym_type: Unique short label curated by PSI-MI

molecular weight estimation by silver staining
type: Class
subclass of: molecular weight estimation by staining
definition: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver.
has_exact_synonym: weight silver stain
has_obo_namespace: PSI-MI
id: MI:0817
in_subset: PSI-MI slim

Axiom
annotated source: molecular weight estimation by silver staining
annotated property: definition
annotated target: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver.
database_cross_reference: PMID:14755292

Axiom
annotated source: molecular weight estimation by silver staining
annotated property: has_exact_synonym
annotated target: weight silver stain
has_synonym_type: Unique short label curated by PSI-MI

molecular weight estimation by coomasie staining
type: Class
subclass of: molecular weight estimation by staining
definition: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye.
has_exact_synonym: weight by comassie
has_obo_namespace: PSI-MI
id: MI:0818
in_subset: PSI-MI slim

Axiom
annotated source: molecular weight estimation by coomasie staining
annotated property: definition
annotated target: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye.
database_cross_reference: PMID:14755292

Axiom
annotated source: molecular weight estimation by coomasie staining
annotated property: has_exact_synonym
annotated target: weight by comassie
has_synonym_type: Unique short label curated by PSI-MI

molecular weight estimation by bromide staining
type: Class
subclass of: molecular weight estimation by staining
definition: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes.
has_exact_synonym: weight by bromide
has_obo_namespace: PSI-MI
id: MI:0819
in_subset: PSI-MI slim

Axiom
annotated source: molecular weight estimation by bromide staining
annotated property: definition
annotated target: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes.
database_cross_reference: PMID:14755292

Axiom
annotated source: molecular weight estimation by bromide staining
annotated property: has_exact_synonym
annotated target: weight by bromide
has_synonym_type: Unique short label curated by PSI-MI

molecular weight estimation by sybr staining
type: Class
subclass of: molecular weight estimation by staining
definition: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes.
has_exact_synonym: safe DNA gel stain
has_exact_synonym: weight by sybr
has_obo_namespace: PSI-MI
id: MI:0820
in_subset: PSI-MI slim

Axiom
annotated source: molecular weight estimation by sybr staining
annotated property: definition
annotated target: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes.
database_cross_reference: PMID:14755292

Axiom
annotated source: molecular weight estimation by sybr staining
annotated property: has_exact_synonym
annotated target: safe DNA gel stain
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: molecular weight estimation by sybr staining
annotated property: has_exact_synonym
annotated target: weight by sybr
has_synonym_type: Unique short label curated by PSI-MI

molecular weight estimation by autoradiography
type: Class
subclass of: confirmation by molecular weight
definition: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography.
has_exact_synonym: weight autoradiogra
has_obo_namespace: PSI-MI
id: MI:0821
in_subset: PSI-MI slim

Axiom
annotated source: molecular weight estimation by autoradiography
annotated property: definition
annotated target: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography.
database_cross_reference: PMID:14755292

Axiom
annotated source: molecular weight estimation by autoradiography
annotated property: has_exact_synonym
annotated target: weight autoradiogra
has_synonym_type: Unique short label curated by PSI-MI

molecular weight estimation by hoechst staining
type: Class
subclass of: molecular weight estimation by staining
definition: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes.
has_exact_synonym: weight by hoechst
has_obo_namespace: PSI-MI
id: MI:0822
in_subset: PSI-MI slim

Axiom
annotated source: molecular weight estimation by hoechst staining
annotated property: definition
annotated target: Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes.
database_cross_reference: PMID:14755292

Axiom
annotated source: molecular weight estimation by hoechst staining
annotated property: has_exact_synonym
annotated target: weight by hoechst
has_synonym_type: Unique short label curated by PSI-MI

predetermined feature
type: Class
subclass of: protein sequence identification
subclass of: Identification by mass spectrometry
subclass of: experimental feature detection
definition: Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s).
has_exact_synonym: predetermined featur
has_obo_namespace: PSI-MI
id: MI:0823
in_subset: PSI-MI slim

Axiom
annotated source: predetermined feature
annotated property: definition
annotated target: Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s).
database_cross_reference: PMID:14755292

Axiom
annotated source: predetermined feature
annotated property: has_exact_synonym
annotated target: predetermined featur
has_synonym_type: Unique short label curated by PSI-MI

x-ray powder diffraction
type: Class
subclass of: x-ray crystallography
definition: Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals.
has_exact_synonym: X-ray
has_exact_synonym: x-ray powder diffrac
has_obo_namespace: PSI-MI
id: MI:0824
in_subset: PSI-MI slim

Axiom
annotated source: x-ray powder diffraction
annotated property: definition
annotated target: Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals.
database_cross_reference: PMID:14755292

Axiom
annotated source: x-ray powder diffraction
annotated property: has_exact_synonym
annotated target: X-ray
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: x-ray powder diffraction
annotated property: has_exact_synonym
annotated target: x-ray powder diffrac
has_synonym_type: Unique short label curated by PSI-MI

x-ray fiber diffraction
type: Class
subclass of: x-ray crystallography
definition: Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray.
has_exact_synonym: X-ray
has_exact_synonym: x-ray fiber diffrac
has_obo_namespace: PSI-MI
id: MI:0825
in_subset: PSI-MI slim

Axiom
annotated source: x-ray fiber diffraction
annotated property: definition
annotated target: Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray.
database_cross_reference: PMID:14755292

Axiom
annotated source: x-ray fiber diffraction
annotated property: has_exact_synonym
annotated target: X-ray
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: x-ray fiber diffraction
annotated property: has_exact_synonym
annotated target: x-ray fiber diffrac
has_synonym_type: Unique short label curated by PSI-MI

x ray scattering
type: Class
subclass of: light scattering
definition: Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles.
has_exact_synonym: saxs
has_obo_namespace: PSI-MI
id: MI:0826
in_subset: PSI-MI slim

Axiom
annotated source: x ray scattering
annotated property: definition
annotated target: Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles.
database_cross_reference: PMID:14755292

Axiom
annotated source: x ray scattering
annotated property: has_exact_synonym
annotated target: saxs
has_synonym_type: Unique short label curated by PSI-MI

x-ray tomography
type: Class
subclass of: imaging technique
definition: X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells.
has_obo_namespace: PSI-MI
id: MI:0827
in_subset: PSI-MI slim

Axiom
annotated source: x-ray tomography
annotated property: definition
annotated target: X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells.
database_cross_reference: PMID:14755292

polyprotein fragment
type: Class
subclass of: biological feature
definition: Subpart of a polyprotein that is naturally cleaved in vivo.
has_exact_synonym: polyprotein frag
has_obo_namespace: PSI-MI
has_related_synonym: chain
id: MI:0828
in_subset: PSI-MI slim

Axiom
annotated source: polyprotein fragment
annotated property: definition
annotated target: Subpart of a polyprotein that is naturally cleaved in vivo.
database_cross_reference: PMID:14577292

Axiom
annotated source: polyprotein fragment
annotated property: has_exact_synonym
annotated target: polyprotein frag
has_synonym_type: Unique short label curated by PSI-MI

multiple parent reference
type: Class
subclass of: cross-reference type
definition: This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules.
has_exact_synonym: multiple parent
has_obo_namespace: PSI-MI
id: MI:0829
in_subset: PSI-MI slim

Axiom
annotated source: multiple parent reference
annotated property: definition
annotated target: This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules.
database_cross_reference: PMID:14755292

Axiom
annotated source: multiple parent reference
annotated property: has_exact_synonym
annotated target: multiple parent
has_synonym_type: Unique short label curated by PSI-MI

tissue list
type: Class
subclass of: participant database
definition: List of tissue used as topic in UniProt RC line. http://www.expasy.org/cgi-bin/lists?tisslist.txt
has_obo_namespace: PSI-MI
id: MI:0830
in_subset: PSI-MI slim

Axiom
annotated source: tissue list
annotated property: definition
annotated target: List of tissue used as topic in UniProt RC line. http://www.expasy.org/cgi-bin/lists?tisslist.txt
database_cross_reference: PMID:14755292

cell ontology
type: Class
subclass of: participant database
definition: Ontology of cell types. http://obo.sourceforge.net/cgi-bin/detail.cgi?cell
has_obo_namespace: PSI-MI
id: MI:0831
in_subset: PSI-MI slim

Axiom
annotated source: cell ontology
annotated property: definition
annotated target: Ontology of cell types. http://obo.sourceforge.net/cgi-bin/detail.cgi?cell
database_cross_reference: PMID:16381901

half cystine
type: Class
definition: A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed
has_exact_synonym: Half of a disulfide bridge
has_obo_namespace: PSI-MI
id: MI:0832
deprecated: true

Axiom
annotated source: half cystine
annotated property: definition
annotated target: A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed
database_cross_reference: MOD:00798
database_cross_reference: RESID:AA0025

Axiom
annotated source: half cystine
annotated property: has_exact_synonym
annotated target: Half of a disulfide bridge
has_synonym_type: Alternate label curated by PSI-MI

autoradiography
type: Class
subclass of: experimental feature detection
subclass of: tag visualisation
definition: Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film.
has_obo_namespace: PSI-MI
id: MI:0833
in_subset: PSI-MI slim

Axiom
annotated source: autoradiography
annotated property: definition
annotated target: Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film.
database_cross_reference: PMID:14755292

ka
type: Class
subclass of: parameter type
definition: Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)
has_exact_synonym: kon
has_obo_namespace: PSI-MI
id: MI:0834
in_subset: PSI-MI slim

Axiom
annotated source: ka
annotated property: definition
annotated target: Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)
database_cross_reference: PMID:14755292

Axiom
annotated source: ka
annotated property: has_exact_synonym
annotated target: kon
has_synonym_type: Unique short label curated by PSI-MI

koff
type: Class
subclass of: parameter type
definition: Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)
has_exact_synonym: koff
has_obo_namespace: PSI-MI
has_related_synonym: Kd
id: MI:0835
in_subset: PSI-MI slim

Axiom
annotated source: koff
annotated property: definition
annotated target: Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)
database_cross_reference: PMID:14755292

Axiom
annotated source: koff
annotated property: has_exact_synonym
annotated target: koff
has_synonym_type: Unique short label curated by PSI-MI

temperature of interaction
type: Class
subclass of: parameter type
definition: Temperature at which interaction was determined. Unit KELVIN (K)
has_exact_synonym: T interaction
has_exact_synonym: Tint
has_exact_synonym: temp interaction
has_obo_namespace: PSI-MI
id: MI:0836
in_subset: PSI-MI slim

Axiom
annotated source: temperature of interaction
annotated property: definition
annotated target: Temperature at which interaction was determined. Unit KELVIN (K)
database_cross_reference: PMID:14755292

Axiom
annotated source: temperature of interaction
annotated property: has_exact_synonym
annotated target: T interaction
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: temperature of interaction
annotated property: has_exact_synonym
annotated target: Tint
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: temperature of interaction
annotated property: has_exact_synonym
annotated target: temp interaction
has_synonym_type: Unique short label curated by PSI-MI

pH of interaction
type: Class
subclass of: parameter type
definition: pH at which interaction was determined.
has_exact_synonym: pHint
has_obo_namespace: PSI-MI
id: MI:0837
in_subset: PSI-MI slim

Axiom
annotated source: pH of interaction
annotated property: definition
annotated target: pH at which interaction was determined.
database_cross_reference: PMID:14755292

Axiom
annotated source: pH of interaction
annotated property: has_exact_synonym
annotated target: pHint
has_synonym_type: Alternate label curated by PSI-MI

kelvin
type: Class
subclass of: parameter unit
definition: The kelvin (K) is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380649×10-23 when expressed in the unit J·K-1, which is equal to kg·m2·s-2·K-1, where the kilogram, metre and second are defined in terms of h, c and caesium frequency. It is equivalent to -273.15°C / -459.67°F.
has_exact_synonym: K
has_obo_namespace: PSI-MI
id: MI:0838
in_subset: PSI-MI slim

Axiom
annotated source: kelvin
annotated property: definition
annotated target: The kelvin (K) is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380649×10-23 when expressed in the unit J·K-1, which is equal to kg·m2·s-2·K-1, where the kilogram, metre and second are defined in terms of h, c and caesium frequency. It is equivalent to -273.15°C / -459.67°F.
database_cross_reference: PMID:14755292

Axiom
annotated source: kelvin
annotated property: has_exact_synonym
annotated target: K
has_synonym_type: Alternate label curated by PSI-MI

per mole per second
type: Class
subclass of: parameter unit
definition: Per mole per second, unit for association rate constant.
has_exact_synonym: M-1s-1
has_obo_namespace: PSI-MI
id: MI:0839
in_subset: PSI-MI slim

Axiom
annotated source: per mole per second
annotated property: definition
annotated target: Per mole per second, unit for association rate constant.
database_cross_reference: PMID:14755292

Axiom
annotated source: per mole per second
annotated property: has_exact_synonym
annotated target: M-1s-1
has_synonym_type: Alternate label curated by PSI-MI

stimulator
type: Class
subclass of: regulator
definition: Molecule stimulating an interaction by interacting with one or more of the participants.
has_obo_namespace: PSI-MI
id: MI:0840
in_subset: PSI-MI slim

Axiom
annotated source: stimulator
annotated property: definition
annotated target: Molecule stimulating an interaction by interacting with one or more of the participants.
database_cross_reference: PMID:14755292

phosphotransferase assay
type: Class
subclass of: enzymatic study
definition: Measures the rate of a phosphate transfer between two molecules.
has_exact_synonym: phosphotransferase
has_obo_namespace: PSI-MI
has_related_synonym: phosphotransfer assay
id: MI:0841
in_subset: PSI-MI slim

Axiom
annotated source: phosphotransferase assay
annotated property: definition
annotated target: Measures the rate of a phosphate transfer between two molecules.
database_cross_reference: PMID:14755292

Axiom
annotated source: phosphotransferase assay
annotated property: has_exact_synonym
annotated target: phosphotransferase
has_synonym_type: Unique short label curated by PSI-MI

phosphate donor
type: Class
subclass of: donor
definition: Any molecule that is able to transfer a phosphate group to another chemical species.
has_obo_namespace: PSI-MI
id: MI:0842
in_subset: PSI-MI slim

Axiom
annotated source: phosphate donor
annotated property: definition
annotated target: Any molecule that is able to transfer a phosphate group to another chemical species.
database_cross_reference: PMID:14755292

phosphate acceptor
type: Class
subclass of: acceptor
definition: Molecule to which a phosphate group may be transferred from a phosphate donor.
has_obo_namespace: PSI-MI
id: MI:0843
in_subset: PSI-MI slim

Axiom
annotated source: phosphate acceptor
annotated property: definition
annotated target: Molecule to which a phosphate group may be transferred from a phosphate donor.
database_cross_reference: PMID:14755292

phosphotransfer reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
has_exact_synonym: phosphotransfer
has_obo_namespace: PSI-MI
id: MI:0844
in_subset: PSI-MI slim

Axiom
annotated source: phosphotransfer reaction
annotated property: definition
annotated target: Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
database_cross_reference: PMID:14755292
database_cross_reference: PMID:16712436

Axiom
annotated source: phosphotransfer reaction
annotated property: has_exact_synonym
annotated target: phosphotransfer
has_synonym_type: Unique short label curated by PSI-MI

spin label
type: Class
subclass of: experimental feature
definition: Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest.
has_obo_namespace: PSI-MI
id: MI:0845
in_subset: PSI-MI slim

Axiom
annotated source: spin label
annotated property: definition
annotated target: Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest.
database_cross_reference: PMID:10966640

r1 spin label
type: Class
subclass of: spin label
definition: Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline- 3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide side chain designated R1.
has_obo_namespace: PSI-MI
id: MI:0846
in_subset: PSI-MI slim

Axiom
annotated source: r1 spin label
annotated property: definition
annotated target: Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline- 3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide side chain designated R1.
database_cross_reference: PMID:10966640

dansyl label
type: Class
subclass of: fluorescent dye label
definition: Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups.
has_exact_synonym: 5-dimethylaminonaphthalene-1-sulfonyl tag
has_exact_synonym: dansyl tag
has_obo_namespace: PSI-MI
id: MI:0847
in_subset: PSI-MI slim

Axiom
annotated source: dansyl label
annotated property: definition
annotated target: Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups.
database_cross_reference: PMID:14755292

Axiom
annotated source: dansyl label
annotated property: has_exact_synonym
annotated target: 5-dimethylaminonaphthalene-1-sulfonyl tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: dansyl label
annotated property: has_exact_synonym
annotated target: dansyl tag
has_synonym_type: Alternate label curated by PSI-MI

125i radiolabel
type: Class
subclass of: radiolabel
definition: Molecule labelled with 125 radio isotope of iodine atoms.
has_exact_synonym: 125I
has_exact_synonym: I125
has_obo_namespace: PSI-MI
id: MI:0848
in_subset: PSI-MI slim

Axiom
annotated source: 125i radiolabel
annotated property: definition
annotated target: Molecule labelled with 125 radio isotope of iodine atoms.
database_cross_reference: PMID:14755292

Axiom
annotated source: 125i radiolabel
annotated property: has_exact_synonym
annotated target: 125I
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: 125i radiolabel
annotated property: has_exact_synonym
annotated target: I125
has_synonym_type: Alternate label curated by PSI-MI

ncbi taxonomy
type: Class
subclass of: participant database
definition: The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available. http://www.ncbi.nlm.nih.gov/Taxonomy/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:0849
in_subset: PSI-MI slim

Axiom
annotated source: ncbi taxonomy
annotated property: definition
annotated target: The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available. http://www.ncbi.nlm.nih.gov/Taxonomy/
database_cross_reference: PMID:10592169

[0-9]+
type: Axiom
annotated source: ncbi taxonomy
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: ncbi taxonomy
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi

encode
type: Class
subclass of: genome databases
definition: ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project. http://www.genome.gov/10005107
has_exact_synonym: ENCODE
has_exact_synonym: Encyclopedia Of DNA Elements
has_obo_namespace: PSI-MI
id: MI:0850
in_subset: PSI-MI slim

Axiom
annotated source: encode
annotated property: definition
annotated target: ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project. http://www.genome.gov/10005107
database_cross_reference: PMID:17372197

Axiom
annotated source: encode
annotated property: has_exact_synonym
annotated target: ENCODE
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: encode
annotated property: has_exact_synonym
annotated target: Encyclopedia Of DNA Elements
has_synonym_type: Alternate label curated by PSI-MI

protein genbank identifier
type: Class
subclass of: genbank identifier
definition: GenBank Identifier or GI numbers for proteins.
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: GenBank Protein GI
has_exact_synonym: genbank protein gi
has_exact_synonym: genbank_protein_gi
has_exact_synonym: genpept id
has_obo_namespace: PSI-MI
id: MI:0851
in_subset: PSI-MI slim

Axiom
annotated source: protein genbank identifier
annotated property: definition
annotated target: GenBank Identifier or GI numbers for proteins.
database_cross_reference: PMID:17170002

[0-9]+
type: Axiom
annotated source: protein genbank identifier
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: protein genbank identifier
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

Axiom
annotated source: protein genbank identifier
annotated property: has_exact_synonym
annotated target: GenBank Protein GI
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein genbank identifier
annotated property: has_exact_synonym
annotated target: genbank protein gi
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: protein genbank identifier
annotated property: has_exact_synonym
annotated target: genbank_protein_gi
has_synonym_type: Unique short label curated by PSI-MI

nucleotide genbank identifier
type: Class
subclass of: genbank identifier
definition: GenBank Identifier or GI numbers for nucleotide.
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: GenBank Nucleotide
has_exact_synonym: genbank nucleotide
has_exact_synonym: genbank_nucl_gi
has_obo_namespace: PSI-MI
id: MI:0852
in_subset: PSI-MI slim

Axiom
annotated source: nucleotide genbank identifier
annotated property: definition
annotated target: GenBank Identifier or GI numbers for nucleotide.
database_cross_reference: PMID:17170002

[0-9]+
type: Axiom
annotated source: nucleotide genbank identifier
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: nucleotide genbank identifier
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi

Axiom
annotated source: nucleotide genbank identifier
annotated property: has_exact_synonym
annotated target: GenBank Nucleotide
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: nucleotide genbank identifier
annotated property: has_exact_synonym
annotated target: genbank nucleotide
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: nucleotide genbank identifier
annotated property: has_exact_synonym
annotated target: genbank_nucl_gi
has_synonym_type: Unique short label curated by PSI-MI

dna overhang
type: Class
subclass of: experimental feature
definition: An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase
has_exact_synonym: cohessive ends
has_exact_synonym: sticky ends
has_obo_namespace: PSI-MI
id: MI:0853
in_subset: PSI-MI slim

Axiom
annotated source: dna overhang
annotated property: definition
annotated target: An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase
database_cross_reference: PMID:14755292

Axiom
annotated source: dna overhang
annotated property: has_exact_synonym
annotated target: cohessive ends
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: dna overhang
annotated property: has_exact_synonym
annotated target: sticky ends
has_synonym_type: Alternate label curated by PSI-MI

3 prime overhang
type: Class
subclass of: dna overhang
definition: An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule.
has_exact_synonym: 3 prime sticky end
has_obo_namespace: PSI-MI
id: MI:0854
in_subset: PSI-MI slim

Axiom
annotated source: 3 prime overhang
annotated property: definition
annotated target: An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: 3 prime overhang
annotated property: has_exact_synonym
annotated target: 3 prime sticky end
has_synonym_type: Alternate label curated by PSI-MI

5 prime overhang
type: Class
subclass of: dna overhang
definition: An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule.
has_exact_synonym: 5 prime sticky end
has_obo_namespace: PSI-MI
id: MI:0855
in_subset: PSI-MI slim

Axiom
annotated source: 5 prime overhang
annotated property: definition
annotated target: An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: 5 prime overhang
annotated property: has_exact_synonym
annotated target: 5 prime sticky end
has_synonym_type: Alternate label curated by PSI-MI

fluorophore
type: Class
subclass of: experimental feature
definition: A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore.
has_obo_namespace: PSI-MI
id: MI:0856
in_subset: PSI-MI slim

Axiom
annotated source: fluorophore
annotated property: definition
annotated target: A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore.
database_cross_reference: PMID:14755292

fluorescent dye label
type: Class
subclass of: dye label
subclass of: fluorophore
definition: Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength.
has_exact_synonym: fluorescent dye
has_obo_namespace: PSI-MI
id: MI:0857
in_subset: PSI-MI slim

Axiom
annotated source: fluorescent dye label
annotated property: definition
annotated target: Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength.
database_cross_reference: PMID:14755292

Axiom
annotated source: fluorescent dye label
annotated property: has_exact_synonym
annotated target: fluorescent dye
has_synonym_type: Unique short label curated by PSI-MI

immunodepleted coimmunoprecipitation
type: Class
subclass of: coimmunoprecipitation
definition: Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex.
has_exact_synonym: immunodepleted coip
has_exact_synonym: immunodepletion
has_obo_namespace: PSI-MI
id: MI:0858
in_subset: PSI-MI slim

Axiom
annotated source: immunodepleted coimmunoprecipitation
annotated property: definition
annotated target: Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex.
database_cross_reference: PMID:17081976

Axiom
annotated source: immunodepleted coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: immunodepleted coip
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: immunodepleted coimmunoprecipitation
annotated property: has_exact_synonym
annotated target: immunodepletion
has_synonym_type: Unique short label curated by PSI-MI

force spectroscopy
type: Class
subclass of: biophysical
subclass of: force measurement
definition: A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force.
has_exact_synonym: intermolecular force
has_obo_namespace: PSI-MI
has_related_synonym: force measurement
has_related_synonym: molecular force measurement
has_related_synonym: single molecule force measurement
has_related_synonym: surface adhesion force measurement
id: MI:0859

Axiom
annotated source: force spectroscopy
annotated property: definition
annotated target: A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force.
database_cross_reference: PMID:18511917

Axiom
annotated source: force spectroscopy
annotated property: has_exact_synonym
annotated target: intermolecular force
has_synonym_type: Alternate label curated by PSI-MI

genbank identifier
type: Class
subclass of: sequence database
definition: edit
database_cross_reference: id-validation-regexp:
has_obo_namespace: PSI-MI
id: MI:0860
in_subset: PSI-MI slim

Axiom
annotated source: genbank identifier
annotated property: definition
annotated target: edit
database_cross_reference: PMID:15078858

ENS[A-Z]+[0-9]{11}
type: Axiom
annotated source: genbank identifier
annotated property: database_cross_reference
annotated target: id-validation-regexp:

protein a tag
type: Class
subclass of: fusion protein
definition: The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis.
has_exact_synonym: protein A
has_obo_namespace: PSI-MI
id: MI:0861
in_subset: PSI-MI slim

Axiom
annotated source: protein a tag
annotated property: definition
annotated target: The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein a tag
annotated property: has_exact_synonym
annotated target: protein A
has_synonym_type: Alternate label curated by PSI-MI

zz tag
type: Class
subclass of: protein a tag
definition: The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain.
has_exact_synonym: ZZ tag
has_obo_namespace: PSI-MI
id: MI:0862
in_subset: PSI-MI slim

Axiom
annotated source: zz tag
annotated property: definition
annotated target: The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain.
database_cross_reference: PMID:11694505

Axiom
annotated source: zz tag
annotated property: has_exact_synonym
annotated target: ZZ tag
has_synonym_type: Alternate label curated by PSI-MI

thiol reactive lanthanide label
type: Class
subclass of: luminscent dye label
definition: Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA.
has_exact_synonym: Tb3+-DTPA-cs124-EMCH
has_exact_synonym: thiol lanthanide
has_obo_namespace: PSI-MI
id: MI:0863
in_subset: PSI-MI slim

Axiom
annotated source: thiol reactive lanthanide label
annotated property: definition
annotated target: Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA.
database_cross_reference: PMID:10077482

Axiom
annotated source: thiol reactive lanthanide label
annotated property: has_exact_synonym
annotated target: Tb3+-DTPA-cs124-EMCH
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: thiol reactive lanthanide label
annotated property: has_exact_synonym
annotated target: thiol lanthanide
has_synonym_type: Unique short label curated by PSI-MI

brenda
type: Class
subclass of: participant database
definition: A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. http://www.brenda-enzymes.info
has_obo_namespace: PSI-MI
id: MI:0864
in_subset: PSI-MI slim

Axiom
annotated source: brenda
annotated property: definition
annotated target: A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. http://www.brenda-enzymes.info
database_cross_reference: PMID:14755292

fluorescence acceptor donor pair
type: Class
subclass of: luminescence acceptor donor pair
definition: Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes.
has_exact_synonym: fret pair
has_obo_namespace: PSI-MI
id: MI:0865
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence acceptor donor pair
annotated property: definition
annotated target: Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes.
database_cross_reference: PMID:14755292

Axiom
annotated source: fluorescence acceptor donor pair
annotated property: has_exact_synonym
annotated target: fret pair
has_synonym_type: Unique short label curated by PSI-MI

tag visualisation
type: Class
subclass of: predetermined participant
definition: Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag.
has_obo_namespace: PSI-MI
id: MI:0866
in_subset: PSI-MI slim

Axiom
annotated source: tag visualisation
annotated property: definition
annotated target: Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag.
database_cross_reference: PMID:14755292

tag visualisation by fluorescence
type: Class
subclass of: tag visualisation
definition: The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction.
has_exact_synonym: tag fluorescence
has_obo_namespace: PSI-MI
id: MI:0867
in_subset: PSI-MI slim

Axiom
annotated source: tag visualisation by fluorescence
annotated property: definition
annotated target: The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: tag visualisation by fluorescence
annotated property: has_exact_synonym
annotated target: tag fluorescence
has_synonym_type: Unique short label curated by PSI-MI

author identifier
type: Class
subclass of: cross-reference type
definition: Author published identifier.
has_obo_namespace: PSI-MI
id: MI:0868
in_subset: PSI-MI slim

Axiom
annotated source: author identifier
annotated property: definition
annotated target: Author published identifier.
database_cross_reference: PMID:14755292

originally assigned identifier
type: Class
subclass of: cross-reference type
definition: Identifier assigned when the record was created by a source database.
has_exact_synonym: original identifier
has_obo_namespace: PSI-MI
id: MI:0869
in_subset: PSI-MI slim

Axiom
annotated source: originally assigned identifier
annotated property: definition
annotated target: Identifier assigned when the record was created by a source database.
database_cross_reference: PMID:14755292

Axiom
annotated source: originally assigned identifier
annotated property: has_exact_synonym
annotated target: original identifier
has_synonym_type: Unique short label curated by PSI-MI

demethylase assay
type: Class
subclass of: enzymatic study
definition: Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule.
has_obo_namespace: PSI-MI
id: MI:0870
in_subset: PSI-MI slim

Axiom
annotated source: demethylase assay
annotated property: definition
annotated target: Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule.
database_cross_reference: PMID:14755292

demethylation reaction
type: Class
subclass of: enzymatic reaction
definition: The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian.
has_exact_synonym: demethylation
has_obo_namespace: PSI-MI
id: MI:0871
in_subset: PSI-MI slim

Axiom
annotated source: demethylation reaction
annotated property: definition
annotated target: The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian.
database_cross_reference: GO:0006482
database_cross_reference: PMID:17277772

Axiom
annotated source: demethylation reaction
annotated property: has_exact_synonym
annotated target: demethylation
has_synonym_type: Unique short label curated by PSI-MI

atomic force microscopy
type: Class
subclass of: imaging technique
definition: The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler. http://en.wikipedia.org/wiki/Atomic_force_microscope
has_exact_synonym: AFM
has_exact_synonym: atomic force microsc
has_obo_namespace: PSI-MI
id: MI:0872
in_subset: PSI-MI slim

Axiom
annotated source: atomic force microscopy
annotated property: definition
annotated target: The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler. http://en.wikipedia.org/wiki/Atomic_force_microscope
database_cross_reference: PMID:17502105

Axiom
annotated source: atomic force microscopy
annotated property: has_exact_synonym
annotated target: AFM
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: atomic force microscopy
annotated property: has_exact_synonym
annotated target: atomic force microsc
has_synonym_type: Unique short label curated by PSI-MI

curation request
type: Class
subclass of: bibliographic attribute name
definition: Annotation of a published paper which has been externally requested.
has_obo_namespace: PSI-MI
id: MI:0873
in_subset: PSI-MI slim

Axiom
annotated source: curation request
annotated property: definition
annotated target: Annotation of a published paper which has been externally requested.
database_cross_reference: PMID:14755292

dataset
type: Class
subclass of: bibliographic attribute name
definition: Targeted curation dataset grouping experiments by topic or dataset origin.
has_obo_namespace: PSI-MI
id: MI:0875
in_subset: PSI-MI slim

Axiom
annotated source: dataset
annotated property: definition
annotated target: Targeted curation dataset grouping experiments by topic or dataset origin.
database_cross_reference: PMID:14755292

author submitted
type: Class
subclass of: experiment attribute name
definition: Data directly submitted by the authors to a database prior to publication.
has_obo_namespace: PSI-MI
id: MI:0878
in_subset: PSI-MI slim

Axiom
annotated source: author submitted
annotated property: definition
annotated target: Data directly submitted by the authors to a database prior to publication.
database_cross_reference: PMID:14755292

nucleoside triphosphatase assay
type: Class
subclass of: enzymatic study
subclass of: phosphatase assay
definition: Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
has_exact_synonym: triphosphatase ass
has_obo_namespace: PSI-MI
id: MI:0879
in_subset: PSI-MI slim

Axiom
annotated source: nucleoside triphosphatase assay
annotated property: definition
annotated target: Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleoside triphosphatase assay
annotated property: has_exact_synonym
annotated target: triphosphatase ass
has_synonym_type: Unique short label curated by PSI-MI

atpase assay
type: Class
subclass of: nucleoside triphosphatase assay
definition: Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate.
has_obo_namespace: PSI-MI
id: MI:0880
in_subset: PSI-MI slim

Axiom
annotated source: atpase assay
annotated property: definition
annotated target: Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate.
database_cross_reference: PMID:14755292

nucleoside triphosphatase reaction
type: Class
subclass of: enzymatic reaction
definition: Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
has_exact_synonym: triphosphatase react
has_obo_namespace: PSI-MI
id: MI:0881
in_subset: PSI-MI slim

Axiom
annotated source: nucleoside triphosphatase reaction
annotated property: definition
annotated target: Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
database_cross_reference: GO:0017111
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleoside triphosphatase reaction
annotated property: has_exact_synonym
annotated target: triphosphatase react
has_synonym_type: Unique short label curated by PSI-MI

atpase reaction
type: Class
subclass of: nucleoside triphosphatase reaction
definition: Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate.
has_obo_namespace: PSI-MI
id: MI:0882
in_subset: PSI-MI slim

Axiom
annotated source: atpase reaction
annotated property: definition
annotated target: Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate.
database_cross_reference: GO:0016887
database_cross_reference: PMID:14755292

gtpase reaction
type: Class
subclass of: nucleoside triphosphatase reaction
definition: Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate.
has_obo_namespace: PSI-MI
id: MI:0883
in_subset: PSI-MI slim

Axiom
annotated source: gtpase reaction
annotated property: definition
annotated target: Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate.
database_cross_reference: GO:0003924
database_cross_reference: PMID:14755292

vsv tag
type: Class
subclass of: tag
definition: Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available.
has_exact_synonym: vesicular stomatitis virus tag
has_obo_namespace: PSI-MI
id: MI:0884
in_subset: PSI-MI slim

Axiom
annotated source: vsv tag
annotated property: definition
annotated target: Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available.
database_cross_reference: PMID:14755292

Axiom
annotated source: vsv tag
annotated property: has_exact_synonym
annotated target: vesicular stomatitis virus tag
has_synonym_type: Alternate label curated by PSI-MI

journal
type: Class
subclass of: bibliographic attribute name
definition: Name and details of a journal from which paper has been taken.
has_obo_namespace: PSI-MI
id: MI:0885
in_subset: PSI-MI slim

Axiom
annotated source: journal
annotated property: definition
annotated target: Name and details of a journal from which paper has been taken.
database_cross_reference: PMID:14755292

publication year
type: Class
subclass of: bibliographic attribute name
definition: Year of publication of a paper.
has_obo_namespace: PSI-MI
id: MI:0886
in_subset: PSI-MI slim

Axiom
annotated source: publication year
annotated property: definition
annotated target: Year of publication of a paper.
database_cross_reference: PMID:14755292

histone acetylase assay
type: Class
subclass of: acetylase assay
definition: In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with "histone acetyltransferase" (HAt)
has_exact_synonym: HAt
has_exact_synonym: hat
has_obo_namespace: PSI-MI
has_related_synonym: histone acetylation
id: MI:0887
in_subset: PSI-MI slim

Axiom
annotated source: histone acetylase assay
annotated property: definition
annotated target: In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with "histone acetyltransferase" (HAt)
database_cross_reference: PMID:14755292

Axiom
annotated source: histone acetylase assay
annotated property: has_exact_synonym
annotated target: HAt
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: histone acetylase assay
annotated property: has_exact_synonym
annotated target: hat
has_synonym_type: Unique short label curated by PSI-MI

small angle neutron scattering
type: Class
subclass of: biophysical
definition: During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample.
has_exact_synonym: SANS
has_exact_synonym: sans
has_obo_namespace: PSI-MI
id: MI:0888
in_subset: PSI-MI slim

Axiom
annotated source: small angle neutron scattering
annotated property: definition
annotated target: During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample.
database_cross_reference: PMID:11578931

Axiom
annotated source: small angle neutron scattering
annotated property: has_exact_synonym
annotated target: SANS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: small angle neutron scattering
annotated property: has_exact_synonym
annotated target: sans
has_synonym_type: Unique short label curated by PSI-MI

acetylase assay
type: Class
subclass of: enzymatic study
definition: Measures the catalysis of the addition of an acetyl group to a target molecule.
has_obo_namespace: PSI-MI
has_related_synonym: acetylation
id: MI:0889
in_subset: PSI-MI slim

Axiom
annotated source: acetylase assay
annotated property: definition
annotated target: Measures the catalysis of the addition of an acetyl group to a target molecule.
database_cross_reference: PMID:14755292

qdot
type: Class
subclass of: fluorescent dye label
definition: Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications.
has_obo_namespace: PSI-MI
id: MI:0890
in_subset: PSI-MI slim

Axiom
annotated source: qdot
annotated property: definition
annotated target: Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications.
database_cross_reference: PMID:17569782

neutron fiber diffraction
type: Class
subclass of: biophysical
definition: Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam.
has_exact_synonym: neutron fiber diff
has_obo_namespace: PSI-MI
id: MI:0891
in_subset: PSI-MI slim

Axiom
annotated source: neutron fiber diffraction
annotated property: definition
annotated target: Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam.
database_cross_reference: PMID:10771422
database_cross_reference: PMID:15272083
database_cross_reference: PMID:15546977
database_cross_reference: PMID:15914673
database_cross_reference: PMID:16041074
database_cross_reference: PMID:16707576

Axiom
annotated source: neutron fiber diffraction
annotated property: has_exact_synonym
annotated target: neutron fiber diff
has_synonym_type: Unique short label curated by PSI-MI

solid phase assay
type: Class
subclass of: affinity technology
definition: Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution.
has_obo_namespace: PSI-MI
id: MI:0892
in_subset: PSI-MI slim

Axiom
annotated source: solid phase assay
annotated property: definition
annotated target: Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution.
database_cross_reference: PMID:14755292

neutron diffraction
type: Class
subclass of: biophysical
definition: Analysis of diffraction pattern using neutron beam
has_obo_namespace: PSI-MI
id: MI:0893
in_subset: PSI-MI slim

Axiom
annotated source: neutron diffraction
annotated property: definition
annotated target: Analysis of diffraction pattern using neutron beam
database_cross_reference: PMID:10771422
database_cross_reference: PMID:15272083
database_cross_reference: PMID:15546977
database_cross_reference: PMID:15914673
database_cross_reference: PMID:16041074
database_cross_reference: PMID:16707576

electron diffraction
type: Class
subclass of: biophysical
definition: Analysis of diffraction pattern using electron beam.
has_obo_namespace: PSI-MI
id: MI:0894
in_subset: PSI-MI slim

Axiom
annotated source: electron diffraction
annotated property: definition
annotated target: Analysis of diffraction pattern using electron beam.
database_cross_reference: PMID:10949309
database_cross_reference: PMID:11034202
database_cross_reference: PMID:11171962
database_cross_reference: PMID:11532455
database_cross_reference: PMID:11700061
database_cross_reference: PMID:15141214
database_cross_reference: PMID:16325200

protein kinase A complementation
type: Class
subclass of: protein complementation assay
definition: This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA.
has_exact_synonym: pka complementation
has_obo_namespace: PSI-MI
id: MI:0895
in_subset: PSI-MI slim

Axiom
annotated source: protein kinase A complementation
annotated property: definition
annotated target: This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA.
database_cross_reference: PMID:17942691

Axiom
annotated source: protein kinase A complementation
annotated property: has_exact_synonym
annotated target: pka complementation
has_synonym_type: Unique short label curated by PSI-MI

renilla luciferase protein tag
type: Class
subclass of: luciferase tag
definition: Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm.
has_exact_synonym: renilla luciferase
has_obo_namespace: PSI-MI
id: MI:0896
in_subset: PSI-MI slim

Axiom
annotated source: renilla luciferase protein tag
annotated property: definition
annotated target: Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm.
database_cross_reference: PMID:14755292

Axiom
annotated source: renilla luciferase protein tag
annotated property: has_exact_synonym
annotated target: renilla luciferase
has_synonym_type: Unique short label curated by PSI-MI

protein modification ontology
type: Class
subclass of: feature database
definition: Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue.
database_cross_reference: id-validation-regexp:
has_exact_synonym: psi-mod
has_obo_namespace: PSI-MI
id: MI:0897
in_subset: PSI-MI slim

Axiom
annotated source: protein modification ontology
annotated property: definition
annotated target: Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue.
database_cross_reference: PMID:14755292

MOD:[0-9]{5}
type: Axiom
annotated source: protein modification ontology
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: protein modification ontology
annotated property: has_exact_synonym
annotated target: psi-mod
has_synonym_type: Unique short label curated by PSI-MI

putative self
type: Class
subclass of: experimental role
subclass of: biological role
definition: Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer).
has_obo_namespace: PSI-MI
id: MI:0898
in_subset: PSI-MI slim

Axiom
annotated source: putative self
annotated property: definition
annotated target: Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer).
database_cross_reference: PMID:14755292

p3 filamentous phage display
type: Class
subclass of: filamentous phage display
definition: pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display.
has_exact_synonym: low valency display
has_exact_synonym: p3 filamentous phage
has_obo_namespace: PSI-MI
id: MI:0899
in_subset: PSI-MI slim

Axiom
annotated source: p3 filamentous phage display
annotated property: definition
annotated target: pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display.
database_cross_reference: PMID:1696028

Axiom
annotated source: p3 filamentous phage display
annotated property: has_exact_synonym
annotated target: low valency display
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: p3 filamentous phage display
annotated property: has_exact_synonym
annotated target: p3 filamentous phage
has_synonym_type: Unique short label curated by PSI-MI

p8 filamentous phage display
type: Class
subclass of: filamentous phage display
definition: pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display.
has_exact_synonym: high valency display
has_exact_synonym: p8 filamentous phage
has_obo_namespace: PSI-MI
id: MI:0900
in_subset: PSI-MI slim

Axiom
annotated source: p8 filamentous phage display
annotated property: definition
annotated target: pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display.
database_cross_reference: PMID:1720463

Axiom
annotated source: p8 filamentous phage display
annotated property: has_exact_synonym
annotated target: high valency display
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: p8 filamentous phage display
annotated property: has_exact_synonym
annotated target: p8 filamentous phage
has_synonym_type: Unique short label curated by PSI-MI

isotope label footprinting
type: Class
subclass of: enzymatic footprinting
definition: Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange.
has_exact_synonym: isotope footprinting
has_obo_namespace: PSI-MI
id: MI:0901
in_subset: PSI-MI slim

Axiom
annotated source: isotope label footprinting
annotated property: definition
annotated target: Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange.
database_cross_reference: PMID:18184591

Axiom
annotated source: isotope label footprinting
annotated property: has_exact_synonym
annotated target: isotope footprinting
has_synonym_type: Unique short label curated by PSI-MI

rna cleavage
type: Class
subclass of: nucleic acid cleavage
definition: Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner.
has_obo_namespace: PSI-MI
id: MI:0902
in_subset: PSI-MI slim

Axiom
annotated source: rna cleavage
annotated property: definition
annotated target: Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner.
database_cross_reference: GO:0006396
database_cross_reference: PMID:14681407

mpidb
type: Class
subclass of: interaction database
subclass of: imex source
definition: The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact).
has_exact_synonym: MPDIB
has_obo_namespace: PSI-MI
id: MI:0903
in_subset: PSI-MI slim

Axiom
annotated source: mpidb
annotated property: definition
annotated target: The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact).
database_cross_reference: PMID:14755292

Axiom
annotated source: mpidb
annotated property: has_exact_synonym
annotated target: MPDIB
has_synonym_type: Alternate label curated by PSI-MI

polysaccharide
type: Class
subclass of: bioactive entity
definition: A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
has_obo_namespace: PSI-MI
id: MI:0904
in_subset: PSI-MI slim

Axiom
annotated source: polysaccharide
annotated property: definition
annotated target: A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
database_cross_reference: PMID:14755292

amplified luminescent proximity homogeneous assay
type: Class
subclass of: fluorescence technology
definition: AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3).
has_exact_synonym: AlphaScreen
has_exact_synonym: alpha-screen
has_obo_namespace: PSI-MI
id: MI:0905
in_subset: PSI-MI slim

Axiom
annotated source: amplified luminescent proximity homogeneous assay
annotated property: definition
annotated target: AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3).
database_cross_reference: PMID:17092917

Axiom
annotated source: amplified luminescent proximity homogeneous assay
annotated property: has_exact_synonym
annotated target: AlphaScreen
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: amplified luminescent proximity homogeneous assay
annotated property: has_exact_synonym
annotated target: alpha-screen
has_synonym_type: Unique short label curated by PSI-MI

au1 tag
type: Class
subclass of: tag
definition: The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available.
has_exact_synonym: DTYRYI epitope tag
has_obo_namespace: PSI-MI
id: MI:0906
in_subset: PSI-MI slim

Axiom
annotated source: au1 tag
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available.
database_cross_reference: PMID:18216269

Axiom
annotated source: au1 tag
annotated property: has_exact_synonym
annotated target: DTYRYI epitope tag
has_synonym_type: Alternate label curated by PSI-MI

conformational status
type: Class
subclass of: experimental preparation
subclass of: Class
  union of: denatured
  union of: native
definition: Statement about the native/denatured conformation of the protein.
has_exact_synonym: conformation
has_obo_namespace: PSI-MI
id: MI:0907
in_subset: PSI-MI slim

Axiom
annotated source: conformational status
annotated property: definition
annotated target: Statement about the native/denatured conformation of the protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: conformational status
annotated property: has_exact_synonym
annotated target: conformation
has_synonym_type: Unique short label curated by PSI-MI

denatured
type: Class
subclass of: conformational status
definition: Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein.
has_obo_namespace: PSI-MI
id: MI:0908
in_subset: PSI-MI slim

Axiom
annotated source: denatured
annotated property: definition
annotated target: Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein.
database_cross_reference: PMID:14755292

native
type: Class
subclass of: conformational status
definition: State of the protein without interference i.e. the natural form.
has_obo_namespace: PSI-MI
id: MI:0909
in_subset: PSI-MI slim

Axiom
annotated source: native
annotated property: definition
annotated target: State of the protein without interference i.e. the natural form.
database_cross_reference: PMID:14755292

nucleic acid cleavage
type: Class
subclass of: cleavage reaction
definition: Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments.
has_exact_synonym: ncl acid cleavage
has_obo_namespace: PSI-MI
id: MI:0910
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid cleavage
annotated property: definition
annotated target: Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid cleavage
annotated property: has_exact_synonym
annotated target: ncl acid cleavage
has_synonym_type: Unique short label curated by PSI-MI

cross linker
type: Class
subclass of: experimental feature
definition: A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed.
has_exact_synonym: crosslinker
has_obo_namespace: PSI-MI
id: MI:0911
in_subset: PSI-MI slim

Axiom
annotated source: cross linker
annotated property: definition
annotated target: A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed.
database_cross_reference: PMID:14755292

Axiom
annotated source: cross linker
annotated property: has_exact_synonym
annotated target: crosslinker
has_synonym_type: Alternate label curated by PSI-MI

spdp cross linker
type: Class
subclass of: cross linker
definition: N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond.
has_exact_synonym: N -Succinimidyl 3-(2-pyridyldithio)-propionate
has_obo_namespace: PSI-MI
id: MI:0912
in_subset: PSI-MI slim

Axiom
annotated source: spdp cross linker
annotated property: definition
annotated target: N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond.
database_cross_reference: PMID:17360572

Axiom
annotated source: spdp cross linker
annotated property: has_exact_synonym
annotated target: N -Succinimidyl 3-(2-pyridyldithio)-propionate
has_synonym_type: Alternate label curated by PSI-MI

lc-spdp cross linker
type: Class
subclass of: spdp cross linker
definition: Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm.
has_exact_synonym: Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate
has_obo_namespace: PSI-MI
id: MI:0913
in_subset: PSI-MI slim

Axiom
annotated source: lc-spdp cross linker
annotated property: definition
annotated target: Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm.
database_cross_reference: PMID:17360572

Axiom
annotated source: lc-spdp cross linker
annotated property: has_exact_synonym
annotated target: Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate
has_synonym_type: Alternate label curated by PSI-MI

association
type: Class
subclass of: molecular association
definition: Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
has_obo_namespace: PSI-MI
id: MI:0914
in_subset: PSI-MI slim

Axiom
annotated source: association
annotated property: definition
annotated target: Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
database_cross_reference: PMID:14755292

physical association
type: Class
subclass of: association
definition: Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other.
has_obo_namespace: PSI-MI
id: MI:0915
in_subset: PSI-MI slim

Axiom
annotated source: physical association
annotated property: definition
annotated target: Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other.
database_cross_reference: PMID:14755292

lexa vp16 complementation
type: Class
subclass of: two hybrid
definition: Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream.
has_exact_synonym: LexA VP16 transcription complementation
has_exact_synonym: lexa vp16 complement
has_obo_namespace: PSI-MI
id: MI:0916
in_subset: PSI-MI slim

Axiom
annotated source: lexa vp16 complementation
annotated property: definition
annotated target: Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream.
database_cross_reference: PMID:9371806

Axiom
annotated source: lexa vp16 complementation
annotated property: has_exact_synonym
annotated target: LexA VP16 transcription complementation
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: lexa vp16 complementation
annotated property: has_exact_synonym
annotated target: lexa vp16 complement
has_synonym_type: Unique short label curated by PSI-MI

matrixdb
type: Class
subclass of: interaction database
subclass of: imex source
definition: Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions. https://matrixdb.univ-lyon1.fr
database_cross_reference: search-url:
has_exact_synonym: MatrixDB
has_obo_namespace: PSI-MI
id: MI:0917
in_subset: PSI-MI slim

Axiom
annotated source: matrixdb
annotated property: definition
annotated target: Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions. https://matrixdb.univ-lyon1.fr
database_cross_reference: PMID:19147664

Axiom
annotated source: matrixdb
annotated property: database_cross_reference
annotated target: search-url:
label: https://matrixdb.univ-lyon1.fr/biomolecule/${ac}

Axiom
annotated source: matrixdb
annotated property: has_exact_synonym
annotated target: MatrixDB
has_synonym_type: Alternate label curated by PSI-MI

donor
type: Class
subclass of: biological role
definition: Molecule which emits active chemical groups, electrons or ions that are transfered to an acceptor molecule.
has_obo_namespace: PSI-MI
id: MI:0918
in_subset: PSI-MI slim

Axiom
annotated source: donor
annotated property: definition
annotated target: Molecule which emits active chemical groups, electrons or ions that are transfered to an acceptor molecule.
database_cross_reference: PMID:14755292

acceptor
type: Class
subclass of: biological role
definition: Molecule able to receive active chemical groups, electrons or ions from a donor molecule.
has_obo_namespace: PSI-MI
id: MI:0919
in_subset: PSI-MI slim

Axiom
annotated source: acceptor
annotated property: definition
annotated target: Molecule able to receive active chemical groups, electrons or ions from a donor molecule.
database_cross_reference: PMID:14755292

ribonuclease assay
type: Class
subclass of: nuclease assay
definition: Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
has_obo_namespace: PSI-MI
id: MI:0920
in_subset: PSI-MI slim

Axiom
annotated source: ribonuclease assay
annotated property: definition
annotated target: Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
database_cross_reference: PMID:14755292

surface plasmon resonance array
type: Class
subclass of: array technology
subclass of: surface plasmon resonance
definition: This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot.
has_exact_synonym: Biacore Flexchip(r)
has_exact_synonym: SPRImager
has_exact_synonym: SPRi-Plex
has_exact_synonym: spr array
has_obo_namespace: PSI-MI
id: MI:0921
in_subset: PSI-MI slim

Axiom
annotated source: surface plasmon resonance array
annotated property: definition
annotated target: This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot.
database_cross_reference: PMID:16510109
database_cross_reference: PMID:16837183
database_cross_reference: PMID:17889820

Axiom
annotated source: surface plasmon resonance array
annotated property: has_exact_synonym
annotated target: Biacore Flexchip(r)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: surface plasmon resonance array
annotated property: has_exact_synonym
annotated target: SPRImager
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: surface plasmon resonance array
annotated property: has_exact_synonym
annotated target: SPRi-Plex
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: surface plasmon resonance array
annotated property: has_exact_synonym
annotated target: spr array
has_synonym_type: Unique short label curated by PSI-MI

imex evidence
type: Class
subclass of: cross-reference type
definition: Experimental evidence supporting an interaction curated and released under the IMEx agreement.
has_obo_namespace: PSI-MI
id: MI:0922
in_subset: PSI-MI slim

Axiom
annotated source: imex evidence
annotated property: definition
annotated target: Experimental evidence supporting an interaction curated and released under the IMEx agreement.
database_cross_reference: PMID:14755292

irefindex
type: Class
subclass of: interaction database
subclass of: source database
definition: iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. http://irefindex.uio.no/
has_exact_synonym: iRefIndex
has_obo_namespace: PSI-MI
id: MI:0923
in_subset: PSI-MI slim

Axiom
annotated source: irefindex
annotated property: definition
annotated target: iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. http://irefindex.uio.no/
database_cross_reference: PMID:18823568

Axiom
annotated source: irefindex
annotated property: has_exact_synonym
annotated target: iRefIndex
has_synonym_type: Alternate label curated by PSI-MI

camjedb
type: Class
subclass of: genome databases
definition: Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni. http://www.sanger.ac.uk/Projects/C_jejuni/
has_obo_namespace: PSI-MI
id: MI:0924
in_subset: PSI-MI slim

Axiom
annotated source: camjedb
annotated property: definition
annotated target: Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni. http://www.sanger.ac.uk/Projects/C_jejuni/
database_cross_reference: PMID:106882042

observed-ptm
type: Class
subclass of: feature attribute name
definition: Post translational modification observed on a protein in the context of an interaction.
has_exact_synonym: observed ptm
has_exact_synonym: observed-ptm
has_obo_namespace: PSI-MI
id: MI:0925
in_subset: PSI-MI slim

Axiom
annotated source: observed-ptm
annotated property: definition
annotated target: Post translational modification observed on a protein in the context of an interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: observed-ptm
annotated property: has_exact_synonym
annotated target: observed ptm
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: observed-ptm
annotated property: has_exact_synonym
annotated target: observed-ptm
has_synonym_type: Unique short label curated by PSI-MI

fiash label
type: Class
subclass of: fluorescent dye label
definition: This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties.
has_exact_synonym: 4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein
has_exact_synonym: FIAsH label
has_obo_namespace: PSI-MI
id: MI:0926
in_subset: PSI-MI slim

Axiom
annotated source: fiash label
annotated property: definition
annotated target: This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties.
database_cross_reference: PMID:9657724

Axiom
annotated source: fiash label
annotated property: has_exact_synonym
annotated target: 4',5'-bis(1,3,2-dithioarsolan-2-yl)fluorescein
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: fiash label
annotated property: has_exact_synonym
annotated target: FIAsH label
has_synonym_type: Alternate label curated by PSI-MI

iaedans label
type: Class
subclass of: fluorescent dye label
definition: IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups.
has_exact_synonym: (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid)
has_exact_synonym: 1,5-IAEDANS
has_exact_synonym: IAEDANS
has_obo_namespace: PSI-MI
id: MI:0927
in_subset: PSI-MI slim

Axiom
annotated source: iaedans label
annotated property: definition
annotated target: IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups.
database_cross_reference: PMID:11052891

Axiom
annotated source: iaedans label
annotated property: has_exact_synonym
annotated target: (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: iaedans label
annotated property: has_exact_synonym
annotated target: 1,5-IAEDANS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: iaedans label
annotated property: has_exact_synonym
annotated target: IAEDANS
has_synonym_type: Alternate label curated by PSI-MI

filter trap assay
type: Class
subclass of: biophysical
subclass of: chromatography technology
definition: Biomolecules are mixed in a buffer and the resulting mixture is passed through a filter. Large aggregates are retained on the filter and the pariticipants may then be identified.
has_exact_synonym: Filter retention assay
has_exact_synonym: filter binding
has_obo_namespace: PSI-MI
has_related_synonym: filter retardation assay
has_related_synonym: membrane filtration
id: MI:0928
in_subset: PSI-MI slim

Axiom
annotated source: filter trap assay
annotated property: definition
annotated target: Biomolecules are mixed in a buffer and the resulting mixture is passed through a filter. Large aggregates are retained on the filter and the pariticipants may then be identified.
database_cross_reference: PMID:10859365

Axiom
annotated source: filter trap assay
annotated property: has_exact_synonym
annotated target: Filter retention assay
has_synonym_type: Alternate label curated by PSI-MI

northern blot
type: Class
subclass of: nucleotide sequence identification
definition: A standard procedure to identify RNA fragments containing specific sequences. In this procedure RNA fragments are separated by electrophoresis, the fragments are transferred to a membrane and the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
has_exact_synonym: northen
has_obo_namespace: PSI-MI
id: MI:0929
in_subset: PSI-MI slim

Axiom
annotated source: northern blot
annotated property: definition
annotated target: A standard procedure to identify RNA fragments containing specific sequences. In this procedure RNA fragments are separated by electrophoresis, the fragments are transferred to a membrane and the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
database_cross_reference: PMID:414220

Axiom
annotated source: northern blot
annotated property: has_exact_synonym
annotated target: northen
has_synonym_type: Alternate label curated by PSI-MI

epistatis
type: Class
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
has_exact_synonym: epistatic genetic interaction
has_obo_namespace: PSI-MI
id: MI:0930
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: epistatis
annotated property: definition
annotated target: An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
database_cross_reference: PMID:11988766

genetic interaction defined by inequality
type: Class
definition: Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship.
has_exact_synonym: genetic inequality
has_obo_namespace: PSI-MI
id: MI:0931
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: genetic interaction defined by inequality
annotated property: definition
annotated target: Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship.
database_cross_reference: PMID:14755292

Axiom
annotated source: genetic interaction defined by inequality
annotated property: has_exact_synonym
annotated target: genetic inequality
has_synonym_type: Unique short label curated by PSI-MI

neutral multigenic phenotype result
type: Class
subclass of: MI 2366
definition: The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype.
has_exact_synonym: expected multigenic phenotypic result
has_exact_synonym: neutral genetic interaction
has_exact_synonym: noninteractive
has_exact_synonym: noninteractive genetic interaction (sensu inequality)
has_exact_synonym: noninteractive genetic interaction defined by inequality
has_obo_namespace: PSI-MI
id: MI:0932
in_subset: PSI-MI slim

Axiom
annotated source: neutral multigenic phenotype result
annotated property: definition
annotated target: The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype.
database_cross_reference: PMID:15833125

Axiom
annotated source: neutral multigenic phenotype result
annotated property: has_exact_synonym
annotated target: noninteractive genetic interaction (sensu inequality)
has_synonym_type: Alternate label curated by PSI-MI

diverging genetic interaction
type: Class
subclass of: genetic interaction (sensu unexpected)
definition: An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E <= wt OR wt <= E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
has_obo_namespace: PSI-MI
id: MI:0933

Axiom
annotated source: diverging genetic interaction
annotated property: definition
annotated target: An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E <= wt OR wt <= E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:14755292

obsolete neutral genetic interaction
type: Class
definition: OBSOLETE: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b [ab != E] OR With respect to two qualitatively different phenotypes, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes.
has_exact_synonym: neutral gent int
has_obo_namespace: PSI-MI
id: MI:0934
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: obsolete neutral genetic interaction
annotated property: definition
annotated target: OBSOLETE: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b [ab != E] OR With respect to two qualitatively different phenotypes, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes.
database_cross_reference: PMID:14755292

Axiom
annotated source: obsolete neutral genetic interaction
annotated property: has_exact_synonym
annotated target: neutral gent int
has_synonym_type: Unique short label curated by PSI-MI

converging genetic interaction
type: Class
subclass of: genetic interaction (sensu unexpected)
definition: An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E < ab <= wt OR wt <= ab < E where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
has_obo_namespace: PSI-MI
id: MI:0935

Axiom
annotated source: converging genetic interaction
annotated property: definition
annotated target: An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E < ab <= wt OR wt <= ab < E where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:14755292

emdb
type: Class
subclass of: pdbe
definition: The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files. https://www.ebi.ac.uk/emdb
database_cross_reference: search-url:
has_exact_synonym: Electron Microscopy Data Bank
has_exact_synonym: eMDB
has_obo_namespace: PSI-MI
id: MI:0936
in_subset: PSI-MI slim

Axiom
annotated source: emdb
annotated property: definition
annotated target: The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files. https://www.ebi.ac.uk/emdb
database_cross_reference: PMID:14643225

Axiom
annotated source: emdb
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.ebi.ac.uk/emdb/${ac}

Axiom
annotated source: emdb
annotated property: has_exact_synonym
annotated target: Electron Microscopy Data Bank
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: emdb
annotated property: has_exact_synonym
annotated target: eMDB
has_synonym_type: Unique short label curated by PSI-MI

glu tag
type: Class
subclass of: tag
definition: This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide.
has_exact_synonym: glu tag
has_obo_namespace: PSI-MI
id: MI:0937
in_subset: PSI-MI slim

Axiom
annotated source: glu tag
annotated property: definition
annotated target: This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide.
database_cross_reference: PMID:8077219

Axiom
annotated source: glu tag
annotated property: has_exact_synonym
annotated target: glu tag
has_synonym_type: Unique short label curated by PSI-MI

rheology measurement
type: Class
subclass of: biophysical
definition: Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules.
has_exact_synonym: rheology
has_obo_namespace: PSI-MI
id: MI:0938
in_subset: PSI-MI slim

Axiom
annotated source: rheology measurement
annotated property: definition
annotated target: Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules.
database_cross_reference: PMID:18445655

Axiom
annotated source: rheology measurement
annotated property: has_exact_synonym
annotated target: rheology
has_synonym_type: Unique short label curated by PSI-MI

fluorescein label
type: Class
subclass of: fluorescent dye label
definition: Fluorescence label used to monitor the presence of a protein.
has_exact_synonym: fluorescein
has_obo_namespace: PSI-MI
id: MI:0939
in_subset: PSI-MI slim

Axiom
annotated source: fluorescein label
annotated property: definition
annotated target: Fluorescence label used to monitor the presence of a protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: fluorescein label
annotated property: has_exact_synonym
annotated target: fluorescein
has_synonym_type: Unique short label curated by PSI-MI

fluorescein-5-maleimide label
type: Class
subclass of: fluorescein label
definition: Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions.
has_exact_synonym: fluor-5-maleimide
has_obo_namespace: PSI-MI
id: MI:0940
in_subset: PSI-MI slim

Axiom
annotated source: fluorescein-5-maleimide label
annotated property: definition
annotated target: Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions.
database_cross_reference: PMID:18066077

Axiom
annotated source: fluorescein-5-maleimide label
annotated property: has_exact_synonym
annotated target: fluor-5-maleimide
has_synonym_type: Unique short label curated by PSI-MI

competitor
type: Class
subclass of: biological role
definition: Binds to an interacting molecule in competition with other interaction candidates, for example at a shared binding site.
has_exact_synonym: competitor
has_obo_namespace: PSI-MI
id: MI:0941
in_subset: PSI-MI slim

Axiom
annotated source: competitor
annotated property: definition
annotated target: Binds to an interacting molecule in competition with other interaction candidates, for example at a shared binding site.
database_cross_reference: PMID:14755292

Axiom
annotated source: competitor
annotated property: has_exact_synonym
annotated target: competitor
has_synonym_type: Unique short label curated by PSI-MI

uniprot taxonomy
type: Class
subclass of: participant database
definition: Based on NCBO Taxonomy but adapted for UniProt http://www.uniprot.org/taxonomy/
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: uniprot taxon
has_obo_namespace: PSI-MI
id: MI:0942
in_subset: PSI-MI slim

Axiom
annotated source: uniprot taxonomy
annotated property: definition
annotated target: Based on NCBO Taxonomy but adapted for UniProt http://www.uniprot.org/taxonomy/
database_cross_reference: PMID:18836194

[0-9]+
type: Axiom
annotated source: uniprot taxonomy
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: uniprot taxonomy
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.uniprot.org/taxonomy/${ac}

Axiom
annotated source: uniprot taxonomy
annotated property: has_exact_synonym
annotated target: uniprot taxon
has_synonym_type: Alternate label curated by PSI-MI

detection by mass spectrometry
type: Class
subclass of: biophysical
definition: 'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer.
has_exact_synonym: ms interact detect
has_obo_namespace: PSI-MI
id: MI:0943
in_subset: PSI-MI slim

Axiom
annotated source: detection by mass spectrometry
annotated property: definition
annotated target: 'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer.
database_cross_reference: PMID:14755292

Axiom
annotated source: detection by mass spectrometry
annotated property: has_exact_synonym
annotated target: ms interact detect
has_synonym_type: Unique short label curated by PSI-MI

mass spectrometry study of hydrogen/deuterium exchange
type: Class
subclass of: detection by mass spectrometry
definition: Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange.
has_exact_synonym: h1-h2 ms
has_obo_namespace: PSI-MI
id: MI:0944
in_subset: PSI-MI slim

Axiom
annotated source: mass spectrometry study of hydrogen/deuterium exchange
annotated property: definition
annotated target: Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange.
database_cross_reference: PMID:18948593

Axiom
annotated source: mass spectrometry study of hydrogen/deuterium exchange
annotated property: has_exact_synonym
annotated target: h1-h2 ms
has_synonym_type: Unique short label curated by PSI-MI

oxidoreductase activity electron transfer reaction
type: Class
subclass of: enzymatic reaction
definition: An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
has_exact_synonym: redox reaction
has_obo_namespace: PSI-MI
id: MI:0945
in_subset: PSI-MI slim

Axiom
annotated source: oxidoreductase activity electron transfer reaction
annotated property: definition
annotated target: An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
database_cross_reference: GO:GO:0016491
database_cross_reference: PMID:14755292

Axiom
annotated source: oxidoreductase activity electron transfer reaction
annotated property: has_exact_synonym
annotated target: redox reaction
has_synonym_type: Unique short label curated by PSI-MI

miniaturized immunoprecipitation
type: Class
subclass of: coimmunoprecipitation
subclass of: protein in situ array
definition: Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) an antibody that recognizes the bait protein or a specific tag is deposited on a circular area inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs.
has_exact_synonym: protein interaction network generator
has_exact_synonym: MITOMI
has_exact_synonym: mIP
has_exact_synonym: ping
has_obo_namespace: PSI-MI
id: MI:0946
in_subset: PSI-MI slim

Axiom
annotated source: miniaturized immunoprecipitation
annotated property: definition
annotated target: Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) an antibody that recognizes the bait protein or a specific tag is deposited on a circular area inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs.
database_cross_reference: PMID:19098921

Axiom
annotated source: miniaturized immunoprecipitation
annotated property: has_exact_synonym
annotated target: MITOMI
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: miniaturized immunoprecipitation
annotated property: has_exact_synonym
annotated target: mIP
has_synonym_type: Unique short label curated by PSI-MI

bead aggregation assay
type: Class
subclass of: solid phase assay
definition: Binding of proteins bound to beads leads to a measurable aggregation of the beads.
has_exact_synonym: bead aggregation
has_obo_namespace: PSI-MI
id: MI:0947
in_subset: PSI-MI slim

Axiom
annotated source: bead aggregation assay
annotated property: definition
annotated target: Binding of proteins bound to beads leads to a measurable aggregation of the beads.
database_cross_reference: PMID:19114658

Axiom
annotated source: bead aggregation assay
annotated property: has_exact_synonym
annotated target: bead aggregation
has_synonym_type: Unique short label curated by PSI-MI

kinetic conditions
type: Class
subclass of: interaction attribute name
definition: A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed.
has_exact_synonym: kinetic_conditions
has_obo_namespace: PSI-MI
id: MI:0948
in_subset: PSI-MI slim

Axiom
annotated source: kinetic conditions
annotated property: definition
annotated target: A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed.
database_cross_reference: PMID:14755292

Axiom
annotated source: kinetic conditions
annotated property: has_exact_synonym
annotated target: kinetic_conditions
has_synonym_type: Unique short label curated by PSI-MI

gdp/gtp exchange assay
type: Class
subclass of: nucleotide exchange assay
definition: Experiments monitoring interactions of GTP-GDP exchange factors with their cognate GTPases.
has_exact_synonym: gdp_gtp exchange
has_exact_synonym: gtp/gdp exchange
has_exact_synonym: guanine nucleotide exchange assay
has_obo_namespace: PSI-MI
id: MI:0949
in_subset: PSI-MI slim

Axiom
annotated source: gdp/gtp exchange assay
annotated property: definition
annotated target: Experiments monitoring interactions of GTP-GDP exchange factors with their cognate GTPases.
database_cross_reference: PMID:17925023

Axiom
annotated source: gdp/gtp exchange assay
annotated property: has_exact_synonym
annotated target: gdp_gtp exchange
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: gdp/gtp exchange assay
annotated property: has_exact_synonym
annotated target: gtp/gdp exchange
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gdp/gtp exchange assay
annotated property: has_exact_synonym
annotated target: guanine nucleotide exchange assay
has_synonym_type: Alternate label curated by PSI-MI

trapping mutant
type: Class
subclass of: experimental feature
definition: Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate.
has_exact_synonym: trap-mutant
has_obo_namespace: PSI-MI
id: MI:0950
in_subset: PSI-MI slim

Axiom
annotated source: trapping mutant
annotated property: definition
annotated target: Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate.
database_cross_reference: PMID:9050838

Axiom
annotated source: trapping mutant
annotated property: has_exact_synonym
annotated target: trap-mutant
has_synonym_type: Unique short label curated by PSI-MI

chain parent sequence reference
type: Class
subclass of: cross-reference type
definition: Reference to the master sequence from which this chain has been derived.
has_exact_synonym: chain-parent
has_obo_namespace: PSI-MI
id: MI:0951
in_subset: PSI-MI slim

Axiom
annotated source: chain parent sequence reference
annotated property: definition
annotated target: Reference to the master sequence from which this chain has been derived.
database_cross_reference: PMID:17925023

Axiom
annotated source: chain parent sequence reference
annotated property: has_exact_synonym
annotated target: chain-parent
has_synonym_type: Unique short label curated by PSI-MI

imex secondary
type: Class
subclass of: cross-reference type
definition: Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier.
has_obo_namespace: PSI-MI
id: MI:0952
in_subset: PSI-MI slim

Axiom
annotated source: imex secondary
annotated property: definition
annotated target: Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier.
database_cross_reference: PMID:17925023

polymerization
type: Class
subclass of: biochemical
definition: Interaction inferred by monitoring polymerization/depolymerization of an interactor
has_exact_synonym: polymerization
has_obo_namespace: PSI-MI
id: MI:0953
in_subset: PSI-MI slim

Axiom
annotated source: polymerization
annotated property: definition
annotated target: Interaction inferred by monitoring polymerization/depolymerization of an interactor
database_cross_reference: PMID:19081060

curation quality
type: Class
subclass of: molecular interaction
definition: An assessment of the depth and extent to which a paper has been curated
has_obo_namespace: PSI-MI
id: MI:0954
in_subset: PSI-MI slim

Axiom
annotated source: curation quality
annotated property: definition
annotated target: An assessment of the depth and extent to which a paper has been curated
database_cross_reference: PMID:17893861

curation depth
type: Class
subclass of: curation quality
definition: Assessment of the depth to which a paper has been curated
has_obo_namespace: PSI-MI
id: MI:0955

Axiom
annotated source: curation depth
annotated property: definition
annotated target: Assessment of the depth to which a paper has been curated
database_cross_reference: PMID:17893861

curation coverage
type: Class
subclass of: curation quality
definition: Assessment to the extent of interactions captured in this paper
has_obo_namespace: PSI-MI
id: MI:0956
in_subset: PSI-MI slim

Axiom
annotated source: curation coverage
annotated property: definition
annotated target: Assessment to the extent of interactions captured in this paper
database_cross_reference: PMID:17893861

full coverage
type: Class
subclass of: curation coverage
definition: All interactions which can be ascribed to an unambiguous identified in this paper have been captured.
has_obo_namespace: PSI-MI
id: MI:0957
in_subset: PSI-MI slim

Axiom
annotated source: full coverage
annotated property: definition
annotated target: All interactions which can be ascribed to an unambiguous identified in this paper have been captured.
database_cross_reference: PMID:17893861

partial coverage
type: Class
subclass of: curation coverage
definition: Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured.
has_obo_namespace: PSI-MI
id: MI:0958
in_subset: PSI-MI slim

Axiom
annotated source: partial coverage
annotated property: definition
annotated target: Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured.
database_cross_reference: PMID:17893861

imex curation
type: Class
subclass of: curation depth
definition: Paper has been curated to full IMEx specifications
has_obo_namespace: PSI-MI
id: MI:0959
in_subset: PSI-MI slim

Axiom
annotated source: imex curation
annotated property: definition
annotated target: Paper has been curated to full IMEx specifications
database_cross_reference: PMID:17893861

mimix curation
type: Class
subclass of: curation depth
definition: Paper has been curated to meet MIMIx specifications
has_obo_namespace: PSI-MI
id: MI:0960
in_subset: PSI-MI slim

Axiom
annotated source: mimix curation
annotated property: definition
annotated target: Paper has been curated to meet MIMIx specifications
database_cross_reference: PMID:17687370

rapid curation
type: Class
subclass of: curation depth
definition: Minimal interaction data has been extracted from the paper
has_obo_namespace: PSI-MI
id: MI:0961
in_subset: PSI-MI slim

Axiom
annotated source: rapid curation
annotated property: definition
annotated target: Minimal interaction data has been extracted from the paper
database_cross_reference: PMID:17687370

strep ii tag
type: Class
subclass of: tag
definition: The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK).
has_exact_synonym: Strep (II)
has_exact_synonym: Strep II
has_obo_namespace: PSI-MI
id: MI:0962
in_subset: PSI-MI slim

Axiom
annotated source: strep ii tag
annotated property: definition
annotated target: The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK).
database_cross_reference: PMID:17571060

Axiom
annotated source: strep ii tag
annotated property: has_exact_synonym
annotated target: Strep (II)
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: strep ii tag
annotated property: has_exact_synonym
annotated target: Strep II
has_synonym_type: Alternate label curated by PSI-MI

interactome parallel affinity capture
type: Class
subclass of: pull down
definition: A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press).
created by: orchard
creation date: 2009-05-14T10:56:21Z
has_exact_synonym: ipac
has_obo_namespace: PSI-MI
id: MI:0963

Axiom
annotated source: interactome parallel affinity capture
annotated property: definition
annotated target: A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press).
database_cross_reference: PMID:14681455

Axiom
annotated source: interactome parallel affinity capture
annotated property: has_exact_synonym
annotated target: ipac
has_synonym_type: Unique short label curated by PSI-MI

infrared spectroscopy
type: Class
subclass of: biophysical
definition: Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum.
created by: orchard
creation date: 2009-10-28T10:55:01Z
has_exact_synonym: ir spectrometry
has_obo_namespace: PSI-MI
id: MI:0964
in_subset: PSI-MI slim

Axiom
annotated source: infrared spectroscopy
annotated property: definition
annotated target: Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum.
database_cross_reference: PMID:15212548

Axiom
annotated source: infrared spectroscopy
annotated property: has_exact_synonym
annotated target: ir spectrometry
has_synonym_type: Unique short label curated by PSI-MI

2d-infrared spectrometry
type: Class
subclass of: infrared spectroscopy
definition: Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles.
created by: orchard
creation date: 2009-10-28T11:05:01Z
has_exact_synonym: 2d-ir
has_obo_namespace: PSI-MI
id: MI:0965
in_subset: PSI-MI slim

Axiom
annotated source: 2d-infrared spectrometry
annotated property: definition
annotated target: Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles.
database_cross_reference: PMID:17502604

Axiom
annotated source: 2d-infrared spectrometry
annotated property: has_exact_synonym
annotated target: 2d-ir
has_synonym_type: Unique short label curated by PSI-MI

ultraviolet-visible spectroscopy
type: Class
subclass of: biophysical
definition: Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges.
created by: orchard
creation date: 2009-10-28T11:12:27Z
has_exact_synonym: UV/Vis
has_exact_synonym: ultraviolet-visible spectrophotometry
has_exact_synonym: uv-vis
has_obo_namespace: PSI-MI
id: MI:0966

Axiom
annotated source: ultraviolet-visible spectroscopy
annotated property: definition
annotated target: Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges.
database_cross_reference: PMID:18799738

Axiom
annotated source: ultraviolet-visible spectroscopy
annotated property: has_exact_synonym
annotated target: uv-vis
has_synonym_type: Unique short label curated by PSI-MI

chembl compound
type: Class
subclass of: chembl
subclass of: bioactive entity reference
definition: ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
created by: orchard
creation date: 2009-10-28T11:20:55Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: chembl
has_obo_namespace: PSI-MI
id: MI:0967
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: chembl compound
annotated property: definition
annotated target: ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
database_cross_reference: PMID:19194660
database_cross_reference: PMID:24214965

[0-9]+
type: Axiom
annotated source: chembl compound
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: chembl compound
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/chembldb/index.php/compound/inspect/${ac}

biosensor
type: Class
subclass of: biophysical
definition: A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component
created by: orchard
creation date: 2009-10-28T11:44:32Z
has_obo_namespace: PSI-MI
id: MI:0968
in_subset: PSI-MI slim

Axiom
annotated source: biosensor
annotated property: definition
annotated target: A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component
database_cross_reference: PMID:10872504

bio-layer interferometry
type: Class
subclass of: biosensor
definition: BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer
created by: orchard
creation date: 2009-10-28T11:48:40Z
has_exact_synonym: bli
has_obo_namespace: PSI-MI
id: MI:0969
in_subset: PSI-MI slim

Axiom
annotated source: bio-layer interferometry
annotated property: definition
annotated target: BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer
database_cross_reference: PMID:19561609

Axiom
annotated source: bio-layer interferometry
annotated property: has_exact_synonym
annotated target: bli
has_synonym_type: Alternate label curated by PSI-MI

inchi key
type: Class
subclass of: checksum
subclass of: structure representation attribute name
definition: InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character
created by: orchard
creation date: 2009-10-28T01:13:25Z
has_exact_synonym: inchi key
has_obo_namespace: PSI-MI
id: MI:0970
in_subset: Drugable

Axiom
annotated source: inchi key
annotated property: definition
annotated target: InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character
database_cross_reference: PMID:15889163

Axiom
annotated source: inchi key
annotated property: has_exact_synonym
annotated target: inchi key
has_synonym_type: Unique short label curated by PSI-MI

phosphopantetheinylation
type: Class
subclass of: enzymatic reaction
definition: The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
created by: orchard
creation date: 2009-10-28T01:20:40Z
has_exact_synonym: p_patetheinylation
has_obo_namespace: PSI-MI
id: MI:0971
in_subset: PSI-MI slim

Axiom
annotated source: phosphopantetheinylation
annotated property: definition
annotated target: The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
database_cross_reference: PMID:19679086

Axiom
annotated source: phosphopantetheinylation
annotated property: has_exact_synonym
annotated target: p_patetheinylation
has_synonym_type: Unique short label curated by PSI-MI

phosphopantetheinylase assay
type: Class
subclass of: enzymatic study
definition: Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
created by: orchard
creation date: 2009-10-28T01:23:19Z
has_exact_synonym: p_pantethinyl assay
has_obo_namespace: PSI-MI
has_related_synonym: phosphopantetheinylation
id: MI:0972

Axiom
annotated source: phosphopantetheinylase assay
annotated property: definition
annotated target: Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
database_cross_reference: PMID:19346479

Axiom
annotated source: phosphopantetheinylase assay
annotated property: has_exact_synonym
annotated target: p_pantethinyl assay
has_synonym_type: Unique short label curated by PSI-MI

imex source
type: Class
subclass of: source database
definition: Databases that contain curated experimental interaction data and exchanging it with other IMEx databases.
created by: orchard
creation date: 2009-12-18T10:24:37Z
has_obo_namespace: PSI-MI
id: MI:0973
in_subset: PSI-MI slim

Axiom
annotated source: imex source
annotated property: definition
annotated target: Databases that contain curated experimental interaction data and exchanging it with other IMEx databases.
database_cross_reference: PMID:17893861

innatedb
type: Class
subclass of: interaction database
subclass of: imex source
definition: Human and mouse experimentally verified interactions and pathways involved in innate immunity.
created by: orchard
creation date: 2010-04-09T03:11:54Z
has_exact_synonym: InnateDB
has_obo_namespace: PSI-MI
id: MI:0974
in_subset: PSI-MI slim

Axiom
annotated source: innatedb
annotated property: definition
annotated target: Human and mouse experimentally verified interactions and pathways involved in innate immunity.
database_cross_reference: PMID:18766178

Axiom
annotated source: innatedb
annotated property: has_exact_synonym
annotated target: InnateDB
has_synonym_type: Alternate label curated by PSI-MI

fc-igg tag
type: Class
subclass of: fusion protein
definition: A fusion protein tag consisting of a portion of the constant region of IgG.
created by: orchard
creation date: 2010-04-21T02:18:04Z
has_obo_namespace: PSI-MI
id: MI:0975
in_subset: PSI-MI slim

Axiom
annotated source: fc-igg tag
annotated property: definition
annotated target: A fusion protein tag consisting of a portion of the constant region of IgG.
database_cross_reference: PMID:11757069

total internal reflection fluorescence spectroscopy
type: Class
subclass of: fluorescence technology
definition: Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface.
created by: orchard
creation date: 2010-04-21T02:30:46Z
has_exact_synonym: tirfs
has_obo_namespace: PSI-MI
id: MI:0976
in_subset: PSI-MI slim

Axiom
annotated source: total internal reflection fluorescence spectroscopy
annotated property: definition
annotated target: Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface.
database_cross_reference: PMID:9013655

Axiom
annotated source: total internal reflection fluorescence spectroscopy
annotated property: has_exact_synonym
annotated target: tirfs
has_synonym_type: Unique short label curated by PSI-MI

no-imex-export
type: Class
subclass of: experiment attribute name
definition: Prevents export of experiment and associated interactions to IMEx
created by: orchard
creation date: 2010-04-21T02:49:48Z
has_obo_namespace: PSI-MI
id: MI:0977
in_subset: PSI-MI slim

Axiom
annotated source: no-imex-export
annotated property: definition
annotated target: Prevents export of experiment and associated interactions to IMEx
database_cross_reference: PMID:17893861

author-name
type: Class
subclass of: participant attribute name
definition: Author given name for a participant, not commonly found in source databases.
created by: orchard
creation date: 2010-04-21T02:55:39Z
has_obo_namespace: PSI-MI
id: MI:0978
in_subset: PSI-MI slim

Axiom
annotated source: author-name
annotated property: definition
annotated target: Author given name for a participant, not commonly found in source databases.
database_cross_reference: PMID:14755292

oxidoreductase assay
type: Class
subclass of: enzymatic study
definition: Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor.
created by: orchard
creation date: 2010-04-21T03:04:54Z
has_exact_synonym: oxidoreduct assay
has_obo_namespace: PSI-MI
id: MI:0979
in_subset: PSI-MI slim

Axiom
annotated source: oxidoreductase assay
annotated property: definition
annotated target: Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor.
database_cross_reference: PMID:14755292

Axiom
annotated source: oxidoreductase assay
annotated property: has_exact_synonym
annotated target: oxidoreduct assay
has_synonym_type: Unique short label curated by PSI-MI

tag visualisation by enzyme assay
type: Class
subclass of: tag visualisation
definition: The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction.
created by: orchard
creation date: 2010-04-21T03:18:09Z
has_exact_synonym: tag enzyme assay
has_obo_namespace: PSI-MI
id: MI:0980
in_subset: PSI-MI slim

Axiom
annotated source: tag visualisation by enzyme assay
annotated property: definition
annotated target: The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: tag visualisation by enzyme assay
annotated property: has_exact_synonym
annotated target: tag enzyme assay
has_synonym_type: Unique short label curated by PSI-MI

tag visualisation by peroxidase activity
type: Class
subclass of: tag visualisation by enzyme assay
definition: The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction.
created by: orchard
creation date: 2010-04-21T03:34:14Z
has_exact_synonym: tag perox activity
has_obo_namespace: PSI-MI
id: MI:0981
in_subset: PSI-MI slim

Axiom
annotated source: tag visualisation by peroxidase activity
annotated property: definition
annotated target: The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: tag visualisation by peroxidase activity
annotated property: has_exact_synonym
annotated target: tag perox activity
has_synonym_type: Unique short label curated by PSI-MI

electrophoretic mobility-based method
type: Class
subclass of: biochemical
definition: Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field.
created by: orchard
creation date: 2010-04-26T10:30:36Z
has_exact_synonym: electrophoresis
has_obo_namespace: PSI-MI
id: MI:0982
in_subset: PSI-MI slim

Axiom
annotated source: electrophoretic mobility-based method
annotated property: definition
annotated target: Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field.
database_cross_reference: PMID:19517512

Axiom
annotated source: electrophoretic mobility-based method
annotated property: has_exact_synonym
annotated target: electrophoresis
has_synonym_type: Unique short label curated by PSI-MI

gemma
type: Class
subclass of: electrophoretic mobility-based method
definition: GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted into the gas phase by a charged reduced electrospray process. The generated particles, each containing one protein molecule with a +1 charge, are separated according to size in a differential mobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry, this method is run at atmospheric pressure and measures the diameter of the particle rather than the mass.
created by: orchard
creation date: 2010-04-26T10:36:41Z
has_obo_namespace: PSI-MI
id: MI:0983
in_subset: PSI-MI slim

Axiom
annotated source: gemma
annotated property: definition
annotated target: GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted into the gas phase by a charged reduced electrospray process. The generated particles, each containing one protein molecule with a +1 charge, are separated according to size in a differential mobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry, this method is run at atmospheric pressure and measures the diameter of the particle rather than the mass.
database_cross_reference: PMID:16861739

deamination assay
type: Class
subclass of: enzymatic study
definition: The measurement of the removal of an amine group from a molecule.
created by: orchard
creation date: 2010-04-26T10:45:01Z
has_exact_synonym: aminase assay
has_exact_synonym: deamination
has_obo_namespace: PSI-MI
id: MI:0984
in_subset: PSI-MI slim

Axiom
annotated source: deamination assay
annotated property: definition
annotated target: The measurement of the removal of an amine group from a molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: deamination assay
annotated property: has_exact_synonym
annotated target: aminase assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: deamination assay
annotated property: has_exact_synonym
annotated target: deamination
has_synonym_type: Unique short label curated by PSI-MI

deamination reaction
type: Class
subclass of: enzymatic reaction
definition: The removal of an amine group from a molecule.
created by: orchard
creation date: 2010-04-26T10:49:06Z
has_exact_synonym: deamination
has_obo_namespace: PSI-MI
id: MI:0985
in_subset: PSI-MI slim

Axiom
annotated source: deamination reaction
annotated property: definition
annotated target: The removal of an amine group from a molecule.
database_cross_reference: PMID:14760721

Axiom
annotated source: deamination reaction
annotated property: has_exact_synonym
annotated target: deamination
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid strand elongation reaction
type: Class
subclass of: enzymatic reaction
definition: The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase.
created by: orchard
creation date: 2010-04-26T10:52:22Z
has_exact_synonym: strand elongation
has_obo_namespace: PSI-MI
id: MI:0986
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid strand elongation reaction
annotated property: definition
annotated target: The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase.
database_cross_reference: PMID:159156

Axiom
annotated source: nucleic acid strand elongation reaction
annotated property: has_exact_synonym
annotated target: strand elongation
has_synonym_type: Unique short label curated by PSI-MI

rna strand elongation
type: Class
subclass of: nucleic acid strand elongation reaction
definition: The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand.
created by: orchard
creation date: 2010-04-26T11:00:08Z
has_exact_synonym: rna elongation
has_obo_namespace: PSI-MI
id: MI:0987
in_subset: PSI-MI slim

Axiom
annotated source: rna strand elongation
annotated property: definition
annotated target: The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand.
database_cross_reference: PMID:14755292

Axiom
annotated source: rna strand elongation
annotated property: has_exact_synonym
annotated target: rna elongation
has_synonym_type: Unique short label curated by PSI-MI

strep tag
type: Class
subclass of: tag
definition: Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK).
created by: orchard
creation date: 2010-04-26T11:07:37Z
has_obo_namespace: PSI-MI
id: MI:0988
in_subset: PSI-MI slim

Axiom
annotated source: strep tag
annotated property: definition
annotated target: Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK).
database_cross_reference: PMID:17571060

amidase assay
type: Class
subclass of: enzymatic study
definition: The measurement of the addition of an amine group to a molecule.
created by: orchard
creation date: 2010-04-26T11:20:23Z
has_exact_synonym: amidation
has_obo_namespace: PSI-MI
id: MI:0989
in_subset: PSI-MI slim

Axiom
annotated source: amidase assay
annotated property: definition
annotated target: The measurement of the addition of an amine group to a molecule.
database_cross_reference: PMID:14760721

Axiom
annotated source: amidase assay
annotated property: has_exact_synonym
annotated target: amidation
has_synonym_type: Unique short label curated by PSI-MI

cleavage assay
type: Class
subclass of: enzymatic study
definition: The cleavage of a biomolecule either into its component parts or sub-parts.
created by: orchard
creation date: 2010-04-26T11:27:22Z
has_exact_synonym: cleavage
has_obo_namespace: PSI-MI
id: MI:0990
in_subset: PSI-MI slim

Axiom
annotated source: cleavage assay
annotated property: definition
annotated target: The cleavage of a biomolecule either into its component parts or sub-parts.
database_cross_reference: PMID:14760721

Axiom
annotated source: cleavage assay
annotated property: has_exact_synonym
annotated target: cleavage
has_synonym_type: Unique short label curated by PSI-MI

lipoprotein cleavage assay
type: Class
subclass of: cleavage assay
definition: The cleavage of a lipid molecule from a larger biomolecule.
created by: orchard
creation date: 2010-04-26T11:30:12Z
has_obo_namespace: PSI-MI
id: MI:0991
in_subset: PSI-MI slim

Axiom
annotated source: lipoprotein cleavage assay
annotated property: definition
annotated target: The cleavage of a lipid molecule from a larger biomolecule.
database_cross_reference: PMID:14760721

defarnesylase assay
type: Class
subclass of: lipoprotein cleavage assay
definition: Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue.
created by: orchard
creation date: 2010-04-26T12:27:47Z
has_exact_synonym: defarnesylation assay
has_obo_namespace: PSI-MI
id: MI:0992
in_subset: PSI-MI slim

Axiom
annotated source: defarnesylase assay
annotated property: definition
annotated target: Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue.
database_cross_reference: PMID:14760721

Axiom
annotated source: defarnesylase assay
annotated property: has_exact_synonym
annotated target: defarnesylation assay
has_synonym_type: Unique short label curated by PSI-MI

degeranylase assay
type: Class
subclass of: lipoprotein cleavage assay
definition: Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue.
created by: orchard
creation date: 2010-04-26T12:36:51Z
has_exact_synonym: degeranylation assay
has_obo_namespace: PSI-MI
id: MI:0993
in_subset: PSI-MI slim

Axiom
annotated source: degeranylase assay
annotated property: definition
annotated target: Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue.
database_cross_reference: PMID:14760721

Axiom
annotated source: degeranylase assay
annotated property: has_exact_synonym
annotated target: degeranylation assay
has_synonym_type: Unique short label curated by PSI-MI

demyristoylase assay
type: Class
subclass of: lipoprotein cleavage assay
definition: measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue.
created by: orchard
creation date: 2010-04-26T12:39:30Z
has_exact_synonym: demyristoylation assay
has_obo_namespace: PSI-MI
id: MI:0994
in_subset: PSI-MI slim

Axiom
annotated source: demyristoylase assay
annotated property: definition
annotated target: measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue.
database_cross_reference: PMID:14760721

Axiom
annotated source: demyristoylase assay
annotated property: has_exact_synonym
annotated target: demyristoylation assay
has_synonym_type: Unique short label curated by PSI-MI

depalmitoylase assay
type: Class
subclass of: lipoprotein cleavage assay
definition: Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues.
created by: orchard
creation date: 2010-04-26T12:42:00Z
has_exact_synonym: depalmitoylation assay
has_obo_namespace: PSI-MI
id: MI:0995
in_subset: PSI-MI slim

Axiom
annotated source: depalmitoylase assay
annotated property: definition
annotated target: Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues.
database_cross_reference: PMID:14760721

Axiom
annotated source: depalmitoylase assay
annotated property: has_exact_synonym
annotated target: depalmitoylation assay
has_synonym_type: Unique short label curated by PSI-MI

deformylase assay
type: Class
subclass of: enzymatic study
definition: Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue.
created by: orchard
creation date: 2010-04-26T12:50:38Z
has_exact_synonym: deformylase reaction
has_obo_namespace: PSI-MI
has_related_synonym: deformylation
id: MI:0996
in_subset: PSI-MI slim

Axiom
annotated source: deformylase assay
annotated property: definition
annotated target: Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue.
database_cross_reference: PMID:14760721

Axiom
annotated source: deformylase assay
annotated property: has_exact_synonym
annotated target: deformylase reaction
has_synonym_type: Unique short label curated by PSI-MI

ubiquitinase assay
type: Class
subclass of: enzymatic study
definition: Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
created by: orchard
creation date: 2010-04-26T12:54:02Z
has_exact_synonym: ubiquitinase assay
has_obo_namespace: PSI-MI
has_related_synonym: ubiquitination
id: MI:0997
in_subset: PSI-MI slim

Axiom
annotated source: ubiquitinase assay
annotated property: definition
annotated target: Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
database_cross_reference: PMID:14760721

Axiom
annotated source: ubiquitinase assay
annotated property: has_exact_synonym
annotated target: ubiquitinase assay
has_synonym_type: Unique short label curated by PSI-MI

deubiquitinase assay
type: Class
subclass of: enzymatic study
definition: Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
created by: orchard
creation date: 2010-04-26T12:56:41Z
has_exact_synonym: deubiquitinase assay
has_obo_namespace: PSI-MI
has_related_synonym: deubiquinase assay
has_related_synonym: deubiquitination
id: MI:0998
in_subset: PSI-MI slim

Axiom
annotated source: deubiquitinase assay
annotated property: definition
annotated target: Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
database_cross_reference: PMID:14760721

Axiom
annotated source: deubiquitinase assay
annotated property: has_exact_synonym
annotated target: deubiquitinase assay
has_synonym_type: Unique short label curated by PSI-MI

formylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group.
created by: orchard
creation date: 2010-04-26T01:01:44Z
has_obo_namespace: PSI-MI
id: MI:0999
in_subset: PSI-MI slim

Axiom
annotated source: formylase assay
annotated property: definition
annotated target: Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group.
database_cross_reference: PMID:14760721

hydroxylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues.
created by: orchard
creation date: 2010-04-26T01:05:19Z
has_obo_namespace: PSI-MI
id: MI:1000
in_subset: PSI-MI slim

Axiom
annotated source: hydroxylase assay
annotated property: definition
annotated target: Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues.
database_cross_reference: PMID:14760721

lipidase assay
type: Class
subclass of: enzymatic study
definition: The covalent binding of a lipid group to a peptide chain.
created by: orchard
creation date: 2010-04-26T01:09:49Z
has_obo_namespace: PSI-MI
has_related_synonym: lipidation
id: MI:1001
in_subset: PSI-MI slim

Axiom
annotated source: lipidase assay
annotated property: definition
annotated target: The covalent binding of a lipid group to a peptide chain.
database_cross_reference: PMID:14760721

myristoylase assay
type: Class
subclass of: lipidase assay
definition: Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid.
created by: orchard
creation date: 2010-04-26T01:16:11Z
has_obo_namespace: PSI-MI
has_related_synonym: myristoylation
id: MI:1002
in_subset: PSI-MI slim

Axiom
annotated source: myristoylase assay
annotated property: definition
annotated target: Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid.
database_cross_reference: PMID:14707621

geranylgeranylase assay
type: Class
subclass of: lipidase assay
definition: Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).
created by: orchard
creation date: 2010-04-26T01:20:07Z
has_exact_synonym: geranylgeranylase
has_obo_namespace: PSI-MI
has_related_synonym: geranylgeranylation
id: MI:1003
in_subset: PSI-MI slim

Axiom
annotated source: geranylgeranylase assay
annotated property: definition
annotated target: Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).
database_cross_reference: PMID:14760721

Axiom
annotated source: geranylgeranylase assay
annotated property: has_exact_synonym
annotated target: geranylgeranylase
has_synonym_type: Unique short label curated by PSI-MI

palmitoylase assay
type: Class
subclass of: lipidase assay
definition: Measurement of the covalent attachment of palmitic acid to a protein.
created by: orchard
creation date: 2010-04-26T01:27:50Z
has_exact_synonym: palmitoylase assay
has_obo_namespace: PSI-MI
has_related_synonym: myristoylation
id: MI:1004
in_subset: PSI-MI slim

Axiom
annotated source: palmitoylase assay
annotated property: definition
annotated target: Measurement of the covalent attachment of palmitic acid to a protein.
database_cross_reference: PMID:14760721

Axiom
annotated source: palmitoylase assay
annotated property: has_exact_synonym
annotated target: palmitoylase assay
has_synonym_type: Unique short label curated by PSI-MI

adp ribosylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the addition of one or more ADP-ribose moieties to molecules.
created by: orchard
creation date: 2010-04-26T01:30:24Z
has_exact_synonym: adp ribosylase
has_obo_namespace: PSI-MI
has_related_synonym: adp ribosylation
id: MI:1005
in_subset: PSI-MI slim

Axiom
annotated source: adp ribosylase assay
annotated property: definition
annotated target: Measurement of the addition of one or more ADP-ribose moieties to molecules.
database_cross_reference: PMID:14760721

Axiom
annotated source: adp ribosylase assay
annotated property: has_exact_synonym
annotated target: adp ribosylase
has_synonym_type: Unique short label curated by PSI-MI

deglycosylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
created by: orchard
creation date: 2010-04-26T01:34:07Z
has_obo_namespace: PSI-MI
id: MI:1006
in_subset: PSI-MI slim

Axiom
annotated source: deglycosylase assay
annotated property: definition
annotated target: Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
database_cross_reference: PMID:14760721

glycosylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
created by: orchard
creation date: 2010-04-26T01:35:37Z
has_obo_namespace: PSI-MI
has_related_synonym: glycosylation
id: MI:1007
in_subset: PSI-MI slim

Axiom
annotated source: glycosylase assay
annotated property: definition
annotated target: Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
database_cross_reference: PMID:14760721

sumoylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
created by: orchard
creation date: 2010-04-26T01:37:31Z
has_obo_namespace: PSI-MI
has_related_synonym: sumoylation
id: MI:1008
in_subset: PSI-MI slim

Axiom
annotated source: sumoylase assay
annotated property: definition
annotated target: Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
database_cross_reference: PMID:14760721

desumoylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
created by: orchard
creation date: 2010-04-26T01:38:56Z
has_obo_namespace: PSI-MI
has_related_synonym: desumylation
id: MI:1009
in_subset: PSI-MI slim

Axiom
annotated source: desumoylase assay
annotated property: definition
annotated target: Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
database_cross_reference: PMID:14760721

neddylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
created by: orchard
creation date: 2010-04-26T01:41:40Z
has_obo_namespace: PSI-MI
has_related_synonym: neddylation
id: MI:1010
in_subset: PSI-MI slim

Axiom
annotated source: neddylase assay
annotated property: definition
annotated target: Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
database_cross_reference: PMID:14760721

deneddylase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
created by: orchard
creation date: 2010-04-26T01:42:49Z
has_obo_namespace: PSI-MI
has_related_synonym: deneddylation
id: MI:1011
in_subset: PSI-MI slim

Axiom
annotated source: deneddylase assay
annotated property: definition
annotated target: Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
database_cross_reference: PMID:14760721

sbp
type: Class
subclass of: tag
definition: 38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide.
created by: orchard
creation date: 2010-04-29T08:42:26Z
has_obo_namespace: PSI-MI
has_related_synonym: steptavidin binding peptide
id: MI:1012
in_subset: PSI-MI slim

Axiom
annotated source: sbp
annotated property: definition
annotated target: 38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide.
database_cross_reference: PMID:117222181

ensemblgenomes
type: Class
subclass of: genome databases
definition: Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range. http://www.ensemblgenomes.org
created by: orchard
creation date: 2010-05-06T08:09:20Z
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:1013
in_subset: PSI-MI slim

Axiom
annotated source: ensemblgenomes
annotated property: definition
annotated target: Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range. http://www.ensemblgenomes.org
database_cross_reference: PMID:19884133

Axiom
annotated source: ensemblgenomes
annotated property: database_cross_reference
annotated target: search-url:
label: http://ensemblgenomes.org/search/eg/${ac}

string
type: Class
subclass of: interaction database
definition: STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins.
created by: orchard
creation date: 2010-07-15T11:00:57Z
has_obo_namespace: PSI-MI
id: MI:1014
in_subset: PSI-MI slim

Axiom
annotated source: string
annotated property: definition
annotated target: STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins.
database_cross_reference: PMID:18940858

dictybase
type: Class
subclass of: genome databases
definition: dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome.
created by: orchard
creation date: 2010-07-29T01:19:40Z
database_cross_reference: id-validation-regexp:
has_obo_namespace: PSI-MI
id: MI:1015
in_subset: PSI-MI slim

DDB_G(0-9){7}
type: Axiom
annotated source: dictybase
annotated property: database_cross_reference
annotated target: id-validation-regexp:

fluorescence recovery after photobleaching
type: Class
subclass of: fluorescence technology
definition: Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction.
created by: orchard
creation date: 2010-11-11T10:39:37Z
has_exact_synonym: frap
has_obo_namespace: PSI-MI
id: MI:1016
in_subset: PSI-MI slim

Axiom
annotated source: fluorescence recovery after photobleaching
annotated property: definition
annotated target: Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction.
database_cross_reference: PMID:15695095
database_cross_reference: PMID:17711354

Axiom
annotated source: fluorescence recovery after photobleaching
annotated property: has_exact_synonym
annotated target: frap
has_synonym_type: Unique short label curated by PSI-MI

rna immunoprecipitation
type: Class
subclass of: coimmunoprecipitation
definition: Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR.
created by: orchard
creation date: 2010-11-11T10:58:47Z
has_exact_synonym: rna-ip
has_obo_namespace: PSI-MI
has_related_synonym: rip
id: MI:1017
in_subset: PSI-MI slim

Axiom
annotated source: rna immunoprecipitation
annotated property: definition
annotated target: Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR.
database_cross_reference: PMID:18265380

Axiom
annotated source: rna immunoprecipitation
annotated property: has_exact_synonym
annotated target: rna-ip
has_synonym_type: Unique short label curated by PSI-MI

deltamass
type: Class
subclass of: feature database
definition: A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home
created by: orchard
creation date: 2010-11-11T11:04:13Z
has_obo_namespace: PSI-MI
id: MI:1018
in_subset: PSI-MI slim

Axiom
annotated source: deltamass
annotated property: definition
annotated target: A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home
database_cross_reference: PMID:8322616

protein phosphatase assay
type: Class
subclass of: phosphatase assay
definition: Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate.
created by: orchard
creation date: 2010-11-11T11:30:47Z
has_obo_namespace: PSI-MI
id: MI:1019
in_subset: PSI-MI slim

hilyte fluor 488
type: Class
subclass of: fluorescent dye label
definition: A carbonyl-reactive fluorescent labelling dye.
created by: orchard
creation date: 2010-11-11T11:35:48Z
has_exact_synonym: hilyte 488
has_obo_namespace: PSI-MI
id: MI:1020
in_subset: PSI-MI slim

Axiom
annotated source: hilyte fluor 488
annotated property: definition
annotated target: A carbonyl-reactive fluorescent labelling dye.
database_cross_reference: PMID:19795889

Axiom
annotated source: hilyte fluor 488
annotated property: has_exact_synonym
annotated target: hilyte 488
has_synonym_type: Unique short label curated by PSI-MI

qx 520
type: Class
subclass of: dye label
definition: Nonfluorescent dye, act as a quencher in FRET assays.
created by: orchard
creation date: 2010-11-11T11:40:16Z
has_obo_namespace: PSI-MI
id: MI:1021
in_subset: PSI-MI slim

field flow fractionation
type: Class
subclass of: cosedimentation
definition: A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids.
created by: orchard
creation date: 2010-11-11T11:55:40Z
has_obo_namespace: PSI-MI
id: MI:1022
in_subset: PSI-MI slim

Axiom
annotated source: field flow fractionation
annotated property: definition
annotated target: A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids.
database_cross_reference: PMID:959835

luminogreen
type: Class
subclass of: dye label
definition: A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell.
created by: orchard
creation date: 2010-11-11T12:10:26Z
has_obo_namespace: PSI-MI
id: MI:1023
in_subset: PSI-MI slim

Axiom
annotated source: luminogreen
annotated property: definition
annotated target: A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell.
database_cross_reference: PMID:19935683

scanning electron microscopy
type: Class
subclass of: electron microscopy
definition: A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity.
created by: orchard
creation date: 2010-11-11T12:17:54Z
has_exact_synonym: sem
has_obo_namespace: PSI-MI
id: MI:1024
in_subset: PSI-MI slim

Axiom
annotated source: scanning electron microscopy
annotated property: definition
annotated target: A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity.
database_cross_reference: PMID:20463740

Axiom
annotated source: scanning electron microscopy
annotated property: has_exact_synonym
annotated target: sem
has_synonym_type: Alternate label curated by PSI-MI

unimod
type: Class
subclass of: feature database
definition: A database of protein modifications for mass spectrometry. www.unimod.org
created by: orchard
creation date: 2010-11-11T12:24:10Z
has_obo_namespace: PSI-MI
id: MI:1025

Axiom
annotated source: unimod
annotated property: definition
annotated target: A database of protein modifications for mass spectrometry. www.unimod.org
database_cross_reference: PMID:15174123

diphtamidase assay
type: Class
subclass of: enzymatic study
definition: Measurement of a modification that converts an L-histidine residue to diphthamide.
created by: orchard
creation date: 2010-11-11T12:33:29Z
has_exact_synonym: diphtamidase
has_obo_namespace: PSI-MI
id: MI:1026
in_subset: PSI-MI slim

Axiom
annotated source: diphtamidase assay
annotated property: definition
annotated target: Measurement of a modification that converts an L-histidine residue to diphthamide.
database_cross_reference: PMID:14760721

Axiom
annotated source: diphtamidase assay
annotated property: has_exact_synonym
annotated target: diphtamidase
has_synonym_type: Unique short label curated by PSI-MI

diphtamidation reaction
type: Class
subclass of: enzymatic reaction
definition: A modification that converts an L-histidine residue to diphthamide.
created by: orchard
creation date: 2010-11-11T12:36:51Z
has_exact_synonym: diphthamidation
has_obo_namespace: PSI-MI
id: MI:1027
in_subset: PSI-MI slim

Axiom
annotated source: diphtamidation reaction
annotated property: definition
annotated target: A modification that converts an L-histidine residue to diphthamide.
database_cross_reference: PMID:14760721

Axiom
annotated source: diphtamidation reaction
annotated property: has_exact_synonym
annotated target: diphthamidation
has_synonym_type: Unique short label curated by PSI-MI

modified chromatin immunoprecipitation
type: Class
subclass of: chromatin immunoprecipitation assay
definition: Chromatin-bound protein networks isolated using magnetic beads coated with antibodies.
created by: orchard
creation date: 2010-11-11T12:58:52Z
has_exact_synonym: mch-ip
has_obo_namespace: PSI-MI
id: MI:1028
in_subset: PSI-MI slim

Axiom
annotated source: modified chromatin immunoprecipitation
annotated property: definition
annotated target: Chromatin-bound protein networks isolated using magnetic beads coated with antibodies.
database_cross_reference: PMID:19106085

Axiom
annotated source: modified chromatin immunoprecipitation
annotated property: has_exact_synonym
annotated target: mch-ip
has_synonym_type: Unique short label curated by PSI-MI

proteomics of isolated chromatin segments
type: Class
subclass of: chromatin immunoprecipitation assay
definition: Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified.
created by: orchard
creation date: 2010-11-11T01:03:21Z
has_exact_synonym: pich
has_obo_namespace: PSI-MI
id: MI:1029
in_subset: PSI-MI slim

Axiom
annotated source: proteomics of isolated chromatin segments
annotated property: definition
annotated target: Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified.
database_cross_reference: PMID:19135898

Axiom
annotated source: proteomics of isolated chromatin segments
annotated property: has_exact_synonym
annotated target: pich
has_synonym_type: Alternate label curated by PSI-MI

excimer fluorescence
type: Class
subclass of: fluorescence technology
definition: Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule.
created by: orchard
creation date: 2010-11-11T01:15:19Z
has_exact_synonym: excimer fluoresc
has_obo_namespace: PSI-MI
id: MI:1030
in_subset: PSI-MI slim

Axiom
annotated source: excimer fluorescence
annotated property: definition
annotated target: Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule.
database_cross_reference: PMID:18480256

Axiom
annotated source: excimer fluorescence
annotated property: has_exact_synonym
annotated target: excimer fluoresc
has_synonym_type: Unique short label curated by PSI-MI

protein folding/unfolding
type: Class
subclass of: affinity technology
definition: A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding.
created by: orchard
creation date: 2010-11-11T01:24:11Z
has_exact_synonym: protein folding
has_obo_namespace: PSI-MI
id: MI:1031
in_subset: PSI-MI slim

Axiom
annotated source: protein folding/unfolding
annotated property: definition
annotated target: A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding.
database_cross_reference: PMID:19940245

Axiom
annotated source: protein folding/unfolding
annotated property: has_exact_synonym
annotated target: protein folding
has_synonym_type: Unique short label curated by PSI-MI

atto 488
type: Class
subclass of: atto label
definition: Fluorescent tag - maleimide couples to thiols.
created by: orchard
creation date: 2010-11-11T01:33:13Z
has_exact_synonym: atto 488 maleimide
has_obo_namespace: PSI-MI
has_related_synonym: atto488
id: MI:1032
in_subset: PSI-MI slim

Axiom
annotated source: atto 488
annotated property: definition
annotated target: Fluorescent tag - maleimide couples to thiols.
database_cross_reference: PMID:14760721

atto 550
type: Class
subclass of: atto label
definition: Fluorescent tag - maleimide couples to thiols.
created by: orchard
creation date: 2010-11-11T01:39:43Z
has_obo_namespace: PSI-MI
has_related_synonym: atto550
id: MI:1033
in_subset: PSI-MI slim

Axiom
annotated source: atto 550
annotated property: definition
annotated target: Fluorescent tag - maleimide couples to thiols.
database_cross_reference: PMID:14760721

nuclease assay
type: Class
subclass of: enzymatic study
definition: Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids.
created by: orchard
creation date: 2010-11-11T01:43:11Z
has_obo_namespace: PSI-MI
id: MI:1034
in_subset: PSI-MI slim

Axiom
annotated source: nuclease assay
annotated property: definition
annotated target: Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids.
database_cross_reference: PMID:14760721

deoxyribonuclease assay
type: Class
subclass of: nuclease assay
definition: Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA.
created by: orchard
creation date: 2010-11-11T01:45:29Z
has_exact_synonym: deoxyribonuclease
has_obo_namespace: PSI-MI
id: MI:1035
in_subset: PSI-MI slim

Axiom
annotated source: deoxyribonuclease assay
annotated property: definition
annotated target: Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA.
database_cross_reference: PMID:14760721

Axiom
annotated source: deoxyribonuclease assay
annotated property: has_exact_synonym
annotated target: deoxyribonuclease
has_synonym_type: Unique short label curated by PSI-MI

nucleotide exchange assay
type: Class
subclass of: biochemical
definition: Experiments monitoring interactions of nucleotide exchange factors with their cognate nucleotidases.
created by: orchard
creation date: 2010-11-11T01:54:00Z
has_exact_synonym: nucleotide exchange
has_obo_namespace: PSI-MI
id: MI:1036
in_subset: PSI-MI slim

Axiom
annotated source: nucleotide exchange assay
annotated property: definition
annotated target: Experiments monitoring interactions of nucleotide exchange factors with their cognate nucleotidases.
database_cross_reference: PMID:14760721

Axiom
annotated source: nucleotide exchange assay
annotated property: has_exact_synonym
annotated target: nucleotide exchange
has_synonym_type: Unique short label curated by PSI-MI

Split renilla luciferase complementation
type: Class
subclass of: split luciferase complementation
definition: The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light.
created by: orchard
creation date: 2010-11-11T02:54:08Z
has_exact_synonym: renilla luciferase
has_obo_namespace: PSI-MI
id: MI:1037
in_subset: PSI-MI slim

Axiom
annotated source: Split renilla luciferase complementation
annotated property: definition
annotated target: The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light.
database_cross_reference: PMID:12705589
database_cross_reference: PMID:22070901

Axiom
annotated source: Split renilla luciferase complementation
annotated property: has_exact_synonym
annotated target: renilla luciferase
has_synonym_type: Alternate label curated by PSI-MI

silicon nanowire field-effect transistor
type: Class
subclass of: biosensor
definition: Measures selective electrical response to molecules binding to the immobilised bait.
created by: orchard
creation date: 2010-11-11T03:11:33Z
has_exact_synonym: nanowire transistor
has_obo_namespace: PSI-MI
id: MI:1038
in_subset: PSI-MI slim

Axiom
annotated source: silicon nanowire field-effect transistor
annotated property: definition
annotated target: Measures selective electrical response to molecules binding to the immobilised bait.
database_cross_reference: PMID:20080536

Axiom
annotated source: silicon nanowire field-effect transistor
annotated property: has_exact_synonym
annotated target: nanowire transistor
has_synonym_type: Alternate label curated by PSI-MI

c-terminal range
type: Class
subclass of: feature range status
definition: The C-terminal region of a sequence, exact coordinates not available.
created by: orchard
creation date: 2010-11-11T03:20:34Z
has_exact_synonym: c-term range
has_obo_namespace: PSI-MI
id: MI:1039
in_subset: PSI-MI slim

Axiom
annotated source: c-terminal range
annotated property: definition
annotated target: The C-terminal region of a sequence, exact coordinates not available.
database_cross_reference: PMID:14760721

Axiom
annotated source: c-terminal range
annotated property: has_exact_synonym
annotated target: c-term range
has_synonym_type: Unique short label curated by PSI-MI

n-terminal range
type: Class
subclass of: feature range status
definition: The N-terminal region of a sequence, exact coordinates not available.
created by: orchard
creation date: 2010-11-11T03:27:57Z
has_exact_synonym: n-term range
has_obo_namespace: PSI-MI
id: MI:1040
in_subset: PSI-MI slim

Axiom
annotated source: n-terminal range
annotated property: definition
annotated target: The N-terminal region of a sequence, exact coordinates not available.
database_cross_reference: PMID:14760721

Axiom
annotated source: n-terminal range
annotated property: has_exact_synonym
annotated target: n-term range
has_synonym_type: Unique short label curated by PSI-MI

synonym
type: Class
subclass of: alias type
definition: Alternative name or descriptor for an entity.
created by: orchard
creation date: 2010-12-02T10:26:35Z
has_obo_namespace: PSI-MI
id: MI:1041
in_subset: PSI-MI slim

Axiom
annotated source: synonym
annotated property: definition
annotated target: Alternative name or descriptor for an entity.
database_cross_reference: PMID:14681455

pubmed central
type: Class
subclass of: literature database
definition: PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals.
created by: orchard
creation date: 2010-12-08T01:20:48Z
database_cross_reference: search-url:
has_exact_synonym: pmc
has_obo_namespace: PSI-MI
id: MI:1042
in_subset: PSI-MI slim

Axiom
annotated source: pubmed central
annotated property: definition
annotated target: PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals.
database_cross_reference: PMID:12519941

Axiom
annotated source: pubmed central
annotated property: database_cross_reference
annotated target: search-url:
label: http://europepmc.org/abstract/PMC/${ac}

Axiom
annotated source: pubmed central
annotated property: has_exact_synonym
annotated target: pmc
has_synonym_type: Unique short label curated by PSI-MI

flannotator
type: Class
subclass of: sequence database
definition: A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier)
created by: orchard
creation date: 2011-01-06T01:16:48Z
database_cross_reference: id-validation-regexp:
has_obo_namespace: PSI-MI
id: MI:1043
in_subset: PSI-MI slim

Axiom
annotated source: flannotator
annotated property: definition
annotated target: A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier)
database_cross_reference: PMID:19126575

CPTO-[0-9]{6}
type: Axiom
annotated source: flannotator
annotated property: database_cross_reference
annotated target: id-validation-regexp:

rice genome annotation project
type: Class
subclass of: genome databases
definition: NSF funded annotation project.
created by: orchard
creation date: 2011-02-11T01:33:28Z
has_obo_namespace: PSI-MI
has_related_synonym: RGAP
id: MI:1044
in_subset: PSI-MI slim

Axiom
annotated source: rice genome annotation project
annotated property: definition
annotated target: NSF funded annotation project.
database_cross_reference: PMID:17145706

curation content
type: Class
subclass of: molecular interaction
definition: Indicates source, depth and standards by which an entry has been added to a database.
created by: orchard
creation date: 2011-03-11T01:16:55Z
has_obo_namespace: PSI-MI
id: MI:1045
in_subset: PSI-MI slim

Axiom
annotated source: curation content
annotated property: definition
annotated target: Indicates source, depth and standards by which an entry has been added to a database.
database_cross_reference: PMID:14755292

interacting molecules
type: Class
subclass of: curation content
definition: Defines an interaction by the type of binary molecule pairs it can generates.
created by: orchard
creation date: 2011-03-11T01:19:27Z
has_obo_namespace: PSI-MI
id: MI:1046
in_subset: PSI-MI slim

Axiom
annotated source: interacting molecules
annotated property: definition
annotated target: Defines an interaction by the type of binary molecule pairs it can generates.
database_cross_reference: PMID:14755292

protein-protein
type: Class
subclass of: interacting molecules
definition: Interaction between a protein or peptide and a corresponding protein or peptide.
created by: orchard
creation date: 2011-03-11T01:21:28Z
has_obo_namespace: PSI-MI
id: MI:1047
in_subset: PSI-MI slim

Axiom
annotated source: protein-protein
annotated property: definition
annotated target: Interaction between a protein or peptide and a corresponding protein or peptide.
database_cross_reference: PMID:14755292

smallmolecule-protein
type: Class
subclass of: interacting molecules
definition: Interaction between a small molecule and a corresponding protein or peptide.
created by: orchard
creation date: 2011-03-11T01:22:36Z
has_obo_namespace: PSI-MI
id: MI:1048
in_subset: PSI-MI slim

Axiom
annotated source: smallmolecule-protein
annotated property: definition
annotated target: Interaction between a small molecule and a corresponding protein or peptide.
database_cross_reference: PMID:14755292

nucleicacid-protein
type: Class
subclass of: interacting molecules
definition: Interaction between a nucleic acid and a corresponding protein or peptide.
created by: orchard
creation date: 2011-03-11T01:23:29Z
has_obo_namespace: PSI-MI
id: MI:1049
in_subset: PSI-MI slim

Axiom
annotated source: nucleicacid-protein
annotated property: definition
annotated target: Interaction between a nucleic acid and a corresponding protein or peptide.
database_cross_reference: PMID:14755292

interaction representation
type: Class
subclass of: curation content
definition: Provides an indication of the level of post-processing of experimental data relating to specific binary pairs
created by: orchard
creation date: 2011-03-11T01:25:29Z
has_obo_namespace: PSI-MI
id: MI:1050
in_subset: PSI-MI slim

Axiom
annotated source: interaction representation
annotated property: definition
annotated target: Provides an indication of the level of post-processing of experimental data relating to specific binary pairs
database_cross_reference: PMID:14755292

evidence
type: Class
subclass of: interaction representation
definition: Binary pair is defined by a single piece of experimental evidence.
created by: orchard
creation date: 2011-03-11T01:27:00Z
has_obo_namespace: PSI-MI
id: MI:1051
in_subset: PSI-MI slim

Axiom
annotated source: evidence
annotated property: definition
annotated target: Binary pair is defined by a single piece of experimental evidence.
database_cross_reference: PMID:14755292

clustered
type: Class
subclass of: interaction representation
definition: Binary pair is defined by multiple pieces of experimental evidence which have been clustered together.
created by: orchard
creation date: 2011-03-11T01:28:50Z
has_obo_namespace: PSI-MI
id: MI:1052
in_subset: PSI-MI slim

Axiom
annotated source: clustered
annotated property: definition
annotated target: Binary pair is defined by multiple pieces of experimental evidence which have been clustered together.
database_cross_reference: PMID:14755292

data source
type: Class
subclass of: curation content
definition: The source of the data entered into the database.
created by: orchard
creation date: 2011-03-11T01:32:16Z
has_obo_namespace: PSI-MI
id: MI:1053
in_subset: PSI-MI slim

Axiom
annotated source: data source
annotated property: definition
annotated target: The source of the data entered into the database.
database_cross_reference: PMID:14755292

experimentally-observed
type: Class
subclass of: data source
definition: Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter.
created by: orchard
creation date: 2011-03-11T01:33:48Z
has_obo_namespace: PSI-MI
id: MI:1054
in_subset: PSI-MI slim

Axiom
annotated source: experimentally-observed
annotated property: definition
annotated target: Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter.
database_cross_reference: PMID:14755292

internally-curated
type: Class
subclass of: data source
definition: Data has been directly curated into this database from the paper describing the experimental evidence
created by: orchard
creation date: 2011-03-11T01:35:12Z
has_obo_namespace: PSI-MI
id: MI:1055
in_subset: PSI-MI slim

Axiom
annotated source: internally-curated
annotated property: definition
annotated target: Data has been directly curated into this database from the paper describing the experimental evidence
database_cross_reference: PMID:14755292

text-mining
type: Class
subclass of: data source
definition: The data has been entered into the database following extraction from the literature by a computational process.
created by: orchard
creation date: 2011-03-11T01:36:34Z
has_obo_namespace: PSI-MI
id: MI:1056
in_subset: PSI-MI slim

Axiom
annotated source: text-mining
annotated property: definition
annotated target: The data has been entered into the database following extraction from the literature by a computational process.
database_cross_reference: PMID:14755292

predicted
type: Class
subclass of: data source
definition: The interaction has been predicted using a specific algorithm.
created by: orchard
creation date: 2011-03-11T01:37:47Z
has_obo_namespace: PSI-MI
id: MI:1057
in_subset: PSI-MI slim

Axiom
annotated source: predicted
annotated property: definition
annotated target: The interaction has been predicted using a specific algorithm.
database_cross_reference: PMID:14755292

imported
type: Class
subclass of: data source
definition: The data has been imported into the database form an external resource.
created by: orchard
creation date: 2011-03-11T01:39:23Z
has_obo_namespace: PSI-MI
id: MI:1058
in_subset: PSI-MI slim

Axiom
annotated source: imported
annotated property: definition
annotated target: The data has been imported into the database form an external resource.
database_cross_reference: PMID:14755292

complex expansion
type: Class
subclass of: curation content
definition: The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export.
created by: orchard
creation date: 2011-03-11T01:41:16Z
has_obo_namespace: PSI-MI
id: MI:1059
in_subset: PSI-MI slim

Axiom
annotated source: complex expansion
annotated property: definition
annotated target: The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export.
database_cross_reference: PMID:14755292

spoke expansion
type: Class
subclass of: complex expansion
definition: Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait.
created by: orchard
creation date: 2011-03-11T01:42:35Z
has_obo_namespace: PSI-MI
id: MI:1060
in_subset: PSI-MI slim

Axiom
annotated source: spoke expansion
annotated property: definition
annotated target: Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait.
database_cross_reference: PMID:14755292

matrix expansion
type: Class
subclass of: complex expansion
definition: Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other.
created by: orchard
creation date: 2011-03-11T01:45:52Z
has_obo_namespace: PSI-MI
id: MI:1061
in_subset: PSI-MI slim

Axiom
annotated source: matrix expansion
annotated property: definition
annotated target: Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other.
database_cross_reference: PMID:14755292

bipartite expansion
type: Class
subclass of: complex expansion
definition: Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity.
created by: orchard
creation date: 2011-03-11T01:49:08Z
has_obo_namespace: PSI-MI
id: MI:1062
in_subset: PSI-MI slim

Axiom
annotated source: bipartite expansion
annotated property: definition
annotated target: Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity.
database_cross_reference: PMID:14755292

consensuspathdb
type: Class
subclass of: pathways database
definition: ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided.
created by: orchard
creation date: 2011-06-21T02:40:16Z
has_obo_namespace: PSI-MI
id: MI:1063
in_subset: PSI-MI slim

Axiom
annotated source: consensuspathdb
annotated property: definition
annotated target: ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided.
database_cross_reference: PMID:21071422

interaction confidence
type: Class
subclass of: molecular interaction
definition: A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction.
created by: orchard
creation date: 2011-07-05T07:13:57Z
has_exact_synonym: confidence
has_exact_synonym: scoring system
has_obo_namespace: PSI-MI
id: MI:1064
in_subset: PSI-MI slim

Axiom
annotated source: interaction confidence
annotated property: definition
annotated target: A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction.
database_cross_reference: PMID:19420069

Axiom
annotated source: interaction confidence
annotated property: has_exact_synonym
annotated target: confidence
has_synonym_type: Unique short label curated by PSI-MI

replication-based confidence
type: Class
subclass of: interaction confidence
definition: Methods based on counting the number of replicates in which an interaction has been observed.
created by: orchard
creation date: 2011-07-05T07:22:02Z
has_exact_synonym: replication score
has_obo_namespace: PSI-MI
has_related_synonym: replication-based scoring system
id: MI:1065
in_subset: PSI-MI slim

Axiom
annotated source: replication-based confidence
annotated property: definition
annotated target: Methods based on counting the number of replicates in which an interaction has been observed.
database_cross_reference: PMID:19420069

Axiom
annotated source: replication-based confidence
annotated property: has_exact_synonym
annotated target: replication score
has_synonym_type: Alternate label curated by PSI-MI

structure-based confidence
type: Class
subclass of: interaction confidence
definition: Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc.
created by: orchard
creation date: 2011-07-05T07:38:50Z
has_exact_synonym: structure score
has_exact_synonym: structure-based scoring system
has_obo_namespace: PSI-MI
id: MI:1066
in_subset: PSI-MI slim

Axiom
annotated source: structure-based confidence
annotated property: definition
annotated target: Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc.
database_cross_reference: PMID:15044803

Axiom
annotated source: structure-based confidence
annotated property: has_exact_synonym
annotated target: structure score
has_synonym_type: Alternate label curated by PSI-MI

function-based confidence
type: Class
subclass of: interaction confidence
subclass of: author-based confidence
definition: Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms.
created by: orchard
creation date: 2011-07-05T07:46:28Z
has_exact_synonym: function score
has_exact_synonym: function-based scoring system
has_obo_namespace: PSI-MI
id: MI:1067
in_subset: PSI-MI slim

Axiom
annotated source: function-based confidence
annotated property: definition
annotated target: Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms.
database_cross_reference: PMID:21443973

Axiom
annotated source: function-based confidence
annotated property: has_exact_synonym
annotated target: function score
has_synonym_type: Unique short label curated by PSI-MI

location-based confidence
type: Class
subclass of: interaction confidence
definition: Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues.
created by: orchard
creation date: 2011-07-05T07:52:36Z
has_exact_synonym: colocation score
has_exact_synonym: location-based scoring system
has_obo_namespace: PSI-MI
id: MI:1068
in_subset: PSI-MI slim

Axiom
annotated source: location-based confidence
annotated property: definition
annotated target: Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues.
database_cross_reference: PMID:18624398

Axiom
annotated source: location-based confidence
annotated property: has_exact_synonym
annotated target: colocation score
has_synonym_type: Unique short label curated by PSI-MI

network-based confidence
type: Class
subclass of: interaction confidence
definition: Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison with genetic interactions.
created by: orchard
creation date: 2011-07-05T07:59:13Z
has_exact_synonym: network score
has_exact_synonym: network-based scoring system
has_obo_namespace: PSI-MI
id: MI:1069
in_subset: PSI-MI slim

Axiom
annotated source: network-based confidence
annotated property: definition
annotated target: Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison with genetic interactions.
database_cross_reference: PMID:19010802

Axiom
annotated source: network-based confidence
annotated property: has_exact_synonym
annotated target: network score
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: network-based confidence
annotated property: has_exact_synonym
annotated target: network-based scoring system
has_synonym_type: Unique short label curated by PSI-MI

standard-based confidence
type: Class
subclass of: interaction confidence
definition: Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules.
created by: orchard
creation date: 2011-07-05T08:09:46Z
has_exact_synonym: standard score
has_exact_synonym: standard-based scoring system
has_obo_namespace: PSI-MI
has_related_synonym: gold standard
id: MI:1070
in_subset: PSI-MI slim

Axiom
annotated source: standard-based confidence
annotated property: definition
annotated target: Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules.
database_cross_reference: PMID:16554755

Axiom
annotated source: standard-based confidence
annotated property: has_exact_synonym
annotated target: standard score
has_synonym_type: Unique short label curated by PSI-MI

literature-based confidence
type: Class
subclass of: interaction confidence
definition: Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining.
created by: orchard
creation date: 2011-07-05T08:24:46Z
has_exact_synonym: literature score
has_exact_synonym: literature-based scoring system
has_obo_namespace: PSI-MI
id: MI:1071
in_subset: PSI-MI slim

Axiom
annotated source: literature-based confidence
annotated property: definition
annotated target: Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining.
database_cross_reference: PMID:18005433

Axiom
annotated source: literature-based confidence
annotated property: has_exact_synonym
annotated target: literature score
has_synonym_type: Unique short label curated by PSI-MI

method-based confidence
type: Class
subclass of: interaction confidence
definition: The confidence of an interaction is assessed on the number of different methods by which it is observed.
created by: orchard
creation date: 2011-07-05T08:42:47Z
has_exact_synonym: method score
has_exact_synonym: method-based scoring system
has_obo_namespace: PSI-MI
id: MI:1072
in_subset: PSI-MI slim

Axiom
annotated source: method-based confidence
annotated property: definition
annotated target: The confidence of an interaction is assessed on the number of different methods by which it is observed.
database_cross_reference: PMID:19420069

Axiom
annotated source: method-based confidence
annotated property: has_exact_synonym
annotated target: method score
has_synonym_type: Unique short label curated by PSI-MI

statistical-based confidence
type: Class
subclass of: interaction confidence
definition: Confidence in an interaction is based on a measure of the probability of these molecules interacting.
created by: orchard
creation date: 2011-07-05T08:50:05Z
has_exact_synonym: statistical score
has_exact_synonym: statistical-based scoring system
has_obo_namespace: PSI-MI
id: MI:1073
in_subset: PSI-MI slim

Axiom
annotated source: statistical-based confidence
annotated property: definition
annotated target: Confidence in an interaction is based on a measure of the probability of these molecules interacting.
database_cross_reference: PMID:19420069

Axiom
annotated source: statistical-based confidence
annotated property: has_exact_synonym
annotated target: statistical score
has_synonym_type: Unique short label curated by PSI-MI

rgs-his tag
type: Class
subclass of: his tag
definition: The protein of interest is expressed as a fusion to a RGS(His)n tag.
created by: orchard
creation date: 2011-07-05T09:52:28Z
has_exact_synonym: rgs-his
has_obo_namespace: PSI-MI
id: MI:1074

Axiom
annotated source: rgs-his tag
annotated property: definition
annotated target: The protein of interest is expressed as a fusion to a RGS(His)n tag.
database_cross_reference: PMID:19223579

Axiom
annotated source: rgs-his tag
annotated property: has_exact_synonym
annotated target: rgs-his
has_synonym_type: Unique short label curated by PSI-MI

beilstein
type: Class
subclass of: bioactive entity reference
definition: The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number.
created by: orchard
creation date: 2011-07-05T10:03:13Z
has_exact_synonym: beilstein
has_obo_namespace: PSI-MI
id: MI:1075
in_subset: PSI-MI slim

Axiom
annotated source: beilstein
annotated property: definition
annotated target: The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number.
database_cross_reference: PMID:ID:11604014

Axiom
annotated source: beilstein
annotated property: has_exact_synonym
annotated target: beilstein
has_synonym_type: Unique short label curated by PSI-MI

einecs
type: Class
subclass of: bioactive entity reference
definition: The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets.
created by: orchard
creation date: 2011-07-05T10:09:35Z
has_exact_synonym: European Inventory of Existing Commercial Chemical Substances
has_exact_synonym: einecs
has_obo_namespace: PSI-MI
id: MI:1076
in_subset: PSI-MI slim

Axiom
annotated source: einecs
annotated property: definition
annotated target: The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets.
database_cross_reference: PMID:17125194

Axiom
annotated source: einecs
annotated property: has_exact_synonym
annotated target: einecs
has_synonym_type: Unique short label curated by PSI-MI

merck index
type: Class
subclass of: bioactive entity reference
definition: Comprehensive information on chemicals, drugs, and biologicals.
created by: orchard
creation date: 2011-07-05T10:15:56Z
has_exact_synonym: merck index
has_obo_namespace: PSI-MI
id: MI:1077
in_subset: PSI-MI slim

Axiom
annotated source: merck index
annotated property: definition
annotated target: Comprehensive information on chemicals, drugs, and biologicals.
database_cross_reference: PMID:17832605

Axiom
annotated source: merck index
annotated property: has_exact_synonym
annotated target: merck index
has_synonym_type: Unique short label curated by PSI-MI

plantgdb
type: Class
subclass of: genome databases
definition: PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.
created by: orchard
creation date: 2011-07-05T10:27:50Z
has_exact_synonym: plantgdb
has_obo_namespace: PSI-MI
id: MI:1078
in_subset: PSI-MI slim

Axiom
annotated source: plantgdb
annotated property: definition
annotated target: PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.
database_cross_reference: PMID:18063570

Axiom
annotated source: plantgdb
annotated property: has_exact_synonym
annotated target: plantgdb
has_synonym_type: Unique short label curated by PSI-MI

ratmap
type: Class
subclass of: genome databases
definition: The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap.
created by: orchard
creation date: 2011-07-05T10:32:10Z
has_exact_synonym: ratmap
has_obo_namespace: PSI-MI
id: MI:1079
in_subset: PSI-MI slim

Axiom
annotated source: ratmap
annotated property: definition
annotated target: The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap.
database_cross_reference: PMID:15608244

Axiom
annotated source: ratmap
annotated property: has_exact_synonym
annotated target: ratmap
has_synonym_type: Unique short label curated by PSI-MI

tair
type: Class
subclass of: genome databases
definition: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.
created by: orchard
creation date: 2011-07-05T10:34:26Z
has_exact_synonym: The Arabidopsis Information Resource
has_exact_synonym: tair
has_obo_namespace: PSI-MI
id: MI:1080
in_subset: PSI-MI slim

Axiom
annotated source: tair
annotated property: definition
annotated target: The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.
database_cross_reference: PMID:20521243

Axiom
annotated source: tair
annotated property: has_exact_synonym
annotated target: tair
has_synonym_type: Unique short label curated by PSI-MI

tigr/jcvi
type: Class
subclass of: genome databases
definition: The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR).
created by: orchard
creation date: 2011-07-05T10:44:11Z
has_exact_synonym: J. Craig Venter Institute
has_exact_synonym: The Institute for Genomic Research
has_exact_synonym: tigr/jcvi
has_obo_namespace: PSI-MI
id: MI:1081
in_subset: PSI-MI slim

Axiom
annotated source: tigr/jcvi
annotated property: definition
annotated target: The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR).
database_cross_reference: PMID:18287690

Axiom
annotated source: tigr/jcvi
annotated property: has_exact_synonym
annotated target: The Institute for Genomic Research
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: tigr/jcvi
annotated property: has_exact_synonym
annotated target: tigr/jcvi
has_synonym_type: Unique short label curated by PSI-MI

zfin
type: Class
subclass of: genome databases
definition: Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools.
created by: orchard
creation date: 2011-07-05T10:53:21Z
has_exact_synonym: The Zebrafish Model Organism Database
has_exact_synonym: zfin
has_obo_namespace: PSI-MI
id: MI:1082

Axiom
annotated source: zfin
annotated property: definition
annotated target: Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools.
database_cross_reference: PMID:21036866

Axiom
annotated source: zfin
annotated property: has_exact_synonym
annotated target: zfin
has_synonym_type: Unique short label curated by PSI-MI

cog
type: Class
subclass of: feature database
definition: Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
created by: orchard
creation date: 2011-07-05T10:59:06Z
has_exact_synonym: Clusters of Orthologous Groups
has_exact_synonym: cogg
has_obo_namespace: PSI-MI
id: MI:1083
in_subset: PSI-MI slim

Axiom
annotated source: cog
annotated property: definition
annotated target: Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
database_cross_reference: PMID:11125040

Axiom
annotated source: cog
annotated property: has_exact_synonym
annotated target: cogg
has_synonym_type: Unique short label curated by PSI-MI

photon donor
type: Class
subclass of: donor
definition: Any molecule that is able to transfer a photon to another chemical species.
created by: orchard
creation date: 2011-07-05T11:03:38Z
has_exact_synonym: photon donor
has_obo_namespace: PSI-MI
id: MI:1084
in_subset: PSI-MI slim

Axiom
annotated source: photon donor
annotated property: definition
annotated target: Any molecule that is able to transfer a photon to another chemical species.
database_cross_reference: PMID:14755292

Axiom
annotated source: photon donor
annotated property: has_exact_synonym
annotated target: photon donor
has_synonym_type: Unique short label curated by PSI-MI

photon acceptor
type: Class
subclass of: acceptor
definition: Molecule to which a photon may be transferred from an photon donor.
created by: orchard
creation date: 2011-07-05T11:06:47Z
has_exact_synonym: photon acceptor
has_obo_namespace: PSI-MI
id: MI:1085
in_subset: PSI-MI slim

Axiom
annotated source: photon acceptor
annotated property: definition
annotated target: Molecule to which a photon may be transferred from an photon donor.
database_cross_reference: PMID:14755292

Axiom
annotated source: photon acceptor
annotated property: has_exact_synonym
annotated target: photon acceptor
has_synonym_type: Unique short label curated by PSI-MI

equilibrium dialysis
type: Class
subclass of: biophysical
definition: Two chambers are separated by a dialysis membrane. The molecular weight cut off (MWCO) of this membrane is chosen such that it will retain the receptor component of the sample (the element which will bind the ligand). A known concentration and volume of ligand is placed into one of the chambers. The ligand is small enough to pass freely through the membrane. A known concentration of receptor is then placed in the remaining chamber in an equivalent volume to that placed in the first chamber. As the ligand diffuses across the membrane some of it will bind to the receptor and some will remain free in solution. The higher the affinity of the interaction, the higher the concentration of ligand that will be bound at any time.
created by: orchard
creation date: 2011-07-05T11:12:25Z
has_exact_synonym: equilib. dialysis
has_obo_namespace: PSI-MI
id: MI:1086

Axiom
annotated source: equilibrium dialysis
annotated property: definition
annotated target: Two chambers are separated by a dialysis membrane. The molecular weight cut off (MWCO) of this membrane is chosen such that it will retain the receptor component of the sample (the element which will bind the ligand). A known concentration and volume of ligand is placed into one of the chambers. The ligand is small enough to pass freely through the membrane. A known concentration of receptor is then placed in the remaining chamber in an equivalent volume to that placed in the first chamber. As the ligand diffuses across the membrane some of it will bind to the receptor and some will remain free in solution. The higher the affinity of the interaction, the higher the concentration of ligand that will be bound at any time.
database_cross_reference: PMID:21609686

Axiom
annotated source: equilibrium dialysis
annotated property: has_exact_synonym
annotated target: equilib. dialysis
has_synonym_type: Unique short label curated by PSI-MI

monoclonal antibody blockade
type: Class
subclass of: affinity technology
subclass of: probe interaction assay
definition: Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule.
created by: orchard
creation date: 2011-07-05T11:19:37Z
has_exact_synonym: mab blockade
has_obo_namespace: PSI-MI
id: MI:1087
in_subset: PSI-MI slim

Axiom
annotated source: monoclonal antibody blockade
annotated property: definition
annotated target: Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: monoclonal antibody blockade
annotated property: has_exact_synonym
annotated target: mab blockade
has_synonym_type: Unique short label curated by PSI-MI

phenotype-based detection assay
type: Class
subclass of: experimental interaction detection
definition: Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor.
created by: orchard
creation date: 2011-07-05T11:24:37Z
has_exact_synonym: phenotype-based
has_obo_namespace: PSI-MI
id: MI:1088

Axiom
annotated source: phenotype-based detection assay
annotated property: definition
annotated target: Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor.
database_cross_reference: PMID:14755292

Axiom
annotated source: phenotype-based detection assay
annotated property: has_exact_synonym
annotated target: phenotype-based
has_synonym_type: Unique short label curated by PSI-MI

nuclear translocation assay
type: Class
subclass of: phenotype-based detection assay
definition: Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules.
created by: orchard
creation date: 2011-07-05T11:27:16Z
has_exact_synonym: nuclear translocation
has_obo_namespace: PSI-MI
id: MI:1089
in_subset: PSI-MI slim

Axiom
annotated source: nuclear translocation assay
annotated property: definition
annotated target: Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules.
database_cross_reference: PMID:21684252

Axiom
annotated source: nuclear translocation assay
annotated property: has_exact_synonym
annotated target: nuclear translocation
has_synonym_type: Unique short label curated by PSI-MI

bimane label
type: Class
subclass of: fluorescent dye label
definition: Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione.
created by: orchard
creation date: 2011-07-05T12:03:52Z
has_exact_synonym: bimane
has_obo_namespace: PSI-MI
id: MI:1090
in_subset: PSI-MI slim

Axiom
annotated source: bimane label
annotated property: definition
annotated target: Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione.
database_cross_reference: PMID:7378449

Axiom
annotated source: bimane label
annotated property: has_exact_synonym
annotated target: bimane
has_synonym_type: Unique short label curated by PSI-MI

publication title
type: Class
subclass of: bibliographic attribute name
definition: Title of the publication.
created by: orchard
creation date: 2011-07-05T12:07:49Z
has_exact_synonym: title
has_obo_namespace: PSI-MI
id: MI:1091
in_subset: PSI-MI slim

Axiom
annotated source: publication title
annotated property: definition
annotated target: Title of the publication.
database_cross_reference: PMID:14755292

Axiom
annotated source: publication title
annotated property: has_exact_synonym
annotated target: title
has_synonym_type: Unique short label curated by PSI-MI

atto label
type: Class
subclass of: fluorescent dye label
definition: Fluorescent dyes - spectral range 500 to 700 nm.
created by: orchard
creation date: 2011-07-05T12:14:52Z
has_exact_synonym: atto label
has_obo_namespace: PSI-MI
id: MI:1092

Axiom
annotated source: atto label
annotated property: definition
annotated target: Fluorescent dyes - spectral range 500 to 700 nm.
database_cross_reference: PMID:14755292

Axiom
annotated source: atto label
annotated property: has_exact_synonym
annotated target: atto label
has_synonym_type: Unique short label curated by PSI-MI

bibliographic attribute name
type: Class
subclass of: experiment attribute name
definition: Attributes specific to the publication.
created by: orchard
creation date: 2011-07-05T12:55:21Z
has_exact_synonym: bib attribute
has_exact_synonym: publication attribute
has_obo_namespace: PSI-MI
id: MI:1093
in_subset: PSI-MI slim

Axiom
annotated source: bibliographic attribute name
annotated property: definition
annotated target: Attributes specific to the publication.
database_cross_reference: PMID:14755292

Axiom
annotated source: bibliographic attribute name
annotated property: has_exact_synonym
annotated target: bib attribute
has_synonym_type: Unique short label curated by PSI-MI

genome databases
type: Class
subclass of: sequence database
definition: Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences.
created by: orchard
creation date: 2011-07-06T07:57:46Z
has_exact_synonym: genome databases
has_obo_namespace: PSI-MI
id: MI:1094
in_subset: PSI-MI slim

Axiom
annotated source: genome databases
annotated property: definition
annotated target: Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences.
database_cross_reference: PMID:14755292

Axiom
annotated source: genome databases
annotated property: has_exact_synonym
annotated target: genome databases
has_synonym_type: Unique short label curated by PSI-MI

hgnc
type: Class
subclass of: gene database
definition: HGNC is the nomenclature committee responsible for the naming of human genes.
created by: orchard
creation date: 2011-07-06T08:02:03Z
has_exact_synonym: Human Genome Nomenclature Committee
has_exact_synonym: hgnc
has_obo_namespace: PSI-MI
id: MI:1095

Axiom
annotated source: hgnc
annotated property: definition
annotated target: HGNC is the nomenclature committee responsible for the naming of human genes.
database_cross_reference: PMID:20929869

Axiom
annotated source: hgnc
annotated property: has_exact_synonym
annotated target: Human Genome Nomenclature Committee
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: hgnc
annotated property: has_exact_synonym
annotated target: hgnc
has_synonym_type: Unique short label curated by PSI-MI

protein sequence databases
type: Class
subclass of: sequence database
definition: Databases dedicated to the collection and annotation of protein sequences.
created by: orchard
creation date: 2011-07-06T08:10:40Z
has_exact_synonym: protein seq db
has_obo_namespace: PSI-MI
id: MI:1096
in_subset: PSI-MI slim

Axiom
annotated source: protein sequence databases
annotated property: definition
annotated target: Databases dedicated to the collection and annotation of protein sequences.
database_cross_reference: PMID:21447597

Axiom
annotated source: protein sequence databases
annotated property: has_exact_synonym
annotated target: protein seq db
has_synonym_type: Unique short label curated by PSI-MI

uniprot
type: Class
subclass of: protein sequence databases
definition: UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation.
created by: orchard
creation date: 2011-07-06T08:14:40Z
has_exact_synonym: uniprot
has_obo_namespace: PSI-MI
id: MI:1097
in_subset: PSI-MI slim

Axiom
annotated source: uniprot
annotated property: definition
annotated target: UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation.
database_cross_reference: PMID:21051339

Axiom
annotated source: uniprot
annotated property: has_exact_synonym
annotated target: uniprot
has_synonym_type: Unique short label curated by PSI-MI

uniprot/swiss-prot
type: Class
subclass of: uniprot knowledge base
definition: UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator. http://www.uniprot.org
created by: orchard
creation date: 2011-07-06T08:17:34Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: UniProt
has_exact_synonym: swiss-prot
has_obo_namespace: PSI-MI
id: MI:1098
in_subset: PSI-MI slim

Axiom
annotated source: uniprot/swiss-prot
annotated property: definition
annotated target: UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator. http://www.uniprot.org
database_cross_reference: PMID:14681372
database_cross_reference: PMID:21447597

(([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?)
type: Axiom
annotated source: uniprot/swiss-prot
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: uniprot/swiss-prot
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.uniprot.org/uniprotkb/${ac}/entry

Axiom
annotated source: uniprot/swiss-prot
annotated property: has_exact_synonym
annotated target: UniProt
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: uniprot/swiss-prot
annotated property: has_exact_synonym
annotated target: swiss-prot
has_synonym_type: Unique short label curated by PSI-MI

uniprot/trembl
type: Class
subclass of: uniprot knowledge base
definition: UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification. http://www.uniprot.org
created by: orchard
creation date: 2011-07-06T08:20:24Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: UniProt
has_exact_synonym: trembl
has_obo_namespace: PSI-MI
id: MI:1099
in_subset: PSI-MI slim

Axiom
annotated source: uniprot/trembl
annotated property: definition
annotated target: UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification. http://www.uniprot.org
database_cross_reference: PMID:14681372
database_cross_reference: PMID:21447597

(([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})(-[0-9]+)?(-PRO_[0-9]{10})?)
type: Axiom
annotated source: uniprot/trembl
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: uniprot/trembl
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.uniprot.org/uniprotkb/${ac}/entry

Axiom
annotated source: uniprot/trembl
annotated property: has_exact_synonym
annotated target: UniProt
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: uniprot/trembl
annotated property: has_exact_synonym
annotated target: trembl
has_synonym_type: Unique short label curated by PSI-MI

bioactive entity
type: Class
subclass of: interactor type
definition: Molecules showing activity in a living system but not encoded by a genomic sequence.
created by: orchard
creation date: 2011-07-06T08:23:48Z
has_exact_synonym: bioactive entity
has_obo_namespace: PSI-MI
id: MI:1100

Axiom
annotated source: bioactive entity
annotated property: definition
annotated target: Molecules showing activity in a living system but not encoded by a genomic sequence.
database_cross_reference: PMID:14760721

Axiom
annotated source: bioactive entity
annotated property: has_exact_synonym
annotated target: bioactive entity
has_synonym_type: Unique short label curated by PSI-MI

standard inchi key
type: Class
subclass of: inchi key
definition: The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes).
created by: orchard
creation date: 2014-01-21T10:14:02Z
has_obo_namespace: PSI-MI
id: MI:1101
in_subset: PSI-MI slim

Axiom
annotated source: standard inchi key
annotated property: definition
annotated target: The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes).
database_cross_reference: PMID:23343401

mapped-identity
type: Class
subclass of: cross-reference type
definition: Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database.
created by: orchard
creation date: 2011-07-06T09:07:02Z
has_exact_synonym: mapped-identity
has_obo_namespace: PSI-MI
id: MI:1102

Axiom
annotated source: mapped-identity
annotated property: definition
annotated target: Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database.
database_cross_reference: PMID:14760721

Axiom
annotated source: mapped-identity
annotated property: has_exact_synonym
annotated target: mapped-identity
has_synonym_type: Unique short label curated by PSI-MI

solution state nmr
type: Class
subclass of: nuclear magnetic resonance
definition: NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp transitions, due to averaging of anisotropic NMR interactions by rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations.
created by: orchard
creation date: 2011-07-06T09:16:45Z
has_exact_synonym: solution nmr
has_exact_synonym: solution state nmr
has_obo_namespace: PSI-MI
id: MI:1103
in_subset: PSI-MI slim

Axiom
annotated source: solution state nmr
annotated property: definition
annotated target: NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp transitions, due to averaging of anisotropic NMR interactions by rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations.
database_cross_reference: PMID:20951674

Axiom
annotated source: solution state nmr
annotated property: has_exact_synonym
annotated target: solution nmr
has_synonym_type: Unique short label curated by PSI-MI

solid state nmr
type: Class
subclass of: nuclear magnetic resonance
definition: Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full effects of anisotropic or orientation-dependent interactions are observed in the spectrum.
created by: orchard
creation date: 2011-07-06T09:23:11Z
has_exact_synonym: solid state nmr
has_exact_synonym: ssnmr
has_obo_namespace: PSI-MI
id: MI:1104
in_subset: PSI-MI slim

Axiom
annotated source: solid state nmr
annotated property: definition
annotated target: Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full effects of anisotropic or orientation-dependent interactions are observed in the spectrum.
database_cross_reference: PMID:20951674

Axiom
annotated source: solid state nmr
annotated property: has_exact_synonym
annotated target: solid state nmr
has_synonym_type: Unique short label curated by PSI-MI

biocyc
type: Class
subclass of: pathways database
definition: BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/).
created by: orchard
creation date: 2011-07-06T09:43:03Z
has_exact_synonym: biocyc
has_obo_namespace: PSI-MI
id: MI:1105
in_subset: PSI-MI slim

Axiom
annotated source: biocyc
annotated property: definition
annotated target: BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/).
database_cross_reference: PMID:19850718

Axiom
annotated source: biocyc
annotated property: has_exact_synonym
annotated target: biocyc
has_synonym_type: Unique short label curated by PSI-MI

pathways database
type: Class
subclass of: interaction database
definition: Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways.
created by: orchard
creation date: 2011-07-07T02:52:18Z
has_exact_synonym: pathways db
has_obo_namespace: PSI-MI
id: MI:1106
in_subset: PSI-MI slim

Axiom
annotated source: pathways database
annotated property: definition
annotated target: Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways.
database_cross_reference: PMID:14755292

Axiom
annotated source: pathways database
annotated property: has_exact_synonym
annotated target: pathways db
has_synonym_type: Unique short label curated by PSI-MI

pid
type: Class
subclass of: pathways database
definition: Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/).
created by: orchard
creation date: 2011-07-07T03:00:27Z
has_exact_synonym: pathways interaction database
has_exact_synonym: pid
has_obo_namespace: PSI-MI
id: MI:1107

Axiom
annotated source: pid
annotated property: definition
annotated target: Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/).
database_cross_reference: PMID:18832364

Axiom
annotated source: pid
annotated property: has_exact_synonym
annotated target: pid
has_synonym_type: Unique short label curated by PSI-MI

biocarta
type: Class
subclass of: pathways database
definition: BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways.
created by: orchard
creation date: 2011-07-07T03:05:55Z
has_exact_synonym: biocarta
has_obo_namespace: PSI-MI
id: MI:1108

Axiom
annotated source: biocarta
annotated property: definition
annotated target: BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways.
database_cross_reference: PMID:14760721

Axiom
annotated source: biocarta
annotated property: has_exact_synonym
annotated target: biocarta
has_synonym_type: Unique short label curated by PSI-MI

gene database
type: Class
subclass of: participant database
definition: Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes.
created by: orchard
creation date: 2011-07-08T08:00:33Z
has_exact_synonym: gene dbs
has_obo_namespace: PSI-MI
id: MI:1109
in_subset: PSI-MI slim

Axiom
annotated source: gene database
annotated property: definition
annotated target: Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes.
database_cross_reference: PMID:14755292

Axiom
annotated source: gene database
annotated property: has_exact_synonym
annotated target: gene dbs
has_synonym_type: Unique short label curated by PSI-MI

predicted interaction
type: Class
subclass of: interaction type
definition: Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method.
created by: orchard
creation date: 2011-08-03T11:14:11Z
has_exact_synonym: predicted
has_obo_namespace: PSI-MI
id: MI:1110
in_subset: PSI-MI slim

Axiom
annotated source: predicted interaction
annotated property: definition
annotated target: Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method.
database_cross_reference: PMID:14755292

Axiom
annotated source: predicted interaction
annotated property: has_exact_synonym
annotated target: predicted
has_synonym_type: Unique short label curated by PSI-MI

two hybrid bait or prey pooling approach
type: Class
subclass of: two hybrid pooling approach
definition: Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
created by: orchard
creation date: 2011-09-29T03:19:21Z
has_obo_namespace: PSI-MI
id: MI:1111
in_subset: PSI-MI slim

Axiom
annotated source: two hybrid bait or prey pooling approach
annotated property: definition
annotated target: Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
database_cross_reference: PMID:11283351
database_cross_reference: PMID:20946815

two hybrid prey pooling approach
type: Class
subclass of: two hybrid bait or prey pooling approach
definition: Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
created by: orchard
creation date: 2011-09-29T03:21:01Z
has_obo_namespace: PSI-MI
id: MI:1112
in_subset: PSI-MI slim

Axiom
annotated source: two hybrid prey pooling approach
annotated property: definition
annotated target: Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
database_cross_reference: PMID:20946815

two hybrid bait and prey pooling approach
type: Class
subclass of: two hybrid pooling approach
definition: def
created by: orchard
creation date: 2011-09-29T03:23:17Z
has_obo_namespace: PSI-MI
id: MI:1113
in_subset: PSI-MI slim

Axiom
annotated source: two hybrid bait and prey pooling approach
annotated property: definition
annotated target: def
database_cross_reference: PMID:10655498

virhostnet
type: Class
subclass of: interaction database
definition: A database of viral-host interactions.
created by: orchard
creation date: 2011-10-19T01:28:24Z
has_obo_namespace: PSI-MI
id: MI:1114
in_subset: PSI-MI slim

Axiom
annotated source: virhostnet
annotated property: definition
annotated target: A database of viral-host interactions.
database_cross_reference: PMID:18984613

spike
type: Class
subclass of: pathways database
definition: SPIKE
created by: orchard
creation date: 2011-11-09T10:27:04Z
has_exact_synonym: Signalling Pathways Integrated Knowledge Engine
has_obo_namespace: PSI-MI
id: MI:1115
in_subset: PSI-MI slim

Axiom
annotated source: spike
annotated property: definition
annotated target: SPIKE
database_cross_reference: PMID:21097778

genemania
type: Class
subclass of: interaction database
definition: GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity.
created by: orchard
creation date: 2011-11-09T02:13:28Z
has_obo_namespace: PSI-MI
id: MI:1116
in_subset: PSI-MI slim

Axiom
annotated source: genemania
annotated property: definition
annotated target: GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity.
database_cross_reference: PMID:20576703

topfind
type: Class
subclass of: interaction database
definition: TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided.
created by: orchard
creation date: 2011-11-16T11:09:25Z
has_exact_synonym: Termini-oriented protein function inferred database
has_obo_namespace: PSI-MI
id: MI:1117
in_subset: PSI-MI slim

Axiom
annotated source: topfind
annotated property: definition
annotated target: TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided.
database_cross_reference: PMID:21822272

enhanced yellow fluorescent protein tag
type: Class
subclass of: yellow fluorescent protein tag
definition: A variation of yellow fluorescent protein derived from eGFP.
created by: orchard
creation date: 2011-11-24T03:17:33Z
has_exact_synonym: eyfp
has_obo_namespace: PSI-MI
id: MI:1118
in_subset: PSI-MI slim

Axiom
annotated source: enhanced yellow fluorescent protein tag
annotated property: definition
annotated target: A variation of yellow fluorescent protein derived from eGFP.
database_cross_reference: PMID:10929120

Axiom
annotated source: enhanced yellow fluorescent protein tag
annotated property: has_exact_synonym
annotated target: eyfp
has_synonym_type: Unique short label curated by PSI-MI

nYFP
type: Class
subclass of: yellow fluorescent protein tag
subclass of: bifc tag
definition: n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
created by: orchard
creation date: 2011-11-24T03:30:18Z
has_obo_namespace: PSI-MI
has_related_synonym: N-terminal part of YFP
id: MI:1119
in_subset: PSI-MI slim

Axiom
annotated source: nYFP
annotated property: definition
annotated target: n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
database_cross_reference: PMID:11983170

cYFP
type: Class
subclass of: yellow fluorescent protein tag
subclass of: bifc tag
definition: c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
created by: orchard
creation date: 2011-11-24T03:43:07Z
has_obo_namespace: PSI-MI
has_related_synonym: C-terminal part of YFP
id: MI:1120
in_subset: PSI-MI slim

Axiom
annotated source: cYFP
annotated property: definition
annotated target: c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
database_cross_reference: PMID:11983170

ceYFP
type: Class
subclass of: enhanced yellow fluorescent protein tag
definition: c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
created by: orchard
creation date: 2011-11-24T03:43:30Z
has_obo_namespace: PSI-MI
has_related_synonym: C-terminal part of EYFP
id: MI:1121
in_subset: PSI-MI slim

Axiom
annotated source: ceYFP
annotated property: definition
annotated target: c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
database_cross_reference: PMID:11983170

neYFP
type: Class
subclass of: enhanced yellow fluorescent protein tag
definition: n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
created by: orchard
creation date: 2011-11-24T03:44:40Z
has_obo_namespace: PSI-MI
has_related_synonym: N-terminal part of EYFP
id: MI:1122
in_subset: PSI-MI slim

Axiom
annotated source: neYFP
annotated property: definition
annotated target: n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
database_cross_reference: PMID:11983170

bindingdb
type: Class
subclass of: interaction database
definition: BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org
created by: orchard
creation date: 2011-11-28T08:55:26Z
has_obo_namespace: PSI-MI
id: MI:1123
in_subset: PSI-MI slim

Axiom
annotated source: bindingdb
annotated property: definition
annotated target: BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org
database_cross_reference: PMID:11812264
database_cross_reference: PMID:11836221
database_cross_reference: PMID:11987162
database_cross_reference: PMID:17145705

pathwaycommons
type: Class
subclass of: pathways database
definition: Allows the user to browse and search pathways across multiple public pathway databases. http://www.pathwaycommons.org
created by: orchard
creation date: 2011-11-30T03:04:14Z
has_exact_synonym: Pathway Commons
has_obo_namespace: PSI-MI
id: MI:1124
in_subset: PSI-MI slim

Axiom
annotated source: pathwaycommons
annotated property: definition
annotated target: Allows the user to browse and search pathways across multiple public pathway databases. http://www.pathwaycommons.org
database_cross_reference: PMID:21071392

direct binding region
type: Class
subclass of: sufficient binding region
definition: The defined region of protein which makes physical contact with the interacting partner.
created by: orchard
creation date: 2012-01-03T01:10:25Z
has_exact_synonym: direct binding
has_obo_namespace: PSI-MI
id: MI:1125
in_subset: PSI-MI slim
comment: Should normally be used with X-ray crystallography or NMR data.

Axiom
annotated source: direct binding region
annotated property: definition
annotated target: The defined region of protein which makes physical contact with the interacting partner.
database_cross_reference: PMID:14755292

Axiom
annotated source: direct binding region
annotated property: has_exact_synonym
annotated target: direct binding
has_synonym_type: Unique short label curated by PSI-MI

self interaction
type: Class
subclass of: direct interaction
definition: Intra-molecular interaction between two or more regions of the same molecule.
created by: orchard
creation date: 2012-01-03T01:19:22Z
has_obo_namespace: PSI-MI
id: MI:1126
in_subset: PSI-MI slim
comment: The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.

Axiom
annotated source: self interaction
annotated property: definition
annotated target: Intra-molecular interaction between two or more regions of the same molecule.
database_cross_reference: PMID:14755292

putative self interaction
type: Class
subclass of: direct interaction
definition: Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules.
created by: orchard
creation date: 2012-01-03T01:21:58Z
has_obo_namespace: PSI-MI
id: MI:1127
in_subset: PSI-MI slim
comment: The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.

Axiom
annotated source: putative self interaction
annotated property: definition
annotated target: Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules.
database_cross_reference: PMID:14755292

mutation disrupting interaction strength
type: Class
subclass of: mutation disrupting interaction
definition: Region of a molecule whose mutation or deletion totally disrupts an interaction strength.
created by: orchard
creation date: 2012-01-03T01:36:37Z
has_exact_synonym: mutation disrupting strength
has_obo_namespace: PSI-MI
id: MI:1128
in_subset: PSI-MI slim

Axiom
annotated source: mutation disrupting interaction strength
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion totally disrupts an interaction strength.
database_cross_reference: PMID:14755292

Axiom
annotated source: mutation disrupting interaction strength
annotated property: has_exact_synonym
annotated target: mutation disrupting strength
has_synonym_type: Unique short label curated by PSI-MI

mutation disrupting interaction rate
type: Class
subclass of: mutation disrupting interaction
definition: Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction)..
created by: orchard
creation date: 2012-01-03T01:37:43Z
has_exact_synonym: mutation disrupting rate
has_obo_namespace: PSI-MI
id: MI:1129
in_subset: PSI-MI slim

Axiom
annotated source: mutation disrupting interaction rate
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction)..
database_cross_reference: PMID:14755292

Axiom
annotated source: mutation disrupting interaction rate
annotated property: has_exact_synonym
annotated target: mutation disrupting rate
has_synonym_type: Unique short label curated by PSI-MI

mutation decreasing interaction rate
type: Class
subclass of: mutation decreasing interaction
definition: Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
created by: orchard
creation date: 2012-01-03T01:38:58Z
has_exact_synonym: mutation decreasing rate
has_obo_namespace: PSI-MI
id: MI:1130
in_subset: PSI-MI slim

Axiom
annotated source: mutation decreasing interaction rate
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
database_cross_reference: PMID:14755292

Axiom
annotated source: mutation decreasing interaction rate
annotated property: has_exact_synonym
annotated target: mutation decreasing rate
has_synonym_type: Unique short label curated by PSI-MI

mutation increasing interaction rate
type: Class
subclass of: mutation increasing interaction
definition: Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
created by: orchard
creation date: 2012-01-03T01:45:09Z
has_exact_synonym: mutation increasing rate
has_obo_namespace: PSI-MI
id: MI:1131
in_subset: PSI-MI slim

Axiom
annotated source: mutation increasing interaction rate
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
database_cross_reference: PMID:14577292

Axiom
annotated source: mutation increasing interaction rate
annotated property: has_exact_synonym
annotated target: mutation increasing rate
has_synonym_type: Unique short label curated by PSI-MI

mutation increasing interaction strength
type: Class
subclass of: mutation increasing interaction
definition: Region of a molecule whose mutation or deletion increases significantly interaction strength.
created by: orchard
creation date: 2012-01-03T01:45:42Z
has_exact_synonym: mutation increasing strength
has_obo_namespace: PSI-MI
id: MI:1132
in_subset: PSI-MI slim

Axiom
annotated source: mutation increasing interaction strength
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion increases significantly interaction strength.
database_cross_reference: PMID:14577292

Axiom
annotated source: mutation increasing interaction strength
annotated property: has_exact_synonym
annotated target: mutation increasing strength
has_synonym_type: Unique short label curated by PSI-MI

mutation decreasing interaction strength
type: Class
subclass of: mutation decreasing interaction
definition: Region of a molecule whose mutation or deletion decreases significantly interaction strength.
created by: orchard
creation date: 2012-01-03T01:48:40Z
has_exact_synonym: mutation decreasing strength
has_obo_namespace: PSI-MI
id: MI:1133
in_subset: PSI-MI slim

Axiom
annotated source: mutation decreasing interaction strength
annotated property: definition
annotated target: Region of a molecule whose mutation or deletion decreases significantly interaction strength.
database_cross_reference: PMID:14755292

Axiom
annotated source: mutation decreasing interaction strength
annotated property: has_exact_synonym
annotated target: mutation decreasing strength
has_synonym_type: Unique short label curated by PSI-MI

mcherry fluorescent protein tag
type: Class
subclass of: red fluorescent protein tag
definition: mCherry is a red monomer which matures extremely rapidly, making it possible to see results very soon after activating transcription. It is highly photostable and resistant to photobleaching. Excitation maximum: 587 nm. Emission maximum: 610 nm.
created by: orchard
creation date: 2012-01-03T02:53:23Z
has_exact_synonym: mcherry
has_obo_namespace: PSI-MI
id: MI:1134

Axiom
annotated source: mcherry fluorescent protein tag
annotated property: has_exact_synonym
annotated target: mcherry
has_synonym_type: Unique short label curated by PSI-MI

venus fluorescent protein tag
type: Class
subclass of: yellow fluorescent protein tag
definition: Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively.
created by: orchard
creation date: 2012-01-03T03:05:01Z
has_exact_synonym: venus
has_obo_namespace: PSI-MI
id: MI:1135
in_subset: PSI-MI slim

Axiom
annotated source: venus fluorescent protein tag
annotated property: definition
annotated target: Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively.
database_cross_reference: PMID:14755292

Axiom
annotated source: venus fluorescent protein tag
annotated property: has_exact_synonym
annotated target: venus
has_synonym_type: Unique short label curated by PSI-MI

kusabira-green protein tag
type: Class
subclass of: green fluorescent protein tag
definition: Monomeric coral fluorescent reporter protein.
created by: orchard
creation date: 2012-01-03T03:10:28Z
has_exact_synonym: kusabira-green
has_obo_namespace: PSI-MI
id: MI:1136
in_subset: PSI-MI slim

Axiom
annotated source: kusabira-green protein tag
annotated property: definition
annotated target: Monomeric coral fluorescent reporter protein.
database_cross_reference: PMID:14755292

Axiom
annotated source: kusabira-green protein tag
annotated property: has_exact_synonym
annotated target: kusabira-green
has_synonym_type: Unique short label curated by PSI-MI

carboxylation assay
type: Class
subclass of: enzymatic study
definition: The measurement of a the introduction of a carboxylic acid group into a substrate.
created by: orchard
creation date: 2012-01-03T03:17:56Z
has_exact_synonym: carboxylation assay
has_obo_namespace: PSI-MI
id: MI:1137
in_subset: PSI-MI slim

Axiom
annotated source: carboxylation assay
annotated property: definition
annotated target: The measurement of a the introduction of a carboxylic acid group into a substrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carboxylation assay
annotated property: has_exact_synonym
annotated target: carboxylation assay
has_synonym_type: Unique short label curated by PSI-MI

decarboxylation assay
type: Class
subclass of: enzymatic study
definition: The measurement of a the introduction of a carboxylic acid group into a substrate.
created by: orchard
creation date: 2012-01-03T03:22:04Z
has_exact_synonym: decarboxxylation assay
has_obo_namespace: PSI-MI
id: MI:1138
in_subset: PSI-MI slim

Axiom
annotated source: decarboxylation assay
annotated property: definition
annotated target: The measurement of a the introduction of a carboxylic acid group into a substrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: decarboxylation assay
annotated property: has_exact_synonym
annotated target: decarboxxylation assay
has_synonym_type: Unique short label curated by PSI-MI

carboxylation reaction
type: Class
subclass of: enzymatic reaction
definition: Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins.
created by: orchard
creation date: 2012-01-03T03:24:05Z
has_exact_synonym: carboxylation
has_obo_namespace: PSI-MI
id: MI:1139
in_subset: PSI-MI slim

Axiom
annotated source: carboxylation reaction
annotated property: definition
annotated target: Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins.
database_cross_reference: PMID:14755292

Axiom
annotated source: carboxylation reaction
annotated property: has_exact_synonym
annotated target: carboxylation
has_synonym_type: Unique short label curated by PSI-MI

decarboxylation reaction
type: Class
subclass of: enzymatic reaction
definition: Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).
created by: orchard
creation date: 2012-01-03T03:31:42Z
has_exact_synonym: decarboxylation
has_obo_namespace: PSI-MI
id: MI:1140
in_subset: PSI-MI slim

Axiom
annotated source: decarboxylation reaction
annotated property: definition
annotated target: Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).
database_cross_reference: PMID:14755292

Axiom
annotated source: decarboxylation reaction
annotated property: has_exact_synonym
annotated target: decarboxylation
has_synonym_type: Unique short label curated by PSI-MI

s tag
type: Class
subclass of: tag
definition: S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser.
created by: orchard
creation date: 2012-01-03T03:37:51Z
has_obo_namespace: PSI-MI
id: MI:1141
in_subset: PSI-MI slim

Axiom
annotated source: s tag
annotated property: definition
annotated target: S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser.
database_cross_reference: PMID:14755292

aminoacylation assay
type: Class
subclass of: enzymatic study
definition: The measurement of the addition of an aminoacyl group to a compound.
created by: orchard
creation date: 2012-01-03T03:46:46Z
has_exact_synonym: aminoacylation
has_obo_namespace: PSI-MI
id: MI:1142
in_subset: PSI-MI slim

Axiom
annotated source: aminoacylation assay
annotated property: definition
annotated target: The measurement of the addition of an aminoacyl group to a compound.
database_cross_reference: PMID:14755292

Axiom
annotated source: aminoacylation assay
annotated property: has_exact_synonym
annotated target: aminoacylation
has_synonym_type: Unique short label curated by PSI-MI

aminoacylation reaction
type: Class
subclass of: enzymatic reaction
definition: Aminoacylation is the process of adding an aminoacyl group to a compound.
created by: orchard
creation date: 2012-01-03T03:49:50Z
has_exact_synonym: aminoacylation
has_obo_namespace: PSI-MI
id: MI:1143
in_subset: PSI-MI slim

Axiom
annotated source: aminoacylation reaction
annotated property: definition
annotated target: Aminoacylation is the process of adding an aminoacyl group to a compound.
database_cross_reference: PMID:14755292

Axiom
annotated source: aminoacylation reaction
annotated property: has_exact_synonym
annotated target: aminoacylation
has_synonym_type: Unique short label curated by PSI-MI

protein a tag visualisation
type: Class
subclass of: tag visualisation
definition: Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A.
created by: orchard
creation date: 2012-01-03T03:54:35Z
has_exact_synonym: protein a visualisation
has_obo_namespace: PSI-MI
id: MI:1144
in_subset: PSI-MI slim

Axiom
annotated source: protein a tag visualisation
annotated property: definition
annotated target: Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A.
database_cross_reference: PMID:14755292

Axiom
annotated source: protein a tag visualisation
annotated property: has_exact_synonym
annotated target: protein a visualisation
has_synonym_type: Unique short label curated by PSI-MI

phospholipase assay
type: Class
subclass of: enzymatic study
definition: A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
created by: orchard
creation date: 2012-01-03T04:04:16Z
has_obo_namespace: PSI-MI
id: MI:1145
in_subset: PSI-MI slim

Axiom
annotated source: phospholipase assay
annotated property: definition
annotated target: A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
database_cross_reference: PMID:14755292

phospholipase reaction
type: Class
subclass of: enzymatic reaction
definition: Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
created by: orchard
creation date: 2012-01-03T04:08:14Z
has_obo_namespace: PSI-MI
id: MI:1146
in_subset: PSI-MI slim

Axiom
annotated source: phospholipase reaction
annotated property: definition
annotated target: Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
database_cross_reference: PMID:14755292

ampylation assay
type: Class
subclass of: enzymatic study
definition: Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
created by: orchard
creation date: 2012-01-03T04:18:27Z
has_exact_synonym: ampylation assay
has_obo_namespace: PSI-MI
id: MI:1147
in_subset: PSI-MI slim

Axiom
annotated source: ampylation assay
annotated property: definition
annotated target: Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
database_cross_reference: PMID:14755292

Axiom
annotated source: ampylation assay
annotated property: has_exact_synonym
annotated target: ampylation assay
has_synonym_type: Unique short label curated by PSI-MI

ampylation reaction
type: Class
subclass of: enzymatic reaction
definition: AMPylation, previously known as adenylylation, is formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
created by: orchard
creation date: 2012-01-03T04:21:12Z
has_exact_synonym: ampylation
has_obo_namespace: PSI-MI
id: MI:1148
in_subset: PSI-MI slim

Axiom
annotated source: ampylation reaction
annotated property: definition
annotated target: AMPylation, previously known as adenylylation, is formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
database_cross_reference: PMID:14755292

Axiom
annotated source: ampylation reaction
annotated property: has_exact_synonym
annotated target: ampylation
has_synonym_type: Unique short label curated by PSI-MI

cooperative interaction
type: Class
subclass of: molecular interaction
definition: A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema.
created by: orchard
creation date: 2012-06-07T12:21:30Z
has_exact_synonym: cooperativity
has_obo_namespace: PSI-MI
id: MI:1149
in_subset: PSI-MI slim

Axiom
annotated source: cooperative interaction
annotated property: definition
annotated target: A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema.
database_cross_reference: PMID:18641616

affected interaction
type: Class
subclass of: interaction attribute name
subclass of: cooperative interaction
definition: For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id.
created by: orchard
creation date: 2012-06-07T12:26:42Z
has_obo_namespace: PSI-MI
id: MI:1150
in_subset: PSI-MI slim

Axiom
annotated source: affected interaction
annotated property: definition
annotated target: For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id.
database_cross_reference: PMID:18641616

participant-ref
type: Class
subclass of: feature attribute name
definition: Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction.
created by: orchard
creation date: 2012-06-07T12:30:48Z
has_obo_namespace: PSI-MI
id: MI:1151
in_subset: PSI-MI slim

Axiom
annotated source: participant-ref
annotated property: definition
annotated target: Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction.
database_cross_reference: PMID:18641616

cooperative effect value
type: Class
subclass of: interaction attribute name
subclass of: cooperative interaction
definition: This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification.
created by: orchard
creation date: 2012-06-07T12:35:01Z
has_exact_synonym: cooperative coupling
has_obo_namespace: PSI-MI
id: MI:1152
in_subset: PSI-MI slim

Axiom
annotated source: cooperative effect value
annotated property: definition
annotated target: This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification.
database_cross_reference: PMID:18706817

cooperative effect outcome
type: Class
subclass of: cooperative interaction
definition: For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished.
created by: orchard
creation date: 2012-06-07T12:40:41Z
has_obo_namespace: PSI-MI
id: MI:1153

Axiom
annotated source: cooperative effect outcome
annotated property: definition
annotated target: For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished.
database_cross_reference: PMID:18706817

positive cooperative effect
type: Class
subclass of: interaction attribute name
subclass of: cooperative effect outcome
definition: This term specifies that an interaction augments a subsequent interaction.
created by: orchard
creation date: 2012-06-07T12:42:19Z
has_obo_namespace: PSI-MI
id: MI:1154

Axiom
annotated source: positive cooperative effect
annotated property: definition
annotated target: This term specifies that an interaction augments a subsequent interaction.
database_cross_reference: PMID:18706817

negative cooperative effect
type: Class
subclass of: interaction attribute name
subclass of: cooperative effect outcome
definition: This term specifies that an interaction diminishes a subsequent interaction.
created by: orchard
creation date: 2012-06-07T12:43:48Z
has_obo_namespace: PSI-MI
id: MI:1155
in_subset: PSI-MI slim

Axiom
annotated source: negative cooperative effect
annotated property: definition
annotated target: This term specifies that an interaction diminishes a subsequent interaction.
database_cross_reference: PMID:18706817

cooperative mechanism
type: Class
subclass of: cooperative interaction
definition: For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect.
created by: orchard
creation date: 2012-06-07T12:46:30Z
has_obo_namespace: PSI-MI
id: MI:1156
in_subset: PSI-MI slim

Axiom
annotated source: cooperative mechanism
annotated property: definition
annotated target: For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect.
database_cross_reference: PMID:18641616

allostery
type: Class
subclass of: interaction attribute name
subclass of: cooperative mechanism
definition: Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event.
created by: orchard
creation date: 2012-06-07T12:50:20Z
has_exact_synonym: allosteric regulation
has_obo_namespace: PSI-MI
id: MI:1157
in_subset: PSI-MI slim

Axiom
annotated source: allostery
annotated property: definition
annotated target: Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event.
database_cross_reference: PMID:18641616
database_cross_reference: PMID:18706817

pre-assembly
type: Class
subclass of: interaction attribute name
subclass of: cooperative mechanism
definition: A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists.
created by: orchard
creation date: 2012-06-07T12:52:44Z
has_obo_namespace: PSI-MI
id: MI:1158
in_subset: PSI-MI slim

Axiom
annotated source: pre-assembly
annotated property: definition
annotated target: A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists.
database_cross_reference: PMID:18641616

allosteric molecule
type: Class
subclass of: biological role
subclass of: interaction attribute name
subclass of: cooperative interaction
definition: A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id.
created by: orchard
creation date: 2012-06-07T12:55:09Z
has_obo_namespace: PSI-MI
id: MI:1159
in_subset: PSI-MI slim

Axiom
annotated source: allosteric molecule
annotated property: definition
annotated target: A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id.
database_cross_reference: PMID:18706817

allosteric effector
type: Class
subclass of: biological role
subclass of: interaction attribute name
subclass of: cooperative interaction
definition: A ligand that elicits an allosteric response upon binding to a target molecule.
created by: orchard
creation date: 2012-06-07T12:57:50Z
has_obo_namespace: PSI-MI
id: MI:1160
in_subset: PSI-MI slim

Axiom
annotated source: allosteric effector
annotated property: definition
annotated target: A ligand that elicits an allosteric response upon binding to a target molecule.
database_cross_reference: PMID:18706817

allosteric response
type: Class
subclass of: cooperative interaction
definition: This term describes the effect of an allosteric binding event. It specifies which properties of the allosteric molecule are altered, i.e. whether the interaction alters either (a) binding or (b) catalytic properties of the allosteric molecule at a site distinct from the allosteric site.
created by: orchard
creation date: 2012-06-07T01:05:17Z
has_obo_namespace: PSI-MI
id: MI:1161
in_subset: PSI-MI slim

allosteric k-type response
type: Class
subclass of: interaction attribute name
subclass of: allosteric response
definition: An allosteric response in which the affinity of a molecule is altered.
created by: orchard
creation date: 2012-06-07T01:08:01Z
has_obo_namespace: PSI-MI
id: MI:1162
in_subset: PSI-MI slim

Axiom
annotated source: allosteric k-type response
annotated property: definition
annotated target: An allosteric response in which the affinity of a molecule is altered.
database_cross_reference: PMID:18706817

allosteric v-type response
type: Class
subclass of: interaction attribute name
subclass of: allosteric response
definition: An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered.
created by: orchard
creation date: 2012-06-07T01:09:07Z
has_obo_namespace: PSI-MI
id: MI:1163
in_subset: PSI-MI slim

Axiom
annotated source: allosteric v-type response
annotated property: definition
annotated target: An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered.
database_cross_reference: PMID:18706817

allosteric mechanism
type: Class
subclass of: cooperative interaction
definition: The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector.
created by: orchard
creation date: 2012-06-07T01:10:45Z
has_obo_namespace: PSI-MI
id: MI:1164

allosteric change in structure
type: Class
subclass of: interaction attribute name
subclass of: allosteric mechanism
definition: The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties.
created by: orchard
creation date: 2012-06-07T01:16:20Z
has_obo_namespace: PSI-MI
id: MI:1165
in_subset: PSI-MI slim

Axiom
annotated source: allosteric change in structure
annotated property: definition
annotated target: The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties.
database_cross_reference: PMID:18706817

allosteric change in dynamics
type: Class
subclass of: interaction attribute name
subclass of: allosteric mechanism
definition: The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties.
created by: orchard
creation date: 2012-06-07T01:17:54Z
has_obo_namespace: PSI-MI
id: MI:1166
in_subset: PSI-MI slim

Axiom
annotated source: allosteric change in dynamics
annotated property: definition
annotated target: The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties.
database_cross_reference: PMID:18706817

allostery type
type: Class
subclass of: cooperative interaction
definition: This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled.
created by: orchard
creation date: 2012-06-07T01:19:57Z
has_obo_namespace: PSI-MI
id: MI:1167
in_subset: PSI-MI slim

Axiom
annotated source: allostery type
annotated property: definition
annotated target: This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled.
database_cross_reference: PMID:18706817

heterotropic allostery
type: Class
subclass of: interaction attribute name
subclass of: allostery type
definition: The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical.
created by: orchard
creation date: 2012-06-07T01:21:25Z
has_obo_namespace: PSI-MI
id: MI:1168
in_subset: PSI-MI slim

Axiom
annotated source: heterotropic allostery
annotated property: definition
annotated target: The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical.
database_cross_reference: PMID:18706817

homotropic allostery
type: Class
subclass of: interaction attribute name
subclass of: allostery type
definition: The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical.
created by: orchard
creation date: 2012-06-07T01:22:35Z
has_obo_namespace: PSI-MI
id: MI:1169
in_subset: PSI-MI slim

Axiom
annotated source: homotropic allostery
annotated property: definition
annotated target: The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical.
database_cross_reference: PMID:18706817

pre-assembly response
type: Class
subclass of: cooperative interaction
definition: This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components.
created by: orchard
creation date: 2012-06-07T01:24:42Z
has_obo_namespace: PSI-MI
id: MI:1170
in_subset: PSI-MI slim

Axiom
annotated source: pre-assembly response
annotated property: definition
annotated target: This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components.
database_cross_reference: PMID:18641616

composite binding site formation
type: Class
subclass of: interaction attribute name
subclass of: pre-assembly response
definition: The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex.
created by: orchard
creation date: 2012-06-07T01:25:50Z
has_obo_namespace: PSI-MI
id: MI:1171
in_subset: PSI-MI slim

Axiom
annotated source: composite binding site formation
annotated property: definition
annotated target: The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex.
database_cross_reference: PMID:18641616

altered physicochemical compatibility
type: Class
subclass of: interaction attribute name
subclass of: pre-assembly response
definition: The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction.
created by: orchard
creation date: 2012-06-07T01:26:56Z
has_obo_namespace: PSI-MI
id: MI:1172
in_subset: PSI-MI slim

Axiom
annotated source: altered physicochemical compatibility
annotated property: definition
annotated target: The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction.
database_cross_reference: PMID:22480932

binding site hiding
type: Class
subclass of: interaction attribute name
subclass of: pre-assembly response
definition: The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present.
created by: orchard
creation date: 2012-06-07T01:28:07Z
has_obo_namespace: PSI-MI
id: MI:1173
in_subset: PSI-MI slim

Axiom
annotated source: binding site hiding
annotated property: definition
annotated target: The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present.
database_cross_reference: PMID:22480932

configurational pre-organization
type: Class
subclass of: interaction attribute name
subclass of: pre-assembly response
definition: Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions.
created by: orchard
creation date: 2012-06-07T01:29:13Z
has_obo_namespace: PSI-MI
id: MI:1174
in_subset: PSI-MI slim

Axiom
annotated source: configurational pre-organization
annotated property: definition
annotated target: Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions.
database_cross_reference: PMID:18641616

allosteric post-translational modification
type: Class
subclass of: biological feature
subclass of: interaction attribute name
subclass of: cooperative interaction
definition: A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id.
created by: orchard
creation date: 2012-06-07T01:33:16Z
has_exact_synonym: allosteric ptm
has_obo_namespace: PSI-MI
id: MI:1175
in_subset: PSI-MI slim

Axiom
annotated source: allosteric post-translational modification
annotated property: definition
annotated target: A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id.
database_cross_reference: PMID:18706817

Axiom
annotated source: allosteric post-translational modification
annotated property: has_exact_synonym
annotated target: allosteric ptm
has_synonym_type: Unique short label curated by PSI-MI

sequence based prediction of gene regulatory region binding sites
type: Class
subclass of: sequence based prediction
definition: Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur.
created by: orchard
creation date: 2012-06-07T01:40:25Z
has_obo_namespace: PSI-MI
has_related_synonym: gene regulatory region prediction
has_related_synonym: sequence based prediction of TG regulatory region binding sites for TF
id: MI:1176
in_subset: PSI-MI slim

Axiom
annotated source: sequence based prediction of gene regulatory region binding sites
annotated property: definition
annotated target: Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur.
database_cross_reference: PMID:15131651

phylogenetic profiling of predicted gene regulatory region binding sites
type: Class
subclass of: sequence based phylogenetic profile
subclass of: sequence based prediction of gene regulatory region binding sites
definition: Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models.
created by: orchard
creation date: 2012-06-07T01:41:59Z
has_exact_synonym: gene regulatory region phylogeny
has_obo_namespace: PSI-MI
has_related_synonym: phylogenetic footprinting
id: MI:1177
in_subset: PSI-MI slim

Axiom
annotated source: phylogenetic profiling of predicted gene regulatory region binding sites
annotated property: definition
annotated target: Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models.
database_cross_reference: PMID:12671656

sequence based prediction of binding of transcription factor to transcribed gene regulatory elements
type: Class
subclass of: sequence based prediction
definition: Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor.
created by: orchard
creation date: 2012-06-07T01:43:57Z
has_exact_synonym: sequence based prediction of binding of TF to TG promoter
has_exact_synonym: transcription factor prediction
has_obo_namespace: PSI-MI
id: MI:1178
in_subset: PSI-MI slim

Axiom
annotated source: sequence based prediction of binding of transcription factor to transcribed gene regulatory elements
annotated property: definition
annotated target: Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor.
database_cross_reference: PMID:16381970

partial nucleotide sequence identification
type: Class
subclass of: nucleotide sequence identification
definition: Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s
created by: orchard
creation date: 2012-06-07T01:47:03Z
has_exact_synonym: partial nucleotide sequence
has_obo_namespace: PSI-MI
id: MI:1179
in_subset: PSI-MI slim

Axiom
annotated source: partial nucleotide sequence identification
annotated property: definition
annotated target: Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s
database_cross_reference: PMID:14755292

Axiom
annotated source: partial nucleotide sequence identification
annotated property: has_exact_synonym
annotated target: partial nucleotide sequence
has_synonym_type: Unique short label curated by PSI-MI

partial DNA sequence identification
type: Class
subclass of: partial nucleotide sequence identification
definition: Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
created by: orchard
creation date: 2012-06-07T01:52:27Z
has_exact_synonym: partial dna sequence
has_obo_namespace: PSI-MI
id: MI:1180
in_subset: PSI-MI slim

Axiom
annotated source: partial DNA sequence identification
annotated property: definition
annotated target: Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
database_cross_reference: PMID:14755292

Axiom
annotated source: partial DNA sequence identification
annotated property: has_exact_synonym
annotated target: partial dna sequence
has_synonym_type: Unique short label curated by PSI-MI

paired end tags sequence identification
type: Class
subclass of: partial DNA sequence identification
definition: Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA.
created by: orchard
creation date: 2012-06-07T01:53:38Z
has_exact_synonym: paired end tags
has_obo_namespace: PSI-MI
id: MI:1181
in_subset: PSI-MI slim

Axiom
annotated source: paired end tags sequence identification
annotated property: definition
annotated target: Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA.
database_cross_reference: PMID:19339662

Axiom
annotated source: paired end tags sequence identification
annotated property: has_exact_synonym
annotated target: paired end tags
has_synonym_type: Unique short label curated by PSI-MI

full identification by RNA sequencing
type: Class
subclass of: nucleotide sequence identification
definition: Sequencing occurs during the course of the experiment. To sequence RNA, the usual method is first to reverse transcribe the sample to generate cDNA fragments.
created by: orchard
creation date: 2012-06-07T02:02:37Z
has_obo_namespace: PSI-MI
id: MI:1182
in_subset: PSI-MI slim

nuclease footprinting
type: Class
subclass of: enzymatic footprinting
definition: Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified.
created by: orchard
creation date: 2012-06-07T02:08:36Z
has_obo_namespace: PSI-MI
has_related_synonym: nuclease protection
id: MI:1183
in_subset: PSI-MI slim

Axiom
annotated source: nuclease footprinting
annotated property: definition
annotated target: Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified.
database_cross_reference: PMID:7685766

dna adenine methyltransferase identification
type: Class
subclass of: proximity labelling technology
definition: DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site.
created by: orchard
creation date: 2012-06-07T02:13:03Z
has_exact_synonym: DamID
has_obo_namespace: PSI-MI
id: MI:1184
in_subset: PSI-MI slim

Axiom
annotated source: dna adenine methyltransferase identification
annotated property: definition
annotated target: DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site.
database_cross_reference: PMID:10748524

Axiom
annotated source: dna adenine methyltransferase identification
annotated property: has_exact_synonym
annotated target: DamID
has_synonym_type: Unique short label curated by PSI-MOD

tag visualisation by dna adenine methyltransferase
type: Class
subclass of: tag visualisation by enzyme assay
definition: Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization.
created by: orchard
creation date: 2012-06-07T02:22:19Z
has_exact_synonym: tag DNA methyltransferase
has_obo_namespace: PSI-MI
id: MI:1185
in_subset: PSI-MI slim

Axiom
annotated source: tag visualisation by dna adenine methyltransferase
annotated property: definition
annotated target: Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization.
database_cross_reference: PMID:10748524

Axiom
annotated source: tag visualisation by dna adenine methyltransferase
annotated property: has_exact_synonym
annotated target: tag DNA methyltransferase
has_synonym_type: Unique short label curated by PSI-MI

dna methyltransferase tag
type: Class
subclass of: enzyme tag
definition: The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites.
created by: orchard
creation date: 2012-06-07T02:32:02Z
has_obo_namespace: PSI-MI
id: MI:1186
in_subset: PSI-MI slim

Axiom
annotated source: dna methyltransferase tag
annotated property: definition
annotated target: The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites.
database_cross_reference: PMID:10748524

damip
type: Class
subclass of: dna adenine methyltransferase identification
definition: A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis.
created by: orchard
creation date: 2012-06-07T02:41:40Z
has_obo_namespace: PSI-MI
id: MI:1187
in_subset: PSI-MI slim

Axiom
annotated source: damip
annotated property: definition
annotated target: A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis.
database_cross_reference: PMID:21472695

tag visualisation by mutated dna adenine methyltransferase
type: Class
subclass of: tag visualisation by dna adenine methyltransferase
definition: A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA.
created by: orchard
creation date: 2012-06-07T02:46:08Z
has_obo_namespace: PSI-MI
id: MI:1188

methylation interference assay
type: Class
subclass of: enzymatic footprinting
definition: In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means "contact points".
created by: orchard
creation date: 2012-06-07T02:54:00Z
has_exact_synonym: methylation interference
has_obo_namespace: PSI-MI
has_related_synonym: contact point analysis
has_related_synonym: methylation protection assay
id: MI:1189
in_subset: PSI-MI slim

Axiom
annotated source: methylation interference assay
annotated property: definition
annotated target: In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means "contact points".
database_cross_reference: PMID:21720958

Axiom
annotated source: methylation interference assay
annotated property: has_exact_synonym
annotated target: methylation interference
has_synonym_type: Unique short label curated by PSI-MI

hydroxy radical footprinting
type: Class
subclass of: chemical footprinting
definition: Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected.
created by: orchard
creation date: 2012-06-07T03:10:48Z
has_obo_namespace: PSI-MI
id: MI:1190
in_subset: PSI-MI slim

Axiom
annotated source: hydroxy radical footprinting
annotated property: definition
annotated target: Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected.
database_cross_reference: PMID:3090544

ultraviolet (uv) footprinting
type: Class
subclass of: footprinting
definition: Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts.
created by: orchard
creation date: 2012-06-07T03:13:02Z
has_obo_namespace: PSI-MI
id: MI:1191
in_subset: PSI-MI slim

Axiom
annotated source: ultraviolet (uv) footprinting
annotated property: definition
annotated target: Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts.
database_cross_reference: PMID:2842760
database_cross_reference: PMID:6728031

antisense oligonucleotides
type: Class
subclass of: post transcriptional interference
definition: This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
created by: orchard
creation date: 2012-06-07T03:19:22Z
has_obo_namespace: PSI-MI
id: MI:1192
in_subset: PSI-MI slim

Axiom
annotated source: antisense oligonucleotides
annotated property: definition
annotated target: This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
database_cross_reference: PMID:14755292

partial RNA sequence identification
type: Class
subclass of: partial nucleotide sequence identification
definition: Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment.
created by: orchard
creation date: 2012-06-07T03:40:14Z
has_exact_synonym: partial rna sequence
has_obo_namespace: PSI-MI
id: MI:1193

Axiom
annotated source: partial RNA sequence identification
annotated property: definition
annotated target: Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment.
database_cross_reference: PMID:14755292

Axiom
annotated source: partial RNA sequence identification
annotated property: has_exact_synonym
annotated target: partial rna sequence
has_synonym_type: Unique short label curated by PSI-MI

reverse transcription pcr
type: Class
subclass of: primer specific pcr
definition: Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR.
created by: orchard
creation date: 2012-06-07T03:47:13Z
has_exact_synonym: RT-PCR
has_obo_namespace: PSI-MI
has_related_synonym: RPCR
has_related_synonym: reverse PCR
id: MI:1194
in_subset: PSI-MI slim

Axiom
annotated source: reverse transcription pcr
annotated property: definition
annotated target: Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR.
database_cross_reference: PMID:12958470

Axiom
annotated source: reverse transcription pcr
annotated property: has_exact_synonym
annotated target: RT-PCR
has_synonym_type: Unique short label curated by PSI-MI

quantitative pcr
type: Class
subclass of: primer specific pcr
definition: Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA.
created by: orchard
creation date: 2012-06-07T03:56:38Z
has_exact_synonym: q-pcr
has_obo_namespace: PSI-MI
has_related_synonym: QRT-PCR
has_related_synonym: RQ-PCR
has_related_synonym: RTQ-PCR
id: MI:1195
in_subset: PSI-MI slim

Axiom
annotated source: quantitative pcr
annotated property: definition
annotated target: Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA.
database_cross_reference: PMID:12958470

Axiom
annotated source: quantitative pcr
annotated property: has_exact_synonym
annotated target: q-pcr
has_synonym_type: Unique short label curated by PSI-MI

quantitative reverse transcription pcr
type: Class
subclass of: reverse transcription pcr
definition: Technique used to measure the quantity of DNA amplified from RNA.
created by: orchard
creation date: 2012-06-07T04:04:42Z
has_exact_synonym: QRT-PCR
has_obo_namespace: PSI-MI
has_related_synonym: RTQ-PCR
id: MI:1196
in_subset: PSI-MI slim

Axiom
annotated source: quantitative reverse transcription pcr
annotated property: definition
annotated target: Technique used to measure the quantity of DNA amplified from RNA.
database_cross_reference: PMID:12958470

Axiom
annotated source: quantitative reverse transcription pcr
annotated property: has_exact_synonym
annotated target: QRT-PCR
has_synonym_type: Unique short label curated by PSI-MI

radioimmunoassay
type: Class
subclass of: identification by antibody
definition: To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or "cold") antigen from the serum to compete with the radiolabeled antigen ("hot") for antibody binding sites. As the concentration of "cold" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured.
created by: orchard
creation date: 2012-06-07T04:13:30Z
has_exact_synonym: RIA
has_obo_namespace: PSI-MI
id: MI:1197

Axiom
annotated source: radioimmunoassay
annotated property: definition
annotated target: To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or "cold") antigen from the serum to compete with the radiolabeled antigen ("hot") for antibody binding sites. As the concentration of "cold" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured.
database_cross_reference: PMID:13846364.

immunohistochemistry
type: Class
subclass of: immunostaining
definition: Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
created by: orchard
creation date: 2012-06-07T04:17:12Z
has_obo_namespace: PSI-MI
id: MI:1198
in_subset: PSI-MI slim

Axiom
annotated source: immunohistochemistry
annotated property: definition
annotated target: Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
database_cross_reference: PMID:16006601

anti-tag immunohistochemistry
type: Class
subclass of: immunohistochemistry
definition: Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
created by: orchard
creation date: 2012-06-07T04:21:23Z
has_obo_namespace: PSI-MI
id: MI:1199
in_subset: PSI-MI slim

Axiom
annotated source: anti-tag immunohistochemistry
annotated property: definition
annotated target: Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
database_cross_reference: PMID:16006601

immunocytochemistry
type: Class
subclass of: immunostaining
definition: Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
created by: orchard
creation date: 2012-06-07T04:22:00Z
has_obo_namespace: PSI-MI
id: MI:1200
in_subset: PSI-MI slim

Axiom
annotated source: immunocytochemistry
annotated property: definition
annotated target: Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
database_cross_reference: PMID:14755292

anti-tag immunocytochemistry
type: Class
subclass of: immunocytochemistry
definition: Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
created by: orchard
creation date: 2012-06-07T04:33:37Z
has_obo_namespace: PSI-MI
id: MI:1201
in_subset: PSI-MI slim

Axiom
annotated source: anti-tag immunocytochemistry
annotated property: definition
annotated target: Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
database_cross_reference: PMID:14755292

one-strep-tag
type: Class
subclass of: tag
definition: Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK)
created by: orchard
creation date: 2012-06-07T04:44:55Z
has_exact_synonym: twin-strep-tag
has_obo_namespace: PSI-MI
id: MI:1202
in_subset: PSI-MI slim

Axiom
annotated source: one-strep-tag
annotated property: definition
annotated target: Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK)
database_cross_reference: PMID:19688738

Axiom
annotated source: one-strep-tag
annotated property: has_exact_synonym
annotated target: twin-strep-tag
has_synonym_type: Alternate label curated by PSI-MI

split luciferase complementation
type: Class
subclass of: protein complementation assay
definition: Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
created by: orchard
creation date: 2012-06-07T04:56:59Z
has_obo_namespace: PSI-MI
id: MI:1203
in_subset: PSI-MI slim

Axiom
annotated source: split luciferase complementation
annotated property: definition
annotated target: Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
database_cross_reference: PMID:20734273

split firefly luciferase complementation
type: Class
subclass of: split luciferase complementation
definition: Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
created by: orchard
creation date: 2012-06-07T05:05:36Z
has_obo_namespace: PSI-MI
id: MI:1204
in_subset: PSI-MI slim

Axiom
annotated source: split firefly luciferase complementation
annotated property: definition
annotated target: Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
database_cross_reference: PMID:20734273
database_cross_reference: PMID:22070901

luciferase tag
type: Class
subclass of: fusion protein
definition: Luciferase is a generic term for the class of oxidative enzymes used in bioluminescence and is distinct from a photoprotein. Luciferase catalyzes a bioluminescent reaction which requires the substrate luciferin as well as Mg2+ and ATP, produces green light with a wavelength of 562 nm.
created by: orchard
creation date: 2012-06-07T05:20:20Z
has_obo_namespace: PSI-MI
id: MI:1205
in_subset: PSI-MI slim

renilla-n
type: Class
subclass of: renilla luciferase protein tag
subclass of: bifc tag
definition: The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: orchard
creation date: 2012-06-07T05:26:34Z
has_obo_namespace: PSI-MI
has_related_synonym: N-terminal fragment of renilla luciferase
id: MI:1206
in_subset: PSI-MI slim

Axiom
annotated source: renilla-n
annotated property: definition
annotated target: The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
database_cross_reference: PMID:12705589

renilla-c
type: Class
subclass of: renilla luciferase protein tag
subclass of: bifc tag
definition: The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: orchard
creation date: 2012-06-07T05:31:32Z
has_exact_synonym: C-terminal fragment of renilla luciferase
has_obo_namespace: PSI-MI
id: MI:1207

Axiom
annotated source: renilla-c
annotated property: definition
annotated target: The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
database_cross_reference: PMID:12705589

firefly luciferase protein tag
type: Class
subclass of: luciferase tag
definition: Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range.
created by: orchard
creation date: 2012-06-07T05:32:53Z
has_obo_namespace: PSI-MI
id: MI:1208
in_subset: PSI-MI slim

Axiom
annotated source: firefly luciferase protein tag
annotated property: definition
annotated target: Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range.
database_cross_reference: PMID:22070901

firefly-c
type: Class
subclass of: firefly luciferase protein tag
subclass of: bifc tag
definition: The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: orchard
creation date: 2012-06-07T05:40:04Z
has_exact_synonym: C-terminal fragment of firefly luciferase
has_obo_namespace: PSI-MI
id: MI:1209
in_subset: PSI-MI slim

Axiom
annotated source: firefly-c
annotated property: definition
annotated target: The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
database_cross_reference: PMID:22070901

firefly-n
type: Class
subclass of: firefly luciferase protein tag
subclass of: bifc tag
definition: The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: orchard
creation date: 2012-06-07T05:41:30Z
has_obo_namespace: PSI-MI
has_related_synonym: N-terminal fragment of firefly luciferase
id: MI:1210
in_subset: PSI-MI slim

Axiom
annotated source: firefly-n
annotated property: definition
annotated target: The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
database_cross_reference: PMID:22070901

liposome binding assay
type: Class
subclass of: cosedimentation
definition: Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out.
created by: orchard
creation date: 2012-06-07T05:51:15Z
has_obo_namespace: PSI-MI
has_related_synonym: liposome centrifugation assay
id: MI:1211
in_subset: PSI-MI slim

Axiom
annotated source: liposome binding assay
annotated property: definition
annotated target: Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out.
database_cross_reference: PMID:14734570

checksum
type: Class
subclass of: participant attribute name
definition: A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing.
created by: orchard
creation date: 2012-06-07T05:54:41Z
has_obo_namespace: PSI-MI
has_related_synonym: hashsum
id: MI:1212
in_subset: PSI-MI slim

Axiom
annotated source: checksum
annotated property: definition
annotated target: A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing.
database_cross_reference: PMID:14755292

n-venus
type: Class
subclass of: venus fluorescent protein tag
subclass of: bifc tag
definition: N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
created by: orchard
creation date: 2012-06-07T06:33:51Z
has_obo_namespace: PSI-MI
id: MI:1213
in_subset: PSI-MI slim

Axiom
annotated source: n-venus
annotated property: definition
annotated target: N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
database_cross_reference: PMID:22229727

c-venus
type: Class
subclass of: venus fluorescent protein tag
subclass of: bifc tag
definition: C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
created by: orchard
creation date: 2012-06-07T06:39:30Z
has_obo_namespace: PSI-MI
id: MI:1214
in_subset: PSI-MI slim

Axiom
annotated source: c-venus
annotated property: definition
annotated target: C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
database_cross_reference: PMID:22229727

bifc tag
type: Class
subclass of: fusion protein
definition: Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured.
created by: orchard
creation date: 2012-06-07T07:13:53Z
has_obo_namespace: PSI-MI
id: MI:1215
in_subset: PSI-MI slim

Axiom
annotated source: bifc tag
annotated property: definition
annotated target: Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured.
database_cross_reference: PMID:17406412

cGFP
type: Class
subclass of: green fluorescent protein tag
subclass of: bifc tag
definition: c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
created by: orchard
creation date: 2012-06-07T07:19:55Z
has_obo_namespace: PSI-MI
id: MI:1216
in_subset: PSI-MI slim

Axiom
annotated source: cGFP
annotated property: definition
annotated target: c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
database_cross_reference: PMID:17406412

nGFP
type: Class
subclass of: green fluorescent protein tag
subclass of: bifc tag
definition: n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
created by: orchard
creation date: 2012-06-07T07:20:57Z
has_obo_namespace: PSI-MI
id: MI:1217
in_subset: PSI-MI slim

Axiom
annotated source: nGFP
annotated property: definition
annotated target: n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
database_cross_reference: PMID:17406412

chromosome conformation capture assay
type: Class
subclass of: cross-linking study
definition: Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library.
created by: orchard
creation date: 2012-06-07T07:25:28Z
has_exact_synonym: chip-3c
has_obo_namespace: PSI-MI
id: MI:1218
in_subset: PSI-MI slim

Axiom
annotated source: chromosome conformation capture assay
annotated property: definition
annotated target: Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library.
database_cross_reference: PMID:11847345

Axiom
annotated source: chromosome conformation capture assay
annotated property: has_exact_synonym
annotated target: chip-3c
has_synonym_type: Unique short label curated by PSI-MI

enzyme-mediated activation of radical sources
type: Class
subclass of: biophysical
definition: Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP).
created by: orchard
creation date: 2012-06-07T07:34:30Z
has_exact_synonym: emars
has_obo_namespace: PSI-MI
id: MI:1219
in_subset: PSI-MI slim

Axiom
annotated source: enzyme-mediated activation of radical sources
annotated property: definition
annotated target: Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP).
database_cross_reference: PMID:21214558

Axiom
annotated source: enzyme-mediated activation of radical sources
annotated property: has_exact_synonym
annotated target: emars
has_synonym_type: Unique short label curated by PSI-MI

tag visualisation by luciferase assay
type: Class
subclass of: tag visualisation by enzyme assay
definition: The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction.
created by: orchard
creation date: 2012-06-11T11:52:57Z
has_exact_synonym: tag luciferase
has_obo_namespace: PSI-MI
id: MI:1220
in_subset: PSI-MI slim

Axiom
annotated source: tag visualisation by luciferase assay
annotated property: definition
annotated target: The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction.
database_cross_reference: PMID:20609414

Axiom
annotated source: tag visualisation by luciferase assay
annotated property: has_exact_synonym
annotated target: tag luciferase
has_synonym_type: Unique short label curated by PSI-MI

author-based confidence
type: Class
subclass of: interaction confidence
definition: A score generated by an author, usually only relevant for that particular dataset.
created by: orchard
creation date: 2012-06-11T11:54:23Z
has_exact_synonym: author score
has_obo_namespace: PSI-MI
id: MI:1221
in_subset: PSI-MI slim

Axiom
annotated source: author-based confidence
annotated property: definition
annotated target: A score generated by an author, usually only relevant for that particular dataset.
database_cross_reference: PMID:14755292

Axiom
annotated source: author-based confidence
annotated property: has_exact_synonym
annotated target: author score
has_synonym_type: Unique short label curated by PSI-MI

mbinfo
type: Class
subclass of: interaction database
subclass of: imex source
definition: MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/).
created by: orchard
creation date: 2012-06-11T12:20:53Z
has_exact_synonym: MBInfo
has_obo_namespace: PSI-MI
id: MI:1222
in_subset: PSI-MI slim

Axiom
annotated source: mbinfo
annotated property: definition
annotated target: MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/).
database_cross_reference: PMID:14755292

Axiom
annotated source: mbinfo
annotated property: has_exact_synonym
annotated target: MBInfo
has_synonym_type: Alternate label curated by PSI-MI

ptm decreasing an interaction
type: Class
subclass of: observed-ptm
definition: Post translational modification on a protein observed to decrease the strength or rate of an interaction.
created by: orchard
creation date: 2012-06-11T12:56:47Z
has_exact_synonym: decreasing-ptm
has_obo_namespace: PSI-MI
id: MI:1223
in_subset: PSI-MI slim

Axiom
annotated source: ptm decreasing an interaction
annotated property: definition
annotated target: Post translational modification on a protein observed to decrease the strength or rate of an interaction.
database_cross_reference: PMID:14744292

Axiom
annotated source: ptm decreasing an interaction
annotated property: has_exact_synonym
annotated target: decreasing-ptm
has_synonym_type: Unique short label curated by PSI-MI

ptm increasing an interaction
type: Class
subclass of: observed-ptm
definition: Post translational modification on a protein observed to increase the strength or rate of an interaction.
created by: orchard
creation date: 2012-06-11T12:58:43Z
has_exact_synonym: increasing-ptm
has_obo_namespace: PSI-MI
id: MI:1224
in_subset: PSI-MI slim

Axiom
annotated source: ptm increasing an interaction
annotated property: definition
annotated target: Post translational modification on a protein observed to increase the strength or rate of an interaction.
database_cross_reference: PMID:14744292

Axiom
annotated source: ptm increasing an interaction
annotated property: has_exact_synonym
annotated target: increasing-ptm
has_synonym_type: Unique short label curated by PSI-MI

ptm disrupting an interaction
type: Class
subclass of: observed-ptm
definition: Post translational modification on a protein observed to disrupt the strength or rate of an interaction.
created by: orchard
creation date: 2012-06-11T12:59:28Z
has_exact_synonym: disrupting-ptm
has_obo_namespace: PSI-MI
id: MI:1225
in_subset: PSI-MI slim

Axiom
annotated source: ptm disrupting an interaction
annotated property: definition
annotated target: Post translational modification on a protein observed to disrupt the strength or rate of an interaction.
database_cross_reference: PMID:14744292

Axiom
annotated source: ptm disrupting an interaction
annotated property: has_exact_synonym
annotated target: disrupting-ptm
has_synonym_type: Unique short label curated by PSI-MI

ampylation assay
type: Class
definition: Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids
created by: orchard
creation date: 2012-06-11T01:06:07Z
has_obo_namespace: PSI-MI
has_related_synonym: ampylation
id: MI:1226
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: ampylation assay
annotated property: definition
annotated target: Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids
database_cross_reference: PMID:14755292

lap tag
type: Class
subclass of: tandem tag
definition: Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification.
created by: orchard
creation date: 2012-06-11T01:16:05Z
has_exact_synonym: lap tag
has_obo_namespace: PSI-MI
has_related_synonym: location and purification tag
id: MI:1227
in_subset: PSI-MI slim

Axiom
annotated source: lap tag
annotated property: definition
annotated target: Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification.
database_cross_reference: PMID:15644491

Axiom
annotated source: lap tag
annotated property: has_exact_synonym
annotated target: lap tag
has_synonym_type: Unique short label curated by PSI-MI

pyo tag
type: Class
subclass of: tag
definition: A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME).
created by: orchard
creation date: 2012-08-10T07:28:55Z
has_obo_namespace: PSI-MI
id: MI:1228
in_subset: PSI-MI slim

Axiom
annotated source: pyo tag
annotated property: definition
annotated target: A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME).
database_cross_reference: PMID:9371754

uridylation assay
type: Class
subclass of: enzymatic study
definition: Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166).
created by: orchard
creation date: 2012-08-10T07:46:07Z
has_obo_namespace: PSI-MI
id: MI:1229
in_subset: PSI-MI slim

Axiom
annotated source: uridylation assay
annotated property: definition
annotated target: Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166).
database_cross_reference: PMID:14755292

uridylation reaction
type: Class
subclass of: enzymatic reaction
definition: The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166).
created by: orchard
creation date: 2012-08-10T07:50:08Z
has_exact_synonym: uridylation
has_obo_namespace: PSI-MI
has_related_synonym: umpylation
id: MI:1230
in_subset: PSI-MI slim

Axiom
annotated source: uridylation reaction
annotated property: definition
annotated target: The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166).
database_cross_reference: PMID:14755292

Axiom
annotated source: uridylation reaction
annotated property: has_exact_synonym
annotated target: uridylation
has_synonym_type: Unique short label curated by PSI-MI

aminomethylcoumarin label
type: Class
subclass of: coumarin label
definition: AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring.
created by: orchard
creation date: 2012-08-10T07:59:18Z
has_exact_synonym: AMC label
has_obo_namespace: PSI-MI
id: MI:1231
in_subset: PSI-MI slim

Axiom
annotated source: aminomethylcoumarin label
annotated property: definition
annotated target: AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring.
database_cross_reference: PMID:14755292

Axiom
annotated source: aminomethylcoumarin label
annotated property: has_exact_synonym
annotated target: AMC label
has_synonym_type: Unique short label curated by PSI-MI

aggregation assay
type: Class
subclass of: biochemical
definition: An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second.
created by: orchard
creation date: 2012-08-10T08:07:15Z
has_exact_synonym: aggregation
has_obo_namespace: PSI-MI
id: MI:1232
in_subset: PSI-MI slim

Axiom
annotated source: aggregation assay
annotated property: definition
annotated target: An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second.
database_cross_reference: PMID:22179788

Axiom
annotated source: aggregation assay
annotated property: has_exact_synonym
annotated target: aggregation
has_synonym_type: Unique short label curated by PSI-MI

resulting-cleavage
type: Class
subclass of: resulting-ptm
definition: The cleavage which results due to the action of a proteolytic enzyme on its substrate.
created by: orchard
creation date: 2012-08-10T08:14:45Z
has_obo_namespace: PSI-MI
id: MI:1233
in_subset: PSI-MI slim
comment: Any feature range given should span the cleavage region e.g. 102-103 if the peptide bond between residues 102 and 103 is cut.

Axiom
annotated source: resulting-cleavage
annotated property: definition
annotated target: The cleavage which results due to the action of a proteolytic enzyme on its substrate.
database_cross_reference: PMID:14755292

silac
type: Class
subclass of: experimental feature detection
definition: SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction.
created by: orchard
creation date: 2012-08-10T08:45:50Z
has_obo_namespace: PSI-MI
id: MI:1234
in_subset: PSI-MI slim

Axiom
annotated source: silac
annotated property: definition
annotated target: SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction.
database_cross_reference: PMID:17139335
database_cross_reference: PMID:18369856

thermal shift binding
type: Class
subclass of: biophysical
definition: Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state.
created by: orchard
creation date: 2012-08-10T08:52:14Z
has_exact_synonym: thermal shift
has_obo_namespace: PSI-MI
has_related_synonym: thermshift binding assay
id: MI:1235
in_subset: PSI-MI slim

Axiom
annotated source: thermal shift binding
annotated property: definition
annotated target: Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state.
database_cross_reference: PMID:22052482

Axiom
annotated source: thermal shift binding
annotated property: has_exact_synonym
annotated target: thermal shift
has_synonym_type: Unique short label curated by PSI-MI

proline isomerase assay
type: Class
subclass of: isomerase assay
definition: Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly.
created by: orchard
creation date: 2012-08-10T08:56:38Z
has_obo_namespace: PSI-MI
id: MI:1236
in_subset: PSI-MI slim

Axiom
annotated source: proline isomerase assay
annotated property: definition
annotated target: Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly.
database_cross_reference: PMID:9344417

proline isomerization reaction
type: Class
subclass of: isomerase reaction
definition: The conversion between cis- and trans- peptide bonds formed by the amine group of a proline.
created by: orchard
creation date: 2012-08-10T09:02:28Z
has_obo_namespace: PSI-MI
id: MI:1237
in_subset: PSI-MI slim

Axiom
annotated source: proline isomerization reaction
annotated property: definition
annotated target: The conversion between cis- and trans- peptide bonds formed by the amine group of a proline.
database_cross_reference: PMID:9344417

mass spectrometry studies of subunit exchange
type: Class
subclass of: mass spectrometry studies of complexes
definition: Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry.
created by: orchard
creation date: 2012-08-10T09:11:36Z
has_exact_synonym: ms subunit exchange
has_obo_namespace: PSI-MI
id: MI:1238
in_subset: PSI-MI slim

Axiom
annotated source: mass spectrometry studies of subunit exchange
annotated property: definition
annotated target: Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry.
database_cross_reference: PMID:20351246

Axiom
annotated source: mass spectrometry studies of subunit exchange
annotated property: has_exact_synonym
annotated target: ms subunit exchange
has_synonym_type: Unique short label curated by PSI-MI

amino-acid variant
type: Class
subclass of: variant
definition: A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events.
created by: orchard
creation date: 2012-08-10T09:20:55Z
has_obo_namespace: PSI-MI
has_related_synonym: SAP
has_related_synonym: single amino-acid polymorphism
id: MI:1239
in_subset: PSI-MI slim

Axiom
annotated source: amino-acid variant
annotated property: definition
annotated target: A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events.
database_cross_reference: PMID:18175334

disease causing amino-acid variant
type: Class
subclass of: amino-acid variant
definition: A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition.
created by: orchard
creation date: 2012-08-10T09:28:06Z
has_exact_synonym: disease aa variant
has_obo_namespace: PSI-MI
has_related_synonym: disease sap
has_related_synonym: disease single amino acid polymorphism
id: MI:1240

Axiom
annotated source: disease causing amino-acid variant
annotated property: definition
annotated target: A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition.
database_cross_reference: PMID:18175334

Axiom
annotated source: disease causing amino-acid variant
annotated property: has_exact_synonym
annotated target: disease aa variant
has_synonym_type: Unique short label curated by PSI-MI

variant
type: Class
subclass of: biological feature
definition: A natural change in a sequence or structure in comparison to a reference entity.
created by: orchard
creation date: 2012-08-10T09:32:29Z
has_obo_namespace: PSI-MI
id: MI:1241

fc-igg1
type: Class
subclass of: fc-igg tag
definition: A fusion protein tag consisting of a portion of the constant region of IgG1.
created by: orchard
creation date: 2012-08-10T10:10:25Z
has_obo_namespace: PSI-MI
id: MI:1242
in_subset: PSI-MI slim

Axiom
annotated source: fc-igg1
annotated property: definition
annotated target: A fusion protein tag consisting of a portion of the constant region of IgG1.
database_cross_reference: PMID:11757069

fc-igg2
type: Class
subclass of: fc-igg tag
definition: A fusion protein tag consisting of a portion of the constant region of IgG2.
created by: orchard
creation date: 2012-08-10T10:14:13Z
has_obo_namespace: PSI-MI
id: MI:1243
in_subset: PSI-MI slim

Axiom
annotated source: fc-igg2
annotated property: definition
annotated target: A fusion protein tag consisting of a portion of the constant region of IgG2.
database_cross_reference: PMID:11757069

mkate2
type: Class
subclass of: red fluorescent protein tag
definition: Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
created by: orchard
creation date: 2012-08-10T11:22:13Z
has_obo_namespace: PSI-MI
id: MI:1244
in_subset: PSI-MI slim

Axiom
annotated source: mkate2
annotated property: definition
annotated target: Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
database_cross_reference: PMID:17721542

mkate
type: Class
subclass of: red fluorescent protein tag
definition: Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
created by: orchard
creation date: 2012-08-10T11:48:12Z
has_obo_namespace: PSI-MI
has_related_synonym: TagFP635
id: MI:1245
in_subset: PSI-MI slim

Axiom
annotated source: mkate
annotated property: definition
annotated target: Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
database_cross_reference: PMID:17721542

ion mobility mass spectrometry of complexes
type: Class
subclass of: mass spectrometry studies of complexes
definition: IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex.
created by: orchard
creation date: 2012-08-10T11:56:05Z
has_exact_synonym: ion mobility mass spec
has_obo_namespace: PSI-MI
has_related_synonym: iM-MS
id: MI:1246
in_subset: PSI-MI slim

Axiom
annotated source: ion mobility mass spectrometry of complexes
annotated property: definition
annotated target: IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex.
database_cross_reference: PMID:18600219

Axiom
annotated source: ion mobility mass spectrometry of complexes
annotated property: has_exact_synonym
annotated target: ion mobility mass spec
has_synonym_type: Unique short label curated by PSI-MI

microscale thermophoresis
type: Class
subclass of: biophysical
definition: Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored.
created by: orchard
creation date: 2012-08-10T12:20:37Z
has_exact_synonym: mst
has_obo_namespace: PSI-MI
id: MI:1247
in_subset: PSI-MI slim

Axiom
annotated source: microscale thermophoresis
annotated property: definition
annotated target: Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored.
database_cross_reference: PMID:17164337

Axiom
annotated source: microscale thermophoresis
annotated property: has_exact_synonym
annotated target: mst
has_synonym_type: Unique short label curated by PSI-MI

bodipy label
type: Class
subclass of: fluorescent dye label
definition: Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields.
created by: orchard
creation date: 2012-08-10T12:34:54Z
has_obo_namespace: PSI-MI
has_related_synonym: 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene
has_related_synonym: boron-dipyrromethene label
id: MI:1248
in_subset: PSI-MI slim

Axiom
annotated source: bodipy label
annotated property: definition
annotated target: Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields.
database_cross_reference: PMID:19067126

isomerase assay
type: Class
subclass of: enzymatic study
definition: Measurement of the catalysis of the structural rearrangement of isomers.
created by: orchard
creation date: 2012-08-10T12:45:27Z
has_obo_namespace: PSI-MI
id: MI:1249
in_subset: PSI-MI slim

Axiom
annotated source: isomerase assay
annotated property: definition
annotated target: Measurement of the catalysis of the structural rearrangement of isomers.
database_cross_reference: PMID:14755292

isomerase reaction
type: Class
subclass of: enzymatic reaction
definition: The catalysis of the structural rearrangement of isomers.
created by: orchard
creation date: 2012-08-10T12:51:00Z
has_obo_namespace: PSI-MI
id: MI:1250
in_subset: PSI-MI slim

Axiom
annotated source: isomerase reaction
annotated property: definition
annotated target: The catalysis of the structural rearrangement of isomers.
database_cross_reference: PMID:14755292

methylmalonyl-CoA isomerase reaction
type: Class
subclass of: isomerase reaction
definition: The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2.
created by: orchard
creation date: 2012-08-10T01:23:35Z
has_obo_namespace: PSI-MI
id: MI:1251
in_subset: PSI-MI slim

Axiom
annotated source: methylmalonyl-CoA isomerase reaction
annotated property: definition
annotated target: The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2.
database_cross_reference: PMID:14755292

methylmalonyl-CoA isomerase asf say
type: Class
subclass of: isomerase assay
definition: The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2
created by: orchard
creation date: 2012-08-10T01:29:23Z
has_obo_namespace: PSI-MI
id: MI:1252
in_subset: PSI-MI slim

Axiom
annotated source: methylmalonyl-CoA isomerase asf say
annotated property: definition
annotated target: The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2
database_cross_reference: PMID:147292

atto 532
type: Class
subclass of: atto label
definition: Fluorescent tag - maleimide couples to thiols.
created by: orchard
creation date: 2012-08-10T01:49:01Z
has_exact_synonym: atto 532 maleimide
has_obo_namespace: PSI-MI
has_related_synonym: atto532
id: MI:1253
in_subset: PSI-MI slim

Axiom
annotated source: atto 532
annotated property: definition
annotated target: Fluorescent tag - maleimide couples to thiols.
database_cross_reference: PMID:14760721

atto 647
type: Class
subclass of: atto label
definition: Fluorescent tag - maleimide couples to thiols.
created by: orchard
creation date: 2012-08-10T01:51:00Z
has_exact_synonym: atto 647 maleimide
has_obo_namespace: PSI-MI
has_related_synonym: atto647
id: MI:1254
in_subset: PSI-MI slim

Axiom
annotated source: atto 647
annotated property: definition
annotated target: Fluorescent tag - maleimide couples to thiols.
database_cross_reference: PMID:14760721

stilbene label
type: Class
subclass of: fluorescent dye label
definition: 1,2-Diphenylethene
created by: orchard
creation date: 2012-08-10T01:56:28Z
has_obo_namespace: PSI-MI
id: MI:1255
in_subset: PSI-MI slim

Axiom
annotated source: stilbene label
annotated property: definition
annotated target: 1,2-Diphenylethene
database_cross_reference: PMID:16287229

luminscent dye label
type: Class
subclass of: dye label
definition: Luminescent dyes such as cyanines,commonly used for DNA labelling.
created by: orchard
creation date: 2012-08-10T02:18:02Z
has_obo_namespace: PSI-MI
id: MI:1256
in_subset: PSI-MI slim

Axiom
annotated source: luminscent dye label
annotated property: definition
annotated target: Luminescent dyes such as cyanines,commonly used for DNA labelling.
database_cross_reference: PMID:14755292

rhodamine label
type: Class
subclass of: fluorescent dye label
definition: Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining.
created by: orchard
creation date: 2012-08-10T02:39:00Z
has_obo_namespace: PSI-MI
id: MI:1257
in_subset: PSI-MI slim

Axiom
annotated source: rhodamine label
annotated property: definition
annotated target: Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining.
database_cross_reference: PMID:12622145

tetramethyl rhodamine label
type: Class
subclass of: rhodamine label
definition: Tetramethyl rhodamine - a derivative of rhodamine.
created by: orchard
creation date: 2012-08-10T02:44:52Z
has_obo_namespace: PSI-MI
id: MI:1258
in_subset: PSI-MI slim

Axiom
annotated source: tetramethyl rhodamine label
annotated property: definition
annotated target: Tetramethyl rhodamine - a derivative of rhodamine.
database_cross_reference: PMID:12622145

acrylodan label
type: Class
subclass of: fluorescent dye label
definition: The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding.
created by: orchard
creation date: 2012-08-10T02:55:26Z
has_obo_namespace: PSI-MI
has_related_synonym: 6-acryloyl-2-dimethylaminonaphthalene
id: MI:1259
in_subset: PSI-MI slim

Axiom
annotated source: acrylodan label
annotated property: definition
annotated target: The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding.
database_cross_reference: PMID:12622145

pyrene label
type: Class
subclass of: fluorescent dye label
definition: Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime.
created by: orchard
creation date: 2012-08-10T03:09:54Z
has_obo_namespace: PSI-MI
id: MI:1260

Axiom
annotated source: pyrene label
annotated property: definition
annotated target: Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime.
database_cross_reference: PMID:12622145

oregon green label
type: Class
subclass of: fluorescein label
definition: Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins
created by: orchard
creation date: 2012-08-10T03:17:05Z
has_obo_namespace: PSI-MI
id: MI:1261
in_subset: PSI-MI slim

Axiom
annotated source: oregon green label
annotated property: definition
annotated target: Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins
database_cross_reference: PMID:12622145

iid
type: Class
subclass of: interaction database
subclass of: imex source
definition: Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions.
created by: orchard
creation date: 2012-10-22T02:57:59Z
database_cross_reference: url:http://iid.ophid.utoronto.ca/iid/
has_exact_synonym: I2D
has_exact_synonym: IID
has_exact_synonym: Interologous Interaction Database
has_obo_namespace: PSI-MI
id: MI:1262
in_subset: PSI-MI slim

Axiom
annotated source: iid
annotated property: definition
annotated target: Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions.
database_cross_reference: PMID:19850753

Axiom
annotated source: iid
annotated property: has_exact_synonym
annotated target: I2D
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: iid
annotated property: has_exact_synonym
annotated target: IID
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: iid
annotated property: has_exact_synonym
annotated target: Interologous Interaction Database
has_synonym_type: Alternate label curated by PSI-MI

molecular connections
type: Class
subclass of: interaction database
subclass of: imex source
definition: Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com
created by: orchard
creation date: 2012-10-22T03:03:01Z
has_exact_synonym: Molecular Connections
has_obo_namespace: PSI-MI
has_related_synonym: MolCon
id: MI:1263
in_subset: PSI-MI slim

Axiom
annotated source: molecular connections
annotated property: definition
annotated target: Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com
database_cross_reference: PMID:22453911

Axiom
annotated source: molecular connections
annotated property: has_exact_synonym
annotated target: Molecular Connections
has_synonym_type: Alternate label curated by PSI-MI

ntnu
type: Class
subclass of: source database
definition: Norwegian University of Science and Technology. www.ntnu.no/home.
created by: orchard
creation date: 2012-10-22T03:15:27Z
has_exact_synonym: NTNU
has_obo_namespace: PSI-MI
id: MI:1264
in_subset: PSI-MI slim

Axiom
annotated source: ntnu
annotated property: definition
annotated target: Norwegian University of Science and Technology. www.ntnu.no/home.
database_cross_reference: PMID:14755292

Axiom
annotated source: ntnu
annotated property: has_exact_synonym
annotated target: NTNU
has_synonym_type: Alternate label curated by PSI-MI

ubiquitin reconstruction tag
type: Class
subclass of: fusion protein
definition: In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases.
created by: orchard
creation date: 2012-10-24T11:08:40Z
has_obo_namespace: PSI-MI
id: MI:1265
in_subset: PSI-MI slim

Axiom
annotated source: ubiquitin reconstruction tag
annotated property: definition
annotated target: In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases.
database_cross_reference: PMID:9560251

cub
type: Class
subclass of: ubiquitin reconstruction tag
definition: A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays.
created by: orchard
creation date: 2012-10-24T11:10:19Z
has_obo_namespace: PSI-MI
has_related_synonym: c-terminal ubiquitin tag
id: MI:1266
in_subset: PSI-MI slim

Axiom
annotated source: cub
annotated property: definition
annotated target: A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays.
database_cross_reference: PMID:9560251

nub
type: Class
subclass of: ubiquitin reconstruction tag
definition: N-terminal ubiquitin moiety (nub, residues 1-34).
created by: orchard
creation date: 2012-10-24T11:12:47Z
has_obo_namespace: PSI-MI
has_related_synonym: N-terminal ubiquitin tag
id: MI:1267
in_subset: PSI-MI slim

Axiom
annotated source: nub
annotated property: definition
annotated target: N-terminal ubiquitin moiety (nub, residues 1-34).
database_cross_reference: PMID:9560251

nubg
type: Class
subclass of: nub
definition: N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation.
created by: orchard
creation date: 2012-10-24T11:31:11Z
has_obo_namespace: PSI-MI
has_related_synonym: Ile13Gly N-terminal ubiquitin tag
id: MI:1268
in_subset: PSI-MI slim

Axiom
annotated source: nubg
annotated property: definition
annotated target: N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation.
database_cross_reference: PMID:9560251

duplicated protein
type: Class
subclass of: set member
definition: An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged.
created by: orchard
creation date: 2012-11-28T03:23:28Z
has_obo_namespace: PSI-MI
id: MI:1269
in_subset: PSI-MI slim

Axiom
annotated source: duplicated protein
annotated property: definition
annotated target: An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged.
database_cross_reference: PMID:21051339

xpress tag
type: Class
subclass of: tag
definition: Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys.
created by: orchard
creation date: 2013-05-30T08:29:27Z
has_obo_namespace: PSI-MI
id: MI:1270
in_subset: PSI-MI slim

Axiom
annotated source: xpress tag
annotated property: definition
annotated target: Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys.
database_cross_reference: PMID:14755292

genetic enhancement (sensu unexpected)
type: Class
subclass of: diverging genetic interaction
subclass of: MI 2380
definition: An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E < wt OR wt < E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T19:12:17Z
has_exact_synonym: enhancing diverging genetic interaction
has_obo_namespace: PSI-MI
has_related_synonym: aggravating interaction
id: MI:1271
in_subset: PSI-MI slim

Axiom
annotated source: genetic enhancement (sensu unexpected)
annotated property: definition
annotated target: An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E < wt OR wt < E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

converging genetic epistasis
type: Class
subclass of: converging genetic interaction
subclass of: quantitative genetic epistasis
subclass of: MI 2385
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:05:15Z
has_obo_namespace: PSI-MI
id: MI:1272
in_subset: PSI-MI slim

Axiom
annotated source: converging genetic epistasis
annotated property: definition
annotated target: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

maximal genetic epistasis
type: Class
subclass of: converging genetic epistasis
definition: An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a* < b < wt OR wt < b < a* = ab where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:11:27Z
has_exact_synonym: cisphenotypic masking genetic interaction
has_obo_namespace: PSI-MI
id: MI:1273
in_subset: PSI-MI slim

Axiom
annotated source: maximal genetic epistasis
annotated property: definition
annotated target: An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a* < b < wt OR wt < b < a* = ab where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

minimal genetic epistasis
type: Class
subclass of: converging genetic epistasis
subclass of: cisphenotypic genetic suppression (partial)
definition: An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab = b < wt OR wt < b = ab < a* where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:13:14Z
has_exact_synonym: cisphenotypic semi-suppressing converging genetic interaction
has_exact_synonym: cisphenotypic semi-suppressing genetic interaction
has_obo_namespace: PSI-MI
id: MI:1274
in_subset: PSI-MI slim

Axiom
annotated source: minimal genetic epistasis
annotated property: definition
annotated target: An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab = b < wt OR wt < b = ab < a* where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

obsolete neutral epistasis
type: Class
definition: OBSOLETE: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) OR (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes.
created by: orchard
creation date: 2013-06-05T20:22:53Z
has_obo_namespace: PSI-MI
id: MI:1275
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: obsolete neutral epistasis
annotated property: definition
annotated target: OBSOLETE: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) OR (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes.
database_cross_reference: PMID:15833125

opposing genetic epistasis
type: Class
subclass of: quantitative genetic epistasis
subclass of: MI 2387
definition: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:25:26Z
has_alternative_id: MI:1285
has_exact_synonym: transphenotypic masking genetic interaction
has_obo_namespace: PSI-MI
id: MI:1276
in_subset: PSI-MI slim

Axiom
annotated source: opposing genetic epistasis
annotated property: definition
annotated target: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

qualitative genetic epistasis
type: Class
subclass of: genetic epistasis (sensu Bateson)
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes.
created by: orchard
creation date: 2013-06-05T20:26:38Z
has_obo_namespace: PSI-MI
id: MI:1277
in_subset: PSI-MI slim

Axiom
annotated source: qualitative genetic epistasis
annotated property: definition
annotated target: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes.
database_cross_reference: PMID:15833125

mutual genetic enhancement (sensu unexpected)
type: Class
subclass of: genetic enhancement (sensu unexpected)
subclass of: MI 2401
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a* <= b < wt [E = a*] OR wt < b <= a* < ab [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:31:30Z
has_exact_synonym: cisphenotypic enhancing diverging genetic interaction
has_obo_namespace: PSI-MI
id: MI:1278
in_subset: PSI-MI slim

Axiom
annotated source: mutual genetic enhancement (sensu unexpected)
annotated property: definition
annotated target: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a* <= b < wt [E = a*] OR wt < b <= a* < ab [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

monophenotypic genetic enhancement
type: Class
subclass of: genetic enhancement (sensu unexpected)
subclass of: MI 2382
definition: An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a < b = wt [E = a] OR wt = b < a < ab [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:33:13Z
has_exact_synonym: monophenotypic enhancing diverging genetic interaction
has_exact_synonym: monophenotypic enhancing genetic interaction
has_exact_synonym: unilateral genetic enhancement
has_obo_namespace: PSI-MI
id: MI:1279
in_subset: PSI-MI slim

Axiom
annotated source: monophenotypic genetic enhancement
annotated property: definition
annotated target: An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a < b = wt [E = a] OR wt = b < a < ab [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

cisphenotypic genetic suppression
type: Class
subclass of: genetic suppression (sensu unexpected)
subclass of: MI 2385
subclass of: MI 2389
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab <= wt) [E = a*] OR (wt < b <= a*) AND (wt <= ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:35:53Z
has_exact_synonym: cisphenotypic suppressing converging genetic interaction
has_exact_synonym: cisphenotypic suppressing genetic interaction
has_obo_namespace: PSI-MI
id: MI:1280
in_subset: PSI-MI slim

Axiom
annotated source: cisphenotypic genetic suppression
annotated property: definition
annotated target: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab <= wt) [E = a*] OR (wt < b <= a*) AND (wt <= ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

mutual genetic suppression (complete)
type: Class
subclass of: genetic suppression (complete)
subclass of: MI 2389
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < ab = wt OR wt = ab < b <= a* OR a < wt = ab < b where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:37:41Z
has_obo_namespace: PSI-MI
id: MI:1281
in_subset: PSI-MI slim

Axiom
annotated source: mutual genetic suppression (complete)
annotated property: definition
annotated target: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < ab = wt OR wt = ab < b <= a* OR a < wt = ab < b where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

cisphenotypic genetic suppression (partial)
type: Class
subclass of: cisphenotypic genetic suppression
subclass of: genetic suppression (partial)
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab < wt) [E = a*] OR (wt < b <= a*) AND (wt < ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:39:12Z
has_exact_synonym: cisphenotypic sub-suppressing converging genetic interaction
has_exact_synonym: cisphenotypic sub-suppressing genetic interaction
has_obo_namespace: PSI-MI
id: MI:1282
in_subset: PSI-MI slim

Axiom
annotated source: cisphenotypic genetic suppression (partial)
annotated property: definition
annotated target: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab < wt) [E = a*] OR (wt < b <= a*) AND (wt < ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

cisphenotypic inter-suppressing genetic interaction
type: Class
subclass of: cisphenotypic genetic suppression (partial)
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < b < wt [E = a*] OR wt < b < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T20:43:52Z
has_exact_synonym: cisphenotypic inter-suppressing converging genetic interaction
has_exact_synonym: genetic suppression-enhancement
has_obo_namespace: PSI-MI
id: MI:1283
in_subset: PSI-MI slim

Axiom
annotated source: cisphenotypic inter-suppressing genetic interaction
annotated property: definition
annotated target: An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < b < wt [E = a*] OR wt < b < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

quantitative genetic epistasis
type: Class
subclass of: genetic epistasis (sensu Bateson)
definition: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes.
created by: orchard
creation date: 2013-06-05T20:47:35Z
has_obo_namespace: PSI-MI
id: MI:1284
in_subset: PSI-MI slim

Axiom
annotated source: quantitative genetic epistasis
annotated property: definition
annotated target: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes.
database_cross_reference: PMID:15833125

obsolete opposing epistasis
type: Class
definition: OBSOLETE: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
IAO_0000231: IAO_0000227
IAO_0100001: opposing genetic epistasis
created by: orchard
creation date: 2013-06-05T20:51:51Z
has_obo_namespace: PSI-MI
id: MI:1285
in_subset: PSI-MI slim
comment: Term replaced by http://purl.obolibrary.org/obo/MI_1276
deprecated: true

Axiom
annotated source: obsolete opposing epistasis
annotated property: definition
annotated target: OBSOLETE: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

surpassing genetic interaction
type: Class
subclass of: genetic interaction (sensu unexpected)
definition: An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < wt < E OR E < wt < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:04:18Z
has_obo_namespace: PSI-MI
id: MI:1286
in_subset: PSI-MI slim

Axiom
annotated source: surpassing genetic interaction
annotated property: definition
annotated target: An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < wt < E OR E < wt < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

mutual genetic over-suppression
type: Class
subclass of: surpassing genetic interaction
subclass of: MI 2385
subclass of: MI 2388
definition: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < wt < ab [E = a*] OR ab < wt < b <= a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:06:09Z
has_exact_synonym: cisphenotypic super-suppressing genetic interaction
has_obo_namespace: PSI-MI
id: MI:1287
in_subset: PSI-MI slim

Axiom
annotated source: mutual genetic over-suppression
annotated property: definition
annotated target: An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < wt < ab [E = a*] OR ab < wt < b <= a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

transphenotypic enhancing genetic interaction
type: Class
subclass of: genetic interaction (sensu unexpected)
subclass of: MI 2387
definition: An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b < ab OR ab < a < wt < b where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:11:03Z
has_exact_synonym: genetic over-suppression-enhancement
has_obo_namespace: PSI-MI
id: MI:1288
in_subset: PSI-MI slim

Axiom
annotated source: transphenotypic enhancing genetic interaction
annotated property: definition
annotated target: An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b < ab OR ab < a < wt < b where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

obsolete phenotype bias
type: Class
definition: OBSOLETE: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (a < ab < b) AND (ab != wt) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:15:34Z
has_obo_namespace: PSI-MI
id: MI:1289
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: obsolete phenotype bias
annotated property: definition
annotated target: OBSOLETE: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (a < ab < b) AND (ab != wt) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

genetic suppression (complete)
type: Class
subclass of: MI 2379
definition: An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = ab != a = E where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:34:57Z
has_exact_synonym: all-suppressing genetic interaction
has_obo_namespace: PSI-MI
id: MI:1290
in_subset: PSI-MI slim

Axiom
annotated source: genetic suppression (complete)
annotated property: definition
annotated target: An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = ab != a = E where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

genetic suppression (partial)
type: Class
subclass of: MI 2379
definition: An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < wt [E = a*] OR wt < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:36:07Z
has_exact_synonym: sub-suppressing genetic interaction
has_obo_namespace: PSI-MI
id: MI:1291
in_subset: PSI-MI slim

Axiom
annotated source: genetic suppression (partial)
annotated property: definition
annotated target: An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < wt [E = a*] OR wt < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

monophenotypic genetic suppression
type: Class
subclass of: genetic suppression (sensu unexpected)
subclass of: MI 2382
definition: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab <= b = wt [E = a] OR wt = b <= ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:37:28Z
has_exact_synonym: monophenotypic suppressing converging genetic interaction
has_exact_synonym: monophenotypic suppressing genetic interaction
has_exact_synonym: unilateral genetic suppression
has_obo_namespace: PSI-MI
id: MI:1292
in_subset: PSI-MI slim

Axiom
annotated source: monophenotypic genetic suppression
annotated property: definition
annotated target: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab <= b = wt [E = a] OR wt = b <= ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

monophenotypic genetic suppression (complete)
type: Class
subclass of: genetic suppression (complete)
subclass of: monophenotypic genetic suppression
definition: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab = b = wt [E = a] OR wt = b = ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:38:36Z
has_exact_synonym: monophenotypic all-suppressing converging genetic interaction
has_exact_synonym: monophenotypic all-suppressing genetic interaction
has_exact_synonym: unilateral genetic suppression (complete)
has_obo_namespace: PSI-MI
id: MI:1293
in_subset: PSI-MI slim

Axiom
annotated source: monophenotypic genetic suppression (complete)
annotated property: definition
annotated target: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab = b = wt [E = a] OR wt = b = ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

monophenotypic genetic suppression (partial)
type: Class
subclass of: monophenotypic genetic suppression
definition: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab < b = wt [E = a] OR wt = b < ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:39:32Z
has_exact_synonym: monophenotypic sub-suppressing converging genetic interaction
has_exact_synonym: monophenotypic sub-suppressing genetic interaction
has_exact_synonym: unilateral genetic suppression (partial)
has_obo_namespace: PSI-MI
id: MI:1294
in_subset: PSI-MI slim

Axiom
annotated source: monophenotypic genetic suppression (partial)
annotated property: definition
annotated target: An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab < b = wt [E = a] OR wt = b < ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

monophenotypic genetic over-suppression
type: Class
subclass of: surpassing genetic interaction
subclass of: MI 2382
subclass of: MI 2388
definition: An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E = a < b = wt < ab OR ab < wt = b < a = E where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
created by: orchard
creation date: 2013-06-05T21:54:08Z
has_exact_synonym: monophenotypic super-suppressing genetic interaction
has_exact_synonym: unilateral genetic over-suppression
has_obo_namespace: PSI-MI
id: MI:1295
in_subset: PSI-MI slim

Axiom
annotated source: monophenotypic genetic over-suppression
annotated property: definition
annotated target: An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E = a < b = wt < ab OR ab < wt = b < a = E where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
database_cross_reference: PMID:15833125

amino acid analysis
type: Class
subclass of: experimental feature detection
definition: The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
created by: orchard
creation date: 2013-06-06T07:49:49Z
has_obo_namespace: PSI-MI
id: MI:1296
in_subset: PSI-MI slim

Axiom
annotated source: amino acid analysis
annotated property: definition
annotated target: The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
database_cross_reference: PMID:19072539

phosphoamino acid analysis
type: Class
subclass of: amino acid analysis
definition: The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
created by: orchard
creation date: 2013-06-06T07:55:30Z
has_obo_namespace: PSI-MI
id: MI:1297
in_subset: PSI-MI slim

Axiom
annotated source: phosphoamino acid analysis
annotated property: definition
annotated target: The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
database_cross_reference: PMID:19072539

complex type
type: Class
subclass of: complex
definition: A classification of the structural characteristics of a macromolecular complex.
created by: orchard
creation date: 2013-06-06T08:52:34Z
has_obo_namespace: PSI-MI
id: MI:1298
in_subset: PSI-MI slim

Axiom
annotated source: complex type
annotated property: definition
annotated target: A classification of the structural characteristics of a macromolecular complex.
database_cross_reference: PMID:12853463

complex composition
type: Class
subclass of: complex
definition: A description of the molecule types of which a macromolecular complex is composed.
created by: orchard
creation date: 2013-06-06T08:55:37Z
has_obo_namespace: PSI-MI
id: MI:1299
in_subset: PSI-MI slim

Axiom
annotated source: complex composition
annotated property: definition
annotated target: A description of the molecule types of which a macromolecular complex is composed.
database_cross_reference: PMID:12853464

obligate complex
type: Class
subclass of: complex type
definition: The protein chains present in the complex are not found as independent stable structures in vivo.
created by: orchard
creation date: 2013-06-06T08:57:32Z
has_obo_namespace: PSI-MI
id: MI:1300
in_subset: PSI-MI slim

Axiom
annotated source: obligate complex
annotated property: definition
annotated target: The protein chains present in the complex are not found as independent stable structures in vivo.
database_cross_reference: PMID:12853463

non-obligate complex
type: Class
subclass of: complex type
definition: Protein chains present in the complex may also be found as independent stable proteins in vivo.
created by: orchard
creation date: 2013-06-06T09:02:52Z
has_obo_namespace: PSI-MI
id: MI:1301
in_subset: PSI-MI slim

Axiom
annotated source: non-obligate complex
annotated property: definition
annotated target: Protein chains present in the complex may also be found as independent stable proteins in vivo.
database_cross_reference: PMID:12853463

stable complex
type: Class
subclass of: complex type
definition: A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo.
created by: orchard
creation date: 2013-06-06T09:05:59Z
has_obo_namespace: PSI-MI
id: MI:1302
in_subset: PSI-MI slim

Axiom
annotated source: stable complex
annotated property: definition
annotated target: A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo.
database_cross_reference: PMID:12853464

transient complex
type: Class
subclass of: complex type
definition: A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium.
created by: orchard
creation date: 2013-06-06T09:09:01Z
has_obo_namespace: PSI-MI
id: MI:1303
in_subset: PSI-MI slim

Axiom
annotated source: transient complex
annotated property: definition
annotated target: A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium.
database_cross_reference: PMID:12853463

molecule set
type: Class
subclass of: interactor type
definition: A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods.
created by: orchard
creation date: 2013-06-06T09:20:00Z
has_obo_namespace: PSI-MI
id: MI:1304
in_subset: PSI-MI slim

Axiom
annotated source: molecule set
annotated property: definition
annotated target: A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods.
database_cross_reference: PMID:14755292

candidate set
type: Class
subclass of: molecule set
definition: A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so.
created by: orchard
creation date: 2013-06-06T10:09:09Z
has_obo_namespace: PSI-MI
id: MI:1305
in_subset: PSI-MI slim

Axiom
annotated source: candidate set
annotated property: definition
annotated target: A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so.
database_cross_reference: PMID:14755292

open set
type: Class
subclass of: molecule set
definition: A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid.
created by: orchard
creation date: 2013-06-06T10:19:10Z
has_obo_namespace: PSI-MI
id: MI:1306
in_subset: PSI-MI slim

Axiom
annotated source: open set
annotated property: definition
annotated target: A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid.
database_cross_reference: PMID:14755292

defined set
type: Class
subclass of: molecule set
definition: Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP).
created by: orchard
creation date: 2013-06-06T10:22:53Z
has_obo_namespace: PSI-MI
id: MI:1307
in_subset: PSI-MI slim

Axiom
annotated source: defined set
annotated property: definition
annotated target: Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP).
database_cross_reference: PMID:14755292

resulting sequence
type: Class
subclass of: feature attribute name
definition: Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description provided in the feature name.
created by: orchard
creation date: 2013-06-06T10:26:19Z
has_obo_namespace: PSI-MI
id: MI:1308
in_subset: PSI-MI slim

Axiom
annotated source: resulting sequence
annotated property: definition
annotated target: Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description provided in the feature name.
database_cross_reference: PMID:14755292

de-ADP-ribosylation assay
type: Class
subclass of: enzymatic study
definition: Hydrolytic reactions that release ADP-ribose.
created by: orchard
creation date: 2013-06-06T10:31:58Z
has_exact_synonym: mono-ADP-ribosylhydrolase
has_obo_namespace: PSI-MI
id: MI:1309
in_subset: PSI-MI slim

Axiom
annotated source: de-ADP-ribosylation assay
annotated property: definition
annotated target: Hydrolytic reactions that release ADP-ribose.
database_cross_reference: PMID:23474712
database_cross_reference: PMID:23474714

de-ADP-ribosylation reaction
type: Class
subclass of: enzymatic reaction
definition: Measure of hydrolytic reactions that release ADP-ribose.
created by: orchard
creation date: 2013-06-06T10:34:18Z
has_obo_namespace: PSI-MI
has_related_synonym: mono-ADP-ribosylhydrolase reaction
id: MI:1310
in_subset: PSI-MI slim

Axiom
annotated source: de-ADP-ribosylation reaction
annotated property: definition
annotated target: Measure of hydrolytic reactions that release ADP-ribose.
database_cross_reference: PMID:23474712
database_cross_reference: PMID:23474714

differential scanning calorimetry
type: Class
subclass of: biophysical
definition: Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants.
created by: orchard
creation date: 2013-06-06T10:39:30Z
has_exact_synonym: dsc
has_obo_namespace: PSI-MI
id: MI:1311
in_subset: PSI-MI slim

Axiom
annotated source: differential scanning calorimetry
annotated property: definition
annotated target: Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants.
database_cross_reference: PMID:10398392

Axiom
annotated source: differential scanning calorimetry
annotated property: has_exact_synonym
annotated target: dsc
has_synonym_type: Unique short label curated by PSI-MI

aut-page
type: Class
subclass of: comigration in gel electrophoresis
definition: Method allowing the detection of interactions between two or more molecules by their very close proximity or the overlap of their respective bands in a SDS gel containing urea as an additional denaturing agent.
created by: orchard
creation date: 2013-06-06T10:43:24Z
has_obo_namespace: PSI-MI
has_related_synonym: acetic acid/urea/triton PAGE
id: MI:1312
in_subset: PSI-MI slim

Axiom
annotated source: aut-page
annotated property: definition
annotated target: Method allowing the detection of interactions between two or more molecules by their very close proximity or the overlap of their respective bands in a SDS gel containing urea as an additional denaturing agent.
database_cross_reference: PMID:12875839

proximity labelling technology
type: Class
subclass of: labelling assay
definition: Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification.
created by: orchard
creation date: 2013-06-06T11:20:43Z
has_obo_namespace: PSI-MI
id: MI:1313
in_subset: PSI-MI slim

Axiom
annotated source: proximity labelling technology
annotated property: definition
annotated target: Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification.
database_cross_reference: PMID:22412018

proximity-dependent biotin identification
type: Class
subclass of: proximity labelling technology
definition: A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification.
created by: orchard
creation date: 2013-06-06T11:23:53Z
has_obo_namespace: PSI-MI
has_related_synonym: BioID
id: MI:1314
in_subset: PSI-MI slim

Axiom
annotated source: proximity-dependent biotin identification
annotated property: definition
annotated target: A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification.
database_cross_reference: PMID:22412018

complex recommended name
type: Class
subclass of: synonym
definition: The most accepted name in the literature for this complex.
created by: orchard
creation date: 2013-10-14T15:00:37Z
has_obo_namespace: PSI-MI
id: MI:1315
in_subset: PSI-MI slim

Axiom
annotated source: complex recommended name
annotated property: definition
annotated target: The most accepted name in the literature for this complex.
database_cross_reference: PMID:14755292

complex systematic name
type: Class
subclass of: synonym
definition: A name for a complex built of the component parts of that complex.
created by: orchard
creation date: 2013-10-14T15:04:57Z
has_obo_namespace: PSI-MI
id: MI:1316
in_subset: PSI-MI slim

eukaryotic linear motif resource
type: Class
subclass of: feature database
definition: The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/
created by: orchard
creation date: 2013-10-22T09:49:10Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: elm
has_obo_namespace: PSI-MI
id: MI:1317

Axiom
annotated source: eukaryotic linear motif resource
annotated property: definition
annotated target: The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/
database_cross_reference: PMID:22110040

[A-Za-z_0-9]+$
type: Axiom
annotated source: eukaryotic linear motif resource
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: eukaryotic linear motif resource
annotated property: database_cross_reference
annotated target: search-url:
label: http://elm.eu.org/elms/elmPages/${ac}.html

Axiom
annotated source: eukaryotic linear motif resource
annotated property: has_exact_synonym
annotated target: elm
has_synonym_type: Unique short label curated by PSI-MI

sulfate donor
type: Class
subclass of: donor
definition: Any molecule that is able to transfer a sulphate group to another chemical species.
created by: orchard
creation date: 2014-01-08T07:51:29Z
has_obo_namespace: PSI-MI
has_related_synonym: sulphate donor
id: MI:1318
in_subset: PSI-MI slim

Axiom
annotated source: sulfate donor
annotated property: definition
annotated target: Any molecule that is able to transfer a sulphate group to another chemical species.
database_cross_reference: PMID:14755292

sulfate acceptor
type: Class
subclass of: acceptor
definition: Molecule to which a sulphate group may be transferred from a sulphate donor.
created by: orchard
creation date: 2014-01-08T07:52:46Z
has_obo_namespace: PSI-MI
has_related_synonym: sulphate acceptor
id: MI:1319
in_subset: PSI-MI slim

Axiom
annotated source: sulfate acceptor
annotated property: definition
annotated target: Molecule to which a sulphate group may be transferred from a sulphate donor.
database_cross_reference: PMID:14755292

membrane yeast two hybrid
type: Class
subclass of: MI 2412
definition: Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners.
created by: orchard
creation date: 2014-01-08T10:14:46Z
has_exact_synonym: MYTH
has_obo_namespace: PSI-MI
id: MI:1320
in_subset: PSI-MI slim

Axiom
annotated source: membrane yeast two hybrid
annotated property: definition
annotated target: Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners.
database_cross_reference: PMID:2261051

ire1 reconstruction
type: Class
subclass of: MI 2412
definition: Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum.
created by: orchard
creation date: 2014-01-08T10:17:38Z
has_obo_namespace: PSI-MI
has_related_synonym: ER-MYTH
has_related_synonym: endoplasmic reticulum membrane yeast-two hybrid
id: MI:1321
in_subset: PSI-MI slim

Axiom
annotated source: ire1 reconstruction
annotated property: definition
annotated target: Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum.
database_cross_reference: PMID:22665516

atto 465
type: Class
subclass of: atto label
definition: Fluorescent tag - maleimide couples to thiols.
created by: orchard
creation date: 2014-01-08T10:27:34Z
has_exact_synonym: atto 465 maleimide
has_exact_synonym: atto465
has_obo_namespace: PSI-MI
id: MI:1322
in_subset: PSI-MI slim

Axiom
annotated source: atto 465
annotated property: definition
annotated target: Fluorescent tag - maleimide couples to thiols.
database_cross_reference: PMID:14755292

tag visualisation by alkaline phosphatase activity
type: Class
subclass of: tag visualisation by enzyme assay
definition: The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction.
created by: orchard
creation date: 2014-01-08T11:00:36Z
has_exact_synonym: tag alk phosphatase activity
has_obo_namespace: PSI-MI
id: MI:1323
in_subset: PSI-MI slim

Axiom
annotated source: tag visualisation by alkaline phosphatase activity
annotated property: definition
annotated target: The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction.
database_cross_reference: PMID:14755292

Axiom
annotated source: tag visualisation by alkaline phosphatase activity
annotated property: has_exact_synonym
annotated target: tag alk phosphatase activity
has_synonym_type: Unique short label curated by PSI-MI

conditioned medium
type: Class
subclass of: sample process
definition: Molecule present in media harvested from cultured cells.
created by: orchard
creation date: 2014-01-08T11:07:44Z
has_obo_namespace: PSI-MI
id: MI:1324
in_subset: PSI-MI slim

Axiom
annotated source: conditioned medium
annotated property: definition
annotated target: Molecule present in media harvested from cultured cells.
database_cross_reference: PMID:14755292

sulfurtransferase assay
type: Class
subclass of: enzymatic study
definition: Measures the rate of a sulphate molecule transfer between two molecules.
created by: orchard
creation date: 2014-01-08T11:13:39Z
has_exact_synonym: sulfertransferase
has_obo_namespace: PSI-MI
has_related_synonym: sulfurtransfer assay
has_related_synonym: sulphurtransferase assay
id: MI:1325
in_subset: PSI-MI slim

Axiom
annotated source: sulfurtransferase assay
annotated property: definition
annotated target: Measures the rate of a sulphate molecule transfer between two molecules.
database_cross_reference: PMID:14755292

Axiom
annotated source: sulfurtransferase assay
annotated property: has_exact_synonym
annotated target: sulfertransferase
has_synonym_type: Unique short label curated by PSI-MI

CLONE OF phosphotransfer reaction
type: Class
definition: Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
created by: orchard
creation date: 2014-01-08T11:15:51Z
has_exact_synonym: phosphotransfer
has_obo_namespace: PSI-MI
id: MI:1326
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: CLONE OF phosphotransfer reaction
annotated property: definition
annotated target: Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
database_cross_reference: PMID:14755292
database_cross_reference: PMID:16712436

Axiom
annotated source: CLONE OF phosphotransfer reaction
annotated property: has_exact_synonym
annotated target: phosphotransfer
has_synonym_type: Unique short label curated by PSI-MI

sulfurtransfer reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction where a sulfate group is transferred between two proteins
created by: orchard
creation date: 2014-01-08T11:16:12Z
has_exact_synonym: sulfurtransfer
has_exact_synonym: sulphurtransfer reaction
has_obo_namespace: PSI-MI
id: MI:1327
in_subset: PSI-MI slim

Axiom
annotated source: sulfurtransfer reaction
annotated property: definition
annotated target: Reaction where a sulfate group is transferred between two proteins
database_cross_reference: GO:GO:0016783
database_cross_reference: PMID:14755292

Axiom
annotated source: sulfurtransfer reaction
annotated property: has_exact_synonym
annotated target: sulfurtransfer
has_synonym_type: Unique short label curated by PSI-MI

coumarin label
type: Class
subclass of: fluorescent dye label
definition: A class of labels derived from the benzopyrone coumarin.
created by: orchard
creation date: 2014-01-08T11:25:00Z
has_obo_namespace: PSI-MI
id: MI:1328
in_subset: PSI-MI slim

Axiom
annotated source: coumarin label
annotated property: definition
annotated target: A class of labels derived from the benzopyrone coumarin.
database_cross_reference: PMID:14755292

cpm
type: Class
subclass of: coumarin label
definition: The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm.
created by: orchard
creation date: 2014-01-08T11:36:48Z
has_exact_synonym: 7-diethylamino-3-(4' maleimidylphenyl)-4-methylcoumarin
has_obo_namespace: PSI-MI
id: MI:1329

Axiom
annotated source: cpm
annotated property: definition
annotated target: The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm.
database_cross_reference: PMID:14755292

dnp
type: Class
subclass of: fluorescent dye label
definition: Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria.
created by: orchard
creation date: 2014-01-08T12:01:24Z
has_exact_synonym: 2, 4-DNP
has_exact_synonym: 2,4-Dinitrophenol
has_exact_synonym: dinitrophenol
has_obo_namespace: PSI-MI
id: MI:1330
in_subset: PSI-MI slim

Axiom
annotated source: dnp
annotated property: definition
annotated target: Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria.
database_cross_reference: PMID:14755292

evidence ontology
type: Class
subclass of: experiment database
definition: The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means.
created by: orchard
creation date: 2014-01-08T12:48:33Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
has_related_synonym: ECO
id: MI:1331
in_subset: PSI-MI slim

Axiom
annotated source: evidence ontology
annotated property: definition
annotated target: The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means.
database_cross_reference: PMID:14755292

ECO:\d{7}$
type: Axiom
annotated source: evidence ontology
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: evidence ontology
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/ols/ontologies/ECO/terms

bhf-ucl
type: Class
subclass of: interaction database
subclass of: imex source
definition: The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium.
created by: orchard
creation date: 2014-01-08T12:56:27Z
has_exact_synonym: BHF-UCL
has_obo_namespace: PSI-MI
has_related_synonym: Cardiovascular Gene Annotation Initiative
id: MI:1332
in_subset: PSI-MI slim

Axiom
annotated source: bhf-ucl
annotated property: definition
annotated target: The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium.
database_cross_reference: PMID:21419760

Axiom
annotated source: bhf-ucl
annotated property: has_exact_synonym
annotated target: BHF-UCL
has_synonym_type: Alternate label curated by PSI-MI

rogid
type: Class
subclass of: checksum
definition: SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value): +/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz Lists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order.
created by: orchard
creation date: 2014-01-09T11:17:18Z
has_obo_namespace: PSI-MI
id: MI:1333
in_subset: PSI-MI slim

Axiom
annotated source: rogid
annotated property: definition
annotated target: SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value): +/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz Lists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order.
database_cross_reference: PMID:18823568

rigid
type: Class
subclass of: interaction attribute name
subclass of: checksum
definition: A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing "=" characters used for padding.
created by: orchard
creation date: 2014-01-09T11:17:32Z
has_obo_namespace: PSI-MI
id: MI:1334
in_subset: PSI-MI slim

Axiom
annotated source: rigid
annotated property: definition
annotated target: A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing "=" characters used for padding.
database_cross_reference: PMID:18823568

hpidb
type: Class
subclass of: interaction database
definition: Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface. http://www.agbase.msstate.edu/hpi/main.html
created by: orchard
creation date: 2014-03-03T11:43:31Z
has_exact_synonym: HPIDB
has_exact_synonym: Host Pathogen Interaction database
has_obo_namespace: PSI-MI
id: MI:1335
in_subset: PSI-MI slim

Axiom
annotated source: hpidb
annotated property: definition
annotated target: Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface. http://www.agbase.msstate.edu/hpi/main.html
database_cross_reference: PMID:20946599

Axiom
annotated source: hpidb
annotated property: has_exact_synonym
annotated target: HPIDB
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: hpidb
annotated property: has_exact_synonym
annotated target: Host Pathogen Interaction database
has_synonym_type: Alternate label curated by PSI-MI

experiment database
type: Class
subclass of: database citation
definition: Databases that contain information used to add additional information to experiments (meta-data).
created by: orchard
creation date: 2014-01-20T11:56:03Z
has_exact_synonym: experiment xref
has_obo_namespace: PSI-MI
id: MI:1336
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: experiment database
annotated property: definition
annotated target: Databases that contain information used to add additional information to experiments (meta-data).
database_cross_reference: PMID:14755292

Axiom
annotated source: experiment database
annotated property: has_exact_synonym
annotated target: experiment xref
has_synonym_type: Unique short label curated by PSI-MI

efo
type: Class
subclass of: experiment database
definition: The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms.
created by: orchard
creation date: 2014-01-20T11:58:47Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: Experimental facto ontology
has_obo_namespace: PSI-MI
id: MI:1337
in_subset: PSI-MI slim

Axiom
annotated source: efo
annotated property: definition
annotated target: The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms.
database_cross_reference: pmid:20200009

([A-Z]+:)?\d{7}$
type: Axiom
annotated source: efo
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: efo
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/ols/ontologies/efo/terms

eef tag
type: Class
subclass of: tag
definition: Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2
created by: orchard
creation date: 2014-01-20T12:13:30Z
has_obo_namespace: PSI-MI
has_related_synonym: Glu-Glu-Phe epitope tag
id: MI:1338
in_subset: PSI-MI slim

Axiom
annotated source: eef tag
annotated property: definition
annotated target: Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2
database_cross_reference: PMID:6204858

supercharged green fluorescent protein
type: Class
subclass of: green fluorescent protein tag
definition: Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation.
created by: orchard
creation date: 2014-01-20T13:13:03Z
has_obo_namespace: PSI-MI
has_related_synonym: stGFP
id: MI:1339
in_subset: PSI-MI slim

Axiom
annotated source: supercharged green fluorescent protein
annotated property: definition
annotated target: Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation.
database_cross_reference: PMID:17665911

human orfeome collection
type: Class
subclass of: protein sequence databases
definition: A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants.
created by: orchard
creation date: 2014-04-08T16:15:19Z
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:1340
in_subset: PSI-MI slim

Axiom
annotated source: human orfeome collection
annotated property: definition
annotated target: A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants.
database_cross_reference: PMID:14755292

Axiom
annotated source: human orfeome collection
annotated property: database_cross_reference
annotated target: search-url:
label: http://horfdb.dfci.harvard.edu/

set member
type: Class
subclass of: cross-reference type
definition: Indicates that this protein is a member of a set of proteins with similar sequence and/or function.
created by: orchard
creation date: 2014-04-25T09:19:21Z
has_obo_namespace: PSI-MI
id: MI:1341
in_subset: PSI-MI slim

Axiom
annotated source: set member
annotated property: definition
annotated target: Indicates that this protein is a member of a set of proteins with similar sequence and/or function.
database_cross_reference: PMID:14755292

qcmd
type: Class
subclass of: biosensor
definition: The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions.
created by: orchard
creation date: 2014-07-17T08:26:51Z
has_exact_synonym: QCM-D
has_exact_synonym: Quartz Crystal Microbalance with Dissipation monitoring
has_obo_namespace: PSI-MI
id: MI:1342
in_subset: PSI-MI slim

Axiom
annotated source: qcmd
annotated property: definition
annotated target: The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions.
database_cross_reference: PMID:19137101
database_cross_reference: PMID:22158962
database_cross_reference: PMID:23504432

enzyme regulator
type: Class
subclass of: regulator
definition: Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits.
created by: orchard
creation date: 2014-07-17T08:43:17Z
has_broad_synonym: enzyme complex regulatory subunit
has_obo_namespace: PSI-MI
id: MI:1343
in_subset: PSI-MI slim

Axiom
annotated source: enzyme regulator
annotated property: definition
annotated target: Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits.
database_cross_reference: PMID:14755292

erythrosin iodoacetamide label
type: Class
subclass of: fluorescein label
definition: Fluoresceine-derived label.
created by: orchard
creation date: 2014-07-17T08:47:44Z
has_exact_synonym: ErIA
has_exact_synonym: erythrosin-5-iodoacetamide
has_obo_namespace: PSI-MI
id: MI:1344

Axiom
annotated source: erythrosin iodoacetamide label
annotated property: definition
annotated target: Fluoresceine-derived label.
database_cross_reference: PMID:14755292

rho tag
type: Class
subclass of: tag
definition: A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope.
created by: orchard
creation date: 2014-09-19T14:24:43Z
has_exact_synonym: 1D4 tag
has_exact_synonym: rho1D4 tag
has_obo_namespace: PSI-MI
id: MI:1345
in_subset: PSI-MI slim

Axiom
annotated source: rho tag
annotated property: definition
annotated target: A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope.
database_cross_reference: PMID:12110672
database_cross_reference: PMID:24943310

Axiom
annotated source: rho tag
annotated property: has_exact_synonym
annotated target: 1D4 tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: rho tag
annotated property: has_exact_synonym
annotated target: rho1D4 tag
has_synonym_type: Alternate label curated by PSI-MI

bmrb
type: Class
subclass of: interaction database
definition: Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US.
created by: orchard
creation date: 2014-09-19T14:42:33Z
has_obo_namespace: PSI-MI
has_related_synonym: BioMagResBank
has_related_synonym: Biological Magnetic Resonance Data Bank
id: MI:1346
in_subset: PSI-MI slim

Axiom
annotated source: bmrb
annotated property: definition
annotated target: Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US.
database_cross_reference: PMID:18288446

protein ontology
type: Class
subclass of: interaction database
definition: PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes.
created by: orchard
creation date: 2014-09-26T14:06:25Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
has_related_synonym: PRO
id: MI:1347
in_subset: PSI-MI slim

Axiom
annotated source: protein ontology
annotated property: definition
annotated target: PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes.
database_cross_reference: PMID:24270789

[0-9]{9}|[A-Z][0-9][A-Z0-9]{3}[0-9]|[A-Z][0-9][A-Z0-9]{3}[0-9]-[1-9]+
type: Axiom
annotated source: protein ontology
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: protein ontology
annotated property: database_cross_reference
annotated target: search-url:
label: http://pir.georgetown.edu/cgi-bin/pro/entry_pro

chembl target
type: Class
subclass of: sequence database
subclass of: chembl
definition: ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
created by: orchard
creation date: 2014-10-16T10:10:03Z
database_cross_reference: regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:1348
in_subset: PSI-MI slim

CHEMBL:[0-9]+
type: Axiom
annotated source: chembl target
annotated property: database_cross_reference
annotated target: regexp:

Axiom
annotated source: chembl target
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/chembldb/index.php/target/inspect/${ac}

chembl
type: Class
subclass of: interaction database
definition: ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
created by: orchard
creation date: 2014-10-16T10:16:54Z
has_obo_namespace: PSI-MI
id: MI:1349
in_subset: PSI-MI slim

Axiom
annotated source: chembl
annotated property: definition
annotated target: ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
database_cross_reference: PMID:24214965

orphanet
type: Class
subclass of: experiment database
definition: Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases.
created by: orchard
creation date: 2014-10-16T10:27:01Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:1350
in_subset: PSI-MI slim

Axiom
annotated source: orphanet
annotated property: definition
annotated target: Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases.
database_cross_reference: PMID:19058507

^\d+$
type: Axiom
annotated source: orphanet
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: orphanet
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/ols/ontologies/ordo/terms

inferred-from
type: Class
subclass of: cross-reference type
definition: Refers to the original experimentally verified object from which the described object has been derived.
created by: orchard
creation date: 2014-10-16T10:39:21Z
has_obo_namespace: PSI-MI
id: MI:1351
in_subset: PSI-MI slim

Axiom
annotated source: inferred-from
annotated property: definition
annotated target: Refers to the original experimentally verified object from which the described object has been derived.
database_cross_reference: PMID:25313161

uracil interference assay
type: Class
subclass of: enzymatic footprinting
definition: In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means "contact points".
created by: orchard
creation date: 2015-01-28T10:12:25Z
has_obo_namespace: PSI-MI
id: MI:1352
in_subset: PSI-MI slim

Axiom
annotated source: uracil interference assay
annotated property: definition
annotated target: In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means "contact points".
database_cross_reference: PMID:18265086

au5 tag
type: Class
subclass of: tag
definition: Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK.
created by: orchard
creation date: 2015-01-28T10:23:06Z
has_obo_namespace: PSI-MI
id: MI:1353
in_subset: PSI-MI slim

Axiom
annotated source: au5 tag
annotated property: definition
annotated target: Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK.
database_cross_reference: PMID:9765280

lipase assay
type: Class
subclass of: cleavage assay
definition: Cleavage (hydrolysis) of a lipid molecule.
created by: orchard
creation date: 2015-02-03T13:18:55Z
has_obo_namespace: PSI-MI
id: MI:1354
in_subset: PSI-MI slim

Axiom
annotated source: lipase assay
annotated property: definition
annotated target: Cleavage (hydrolysis) of a lipid molecule.
database_cross_reference: PMID:14760721

lipid cleavage
type: Class
subclass of: cleavage reaction
definition: Reaction monitoring the cleavage (hydrolysis) or a lipid molecule.
created by: orchard
creation date: 2015-02-03T13:25:21Z
has_obo_namespace: PSI-MI
id: MI:1355
in_subset: PSI-MI slim

Axiom
annotated source: lipid cleavage
annotated property: definition
annotated target: Reaction monitoring the cleavage (hydrolysis) or a lipid molecule.
database_cross_reference: PMID:14760721

validated two hybrid
type: Class
subclass of: two hybrid
definition: The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique.
created by: orchard
creation date: 2015-02-03T13:36:20Z
has_obo_namespace: PSI-MI
id: MI:1356
in_subset: PSI-MI slim

Axiom
annotated source: validated two hybrid
annotated property: definition
annotated target: The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique.
database_cross_reference: PMID:25416956

RNAcentral
type: Class
subclass of: sequence database
definition: Provides unified access to the ncRNA sequence data supplied by the expert databases.
created by: orchard
creation date: 2015-02-03T13:37:23Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_obo_namespace: PSI-MI
id: MI:1357
in_subset: PSI-MI slim

Axiom
annotated source: RNAcentral
annotated property: definition
annotated target: Provides unified access to the ncRNA sequence data supplied by the expert databases.
database_cross_reference: PMID:25352543

/URS[0-9A-F]{10}/i
type: Axiom
annotated source: RNAcentral
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: RNAcentral
annotated property: database_cross_reference
annotated target: search-url:
label: http://rnacentral.org/rna/${ac}

drugbank
type: Class
subclass of: bioactive entity reference
definition: DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins.
has_obo_namespace: PSI-MI
id: MI:2002
in_subset: Drugable

Axiom
annotated source: drugbank
annotated property: definition
annotated target: DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins.
database_cross_reference: PMID:14755292

commercial name
type: Class
subclass of: synonym
definition: Standard name of drug or any reagent as provided by its manufacturer.
has_exact_synonym: generic name
has_obo_namespace: PSI-MI
id: MI:2003
in_subset: Drugable

Axiom
annotated source: commercial name
annotated property: definition
annotated target: Standard name of drug or any reagent as provided by its manufacturer.
database_cross_reference: PMID:14755292

Axiom
annotated source: commercial name
annotated property: has_exact_synonym
annotated target: generic name
has_synonym_type: Alternate label curated by PSI-MI

drug brand name
type: Class
subclass of: synonym
definition: Alternate names of the drug, brand names from different manufacturers.
has_obo_namespace: PSI-MI
id: MI:2004
in_subset: Drugable

Axiom
annotated source: drug brand name
annotated property: definition
annotated target: Alternate names of the drug, brand names from different manufacturers.
database_cross_reference: PMID:14755292

drug mixture brand name
type: Class
subclass of: synonym
definition: Brand names and composition of mixtures that include the drug described in this DrugCard file.
has_exact_synonym: mix brand name
has_obo_namespace: PSI-MI
id: MI:2005
in_subset: Drugable

Axiom
annotated source: drug mixture brand name
annotated property: definition
annotated target: Brand names and composition of mixtures that include the drug described in this DrugCard file.
database_cross_reference: PMID:14755292

Axiom
annotated source: drug mixture brand name
annotated property: has_exact_synonym
annotated target: mix brand name
has_synonym_type: Unique short label curated by PSI-MI

biotech product preparation
type: Class
subclass of: bioactive entity attribute name
definition: Description of the drug (for biotech drugs) describing its composition and/or preparation.
has_exact_synonym: biotech prep
has_obo_namespace: PSI-MI
id: MI:2006
in_subset: Drugable

Axiom
annotated source: biotech product preparation
annotated property: definition
annotated target: Description of the drug (for biotech drugs) describing its composition and/or preparation.
database_cross_reference: PMID:14755292

Axiom
annotated source: biotech product preparation
annotated property: has_exact_synonym
annotated target: biotech prep
has_synonym_type: Unique short label curated by PSI-MI

iupac name
type: Class
subclass of: synonym
definition: IUPAC or standard chemical name for a drug, or a chemical.
has_obo_namespace: PSI-MI
id: MI:2007
in_subset: Drugable

Axiom
annotated source: iupac name
annotated property: definition
annotated target: IUPAC or standard chemical name for a drug, or a chemical.
database_cross_reference: PMID:14755292

chemical formula
type: Class
subclass of: physicochemical attribute name
definition: Chemical formula describing atomic or elemental composition
has_obo_namespace: PSI-MI
id: MI:2008
in_subset: Drugable

Axiom
annotated source: chemical formula
annotated property: definition
annotated target: Chemical formula describing atomic or elemental composition
database_cross_reference: PMID:14755292

chemical structure
type: Class
subclass of: physicochemical attribute name
definition: Image of the drug structure (if small molecule) or its sequence (if biotech drug)
has_obo_namespace: PSI-MI
id: MI:2009
in_subset: Drugable

Axiom
annotated source: chemical structure
annotated property: definition
annotated target: Image of the drug structure (if small molecule) or its sequence (if biotech drug)
database_cross_reference: PMID:14755292

standard inchi
type: Class
subclass of: checksum
subclass of: structure representation attribute name
definition: IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03.
has_exact_synonym: standard inchi
has_obo_namespace: PSI-MI
has_related_synonym: inchi id
id: MI:2010
in_subset: PSI-MI slim

Axiom
annotated source: standard inchi
annotated property: definition
annotated target: IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03.
database_cross_reference: PMID:14755292

Axiom
annotated source: standard inchi
annotated property: has_exact_synonym
annotated target: standard inchi
has_synonym_type: Unique short label curated by PSI-MI

cas registry number
type: Class
subclass of: bioactive entity reference
definition: Chemical Abstract Service identification number
has_obo_namespace: PSI-MI
id: MI:2011
in_subset: Drugable

Axiom
annotated source: cas registry number
annotated property: definition
annotated target: Chemical Abstract Service identification number
database_cross_reference: PMID:14755292

kegg compound
type: Class
subclass of: kegg
definition: Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)
has_exact_synonym: KEGG Compound ID
has_obo_namespace: PSI-MI
id: MI:2012
in_subset: Drugable

Axiom
annotated source: kegg compound
annotated property: definition
annotated target: Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)
database_cross_reference: PMID:14755292

Axiom
annotated source: kegg compound
annotated property: has_exact_synonym
annotated target: KEGG Compound ID
has_synonym_type: Alternate label curated by PSI-MI

pubchem
type: Class
definition: NCBI's PubChem database identification number (if molecule is in PubChem). OBSOLETE as redudant with MI:0730
has_exact_synonym: PubChem ID
has_obo_namespace: PSI-MI
id: MI:2013
in_subset: Drugable
deprecated: true

Axiom
annotated source: pubchem
annotated property: definition
annotated target: NCBI's PubChem database identification number (if molecule is in PubChem). OBSOLETE as redudant with MI:0730
database_cross_reference: PMID:14755292

Axiom
annotated source: pubchem
annotated property: has_exact_synonym
annotated target: PubChem ID
has_synonym_type: Alternate label curated by PSI-MI

pharmgkb
type: Class
subclass of: bioactive entity reference
definition: Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)
has_obo_namespace: PSI-MI
id: MI:2015
in_subset: Drugable

Axiom
annotated source: pharmgkb
annotated property: definition
annotated target: Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)
database_cross_reference: PMID:14755292

bind smid
type: Class
subclass of: bioactive entity reference
definition: BIND database Small Molecule Identification number (if molecule is in BIND)
has_obo_namespace: PSI-MI
id: MI:2016
in_subset: Drugable
comment: May not be publicly available any more since now owned by Thompson Scientific.

Axiom
annotated source: bind smid
annotated property: definition
annotated target: BIND database Small Molecule Identification number (if molecule is in BIND)
database_cross_reference: PMID:14755292

heterogen
type: Class
subclass of: rcsb pdb
subclass of: pdbe
subclass of: pdbj
definition: The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are: - not one of the standard amino acids, and - not one of the nucleic acids (C, G, A, T, U, and I), and - not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and - not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name. Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK.
has_exact_synonym: het
has_obo_namespace: PSI-MI
id: MI:2017
in_subset: Drugable

Axiom
annotated source: heterogen
annotated property: definition
annotated target: The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are: - not one of the standard amino acids, and - not one of the nucleic acids (C, G, A, T, U, and I), and - not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and - not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name. Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK.
database_cross_reference: PMID:14755292

Axiom
annotated source: heterogen
annotated property: has_exact_synonym
annotated target: het
has_synonym_type: Unique short label curated by PSI-MI

canadian drug identification number
type: Class
subclass of: bioactive entity reference
definition: Drug Identification Number (Canadian Drug ID system)
has_exact_synonym: din
has_obo_namespace: PSI-MI
id: MI:2020
in_subset: Drugable

Axiom
annotated source: canadian drug identification number
annotated property: definition
annotated target: Drug Identification Number (Canadian Drug ID system)
database_cross_reference: PMID:14755292

Axiom
annotated source: canadian drug identification number
annotated property: has_exact_synonym
annotated target: din
has_synonym_type: Unique short label curated by PSI-MI

rxlist link
type: Class
subclass of: bioactive entity reference
definition: Hyperlink to RxList entry for the given drug (if it exists)
has_obo_namespace: PSI-MI
id: MI:2021
in_subset: Drugable

Axiom
annotated source: rxlist link
annotated property: definition
annotated target: Hyperlink to RxList entry for the given drug (if it exists)
database_cross_reference: PMID:14755292

material safety data sheet
type: Class
subclass of: physicochemical attribute name
definition: Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs.
has_exact_synonym: MSDS Material Safety Sheet
has_exact_synonym: msds
has_obo_namespace: PSI-MI
id: MI:2023
in_subset: Drugable

Axiom
annotated source: material safety data sheet
annotated property: definition
annotated target: Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs.
database_cross_reference: PMID:14755292

Axiom
annotated source: material safety data sheet
annotated property: has_exact_synonym
annotated target: MSDS Material Safety Sheet
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: material safety data sheet
annotated property: has_exact_synonym
annotated target: msds
has_synonym_type: Unique short label curated by PSI-MI

patent number
type: Class
subclass of: cross-reference type
definition: number of the patent describing a drug's synthesis or use.
has_obo_namespace: PSI-MI
id: MI:2024
in_subset: Drugable

Axiom
annotated source: patent number
annotated property: definition
annotated target: number of the patent describing a drug's synthesis or use.
database_cross_reference: PMID:14755292

molecular weight
type: Class
subclass of: parameter type
definition: Molecular weight in g/mol, determined from molecular formula or sequence.
has_obo_namespace: PSI-MI
id: MI:2025
in_subset: Drugable

Axiom
annotated source: molecular weight
annotated property: definition
annotated target: Molecular weight in g/mol, determined from molecular formula or sequence.
database_cross_reference: PMID:14755292

melting point
type: Class
subclass of: parameter type
definition: The melting point of a solid is the temperature range at which it changes state from solid to liquid.
has_obo_namespace: PSI-MI
id: MI:2026
in_subset: Drugable

Axiom
annotated source: melting point
annotated property: definition
annotated target: The melting point of a solid is the temperature range at which it changes state from solid to liquid.
database_cross_reference: PMID:14755292

water solubility
type: Class
subclass of: logs
definition: Water solubility in mg/mL or g/L
has_exact_synonym: logSw
has_obo_namespace: PSI-MI
id: MI:2027
in_subset: Drugable

Axiom
annotated source: water solubility
annotated property: definition
annotated target: Water solubility in mg/mL or g/L
database_cross_reference: PMID:14755292

Axiom
annotated source: water solubility
annotated property: has_exact_synonym
annotated target: logSw
has_synonym_type: Alternate label curated by PSI-MI

logp
type: Class
subclass of: parameter type
definition: Water/octanol partition coefficient of a small molecule.
has_obo_namespace: PSI-MI
id: MI:2029
in_subset: Drugable

Axiom
annotated source: logp
annotated property: definition
annotated target: Water/octanol partition coefficient of a small molecule.
database_cross_reference: PMID:14755292

isoelectric point
type: Class
subclass of: parameter type
definition: The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule.
has_obo_namespace: PSI-MI
id: MI:2030
in_subset: Drugable

Axiom
annotated source: isoelectric point
annotated property: definition
annotated target: The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule.
database_cross_reference: PMID:14755292

hydrophobicity
type: Class
subclass of: parameter type
definition: Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score.
has_obo_namespace: PSI-MI
id: MI:2033
in_subset: Drugable

Axiom
annotated source: hydrophobicity
annotated property: definition
annotated target: Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score.
database_cross_reference: PMID:14755292

boiling point
type: Class
subclass of: parameter type
definition: The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure.
has_obo_namespace: PSI-MI
id: MI:2036
in_subset: Drugable

Axiom
annotated source: boiling point
annotated property: definition
annotated target: The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure.
database_cross_reference: PMID:14755292

smiles string
type: Class
subclass of: checksum
subclass of: structure representation attribute name
definition: SMILES string corresponding to drug structure
has_obo_namespace: PSI-MI
id: MI:2039
in_subset: Drugable

Axiom
annotated source: smiles string
annotated property: definition
annotated target: SMILES string corresponding to drug structure
database_cross_reference: PMID:14755292

drug type
type: Class
subclass of: bioactive entity attribute name
definition: Type of drug (approved, experimental, biotech, nutraceutical)
has_obo_namespace: PSI-MI
id: MI:2040
in_subset: Drugable

Axiom
annotated source: drug type
annotated property: definition
annotated target: Type of drug (approved, experimental, biotech, nutraceutical)
database_cross_reference: PMID:14755292

drug category
type: Class
subclass of: bioactive entity attribute name
definition: Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.).
has_obo_namespace: PSI-MI
id: MI:2041
in_subset: Drugable

Axiom
annotated source: drug category
annotated property: definition
annotated target: Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.).
database_cross_reference: PMID:14755292

disease indication
type: Class
subclass of: bioactive entity attribute name
definition: Description or common names of diseases that the drug is used to treat.
has_obo_namespace: PSI-MI
id: MI:2042
in_subset: Drugable
comment: Source of further terms could be MeSH term or SNOWMAN.

Axiom
annotated source: disease indication
annotated property: definition
annotated target: Description or common names of diseases that the drug is used to treat.
database_cross_reference: PMID:14755292

pharmacology
type: Class
subclass of: bioactive entity attribute name
definition: Text description of how the drug works at a clinical or physiological level.
has_obo_namespace: PSI-MI
id: MI:2043
in_subset: Drugable

Axiom
annotated source: pharmacology
annotated property: definition
annotated target: Text description of how the drug works at a clinical or physiological level.
database_cross_reference: PMID:14755292

mechanism of action
type: Class
subclass of: bioactive entity attribute name
definition: Description of how the drug works or what it binds to at a molecular level.
has_obo_namespace: PSI-MI
id: MI:2044
in_subset: Drugable

Axiom
annotated source: mechanism of action
annotated property: definition
annotated target: Description of how the drug works or what it binds to at a molecular level.
database_cross_reference: PMID:14755292

drug absorption
type: Class
subclass of: parameter type
definition: Determination of how quickly and how much of a drug reaches its intended target (site) of action.
has_obo_namespace: PSI-MI
id: MI:2045
in_subset: Drugable

Axiom
annotated source: drug absorption
annotated property: definition
annotated target: Determination of how quickly and how much of a drug reaches its intended target (site) of action.
database_cross_reference: PMID:14755292

lethal dose 50
type: Class
subclass of: parameter type
definition: The LD50 is the dose that kills half (50%) of the animals tested
has_exact_synonym: ld50
has_exact_synonym: lethal dose 50 %
has_obo_namespace: PSI-MI
id: MI:2046
in_subset: Drugable

Axiom
annotated source: lethal dose 50
annotated property: definition
annotated target: The LD50 is the dose that kills half (50%) of the animals tested
database_cross_reference: PMID:14755292

Axiom
annotated source: lethal dose 50
annotated property: has_exact_synonym
annotated target: ld50
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: lethal dose 50
annotated property: has_exact_synonym
annotated target: lethal dose 50 %
has_synonym_type: Alternate label curated by PSI-MI

percentage of plasma protein binding
type: Class
subclass of: parameter type
definition: Percentage of the drug that is bound in plasma proteins
has_exact_synonym: plasma prot binding
has_exact_synonym: protein binding %
has_obo_namespace: PSI-MI
id: MI:2047
in_subset: Drugable

Axiom
annotated source: percentage of plasma protein binding
annotated property: definition
annotated target: Percentage of the drug that is bound in plasma proteins
database_cross_reference: PMID:14755292

Axiom
annotated source: percentage of plasma protein binding
annotated property: has_exact_synonym
annotated target: plasma prot binding
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: percentage of plasma protein binding
annotated property: has_exact_synonym
annotated target: protein binding %
has_synonym_type: Alternate label curated by PSI-MI

drug biotransformation
type: Class
subclass of: pharmacokinetics attribute name
definition: The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media.
has_exact_synonym: drug metabolism
has_obo_namespace: PSI-MI
id: MI:2048
in_subset: Drugable

Axiom
annotated source: drug biotransformation
annotated property: definition
annotated target: The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media.
database_cross_reference: PMID:14755292

Axiom
annotated source: drug biotransformation
annotated property: has_exact_synonym
annotated target: drug metabolism
has_synonym_type: Unique short label curated by PSI-MI

elimination half life
type: Class
subclass of: parameter type
definition: Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%.
has_exact_synonym: distribution halflife
has_exact_synonym: elimin half life
has_exact_synonym: t1/2
has_obo_namespace: PSI-MI
id: MI:2049
in_subset: Drugable

Axiom
annotated source: elimination half life
annotated property: definition
annotated target: Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%.
database_cross_reference: PMID:14755292

Axiom
annotated source: elimination half life
annotated property: has_exact_synonym
annotated target: distribution halflife
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: elimination half life
annotated property: has_exact_synonym
annotated target: elimin half life
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: elimination half life
annotated property: has_exact_synonym
annotated target: t1/2
has_synonym_type: Alternate label curated by PSI-MI

dosage form
type: Class
subclass of: bioactive entity attribute name
definition: How the drug is dispensed (tablets, capsules, solutions), packing material.
has_obo_namespace: PSI-MI
id: MI:2050
in_subset: Drugable

Axiom
annotated source: dosage form
annotated property: definition
annotated target: How the drug is dispensed (tablets, capsules, solutions), packing material.
database_cross_reference: PMID:14755292

patient information
type: Class
subclass of: bioactive entity attribute name
definition: Information on the disease indications and treatment regime for the drug. May also include contra-indications.
has_obo_namespace: PSI-MI
id: MI:2051
in_subset: Drugable

Axiom
annotated source: patient information
annotated property: definition
annotated target: Information on the disease indications and treatment regime for the drug. May also include contra-indications.
database_cross_reference: PMID:14755292

contraindications
type: Class
subclass of: bioactive entity attribute name
definition: Cautions or conditions indicating why or when the drug should not be taken or prescribed.
has_obo_namespace: PSI-MI
id: MI:2053
in_subset: Drugable

Axiom
annotated source: contraindications
annotated property: definition
annotated target: Cautions or conditions indicating why or when the drug should not be taken or prescribed.
database_cross_reference: PMID:14755292

bioactive entity reference
type: Class
subclass of: participant database
definition: General on-line reference to other details about a drug or other bioactive entity.
has_exact_synonym: bioactive entity ref
has_obo_namespace: PSI-MI
id: MI:2054
in_subset: Drugable
in_subset: PSI-MI slim

Axiom
annotated source: bioactive entity reference
annotated property: definition
annotated target: General on-line reference to other details about a drug or other bioactive entity.
database_cross_reference: PMID:14755292

Axiom
annotated source: bioactive entity reference
annotated property: has_exact_synonym
annotated target: bioactive entity ref
has_synonym_type: Unique short label curated by PSI-MI

chemical stability
type: Class
subclass of: physicochemical attribute name
definition: chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent.
has_exact_synonym: thermodynamic stability
has_obo_namespace: PSI-MI
id: MI:2055
in_subset: Drugable

Axiom
annotated source: chemical stability
annotated property: definition
annotated target: chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent.
database_cross_reference: PMID:14755292

Axiom
annotated source: chemical stability
annotated property: has_exact_synonym
annotated target: thermodynamic stability
has_synonym_type: Alternate label curated by PSI-MI

solubility
type: Class
subclass of: parameter type
definition: Potential ability of a substance to dissolve in a liquid.
has_exact_synonym: dt theoretical pi
has_obo_namespace: PSI-MI
id: MI:2064
in_subset: Drugable

Axiom
annotated source: solubility
annotated property: definition
annotated target: Potential ability of a substance to dissolve in a liquid.
database_cross_reference: PMID:14755292

Axiom
annotated source: solubility
annotated property: has_exact_synonym
annotated target: dt theoretical pi
has_synonym_type: Unique short label curated by PSI-MI

organisms affected
type: Class
subclass of: bioactive entity attribute name
definition: Names of organisms which are affected, positively or negatively, by the drug.
has_obo_namespace: PSI-MI
id: MI:2084
in_subset: Drugable

Axiom
annotated source: organisms affected
annotated property: definition
annotated target: Names of organisms which are affected, positively or negatively, by the drug.
database_cross_reference: PMID:14755292

physicochemical attribute name
type: Class
subclass of: attribute name
definition: Chemical and physical properties of a molecule.
has_exact_synonym: physicochemical att
has_obo_namespace: PSI-MI
id: MI:2086
in_subset: Drugable

Axiom
annotated source: physicochemical attribute name
annotated property: definition
annotated target: Chemical and physical properties of a molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: physicochemical attribute name
annotated property: has_exact_synonym
annotated target: physicochemical att
has_synonym_type: Unique short label curated by PSI-MI

bioactive entity attribute name
type: Class
subclass of: attribute name
definition: Properties of a chemical tested or used as a drug, herbicide, insecticide etc.
has_exact_synonym: bioactive entity att
has_obo_namespace: PSI-MI
id: MI:2089
in_subset: Drugable

Axiom
annotated source: bioactive entity attribute name
annotated property: definition
annotated target: Properties of a chemical tested or used as a drug, herbicide, insecticide etc.
database_cross_reference: PMID:14755292

Axiom
annotated source: bioactive entity attribute name
annotated property: has_exact_synonym
annotated target: bioactive entity att
has_synonym_type: Unique short label curated by PSI-MI

structure representation attribute name
type: Class
subclass of: attribute name
definition: Human artefact to describe and report the structure of a molecule.
has_exact_synonym: struc representation
has_obo_namespace: PSI-MI
id: MI:2091
in_subset: Drugable

Axiom
annotated source: structure representation attribute name
annotated property: definition
annotated target: Human artefact to describe and report the structure of a molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: structure representation attribute name
annotated property: has_exact_synonym
annotated target: struc representation
has_synonym_type: Unique short label curated by PSI-MI

anti-convulsant
type: Class
subclass of: drug category
definition: Therapeutic category or general category of drug -anti-convulsant
has_obo_namespace: PSI-MI
id: MI:2097
in_subset: Drugable

Axiom
annotated source: anti-convulsant
annotated property: definition
annotated target: Therapeutic category or general category of drug -anti-convulsant
database_cross_reference: PMID:14755292

anti-bacterial
type: Class
subclass of: drug category
definition: Therapeutic category or general category of drug -anti-bacterial
has_obo_namespace: PSI-MI
id: MI:2098
in_subset: Drugable

Axiom
annotated source: anti-bacterial
annotated property: definition
annotated target: Therapeutic category or general category of drug -anti-bacterial
database_cross_reference: PMID:14755292

fda approved drug
type: Class
subclass of: drug type
definition: A drug licensed for sale in the USA by the FDA.
has_obo_namespace: PSI-MI
id: MI:2099
in_subset: Drugable

Axiom
annotated source: fda approved drug
annotated property: definition
annotated target: A drug licensed for sale in the USA by the FDA.
database_cross_reference: PMID:14755292

experimental drug
type: Class
subclass of: drug type
definition: A drug which has yet to be formally approved for the indication which it is currently being used to treat.
has_obo_namespace: PSI-MI
id: MI:2100
in_subset: Drugable

Axiom
annotated source: experimental drug
annotated property: definition
annotated target: A drug which has yet to be formally approved for the indication which it is currently being used to treat.
database_cross_reference: PMID:14755292

biotech drug
type: Class
subclass of: drug type
definition: A natural product, such as a protein or peptide, which is produced used biotechnology as a drug.
has_obo_namespace: PSI-MI
id: MI:2101
in_subset: Drugable

Axiom
annotated source: biotech drug
annotated property: definition
annotated target: A natural product, such as a protein or peptide, which is produced used biotechnology as a drug.
database_cross_reference: PMID:14755292

nutraceutical drug
type: Class
subclass of: drug type
definition: A drug which may also be regarded as a foodstuff.
has_obo_namespace: PSI-MI
id: MI:2102
in_subset: Drugable

Axiom
annotated source: nutraceutical drug
annotated property: definition
annotated target: A drug which may also be regarded as a foodstuff.
database_cross_reference: PMID:14755292

pka
type: Class
subclass of: parameter type
definition: Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid.
has_obo_namespace: PSI-MI
id: MI:2105
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: pka
annotated property: definition
annotated target: Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid.
database_cross_reference: PMID:14755292

degree of ionisation ph 7.4
type: Class
subclass of: parameter type
definition: The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4
has_exact_synonym: ionisation ph 7.4
has_obo_namespace: PSI-MI
id: MI:2106
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: degree of ionisation ph 7.4
annotated property: definition
annotated target: The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4
database_cross_reference: PMID:14755292

Axiom
annotated source: degree of ionisation ph 7.4
annotated property: has_exact_synonym
annotated target: ionisation ph 7.4
has_synonym_type: Unique short label curated by PSI-MI

logd
type: Class
subclass of: parameter type
definition: The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4
has_obo_namespace: PSI-MI
id: MI:2107
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: logd
annotated property: definition
annotated target: The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4
database_cross_reference: PMID:14755292

solubility ph 7.4
type: Class
subclass of: solubility
definition: Solubility pH 7.4
has_obo_namespace: PSI-MI
id: MI:2108
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: solubility ph 7.4
annotated property: definition
annotated target: Solubility pH 7.4
database_cross_reference: PMID:14755292

solubility in dmso
type: Class
subclass of: solubility
definition: Solubility in DMSO
has_obo_namespace: PSI-MI
id: MI:2109
in_subset: Drugable

Axiom
annotated source: solubility in dmso
annotated property: definition
annotated target: Solubility in DMSO
database_cross_reference: PMID:14755292

diffusion coefficient
type: Class
subclass of: parameter type
definition: Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s.
has_exact_synonym: diffusion coeff
has_obo_namespace: PSI-MI
id: MI:2111
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: diffusion coefficient
annotated property: definition
annotated target: Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s.
database_cross_reference: PMID:14755292

Axiom
annotated source: diffusion coefficient
annotated property: has_exact_synonym
annotated target: diffusion coeff
has_synonym_type: Unique short label curated by PSI-MI

chemical stability at pH 2
type: Class
subclass of: chemical stability
definition: Chemical stability at pH 2
has_exact_synonym: chem stab ph 2
has_obo_namespace: PSI-MI
id: MI:2112
in_subset: Drugable
comment: Qualitative prediction of this parameter is possible.

Axiom
annotated source: chemical stability at pH 2
annotated property: definition
annotated target: Chemical stability at pH 2
database_cross_reference: PMID:14755292

Axiom
annotated source: chemical stability at pH 2
annotated property: has_exact_synonym
annotated target: chem stab ph 2
has_synonym_type: Unique short label curated by PSI-MI

dissolution profile
type: Class
subclass of: parameter type
definition: The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations.
has_obo_namespace: PSI-MI
id: MI:2113
in_subset: Drugable
comment: The prediction of the value for this paramter is currently not possible.

Axiom
annotated source: dissolution profile
annotated property: definition
annotated target: The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations.
database_cross_reference: PMID:14755292

pharmacokinetics attribute name
type: Class
subclass of: physicochemical attribute name
definition: Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug.
has_obo_namespace: PSI-MI
id: MI:2115
in_subset: Drugable

Axiom
annotated source: pharmacokinetics attribute name
annotated property: definition
annotated target: Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug.
database_cross_reference: PMID:14755292

cell permeability
type: Class
subclass of: parameter type
definition: The permitting or activating of the passage of substances into, out of, or through cells.
has_obo_namespace: PSI-MI
id: MI:2116
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: cell permeability
annotated property: definition
annotated target: The permitting or activating of the passage of substances into, out of, or through cells.
database_cross_reference: PMID:14755292

volume of distribution
type: Class
subclass of: parameter type
definition: The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd.
has_exact_synonym: distribution volume
has_exact_synonym: vd
has_exact_synonym: vol of distribution
has_obo_namespace: PSI-MI
id: MI:2118
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: volume of distribution
annotated property: definition
annotated target: The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd.
database_cross_reference: PMID:14755292

Axiom
annotated source: volume of distribution
annotated property: has_exact_synonym
annotated target: distribution volume
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: volume of distribution
annotated property: has_exact_synonym
annotated target: vd
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: volume of distribution
annotated property: has_exact_synonym
annotated target: vol of distribution
has_synonym_type: Unique short label curated by PSI-MI

tissue distribution
type: Class
subclass of: parameter type
definition: Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
has_obo_namespace: PSI-MI
id: MI:2120
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: tissue distribution
annotated property: definition
annotated target: Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
database_cross_reference: PMID:14755292

transporter binding
type: Class
subclass of: pharmacokinetics attribute name
definition: Substrate of a carrier system allowing the intake of an agent into an organ or part of body.
has_obo_namespace: PSI-MI
id: MI:2121
in_subset: Drugable
comment: The prediction of the value for this parameter is currently not possible.

Axiom
annotated source: transporter binding
annotated property: definition
annotated target: Substrate of a carrier system allowing the intake of an agent into an organ or part of body.
database_cross_reference: PMID:14755292

clearance
type: Class
subclass of: parameter type
definition: The ratio of excretion is or measure of the speed at which a constituent is lost from the body.
has_obo_namespace: PSI-MI
id: MI:2122
in_subset: Drugable

Axiom
annotated source: clearance
annotated property: definition
annotated target: The ratio of excretion is or measure of the speed at which a constituent is lost from the body.
database_cross_reference: PMID:14755292

renal clearance
type: Class
subclass of: parameter type
definition: The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine.
has_obo_namespace: PSI-MI
id: MI:2123
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: renal clearance
annotated property: definition
annotated target: The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine.
database_cross_reference: PMID:14755292

total clearance
type: Class
subclass of: parameter type
definition: The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood.
has_exact_synonym: cl
has_exact_synonym: clearance
has_obo_namespace: PSI-MI
id: MI:2124
in_subset: Drugable
comment: The prediction of the value for this paramter is currently not possible.

Axiom
annotated source: total clearance
annotated property: definition
annotated target: The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood.
database_cross_reference: PMID:14755292

Axiom
annotated source: total clearance
annotated property: has_exact_synonym
annotated target: cl
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: total clearance
annotated property: has_exact_synonym
annotated target: clearance
has_synonym_type: Alternate label curated by PSI-MI

maximum absorbable dose
type: Class
subclass of: parameter type
definition: The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier.
has_exact_synonym: mad
has_obo_namespace: PSI-MI
id: MI:2125
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: maximum absorbable dose
annotated property: definition
annotated target: The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier.
database_cross_reference: PMID:8987073

Axiom
annotated source: maximum absorbable dose
annotated property: has_exact_synonym
annotated target: mad
has_synonym_type: Unique short label curated by PSI-MI

paracellular absorption
type: Class
subclass of: parameter type
definition: Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion.
has_exact_synonym: paracellular absorp
has_obo_namespace: PSI-MI
id: MI:2126
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: paracellular absorption
annotated property: definition
annotated target: Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion.
database_cross_reference: PMID:14755292

Axiom
annotated source: paracellular absorption
annotated property: has_exact_synonym
annotated target: paracellular absorp
has_synonym_type: Unique short label curated by PSI-MI

tmax/cmax
type: Class
subclass of: parameter type
definition: Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself.
has_obo_namespace: PSI-MI
id: MI:2127
in_subset: Drugable
comment: The prediction of the value for this paramter is currently not possible.

Axiom
annotated source: tmax/cmax
annotated property: definition
annotated target: Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself.
database_cross_reference: PMID:14755292

ABCB1 transporter substrate
type: Class
subclass of: transporter binding
definition: Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile.
has_exact_synonym: abcb1 substrate
has_exact_synonym: pgp(mdr1) substrate
has_obo_namespace: PSI-MI
id: MI:2128
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: ABCB1 transporter substrate
annotated property: definition
annotated target: Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile.
database_cross_reference: PMID:14755292

Axiom
annotated source: ABCB1 transporter substrate
annotated property: has_exact_synonym
annotated target: abcb1 substrate
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: ABCB1 transporter substrate
annotated property: has_exact_synonym
annotated target: pgp(mdr1) substrate
has_synonym_type: Alternate label curated by PSI-MI

bile transporter substrate
type: Class
subclass of: transporter binding
definition: Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
has_exact_synonym: bile trans substrate
has_obo_namespace: PSI-MI
id: MI:2129
in_subset: Drugable
comment: The prediction of the value for this paramater is currently not possible.

Axiom
annotated source: bile transporter substrate
annotated property: definition
annotated target: Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
database_cross_reference: PMID:14755292

Axiom
annotated source: bile transporter substrate
annotated property: has_exact_synonym
annotated target: bile trans substrate
has_synonym_type: Unique short label curated by PSI-MI

cyp-450 inhibition
type: Class
subclass of: toxicity attribute name
definition: Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds.
has_exact_synonym: Cytochrome P450 inhibition
has_exact_synonym: cyp-450 inhibition
has_obo_namespace: PSI-MI
id: MI:2130
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: cyp-450 inhibition
annotated property: definition
annotated target: Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds.
database_cross_reference: PMID:14755292

Axiom
annotated source: cyp-450 inhibition
annotated property: has_exact_synonym
annotated target: Cytochrome P450 inhibition
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cyp-450 inhibition
annotated property: has_exact_synonym
annotated target: cyp-450 inhibition
has_synonym_type: Alternate label curated by PSI-MI

metabolite identification
type: Class
subclass of: pharmacokinetics attribute name
definition: Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body
has_exact_synonym: metabolite identific
has_obo_namespace: PSI-MI
id: MI:2131
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: metabolite identification
annotated property: definition
annotated target: Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body
database_cross_reference: PMID:14755292

Axiom
annotated source: metabolite identification
annotated property: has_exact_synonym
annotated target: metabolite identific
has_synonym_type: Unique short label curated by PSI-MI

gsh adducts
type: Class
subclass of: pharmacokinetics attribute name
definition: Derivative molecule which has formed from a reaction with glutathione.
has_obo_namespace: PSI-MI
id: MI:2132
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: gsh adducts
annotated property: definition
annotated target: Derivative molecule which has formed from a reaction with glutathione.
database_cross_reference: PMID:14755292

neutralization by glucuronidation or sulfatation
type: Class
subclass of: drug biotransformation
definition: Neutralization of a compound occuring via its glucuronidation or sulfatation.
has_exact_synonym: neutraliz gluc/sulf
has_obo_namespace: PSI-MI
id: MI:2133
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: neutralization by glucuronidation or sulfatation
annotated property: definition
annotated target: Neutralization of a compound occuring via its glucuronidation or sulfatation.
database_cross_reference: PMID:14755292

Axiom
annotated source: neutralization by glucuronidation or sulfatation
annotated property: has_exact_synonym
annotated target: neutraliz gluc/sulf
has_synonym_type: Unique short label curated by PSI-MI

toxicity attribute name
type: Class
subclass of: bioactive entity attribute name
definition: The mechanism by which a substance can harm humans or animals.
has_obo_namespace: PSI-MI
id: MI:2135
in_subset: Drugable

Axiom
annotated source: toxicity attribute name
annotated property: definition
annotated target: The mechanism by which a substance can harm humans or animals.
database_cross_reference: PMID:14755292

herg binding
type: Class
subclass of: toxicity attribute name
definition: Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential.
has_obo_namespace: PSI-MI
id: MI:2136
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: herg binding
annotated property: definition
annotated target: Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential.
database_cross_reference: PMID:14755292

genotoxicity
type: Class
subclass of: toxicity attribute name
definition: Tendency of a bioactive entity to induce damage at the level of the gene.
has_obo_namespace: PSI-MI
id: MI:2137
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: genotoxicity
annotated property: definition
annotated target: Tendency of a bioactive entity to induce damage at the level of the gene.
database_cross_reference: PMID:14755292

mutagenicity
type: Class
subclass of: toxicity attribute name
definition: Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences.
has_obo_namespace: PSI-MI
id: MI:2138
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: mutagenicity
annotated property: definition
annotated target: Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences.
database_cross_reference: PMID:14755292

carcinogenicity
type: Class
subclass of: toxicity attribute name
definition: Tendency of a bioactive entity to induce a cancer.
has_exact_synonym: cancerogenicity
has_obo_namespace: PSI-MI
id: MI:2139
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: carcinogenicity
annotated property: definition
annotated target: Tendency of a bioactive entity to induce a cancer.
database_cross_reference: PMID:14755292

Axiom
annotated source: carcinogenicity
annotated property: has_exact_synonym
annotated target: cancerogenicity
has_synonym_type: Alternate label curated by PSI-MI

chromosome damage
type: Class
subclass of: toxicity attribute name
definition: Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number.
has_obo_namespace: PSI-MI
id: MI:2140
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: chromosome damage
annotated property: definition
annotated target: Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number.
database_cross_reference: PMID:14755292

hepatotoxicity
type: Class
subclass of: toxicity attribute name
definition: Tendency of a bioactive entity to affect liver function.
has_obo_namespace: PSI-MI
id: MI:2141
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: hepatotoxicity
annotated property: definition
annotated target: Tendency of a bioactive entity to affect liver function.
database_cross_reference: PMID:14755292

phospholipidosis
type: Class
subclass of: toxicity attribute name
definition: Causes excess phospholipids to accumulate within cells.
has_obo_namespace: PSI-MI
id: MI:2142
in_subset: Drugable
comment: Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.

Axiom
annotated source: phospholipidosis
annotated property: definition
annotated target: Causes excess phospholipids to accumulate within cells.
database_cross_reference: PMID:14755292

solubility ph 6.5
type: Class
subclass of: solubility
definition: Solubility pH 6.5.
has_obo_namespace: PSI-MI
id: MI:2145
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: solubility ph 6.5
annotated property: definition
annotated target: Solubility pH 6.5.
database_cross_reference: PMID:14755292

solubility ph 2.0
type: Class
subclass of: solubility
definition: Solubility pH 2.0
has_exact_synonym: solubility ph2.0
has_obo_namespace: PSI-MI
id: MI:2146
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: solubility ph 2.0
annotated property: definition
annotated target: Solubility pH 2.0
database_cross_reference: PMID:14755292

Axiom
annotated source: solubility ph 2.0
annotated property: has_exact_synonym
annotated target: solubility ph2.0
has_synonym_type: Alternate label curated by PSI-MI

chemical stability at pH 7.4
type: Class
subclass of: chemical stability
definition: Chemical stabilityat at pH 7.4
has_exact_synonym: chem stab ph 7.4
has_obo_namespace: PSI-MI
id: MI:2147
in_subset: Drugable
comment: Qualitative prediction of this parameter is possible.

Axiom
annotated source: chemical stability at pH 7.4
annotated property: definition
annotated target: Chemical stabilityat at pH 7.4
database_cross_reference: PMID:14755292

Axiom
annotated source: chemical stability at pH 7.4
annotated property: has_exact_synonym
annotated target: chem stab ph 7.4
has_synonym_type: Unique short label curated by PSI-MI

investigational drug
type: Class
subclass of: drug type
definition: A drug currently under clinical development.
has_obo_namespace: PSI-MI
id: MI:2148
in_subset: Drugable
comment: Intact.

Axiom
annotated source: investigational drug
annotated property: definition
annotated target: A drug currently under clinical development.
database_cross_reference: PMID:14755292

withdrawn drug
type: Class
subclass of: drug type
definition: A drug for which the licencing for prescriptive use has been withdrawn.
has_obo_namespace: PSI-MI
id: MI:2149
in_subset: Drugable
comment: Intact.

Axiom
annotated source: withdrawn drug
annotated property: definition
annotated target: A drug for which the licencing for prescriptive use has been withdrawn.
database_cross_reference: PMID:14755292

illicit drug
type: Class
subclass of: drug type
definition: A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription.
has_obo_namespace: PSI-MI
id: MI:2150
in_subset: Drugable

Axiom
annotated source: illicit drug
annotated property: definition
annotated target: A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription.
database_cross_reference: PMID:14755292

other drug interaction
type: Class
subclass of: bioactive entity attribute name
definition: Effect of additional drug treatments on a given drug action.
has_exact_synonym: drug interaction
has_obo_namespace: PSI-MI
id: MI:2151
in_subset: Drugable

Axiom
annotated source: other drug interaction
annotated property: definition
annotated target: Effect of additional drug treatments on a given drug action.
database_cross_reference: PMID:14755292

Axiom
annotated source: other drug interaction
annotated property: has_exact_synonym
annotated target: drug interaction
has_synonym_type: Unique short label curated by PSI-MI

food interaction
type: Class
subclass of: bioactive entity attribute name
definition: Effect of food ingestion on a given drug treatment.
has_obo_namespace: PSI-MI
id: MI:2152
in_subset: Drugable
comment: IntAct MeSH term or SNOWMAN.

Axiom
annotated source: food interaction
annotated property: definition
annotated target: Effect of food ingestion on a given drug treatment.
database_cross_reference: PMID:14755292

pdr health
type: Class
subclass of: bioactive entity reference
definition: Hyperlink to PDRhealth entry for the given drug (if it exists)
has_exact_synonym: PDRhealth
has_obo_namespace: PSI-MI
id: MI:2153
in_subset: Drugable

Axiom
annotated source: pdr health
annotated property: definition
annotated target: Hyperlink to PDRhealth entry for the given drug (if it exists)
database_cross_reference: PMID:14755292

Axiom
annotated source: pdr health
annotated property: has_exact_synonym
annotated target: PDRhealth
has_synonym_type: Alternate label curated by PSI-MI

wikipedia
type: Class
subclass of: bioactive entity reference
definition: Hyperlink to wikipedia entry for the given drug (if it exists)
has_obo_namespace: PSI-MI
id: MI:2154
in_subset: Drugable

Axiom
annotated source: wikipedia
annotated property: definition
annotated target: Hyperlink to wikipedia entry for the given drug (if it exists)
database_cross_reference: PMID:14755292

average molecular weight
type: Class
subclass of: molecular weight
definition: Molecular weight in g/mol, determined from molecular formula or sequence.
has_exact_synonym: avrg mol weight
has_obo_namespace: PSI-MI
id: MI:2155
in_subset: Drugable

Axiom
annotated source: average molecular weight
annotated property: definition
annotated target: Molecular weight in g/mol, determined from molecular formula or sequence.
database_cross_reference: PMID:14755292

Axiom
annotated source: average molecular weight
annotated property: has_exact_synonym
annotated target: avrg mol weight
has_synonym_type: Unique short label curated by PSI-MI

monoisotopic molecular weight
type: Class
subclass of: molecular weight
definition: Molecular weight in g/mol, determined from molecular formula or sequence.
has_exact_synonym: monoisotopic mol wgt
has_obo_namespace: PSI-MI
id: MI:2156
in_subset: Drugable

Axiom
annotated source: monoisotopic molecular weight
annotated property: definition
annotated target: Molecular weight in g/mol, determined from molecular formula or sequence.
database_cross_reference: PMID:14755292

Axiom
annotated source: monoisotopic molecular weight
annotated property: has_exact_synonym
annotated target: monoisotopic mol wgt
has_synonym_type: Unique short label curated by PSI-MI

experimental water solubility
type: Class
subclass of: water solubility
subclass of: experimental logs
definition: Water solubility in mg/mL or g/L.
has_exact_synonym: exp h2o solubilty
has_exact_synonym: experimental h2o solubility
has_obo_namespace: PSI-MI
id: MI:2157
in_subset: Drugable

Axiom
annotated source: experimental water solubility
annotated property: definition
annotated target: Water solubility in mg/mL or g/L.
database_cross_reference: PMID:14755292

Axiom
annotated source: experimental water solubility
annotated property: has_exact_synonym
annotated target: exp h2o solubilty
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: experimental water solubility
annotated property: has_exact_synonym
annotated target: experimental h2o solubility
has_synonym_type: Alternate label curated by PSI-MI

predicted water solubility
type: Class
subclass of: water solubility
definition: Water solubility in mg/mL or g/L
has_exact_synonym: predicted h2o solub
has_exact_synonym: predicted h2o solubility
has_obo_namespace: PSI-MI
id: MI:2158
in_subset: Drugable

Axiom
annotated source: predicted water solubility
annotated property: definition
annotated target: Water solubility in mg/mL or g/L
database_cross_reference: PMID:14755292

Axiom
annotated source: predicted water solubility
annotated property: has_exact_synonym
annotated target: predicted h2o solub
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: predicted water solubility
annotated property: has_exact_synonym
annotated target: predicted h2o solubility
has_synonym_type: Alternate label curated by PSI-MI

logs
type: Class
subclass of: parameter type
definition: Solubility of a molecule in a given solvant.
has_exact_synonym: logS
has_obo_namespace: PSI-MI
id: MI:2160
in_subset: Drugable

Axiom
annotated source: logs
annotated property: definition
annotated target: Solubility of a molecule in a given solvant.
database_cross_reference: PMID:14755292

Axiom
annotated source: logs
annotated property: has_exact_synonym
annotated target: logS
has_synonym_type: Alternate label curated by PSI-MI

experimental logs
type: Class
subclass of: logs
definition: Experimental derived value for the solubility of a molecule in a given solvant.
has_exact_synonym: experimental logS
has_obo_namespace: PSI-MI
id: MI:2161
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: experimental logs
annotated property: definition
annotated target: Experimental derived value for the solubility of a molecule in a given solvant.
database_cross_reference: PMID:14755292

Axiom
annotated source: experimental logs
annotated property: has_exact_synonym
annotated target: experimental logS
has_synonym_type: Alternate label curated by PSI-MI

experimental CaCO2 permeability
type: Class
subclass of: parameter type
definition: Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption
has_exact_synonym: caco2 permeability
has_obo_namespace: PSI-MI
id: MI:2162
in_subset: Drugable
comment: Quantitative prediction of this parameter is possible.

Axiom
annotated source: experimental CaCO2 permeability
annotated property: definition
annotated target: Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption
database_cross_reference: PMID:14755292

Axiom
annotated source: experimental CaCO2 permeability
annotated property: has_exact_synonym
annotated target: caco2 permeability
has_synonym_type: Unique short label curated by PSI-MI

by homology
type: Class
subclass of: cross-reference type
definition: Reference assigned to a molecule by sequence homology with another similar sequence.
has_obo_namespace: PSI-MI
id: MI:2163
in_subset: Drugable

Axiom
annotated source: by homology
annotated property: definition
annotated target: Reference assigned to a molecule by sequence homology with another similar sequence.
database_cross_reference: PMID:14755292

mind
type: Class
subclass of: interaction database
definition: The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php
created by: orchard
creation date: 2013-02-26T12:27:35Z
has_obo_namespace: PSI-MI
id: MI:2164
in_subset: PSI-MI slim

Axiom
annotated source: mind
annotated property: definition
annotated target: The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php
database_cross_reference: PMID:14755292

bar
type: Class
subclass of: interaction database
definition: The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi" [PMID:15960624]
created by: orchard
creation date: 2013-02-26T12:49:13Z
has_exact_synonym: bar-arabidopsis interactions viewer
has_obo_namespace: PSI-MI
id: MI:2165
in_subset: PSI-MI slim

Axiom
annotated source: bar
annotated property: definition
annotated target: The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi" [PMID:15960624]
database_cross_reference: PMID:15960624

ai
type: Class
subclass of: interaction database
definition: The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. http://interactome.dfci.harvard.edu/A_thaliana/index.php
created by: orchard
creation date: 2013-02-26T12:54:32Z
has_exact_synonym: AI
has_obo_namespace: PSI-MI
id: MI:2166
in_subset: PSI-MI slim

Axiom
annotated source: ai
annotated property: definition
annotated target: The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. http://interactome.dfci.harvard.edu/A_thaliana/index.php
database_cross_reference: PMID:21798944

kinetic exclusion assay
type: Class
subclass of: solid phase assay
definition: In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag.
created by: ppm
creation date: 2015-04-27T15:51:46Z
has_exact_synonym: kinetic exclusion
has_exact_synonym: kinexa
has_obo_namespace: PSI-MI
id: MI:2167
in_subset: PSI-MI slim

Axiom
annotated source: kinetic exclusion assay
annotated property: definition
annotated target: In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag.
database_cross_reference: PMID:15674023

Axiom
annotated source: kinetic exclusion assay
annotated property: has_exact_synonym
annotated target: kinetic exclusion
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: kinetic exclusion assay
annotated property: has_exact_synonym
annotated target: kinexa
has_synonym_type: Alternate label curated by PSI-MI

conditional site labelling
type: Class
subclass of: proximity labelling technology
definition: The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection.
created by: ppm
creation date: 2015-04-29T10:19:28Z
has_obo_namespace: PSI-MI
has_related_synonym: active site labelling
id: MI:2168
in_subset: PSI-MI slim

Axiom
annotated source: conditional site labelling
annotated property: definition
annotated target: The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection.
database_cross_reference: PMID:19416890

luminiscence technology
type: Class
subclass of: biophysical
definition: Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin.
created by: ppm
creation date: 2015-04-29T11:50:41Z
has_obo_namespace: PSI-MI
id: MI:2169

Axiom
annotated source: luminiscence technology
annotated property: definition
annotated target: Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin.
database_cross_reference: PMID:24166364

bimolecular luminiscence complementation
type: Class
subclass of: luminiscence technology
definition: The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection.
created by: ppm
creation date: 2015-04-29T12:03:27Z
has_exact_synonym: bilc
has_exact_synonym: bioluminescence complementation
has_exact_synonym: bioluminescence complementation assay
has_exact_synonym: luminescence complementation assay
has_exact_synonym: luminiscence complementation
has_obo_namespace: PSI-MI
has_related_synonym: split-luciferase complementation
has_related_synonym: split-luciferase complementation assay
id: MI:2170

Axiom
annotated source: bimolecular luminiscence complementation
annotated property: definition
annotated target: The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection.
database_cross_reference: PMID:25859972

Axiom
annotated source: bimolecular luminiscence complementation
annotated property: has_exact_synonym
annotated target: bilc
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: bimolecular luminiscence complementation
annotated property: has_exact_synonym
annotated target: bioluminescence complementation
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: bimolecular luminiscence complementation
annotated property: has_exact_synonym
annotated target: bioluminescence complementation assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: bimolecular luminiscence complementation
annotated property: has_exact_synonym
annotated target: luminescence complementation assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: bimolecular luminiscence complementation
annotated property: has_exact_synonym
annotated target: luminiscence complementation
has_synonym_type: Alternate label curated by PSI-MI

complemented donor-acceptor resonance energy transfer
type: Class
subclass of: fluorescence technology
subclass of: luminiscence technology
definition: This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished.
created by: ppm
creation date: 2015-04-29T13:25:55Z
has_exact_synonym: bret complementation
has_exact_synonym: bret complementation assay
has_exact_synonym: copa-ret
has_obo_namespace: PSI-MI
id: MI:2171
in_subset: PSI-MI slim

Axiom
annotated source: complemented donor-acceptor resonance energy transfer
annotated property: definition
annotated target: This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished.
database_cross_reference: PMID:21785426
database_cross_reference: PMID:25706338

Axiom
annotated source: complemented donor-acceptor resonance energy transfer
annotated property: has_exact_synonym
annotated target: bret complementation
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: complemented donor-acceptor resonance energy transfer
annotated property: has_exact_synonym
annotated target: bret complementation assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: complemented donor-acceptor resonance energy transfer
annotated property: has_exact_synonym
annotated target: copa-ret
has_synonym_type: Unique short label curated by PSI-MI

aspgd
type: Class
subclass of: interaction database
definition: AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species. www.aspergillusgenome.org/
created by: ppm
creation date: 2015-05-05T14:28:59Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: AspGD
has_exact_synonym: Aspergillus Genome Database
has_exact_synonym: aspgd
has_obo_namespace: PSI-MI
id: MI:2172

Axiom
annotated source: aspgd
annotated property: definition
annotated target: AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species. www.aspergillusgenome.org/
database_cross_reference: PMID:24194595

ASPL[0-9]{10}
type: Axiom
annotated source: aspgd
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: aspgd
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.aspergillusgenome.org/cgi-bin/locus.pl

Axiom
annotated source: aspgd
annotated property: has_exact_synonym
annotated target: AspGD
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: aspgd
annotated property: has_exact_synonym
annotated target: Aspergillus Genome Database
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: aspgd
annotated property: has_exact_synonym
annotated target: aspgd
has_synonym_type: Unique short label curated by PSI-MI

cgd
type: Class
subclass of: interaction database
definition: Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health. www.candidagenome.org/
created by: ppm
creation date: 2015-05-05T14:41:00Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: CGD
has_exact_synonym: Candida Genome Database
has_exact_synonym: cgd
has_obo_namespace: PSI-MI
id: MI:2173

Axiom
annotated source: cgd
annotated property: definition
annotated target: Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health. www.candidagenome.org/
database_cross_reference: PMID:22064862

(CAL|CAF)[0-9]{7}
type: Axiom
annotated source: cgd
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: cgd
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.candidagenome.org/cgi-bin/locus.pl

Axiom
annotated source: cgd
annotated property: has_exact_synonym
annotated target: CGD
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cgd
annotated property: has_exact_synonym
annotated target: Candida Genome Database
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cgd
annotated property: has_exact_synonym
annotated target: cgd
has_synonym_type: Unique short label curated by PSI-MI

ecoliwiki
type: Class
subclass of: interaction database
definition: Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about everything related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. http://ecoliwiki.net/colipedia/
created by: ppm
creation date: 2015-05-05T14:55:06Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: EcoliWiki
has_exact_synonym: ecoliwiki
has_obo_namespace: PSI-MI
id: MI:2174

Axiom
annotated source: ecoliwiki
annotated property: definition
annotated target: Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about everything related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. http://ecoliwiki.net/colipedia/
database_cross_reference: PMID:22064863

[A-Za-z]{3,4}
type: Axiom
annotated source: ecoliwiki
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: ecoliwiki
annotated property: database_cross_reference
annotated target: search-url:
label: http://ecoliwiki.net/colipedia/${ac}

Axiom
annotated source: ecoliwiki
annotated property: has_exact_synonym
annotated target: EcoliWiki
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ecoliwiki
annotated property: has_exact_synonym
annotated target: ecoliwiki
has_synonym_type: Unique short label curated by PSI-MI

genedb
type: Class
subclass of: interaction database
definition: The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are: -to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group. -to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data. GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. www.genedb.org
created by: ppm
creation date: 2015-05-05T15:04:16Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: GeneDB
has_exact_synonym: genedb
has_obo_namespace: PSI-MI
id: MI:2175

Axiom
annotated source: genedb
annotated property: definition
annotated target: The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are: -to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group. -to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data. GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. www.genedb.org
database_cross_reference: PMID:22116062

((LmjF|LinJ|LmxM)\.[0-9]{2}\.[0-9]{4})|(PF3D7_[0-9]{7})|(Tb[0-9]+\.[A-Za-z0-9]+\.[0-9]+)|(TcCLB\.[0-9]{6}\.[0-9]+)
type: Axiom
annotated source: genedb
annotated property: database_cross_reference
annotated target: id-validation-regexp:

www.genedb.org/gene/${ac}
type: Axiom
annotated source: genedb
annotated property: database_cross_reference
annotated target: search-url:

Axiom
annotated source: genedb
annotated property: has_exact_synonym
annotated target: GeneDB
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: genedb
annotated property: has_exact_synonym
annotated target: genedb
has_synonym_type: Unique short label curated by PSI-MI

gramene
type: Class
subclass of: interaction database
definition: Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. http://www.gramene.org
created by: ppm
creation date: 2015-05-05T15:12:03Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: Gramene
has_exact_synonym: gramene
has_obo_namespace: PSI-MI
id: MI:2176

Axiom
annotated source: gramene
annotated property: definition
annotated target: Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. http://www.gramene.org
database_cross_reference: PMID:24217918

[A-Z][0-9][A-Z0-9]{3}[0-9]
type: Axiom
annotated source: gramene
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: gramene
annotated property: database_cross_reference
annotated target: search-url:
label: http://tools.gramene.org/search

Axiom
annotated source: gramene
annotated property: has_exact_synonym
annotated target: Gramene
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gramene
annotated property: has_exact_synonym
annotated target: gramene
has_synonym_type: Unique short label curated by PSI-MI

pombase
type: Class
subclass of: interaction database
definition: PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets. www.pombase.org
created by: ppm
creation date: 2015-05-05T15:17:42Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: PomBase
has_exact_synonym: pombase
has_obo_namespace: PSI-MI
id: MI:2177

Axiom
annotated source: pombase
annotated property: definition
annotated target: PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets. www.pombase.org
database_cross_reference: PMID:22039153

S\w+(\.)?\w+(\.)?
type: Axiom
annotated source: pombase
annotated property: database_cross_reference
annotated target: id-validation-regexp:

www.pombase.org/spombe/result/${ac}
type: Axiom
annotated source: pombase
annotated property: database_cross_reference
annotated target: search-url:

Axiom
annotated source: pombase
annotated property: has_exact_synonym
annotated target: PomBase
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: pombase
annotated property: has_exact_synonym
annotated target: pombase
has_synonym_type: Unique short label curated by PSI-MI

agi_locuscode
type: Class
subclass of: interaction database
definition: The Arabidopsis Genome Initiative comprises TAIR, TIGR and MIPS.
created by: ppm
creation date: 2015-05-05T16:12:18Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: AGI_LocusCode
has_exact_synonym: Arabidopsis Genome Initiative
has_exact_synonym: agi_locuscode
has_obo_namespace: PSI-MI
id: MI:2178

A[Tt][MmCc0-5][Gg][0-9]{5}(\.[0-9]{1})?
type: Axiom
annotated source: agi_locuscode
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: agi_locuscode
annotated property: database_cross_reference
annotated target: search-url:
label: http://arabidopsis.org/servlets/TairObject

Axiom
annotated source: agi_locuscode
annotated property: has_exact_synonym
annotated target: AGI_LocusCode
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: agi_locuscode
annotated property: has_exact_synonym
annotated target: Arabidopsis Genome Initiative
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: agi_locuscode
annotated property: has_exact_synonym
annotated target: agi_locuscode
has_synonym_type: Unique short label curated by PSI-MI

subset
type: Class
subclass of: cross-reference type
definition: Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex).
created by: ppm
creation date: 2015-05-11T09:59:36Z
has_exact_synonym: part of
has_exact_synonym: subset
has_obo_namespace: PSI-MI
id: MI:2179
in_subset: PSI-MI slim

Axiom
annotated source: subset
annotated property: definition
annotated target: Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex).
database_cross_reference: PMID:14755292

Axiom
annotated source: subset
annotated property: has_exact_synonym
annotated target: part of
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: subset
annotated property: has_exact_synonym
annotated target: subset
has_synonym_type: Unique short label curated by PSI-MI

agbase
type: Class
subclass of: interaction database
definition: AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation. http://www.agbase.msstate.edu/
created by: ppm
creation date: 2015-05-11T10:23:14Z
database_cross_reference: search-url:
has_exact_synonym: AgBase
has_exact_synonym: agbase
has_obo_namespace: PSI-MI
id: MI:2180
in_subset: PSI-MI slim

Axiom
annotated source: agbase
annotated property: definition
annotated target: AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation. http://www.agbase.msstate.edu/
database_cross_reference: PMID:21075795

Axiom
annotated source: agbase
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.agbase.msstate.edu/cgi-bin/getEntry.pl

Axiom
annotated source: agbase
annotated property: has_exact_synonym
annotated target: AgBase
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: agbase
annotated property: has_exact_synonym
annotated target: agbase
has_synonym_type: Unique short label curated by PSI-MI

cacao
type: Class
subclass of: interaction database
definition: The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition. http://gowiki.tamu.edu/wiki/index.php/Category:CACAO
created by: ppm
creation date: 2015-05-11T10:51:57Z
database_cross_reference: search-url:
has_exact_synonym: CACAO
has_exact_synonym: Community Assessment of Community Annotation with Ontologies
has_exact_synonym: cacao
has_obo_namespace: PSI-MI
id: MI:2181
in_subset: PSI-MI slim

Axiom
annotated source: cacao
annotated property: database_cross_reference
annotated target: search-url:
label: http://gowiki.tamu.edu/wiki/index.php/${ac}

Axiom
annotated source: cacao
annotated property: has_exact_synonym
annotated target: CACAO
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cacao
annotated property: has_exact_synonym
annotated target: Community Assessment of Community Annotation with Ontologies
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: cacao
annotated property: has_exact_synonym
annotated target: cacao
has_synonym_type: Unique short label curated by PSI-MI

dflat
type: Class
subclass of: participant database
definition: Database dedicated to annotating gene function related to human fetal development using the Gene Ontology for functional annotation. http://bcb.cs.tufts.edu/dflat/
created by: ppm
creation date: 2015-05-11T11:01:34Z
has_exact_synonym: DFLAT
has_exact_synonym: Developmental FunctionaL Annotation at Tufts
has_exact_synonym: dflat
has_obo_namespace: PSI-MI
id: MI:2182
in_subset: PSI-MI slim

Axiom
annotated source: dflat
annotated property: has_exact_synonym
annotated target: DFLAT
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: dflat
annotated property: has_exact_synonym
annotated target: Developmental FunctionaL Annotation at Tufts
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: dflat
annotated property: has_exact_synonym
annotated target: dflat
has_synonym_type: Unique short label curated by PSI-MI

go_central
type: Class
subclass of: gene ontology
definition: The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool. http://www.geneontology.org/GO.refgenome.shtml
created by: ppm
creation date: 2015-05-11T11:10:30Z
has_exact_synonym: GO central
has_exact_synonym: GO_central
has_exact_synonym: The Reference Genome Annotation Project
has_exact_synonym: go_central
has_obo_namespace: PSI-MI
id: MI:2183
in_subset: PSI-MI slim

Axiom
annotated source: go_central
annotated property: definition
annotated target: The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool. http://www.geneontology.org/GO.refgenome.shtml
database_cross_reference: PMID:19578431

Axiom
annotated source: go_central
annotated property: has_exact_synonym
annotated target: GO central
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: go_central
annotated property: has_exact_synonym
annotated target: GO_central
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: go_central
annotated property: has_exact_synonym
annotated target: The Reference Genome Annotation Project
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: go_central
annotated property: has_exact_synonym
annotated target: go_central
has_synonym_type: Unique short label curated by PSI-MI

mtbbase
type: Class
subclass of: interaction database
definition: Collection and Refinement of Physiological Data on Mycobacterium tuberculosis in the form of GO annitations. MTBBASE data has also been rendered as pathway information in Reactome. http://www.ark.in-berlin.de/Site/MTBbase.html http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121237.1
created by: ppm
creation date: 2015-05-11T11:34:15Z
has_exact_synonym: MTBBASE
has_exact_synonym: mtbbase
has_obo_namespace: PSI-MI
id: MI:2184
in_subset: PSI-MI slim

Axiom
annotated source: mtbbase
annotated property: has_exact_synonym
annotated target: MTBBASE
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: mtbbase
annotated property: has_exact_synonym
annotated target: mtbbase
has_synonym_type: Unique short label curated by PSI-MI

parkinsonsuk-ucl
type: Class
subclass of: interaction database
definition: The Parkinson's UK Gene Ontology Project represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by Parkinson's UK. This annotation group is a member of the IMEx Consortium. http://www.ucl.ac.uk/functional-gene-annotation/neurological
created by: ppm
creation date: 2015-05-11T11:45:34Z
has_exact_synonym: Parkinson-UCL
has_exact_synonym: Parkinsons Disease Gene Ontology Initiative
has_exact_synonym: ParkinsonsUK-UCL
has_exact_synonym: parkinsonsuk-ucl
has_obo_namespace: PSI-MI
id: MI:2185
in_subset: PSI-MI slim

Axiom
annotated source: parkinsonsuk-ucl
annotated property: has_exact_synonym
annotated target: Parkinson-UCL
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: parkinsonsuk-ucl
annotated property: has_exact_synonym
annotated target: Parkinsons Disease Gene Ontology Initiative
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: parkinsonsuk-ucl
annotated property: has_exact_synonym
annotated target: ParkinsonsUK-UCL
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: parkinsonsuk-ucl
annotated property: has_exact_synonym
annotated target: parkinsonsuk-ucl
has_synonym_type: Unique short label curated by PSI-MI

alut
type: Class
subclass of: interaction database
definition: The Alzheimers-University of Toronto project adds functional annotation to Alzheimer's related gene products using the Gene Ontology. http://www.ims.utoronto.ca/
created by: ppm
creation date: 2015-05-11T13:13:02Z
has_exact_synonym: Alzheimers Project at University of Toronto
has_exact_synonym: Alzheimers University of Toronto
has_exact_synonym: Alzheimers_University_of_Toronto
has_exact_synonym: alut
has_obo_namespace: PSI-MI
id: MI:2186
in_subset: PSI-MI slim

Axiom
annotated source: alut
annotated property: has_exact_synonym
annotated target: Alzheimers Project at University of Toronto
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: alut
annotated property: has_exact_synonym
annotated target: Alzheimers University of Toronto
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: alut
annotated property: has_exact_synonym
annotated target: Alzheimers_University_of_Toronto
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: alut
annotated property: has_exact_synonym
annotated target: alut
has_synonym_type: Unique short label curated by PSI-MI

ri
type: Class
subclass of: interaction database
definition: The Roslin Institute uses the Gene Ontology to add functional annotation to different gene products. http://www.roslin.ac.uk/
created by: ppm
creation date: 2015-05-11T13:18:36Z
has_exact_synonym: RI
has_exact_synonym: Roslin Institute
has_exact_synonym: Roslin_Institute
has_exact_synonym: ri
has_exact_synonym: roslin_institute
has_obo_namespace: PSI-MI
id: MI:2187
in_subset: PSI-MI slim

Axiom
annotated source: ri
annotated property: has_exact_synonym
annotated target: RI
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ri
annotated property: has_exact_synonym
annotated target: Roslin Institute
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ri
annotated property: has_exact_synonym
annotated target: Roslin_Institute
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ri
annotated property: has_exact_synonym
annotated target: ri
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: ri
annotated property: has_exact_synonym
annotated target: roslin_institute
has_synonym_type: Alternate label curated by PSI-MI

par-clip
type: Class
subclass of: clip
definition: Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology. http://en.wikipedia.org/wiki/PAR-CLIP
created by: ppm
creation date: 2015-05-11T15:13:05Z
has_exact_synonym: PAR-CLIP
has_exact_synonym: Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation
has_exact_synonym: par-clip
has_obo_namespace: PSI-MI
id: MI:2188
in_subset: PSI-MI slim

Axiom
annotated source: par-clip
annotated property: definition
annotated target: Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology. http://en.wikipedia.org/wiki/PAR-CLIP
database_cross_reference: PMID:20371350
database_cross_reference: PMID:20644507

Axiom
annotated source: par-clip
annotated property: has_exact_synonym
annotated target: PAR-CLIP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: par-clip
annotated property: has_exact_synonym
annotated target: Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: par-clip
annotated property: has_exact_synonym
annotated target: par-clip
has_synonym_type: Unique short label curated by PSI-MI

avexis
type: Class
subclass of: solid phase assay
definition: Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates.
created by: ppm
creation date: 2015-06-01T15:05:13Z
has_exact_synonym: AVidity-based EXtracellular Interaction Screen
has_exact_synonym: avexis
has_exact_synonym: avidity-based extracellular interaction screen
has_obo_namespace: PSI-MI
id: MI:2189

Axiom
annotated source: avexis
annotated property: definition
annotated target: Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates.
database_cross_reference: pmid:22414956

Axiom
annotated source: avexis
annotated property: has_exact_synonym
annotated target: AVidity-based EXtracellular Interaction Screen
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: avexis
annotated property: has_exact_synonym
annotated target: avexis
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: avexis
annotated property: has_exact_synonym
annotated target: avidity-based extracellular interaction screen
has_synonym_type: Alternate label curated by PSI-MI

long non-coding ribonucleic acid
type: Class
subclass of: ribonucleic acid
definition: Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far.
created by: ppm
creation date: 2015-06-02T11:33:27Z
has_exact_synonym: lncRNA
has_exact_synonym: lncrna
has_exact_synonym: long non coding RNA
has_exact_synonym: long non coding ribonucleic acid
has_exact_synonym: long non-coding RNA
has_obo_namespace: PSI-MI
id: MI:2190

Axiom
annotated source: long non-coding ribonucleic acid
annotated property: definition
annotated target: Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far.
database_cross_reference: PMID:23750541

Axiom
annotated source: long non-coding ribonucleic acid
annotated property: has_exact_synonym
annotated target: lncRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: long non-coding ribonucleic acid
annotated property: has_exact_synonym
annotated target: lncrna
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: long non-coding ribonucleic acid
annotated property: has_exact_synonym
annotated target: long non coding RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: long non-coding ribonucleic acid
annotated property: has_exact_synonym
annotated target: long non coding ribonucleic acid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: long non-coding ribonucleic acid
annotated property: has_exact_synonym
annotated target: long non-coding RNA
has_synonym_type: Alternate label curated by PSI-MI

clip
type: Class
subclass of: nucleic acid uv cross-linking assay
definition: Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA. https://en.wikipedia.org/wiki/CLIP
created by: ppm
creation date: 2015-06-15T10:17:34Z
has_exact_synonym: CLIP
has_exact_synonym: clip
has_exact_synonym: cross linking immunoprecipitation
has_exact_synonym: cross-linking immunoprecipitation
has_obo_namespace: PSI-MI
id: MI:2191
in_subset: PSI-MI slim

Axiom
annotated source: clip
annotated property: definition
annotated target: Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA. https://en.wikipedia.org/wiki/CLIP
database_cross_reference: PMID:14615540

Axiom
annotated source: clip
annotated property: has_exact_synonym
annotated target: CLIP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: clip
annotated property: has_exact_synonym
annotated target: clip
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: clip
annotated property: has_exact_synonym
annotated target: cross linking immunoprecipitation
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: clip
annotated property: has_exact_synonym
annotated target: cross-linking immunoprecipitation
has_synonym_type: Alternate label curated by PSI-MI

clip-seq
type: Class
subclass of: clip
definition: This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins. https://en.wikipedia.org/wiki/HITS-CLIP
created by: ppm
creation date: 2015-06-15T10:44:44Z
has_exact_synonym: CLIP-Seq
has_exact_synonym: HITS-CLIP
has_exact_synonym: UV cross-linking immunoprecipitation combined with high-throughput sequencing
has_exact_synonym: clip-seq
has_obo_namespace: PSI-MI
id: MI:2192
in_subset: PSI-MI slim

Axiom
annotated source: clip-seq
annotated property: definition
annotated target: This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins. https://en.wikipedia.org/wiki/HITS-CLIP
database_cross_reference: PMID:18978773
database_cross_reference: PMID:21633356

Axiom
annotated source: clip-seq
annotated property: has_exact_synonym
annotated target: CLIP-Seq
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: clip-seq
annotated property: has_exact_synonym
annotated target: HITS-CLIP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: clip-seq
annotated property: has_exact_synonym
annotated target: UV cross-linking immunoprecipitation combined with high-throughput sequencing
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: clip-seq
annotated property: has_exact_synonym
annotated target: clip-seq
has_synonym_type: Unique short label curated by PSI-MOD

iclip
type: Class
subclass of: clip
definition: iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution. https://en.wikipedia.org/wiki/ICLIP
created by: ppm
creation date: 2015-06-15T11:17:22Z
has_exact_synonym: iCLIP
has_exact_synonym: iclip
has_exact_synonym: individual-nucleotide resolution cross-linking and immunoprecipitation
has_obo_namespace: PSI-MI
id: MI:2193
in_subset: PSI-MI slim

Axiom
annotated source: iclip
annotated property: definition
annotated target: iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution. https://en.wikipedia.org/wiki/ICLIP
database_cross_reference: PMID:20601959

Axiom
annotated source: iclip
annotated property: has_exact_synonym
annotated target: iCLIP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: iclip
annotated property: has_exact_synonym
annotated target: iclip
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: iclip
annotated property: has_exact_synonym
annotated target: individual-nucleotide resolution cross-linking and immunoprecipitation
has_synonym_type: Alternate label curated by PSI-MI

crac
type: Class
subclass of: nucleic acid uv cross-linking assay
definition: Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.
created by: ppm
creation date: 2015-06-15T11:26:33Z
has_exact_synonym: CRAC
has_exact_synonym: crac
has_exact_synonym: cross-linking and analysis of cDNAs
has_obo_namespace: PSI-MI
id: MI:2194

Axiom
annotated source: crac
annotated property: definition
annotated target: Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.
database_cross_reference: PMID:19482942

Axiom
annotated source: crac
annotated property: has_exact_synonym
annotated target: CRAC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: crac
annotated property: has_exact_synonym
annotated target: crac
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: crac
annotated property: has_exact_synonym
annotated target: cross-linking and analysis of cDNAs
has_synonym_type: Alternate label curated by PSI-MI

clash
type: Class
subclass of: crac
definition: This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs.
created by: ppm
creation date: 2015-06-15T11:45:38Z
has_exact_synonym: CLASH
has_exact_synonym: clash
has_exact_synonym: cross-linking, ligation, and sequencing of hybrids
has_obo_namespace: PSI-MI
id: MI:2195
in_subset: PSI-MI slim

Axiom
annotated source: clash
annotated property: definition
annotated target: This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs.
database_cross_reference: PMID:21610164

Axiom
annotated source: clash
annotated property: has_exact_synonym
annotated target: CLASH
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: clash
annotated property: has_exact_synonym
annotated target: clash
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: clash
annotated property: has_exact_synonym
annotated target: cross-linking, ligation, and sequencing of hybrids
has_synonym_type: Alternate label curated by PSI-MI

quartz crystal microbalance
type: Class
subclass of: biosensor
definition: A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator.
created by: ppm
creation date: 2015-07-07T09:46:51Z
has_exact_synonym: QCM
has_exact_synonym: qcm
has_obo_namespace: PSI-MI
id: MI:2196
in_subset: PSI-MI slim

Axiom
annotated source: quartz crystal microbalance
annotated property: definition
annotated target: A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator.
database_cross_reference: PMID:23504432

Axiom
annotated source: quartz crystal microbalance
annotated property: has_exact_synonym
annotated target: QCM
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: quartz crystal microbalance
annotated property: has_exact_synonym
annotated target: qcm
has_synonym_type: Unique short label curated by PSI-MI

probe interaction assay
type: Class
subclass of: biochemical
definition: An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study.
created by: ppm
creation date: 2015-07-07T10:11:26Z
has_exact_synonym: probe interaction assay
has_obo_namespace: PSI-MI
id: MI:2197
in_subset: PSI-MI slim

Axiom
annotated source: probe interaction assay
annotated property: definition
annotated target: An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study.
database_cross_reference: PMID:14755292

Axiom
annotated source: probe interaction assay
annotated property: has_exact_synonym
annotated target: probe interaction assay
has_synonym_type: Unique short label curated by PSI-MI

labelling assay
type: Class
subclass of: probe interaction assay
definition: The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners.
created by: ppm
creation date: 2015-07-07T10:14:29Z
has_exact_synonym: labelling assay
has_obo_namespace: PSI-MI
id: MI:2198
in_subset: PSI-MI slim

Axiom
annotated source: labelling assay
annotated property: definition
annotated target: The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners.
database_cross_reference: PMID:14755292

Axiom
annotated source: labelling assay
annotated property: has_exact_synonym
annotated target: labelling assay
has_synonym_type: Unique short label curated by PSI-MI

specific site-labelling technology
type: Class
subclass of: labelling assay
definition: The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label
created by: ppm
creation date: 2015-07-07T11:51:57Z
has_exact_synonym: site-labelling technology
has_exact_synonym: specific site-labelling technology
has_obo_namespace: PSI-MI
id: MI:2199
in_subset: PSI-MI slim

Axiom
annotated source: specific site-labelling technology
annotated property: definition
annotated target: The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label
database_cross_reference: PMID:8441405

Axiom
annotated source: specific site-labelling technology
annotated property: has_exact_synonym
annotated target: site-labelling technology
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: specific site-labelling technology
annotated property: has_exact_synonym
annotated target: specific site-labelling technology
has_synonym_type: Alternate label curated by PSI-MI

primesdb
type: Class
subclass of: interaction database
definition: PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks. http://primesdb.eu/
created by: ppm
creation date: 2015-07-13T16:36:21Z
has_exact_synonym: PRIMESDB
has_exact_synonym: primesdb
has_obo_namespace: PSI-MI
id: MI:2200

Axiom
annotated source: primesdb
annotated property: definition
annotated target: PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks. http://primesdb.eu/
database_cross_reference: PMID:22453911

Axiom
annotated source: primesdb
annotated property: has_exact_synonym
annotated target: PRIMESDB
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: primesdb
annotated property: has_exact_synonym
annotated target: primesdb
has_synonym_type: Unique short label curated by PSI-MI

DNA chemical modification
type: Class
subclass of: biological feature
definition: Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification.
created by: ppm
creation date: 2015-08-11T15:37:49Z
has_exact_synonym: DNA chemical modification
has_exact_synonym: DNA epigenetic modification
has_exact_synonym: dna chemical modification
has_obo_namespace: PSI-MI
id: MI:2201
in_subset: PSI-MI slim

Axiom
annotated source: DNA chemical modification
annotated property: definition
annotated target: Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification.
database_cross_reference: PMID:14755292

Axiom
annotated source: DNA chemical modification
annotated property: has_exact_synonym
annotated target: DNA chemical modification
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: DNA chemical modification
annotated property: has_exact_synonym
annotated target: DNA epigenetic modification
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: DNA chemical modification
annotated property: has_exact_synonym
annotated target: dna chemical modification
has_synonym_type: Unique short label curated by PSI-MI

RNA chemical modification
type: Class
subclass of: biological feature
definition: Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation).
created by: ppm
creation date: 2015-08-11T15:55:40Z
has_exact_synonym: RNA chemical modification
has_exact_synonym: post-transcriptional modification
has_exact_synonym: rna chemical modification
has_obo_namespace: PSI-MI
id: MI:2202
in_subset: PSI-MI slim

Axiom
annotated source: RNA chemical modification
annotated property: definition
annotated target: Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation).
database_cross_reference: PMID:14755292

Axiom
annotated source: RNA chemical modification
annotated property: has_exact_synonym
annotated target: RNA chemical modification
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: RNA chemical modification
annotated property: has_exact_synonym
annotated target: post-transcriptional modification
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: RNA chemical modification
annotated property: has_exact_synonym
annotated target: rna chemical modification
has_synonym_type: Unique short label curated by PSI-MI

primer extension assay
type: Class
subclass of: partial RNA sequence identification
definition: Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site.
created by: ppm
creation date: 2015-08-11T17:22:38Z
has_exact_synonym: primer extension assay
has_obo_namespace: PSI-MI
id: MI:2203
in_subset: PSI-MI slim

Axiom
annotated source: primer extension assay
annotated property: definition
annotated target: Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site.
database_cross_reference: PMID:23378648

Axiom
annotated source: primer extension assay
annotated property: has_exact_synonym
annotated target: primer extension assay
has_synonym_type: Unique short label curated by PSI-MI

micro rna
type: Class
subclass of: ribonucleic acid
definition: A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression.
created by: ppm
creation date: 2016-01-20T16:25:10Z
database_cross_reference: url:
has_exact_synonym: miRNA
has_exact_synonym: micro RNA
has_exact_synonym: micro-RNA
has_exact_synonym: micro-rna
has_exact_synonym: mirna
has_obo_namespace: PSI-MI
id: MI:2204
in_subset: PSI-MI slim

Axiom
annotated source: micro rna
annotated property: definition
annotated target: A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression.
database_cross_reference: PMID:14744438

Axiom
annotated source: micro rna
annotated property: database_cross_reference
annotated target: url:
label: https://en.wikipedia.org/wiki/MicroRNA

Axiom
annotated source: micro rna
annotated property: has_exact_synonym
annotated target: miRNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: micro rna
annotated property: has_exact_synonym
annotated target: micro RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: micro rna
annotated property: has_exact_synonym
annotated target: micro-RNA
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: micro rna
annotated property: has_exact_synonym
annotated target: micro-rna
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: micro rna
annotated property: has_exact_synonym
annotated target: mirna
has_synonym_type: Unique short label curated by PSI-MI

pir
type: Class
subclass of: protein sequence databases
definition: The PIR-International Protein Sequence Database (PIR-PSD) was the world's first database of classified and functionally annotated protein sequences that grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. Produced and distributed by the Protein Information Resource in collaboration with MIPS (Munich Information Center for Protein Sequences) and JIPID (Japan International Protein Information Database), PIR-PSD has been the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years. In 2002, PIR joined EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase. Bi-directional cross-references between UniProt (UniProt Knowledgebase and/or UniParc) and PIR-PSD are established to allow easy tracking of former PIR-PSD entries. PIR-PSD unique sequences, reference citations, and experimentally-verified data can now be found in the relevant UniProt records. Legacy data can be found at http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml
created by: ppm
creation date: 2016-01-20T16:48:10Z
has_exact_synonym: PIR
has_exact_synonym: Protein Information Resource
has_exact_synonym: pir
has_obo_namespace: PSI-MI
id: MI:2205
in_subset: PSI-MI slim

Axiom
annotated source: pir
annotated property: has_exact_synonym
annotated target: PIR
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: pir
annotated property: has_exact_synonym
annotated target: Protein Information Resource
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: pir
annotated property: has_exact_synonym
annotated target: pir
has_synonym_type: Unique short label curated by PSI-MI

observed nucleic acid chemical modification
type: Class
subclass of: feature attribute name
definition: Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
created by: ppm
creation date: 2016-01-21T14:50:29Z
has_exact_synonym: observed na chemical modification
has_exact_synonym: observed nucleic acid chemical modification
has_obo_namespace: PSI-MI
id: MI:2206
in_subset: PSI-MI slim

Axiom
annotated source: observed nucleic acid chemical modification
annotated property: definition
annotated target: Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
database_cross_reference: PMID:14755292

Axiom
annotated source: observed nucleic acid chemical modification
annotated property: has_exact_synonym
annotated target: observed na chemical modification
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: observed nucleic acid chemical modification
annotated property: has_exact_synonym
annotated target: observed nucleic acid chemical modification
has_synonym_type: Unique short label curated by PSI-MI

resulting nucleic acid chemical modification
type: Class
subclass of: observed nucleic acid chemical modification
definition: Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
created by: ppm
creation date: 2016-01-21T15:02:23Z
has_exact_synonym: resulting na chemical modification
has_exact_synonym: resulting nucleic acid chemical modification
has_obo_namespace: PSI-MI
id: MI:2207
in_subset: PSI-MI slim

Axiom
annotated source: resulting nucleic acid chemical modification
annotated property: definition
annotated target: Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
database_cross_reference: PMID:14755292

Axiom
annotated source: resulting nucleic acid chemical modification
annotated property: has_exact_synonym
annotated target: resulting na chemical modification
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: resulting nucleic acid chemical modification
annotated property: has_exact_synonym
annotated target: resulting nucleic acid chemical modification
has_synonym_type: Unique short label curated by PSI-MI

prerequisite-nucleic acid chemical modification
type: Class
subclass of: observed nucleic acid chemical modification
definition: Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
created by: ppm
creation date: 2016-01-21T15:12:35Z
has_exact_synonym: prerequisite-na chemical modification
has_exact_synonym: prerequisite-nucleic acid chemical modification
has_obo_namespace: PSI-MI
id: MI:2208
in_subset: PSI-MI slim

Axiom
annotated source: prerequisite-nucleic acid chemical modification
annotated property: definition
annotated target: Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
database_cross_reference: PMID:14755292

Axiom
annotated source: prerequisite-nucleic acid chemical modification
annotated property: has_exact_synonym
annotated target: prerequisite-na chemical modification
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: prerequisite-nucleic acid chemical modification
annotated property: has_exact_synonym
annotated target: prerequisite-nucleic acid chemical modification
has_synonym_type: Unique short label curated by PSI-MI

nucleic acid chemical modification decreasing an interaction
type: Class
subclass of: observed nucleic acid chemical modification
definition: Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
created by: ppm
creation date: 2016-01-21T15:17:08Z
has_exact_synonym: na chemical modification decreasing
has_exact_synonym: nucleic acid chemical modification decreasing an interaction
has_obo_namespace: PSI-MI
id: MI:2209

Axiom
annotated source: nucleic acid chemical modification decreasing an interaction
annotated property: definition
annotated target: Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid chemical modification decreasing an interaction
annotated property: has_exact_synonym
annotated target: na chemical modification decreasing
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: nucleic acid chemical modification decreasing an interaction
annotated property: has_exact_synonym
annotated target: nucleic acid chemical modification decreasing an interaction
has_synonym_type: Alternate label curated by PSI-MI

nucleic acid chemical modification disrupting an interaction
type: Class
subclass of: observed nucleic acid chemical modification
definition: Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
created by: ppm
creation date: 2016-01-21T15:18:52Z
has_exact_synonym: na chemical modification disrupting
has_exact_synonym: nucleic acid chemical modification disrupting an interaction
has_obo_namespace: PSI-MI
id: MI:2210
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid chemical modification disrupting an interaction
annotated property: definition
annotated target: Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid chemical modification disrupting an interaction
annotated property: has_exact_synonym
annotated target: na chemical modification disrupting
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: nucleic acid chemical modification disrupting an interaction
annotated property: has_exact_synonym
annotated target: nucleic acid chemical modification disrupting an interaction
has_synonym_type: Alternate label curated by PSI-MI

nucleic acid chemical modification increasing an interaction
type: Class
subclass of: observed nucleic acid chemical modification
definition: Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
created by: ppm
creation date: 2016-01-21T15:25:51Z
has_exact_synonym: na chemical modification increasing
has_exact_synonym: nucleic acid chemical modification increasing an interaction
has_obo_namespace: PSI-MI
id: MI:2211
in_subset: PSI-MI slim

Axiom
annotated source: nucleic acid chemical modification increasing an interaction
annotated property: definition
annotated target: Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
database_cross_reference: PMID:14755292

Axiom
annotated source: nucleic acid chemical modification increasing an interaction
annotated property: has_exact_synonym
annotated target: na chemical modification increasing
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: nucleic acid chemical modification increasing an interaction
annotated property: has_exact_synonym
annotated target: nucleic acid chemical modification increasing an interaction
has_synonym_type: Alternate label curated by PSI-MI

proteomexchange
type: Class
subclass of: peptide sequence database
definition: The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE. http://www.proteomexchange.org
created by: ppm
creation date: 2016-02-02T13:52:54Z
has_exact_synonym: ProteomExchange
has_exact_synonym: proteomexchange
has_obo_namespace: PSI-MI
id: MI:2212
in_subset: PSI-MI slim

Axiom
annotated source: proteomexchange
annotated property: definition
annotated target: The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE. http://www.proteomexchange.org
database_cross_reference: PMID:25047258

Axiom
annotated source: proteomexchange
annotated property: has_exact_synonym
annotated target: ProteomExchange
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: proteomexchange
annotated property: has_exact_synonym
annotated target: proteomexchange
has_synonym_type: Unique short label curated by PSI-MI

super-resolution microscopy
type: Class
subclass of: imaging technique
definition: Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: "true" super-resolution techniques, which capture information contained in evanescent waves, and "functional" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image.
created by: ppm
creation date: 2016-02-11T11:10:32Z
has_exact_synonym: super resolution microscopy
has_exact_synonym: super-resolution microscopy
has_obo_namespace: PSI-MI
id: MI:2213

Axiom
annotated source: super-resolution microscopy
annotated property: definition
annotated target: Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: "true" super-resolution techniques, which capture information contained in evanescent waves, and "functional" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image.
database_cross_reference: PMID:14755292

Axiom
annotated source: super-resolution microscopy
annotated property: has_exact_synonym
annotated target: super resolution microscopy
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: super-resolution microscopy
annotated property: has_exact_synonym
annotated target: super-resolution microscopy
has_synonym_type: Unique short label curated by PSI-MI

signor
type: Class
subclass of: pathways database
definition: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.
created by: ppm
creation date: 2016-03-15T15:31:08Z
database_cross_reference: search-url:
has_exact_synonym: SIGNOR
has_exact_synonym: SIGnaling Network Open Resource
has_exact_synonym: signaling network open resource
has_exact_synonym: signor
has_obo_namespace: PSI-MI
id: MI:2214
in_subset: PSI-MI slim

Axiom
annotated source: signor
annotated property: definition
annotated target: SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.
database_cross_reference: PMID:26467481

Axiom
annotated source: signor
annotated property: database_cross_reference
annotated target: search-url:
label: http://signor.uniroma2.it/relation_result.php

Axiom
annotated source: signor
annotated property: has_exact_synonym
annotated target: SIGNOR
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: signor
annotated property: has_exact_synonym
annotated target: SIGnaling Network Open Resource
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: signor
annotated property: has_exact_synonym
annotated target: signaling network open resource
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: signor
annotated property: has_exact_synonym
annotated target: signor
has_synonym_type: Unique short label curated by PSI-MI

barcode fusion genetics two hybrid
type: Class
subclass of: two hybrid bait and prey pooling approach
definition: This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs.
created by: ppm
creation date: 2016-05-05T14:33:32Z
has_exact_synonym: BGF-2h
has_exact_synonym: barcode fusion genetics two hybrid
has_exact_synonym: bfg two hybrid
has_exact_synonym: bfg-2h
has_obo_namespace: PSI-MI
id: MI:2215

Axiom
annotated source: barcode fusion genetics two hybrid
annotated property: definition
annotated target: This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs.
database_cross_reference: PMID:27107012

Axiom
annotated source: barcode fusion genetics two hybrid
annotated property: has_exact_synonym
annotated target: BGF-2h
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: barcode fusion genetics two hybrid
annotated property: has_exact_synonym
annotated target: barcode fusion genetics two hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: barcode fusion genetics two hybrid
annotated property: has_exact_synonym
annotated target: bfg two hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: barcode fusion genetics two hybrid
annotated property: has_exact_synonym
annotated target: bfg-2h
has_synonym_type: Unique short label curated by PSI-MI

deampylation assay
type: Class
subclass of: enzymatic study
definition: Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
created by: ppm
creation date: 2016-05-09T09:40:07Z
has_exact_synonym: de-AMPylation assay
has_exact_synonym: de-ampylation assay
has_exact_synonym: deAMPylation assay
has_exact_synonym: deampylation assay
has_obo_namespace: PSI-MI
id: MI:2216
in_subset: PSI-MI slim

Axiom
annotated source: deampylation assay
annotated property: definition
annotated target: Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
database_cross_reference: PMID:14755292

Axiom
annotated source: deampylation assay
annotated property: has_exact_synonym
annotated target: de-AMPylation assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: deampylation assay
annotated property: has_exact_synonym
annotated target: de-ampylation assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: deampylation assay
annotated property: has_exact_synonym
annotated target: deAMPylation assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: deampylation assay
annotated property: has_exact_synonym
annotated target: deampylation assay
has_synonym_type: Unique short label curated by PSI-MI

luciferase-c
type: Class
subclass of: luciferase tag
definition: The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: ppm
creation date: 2016-05-09T09:45:05Z
has_exact_synonym: luciferase-c
has_obo_namespace: PSI-MI
id: MI:2217
in_subset: PSI-MI slim

Axiom
annotated source: luciferase-c
annotated property: definition
annotated target: The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
database_cross_reference: PMID:22070901

Axiom
annotated source: luciferase-c
annotated property: has_exact_synonym
annotated target: luciferase-c
has_synonym_type: Unique short label curated by PSI-MI

luciferase-n
type: Class
subclass of: luciferase tag
definition: The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: ppm
creation date: 2016-05-09T09:45:23Z
has_exact_synonym: luciferase-n
has_obo_namespace: PSI-MI
id: MI:2218
in_subset: PSI-MI slim

Axiom
annotated source: luciferase-n
annotated property: definition
annotated target: The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
database_cross_reference: PMID:22070901

Axiom
annotated source: luciferase-n
annotated property: has_exact_synonym
annotated target: luciferase-n
has_synonym_type: Unique short label curated by PSI-MI

gaussia luciferase protein tag
type: Class
subclass of: luciferase tag
definition: Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range.
created by: ppm
creation date: 2016-05-09T10:05:39Z
has_exact_synonym: GLuc tag
has_exact_synonym: gaussia luciferase
has_exact_synonym: gaussia luciferase protein tag
has_exact_synonym: gluc tag
has_obo_namespace: PSI-MI
id: MI:2219

Axiom
annotated source: gaussia luciferase protein tag
annotated property: definition
annotated target: Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range.
database_cross_reference: PMID:26025768

Axiom
annotated source: gaussia luciferase protein tag
annotated property: has_exact_synonym
annotated target: GLuc tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gaussia luciferase protein tag
annotated property: has_exact_synonym
annotated target: gaussia luciferase
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: gaussia luciferase protein tag
annotated property: has_exact_synonym
annotated target: gaussia luciferase protein tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gaussia luciferase protein tag
annotated property: has_exact_synonym
annotated target: gluc tag
has_synonym_type: Alternate label curated by PSI-MOD

gaussia-c
type: Class
subclass of: gaussia luciferase protein tag
definition: The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: ppm
creation date: 2016-05-09T10:13:06Z
has_exact_synonym: gaussia-c
has_obo_namespace: PSI-MI
id: MI:2220

Axiom
annotated source: gaussia-c
annotated property: definition
annotated target: The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
database_cross_reference: PMID:17099704

Axiom
annotated source: gaussia-c
annotated property: has_exact_synonym
annotated target: gaussia-c
has_synonym_type: Unique short label curated by PSI-MI

gaussia-n
type: Class
subclass of: gaussia luciferase protein tag
definition: The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: ppm
creation date: 2016-05-09T10:13:23Z
has_exact_synonym: gaussia-n
has_obo_namespace: PSI-MI
id: MI:2221

Axiom
annotated source: gaussia-n
annotated property: definition
annotated target: The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
database_cross_reference: PMID:17099704

Axiom
annotated source: gaussia-n
annotated property: has_exact_synonym
annotated target: gaussia-n
has_synonym_type: Unique short label curated by PSI-MI

inference by socio-affinity scoring
type: Class
subclass of: inferred by author
definition: Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set.
created by: ppm
creation date: 2016-05-13T16:16:06Z
has_exact_synonym: inference by socio-affinity scoring
has_exact_synonym: socio-affinity index inference
has_exact_synonym: socio-affinity inference
has_exact_synonym: socioaffinity index scoring
has_exact_synonym: socioaffinity inference
has_obo_namespace: PSI-MI
id: MI:2222
in_subset: PSI-MI slim

Axiom
annotated source: inference by socio-affinity scoring
annotated property: definition
annotated target: Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set.
database_cross_reference: PMID:16429126

Axiom
annotated source: inference by socio-affinity scoring
annotated property: has_exact_synonym
annotated target: inference by socio-affinity scoring
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: inference by socio-affinity scoring
annotated property: has_exact_synonym
annotated target: socio-affinity index inference
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: inference by socio-affinity scoring
annotated property: has_exact_synonym
annotated target: socio-affinity inference
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: inference by socio-affinity scoring
annotated property: has_exact_synonym
annotated target: socioaffinity index scoring
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: inference by socio-affinity scoring
annotated property: has_exact_synonym
annotated target: socioaffinity inference
has_synonym_type: Unique short label curated by PSI-MI

inference by quantitative co-purification
type: Class
subclass of: inferred by author
definition: This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs.
created by: ppm
creation date: 2016-05-17T10:36:05Z
has_exact_synonym: inference by quantitative co-purification
has_exact_synonym: quantitative tagless co - purification
has_obo_namespace: PSI-MI
id: MI:2223
in_subset: PSI-MI slim

Axiom
annotated source: inference by quantitative co-purification
annotated property: definition
annotated target: This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs.
database_cross_reference: PMID:27099342

Axiom
annotated source: inference by quantitative co-purification
annotated property: has_exact_synonym
annotated target: inference by quantitative co-purification
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: inference by quantitative co-purification
annotated property: has_exact_synonym
annotated target: quantitative tagless co - purification
has_synonym_type: Alternate label curated by PSI-MI

chemical rna modification plus base pairing prediction
type: Class
subclass of: genetic interference
definition: In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified.
created by: ppm
creation date: 2016-05-23T13:32:07Z
has_exact_synonym: chemical rna modification plus base pairing prediction
has_obo_namespace: PSI-MI
id: MI:2224
in_subset: PSI-MI slim

Axiom
annotated source: chemical rna modification plus base pairing prediction
annotated property: definition
annotated target: In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified.
database_cross_reference: PMID:10024243

Axiom
annotated source: chemical rna modification plus base pairing prediction
annotated property: has_exact_synonym
annotated target: chemical rna modification plus base pairing prediction
has_synonym_type: Unique short label curated by PSI-MI

zinc
type: Class
subclass of: interaction database
definition: ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology. http://zinc15.docking.org/
created by: ppm
creation date: 2016-06-13T15:47:30Z
database_cross_reference: id-validation-regexp:
database_cross_reference: search-url:
has_exact_synonym: ZINC
has_exact_synonym: zinc
has_obo_namespace: PSI-MI
id: MI:2225
in_subset: PSI-MI slim

Axiom
annotated source: zinc
annotated property: definition
annotated target: ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology. http://zinc15.docking.org/
database_cross_reference: PMID:26479676

[0-9]*
type: Axiom
annotated source: zinc
annotated property: database_cross_reference
annotated target: id-validation-regexp:

Axiom
annotated source: zinc
annotated property: database_cross_reference
annotated target: search-url:
label: http://zinc15.docking.org/substances/${ac}

Axiom
annotated source: zinc
annotated property: has_exact_synonym
annotated target: ZINC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: zinc
annotated property: has_exact_synonym
annotated target: zinc
has_synonym_type: Unique short label curated by PSI-MI

mutation with no effect
type: Class
subclass of: mutation
definition: A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type.
created by: ppm
creation date: 2016-06-13T15:57:12Z
has_exact_synonym: mutation not affecting interaction
has_exact_synonym: mutation with no effect
has_obo_namespace: PSI-MI
id: MI:2226
in_subset: PSI-MI slim

Axiom
annotated source: mutation with no effect
annotated property: definition
annotated target: A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type.
database_cross_reference: PMID:14577292

Axiom
annotated source: mutation with no effect
annotated property: has_exact_synonym
annotated target: mutation not affecting interaction
has_synonym_type: Alternate label curated by PSI-MOD

Axiom
annotated source: mutation with no effect
annotated property: has_exact_synonym
annotated target: mutation with no effect
has_synonym_type: Unique short label curated by PSI-MI

mutation causing an interaction
type: Class
subclass of: mutation
definition: A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact.
created by: ppm
creation date: 2016-06-13T16:25:47Z
has_exact_synonym: mutation causing
has_exact_synonym: mutation causing an interaction
has_exact_synonym: mutation enabling interaction
has_obo_namespace: PSI-MI
id: MI:2227

Axiom
annotated source: mutation causing an interaction
annotated property: definition
annotated target: A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact.
database_cross_reference: PMID:14755292

Axiom
annotated source: mutation causing an interaction
annotated property: has_exact_synonym
annotated target: mutation causing
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: mutation causing an interaction
annotated property: has_exact_synonym
annotated target: mutation causing an interaction
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: mutation causing an interaction
annotated property: has_exact_synonym
annotated target: mutation enabling interaction
has_synonym_type: Alternate label curated by PSI-MI

ceitec
type: Class
subclass of: interaction database
definition: Interactions and complexes curated by scientists at the Central European Institute of Technology (CEITEC).
created by: ppm
creation date: 2016-09-14T10:41:07Z
database_cross_reference: search-url:
has_exact_synonym: CEITEC
has_exact_synonym: Central European Institute of Technology
has_exact_synonym: ceitec
has_obo_namespace: PSI-MI
id: MI:2228

www.ceitec.eu/
type: Axiom
annotated source: ceitec
annotated property: database_cross_reference
annotated target: search-url:

Axiom
annotated source: ceitec
annotated property: has_exact_synonym
annotated target: CEITEC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ceitec
annotated property: has_exact_synonym
annotated target: Central European Institute of Technology
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: ceitec
annotated property: has_exact_synonym
annotated target: ceitec
has_synonym_type: Unique short label curated by PSI-MI

nucleicacid-gene
type: Class
subclass of: interacting molecules
definition: Interaction between a nucleic acid and a gene region.
created by: ppm
creation date: 2016-09-21T11:39:49Z
has_obo_namespace: PSI-MI
id: MI:2229
in_subset: PSI-MI slim

Axiom
annotated source: nucleicacid-gene
annotated property: definition
annotated target: Interaction between a nucleic acid and a gene region.
database_cross_reference: PMID:14755292

nucleicacid-nucleicacid
type: Class
subclass of: interacting molecules
definition: Interaction between a nucleic acid and a corresponding nucleic acid.
created by: ppm
creation date: 2016-09-21T11:41:03Z
has_obo_namespace: PSI-MI
id: MI:2230
in_subset: PSI-MI slim

Axiom
annotated source: nucleicacid-nucleicacid
annotated property: definition
annotated target: Interaction between a nucleic acid and a corresponding nucleic acid.
database_cross_reference: PMID:14755292

coexpression
type: Class
subclass of: experimental knowledge based
definition: This approach infers interacting pairs of proteins looking at expression data coming from transcript expression datasets. Co-expressed pairs of genes are ranked and predicted to be interacting proteins as well.
created by: ppm
creation date: 2016-10-05T11:48:53Z
has_exact_synonym: co-expression
has_exact_synonym: coexpression
has_exact_synonym: coexpression prediction
has_obo_namespace: PSI-MI
id: MI:2231
in_subset: PSI-MI slim

Axiom
annotated source: coexpression
annotated property: has_exact_synonym
annotated target: co-expression
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: coexpression
annotated property: has_exact_synonym
annotated target: coexpression
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: coexpression
annotated property: has_exact_synonym
annotated target: coexpression prediction
has_synonym_type: Alternate label curated by PSI-MI

molecular association
type: Class
subclass of: interaction type
definition: A particular way two or more molecules influence one another.
created by: ppm
creation date: 2016-12-08T15:17:45Z
has_exact_synonym: molecular association
has_obo_namespace: PSI-MI
id: MI:2232
in_subset: PSI-MI slim

Axiom
annotated source: molecular association
annotated property: has_exact_synonym
annotated target: molecular association
has_synonym_type: Unique short label curated by PSI-MI

causal interaction
type: Class
subclass of: molecular interaction
definition: Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema.
created by: ppm
creation date: 2017-01-19T13:17:37Z
has_exact_synonym: causal interaction
has_obo_namespace: PSI-MI
id: MI:2233
in_subset: PSI-MI slim

Axiom
annotated source: causal interaction
annotated property: definition
annotated target: Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema.
database_cross_reference: DOI:10.1142/S0219525908001465

Axiom
annotated source: causal interaction
annotated property: has_exact_synonym
annotated target: causal interaction
has_synonym_type: Unique short label curated by PSI-MI

causal statement
type: Class
subclass of: causal interaction
definition: The effect of modulator entity A on a modulated entity B.
created by: ppm
creation date: 2017-01-19T13:20:22Z
has_exact_synonym: causal statement
has_obo_namespace: PSI-MI
id: MI:2234

Axiom
annotated source: causal statement
annotated property: definition
annotated target: The effect of modulator entity A on a modulated entity B.
database_cross_reference: PMID:26467481

Axiom
annotated source: causal statement
annotated property: has_exact_synonym
annotated target: causal statement
has_synonym_type: Unique short label curated by PSI-MI

up-regulates
type: Class
subclass of: causal statement
definition: The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B.
created by: ppm
creation date: 2017-01-19T13:47:54Z
has_exact_synonym: up regulates
has_exact_synonym: up-regulates
has_narrow_synonym: activates
has_obo_namespace: PSI-MI
id: MI:2235
in_subset: PSI-MI slim

Axiom
annotated source: up-regulates
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B.
database_cross_reference: PMID:26467481

Axiom
annotated source: up-regulates
annotated property: has_exact_synonym
annotated target: up regulates
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: up-regulates
annotated property: has_exact_synonym
annotated target: up-regulates
has_synonym_type: Unique short label curated by PSI-MI

up-regulates activity
type: Class
subclass of: up-regulates
definition: The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
created by: ppm
creation date: 2017-01-19T13:50:43Z
database_cross_reference: GO:GO:0044093
has_exact_synonym: activates activity
has_exact_synonym: up-regulates activity
has_obo_namespace: PSI-MI
id: MI:2236
in_subset: PSI-MI slim

Axiom
annotated source: up-regulates activity
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
database_cross_reference: PMID:26467481

Axiom
annotated source: up-regulates activity
annotated property: has_exact_synonym
annotated target: activates activity
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: up-regulates activity
annotated property: has_exact_synonym
annotated target: up-regulates activity
has_synonym_type: Unique short label curated by PSI-MI

up-regulates quantity
type: Class
subclass of: up-regulates
definition: The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B.
created by: ppm
creation date: 2017-01-19T13:53:41Z
has_exact_synonym: increases quantity
has_exact_synonym: up-regulates quantity
has_obo_namespace: PSI-MI
id: MI:2237
in_subset: PSI-MI slim

Axiom
annotated source: up-regulates quantity
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B.
database_cross_reference: PMID:26467481

Axiom
annotated source: up-regulates quantity
annotated property: has_exact_synonym
annotated target: increases quantity
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: up-regulates quantity
annotated property: has_exact_synonym
annotated target: up-regulates quantity
has_synonym_type: Unique short label curated by PSI-MI

up-regulates quantity by expression
type: Class
subclass of: up-regulates quantity
definition: The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression.
created by: ppm
creation date: 2017-01-19T13:56:00Z
has_exact_synonym: increases quantity by expression
has_exact_synonym: up-regulates quantity by expression
has_obo_namespace: PSI-MI
id: MI:2238
in_subset: PSI-MI slim

Axiom
annotated source: up-regulates quantity by expression
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression.
database_cross_reference: PMID:26467481

Axiom
annotated source: up-regulates quantity by expression
annotated property: has_exact_synonym
annotated target: increases quantity by expression
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: up-regulates quantity by expression
annotated property: has_exact_synonym
annotated target: up-regulates quantity by expression
has_synonym_type: Unique short label curated by PSI-MI

up-regulates quantity by stabilization
type: Class
subclass of: up-regulates quantity
definition: The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation.
created by: ppm
creation date: 2017-01-19T13:58:03Z
has_exact_synonym: increases quantity by stabilization
has_exact_synonym: up-regulates quantity by stabilization
has_obo_namespace: PSI-MI
id: MI:2239
in_subset: PSI-MI slim

Axiom
annotated source: up-regulates quantity by stabilization
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation.
database_cross_reference: PMID:26467481

Axiom
annotated source: up-regulates quantity by stabilization
annotated property: has_exact_synonym
annotated target: increases quantity by stabilization
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: up-regulates quantity by stabilization
annotated property: has_exact_synonym
annotated target: up-regulates quantity by stabilization
has_synonym_type: Unique short label curated by PSI-MI

down-regulates
type: Class
subclass of: causal statement
definition: The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B.
created by: ppm
creation date: 2017-01-19T14:00:20Z
has_exact_synonym: down regulates
has_exact_synonym: down-regulates
has_obo_namespace: PSI-MI
id: MI:2240
in_subset: PSI-MI slim

Axiom
annotated source: down-regulates
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B.
database_cross_reference: PMID:26467481

Axiom
annotated source: down-regulates
annotated property: has_exact_synonym
annotated target: down regulates
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: down-regulates
annotated property: has_exact_synonym
annotated target: down-regulates
has_synonym_type: Unique short label curated by PSI-MI

down-regulates activity
type: Class
subclass of: down-regulates
definition: The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
created by: ppm
creation date: 2017-01-19T14:13:34Z
database_cross_reference: GO:GO:0044093
has_exact_synonym: down-regulates activity
has_exact_synonym: inhibits activity
has_obo_namespace: PSI-MI
id: MI:2241
in_subset: PSI-MI slim

Axiom
annotated source: down-regulates activity
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
database_cross_reference: PMID:26467481

Axiom
annotated source: down-regulates activity
annotated property: has_exact_synonym
annotated target: down-regulates activity
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: down-regulates activity
annotated property: has_exact_synonym
annotated target: inhibits activity
has_synonym_type: Alternate label curated by PSI-MI

down-regulates quantity
type: Class
subclass of: down-regulates
definition: The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B.
created by: ppm
creation date: 2017-01-19T14:15:10Z
has_exact_synonym: decreases quantity
has_exact_synonym: down-regulates quantity
has_obo_namespace: PSI-MI
id: MI:2242
in_subset: PSI-MI slim

Axiom
annotated source: down-regulates quantity
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B.
database_cross_reference: PMID:26467481

Axiom
annotated source: down-regulates quantity
annotated property: has_exact_synonym
annotated target: decreases quantity
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: down-regulates quantity
annotated property: has_exact_synonym
annotated target: down-regulates quantity
has_synonym_type: Unique short label curated by PSI-MI

down-regulates quantity by repression
type: Class
subclass of: down-regulates quantity
definition: The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression.
created by: ppm
creation date: 2017-01-19T14:25:28Z
has_exact_synonym: Decrease quantity by repression
has_exact_synonym: down-regulates quantity by repression
has_obo_namespace: PSI-MI
id: MI:2243
in_subset: PSI-MI slim

Axiom
annotated source: down-regulates quantity by repression
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression.
database_cross_reference: PMID:26467481

Axiom
annotated source: down-regulates quantity by repression
annotated property: has_exact_synonym
annotated target: Decrease quantity by repression
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: down-regulates quantity by repression
annotated property: has_exact_synonym
annotated target: down-regulates quantity by repression
has_synonym_type: Unique short label curated by PSI-MI

down-regulates quantity by destabilization
type: Class
subclass of: down-regulates quantity
definition: The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation.
created by: ppm
creation date: 2017-01-19T14:28:52Z
has_exact_synonym: decrease quantity by destabilization
has_exact_synonym: down-regulates quantity by destabilization
has_obo_namespace: PSI-MI
id: MI:2244
in_subset: PSI-MI slim

Axiom
annotated source: down-regulates quantity by destabilization
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation.
database_cross_reference: PMID:26467481

Axiom
annotated source: down-regulates quantity by destabilization
annotated property: has_exact_synonym
annotated target: decrease quantity by destabilization
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: down-regulates quantity by destabilization
annotated property: has_exact_synonym
annotated target: down-regulates quantity by destabilization
has_synonym_type: Unique short label curated by PSI-MI

causal regulatory mechanism
type: Class
subclass of: causal interaction
definition: Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B.
created by: ppm
creation date: 2017-01-19T15:44:29Z
has_exact_synonym: causal regulatory mechanism
has_exact_synonym: indirect causal regulation
has_obo_namespace: PSI-MI
id: MI:2245

Axiom
annotated source: causal regulatory mechanism
annotated property: definition
annotated target: Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B.
database_cross_reference: PMID:26467481

Axiom
annotated source: causal regulatory mechanism
annotated property: has_exact_synonym
annotated target: causal regulatory mechanism
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: causal regulatory mechanism
annotated property: has_exact_synonym
annotated target: indirect causal regulation
has_synonym_type: Alternate label curated by PSI-MI

indirect causal regulation
type: Class
definition: The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B.
created by: ppm
creation date: 2017-01-19T15:45:44Z
has_exact_synonym: indirect
has_exact_synonym: indirect causal regulation
has_obo_namespace: PSI-MI
id: MI:2246
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: indirect causal regulation
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B.
database_cross_reference: PMID:15845847

Axiom
annotated source: indirect causal regulation
annotated property: has_exact_synonym
annotated target: indirect
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: indirect causal regulation
annotated property: has_exact_synonym
annotated target: indirect causal regulation
has_synonym_type: Unique short label curated by PSI-MI

transcriptional regulation
type: Class
subclass of: causal regulatory mechanism
definition: Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
created by: ppm
creation date: 2017-01-19T15:47:39Z
has_exact_synonym: transcriptional regulation
has_obo_namespace: PSI-MI
id: MI:2247
in_subset: PSI-MI slim

Axiom
annotated source: transcriptional regulation
annotated property: definition
annotated target: Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
database_cross_reference: PMID:25428369

Axiom
annotated source: transcriptional regulation
annotated property: has_exact_synonym
annotated target: transcriptional regulation
has_synonym_type: Unique short label curated by PSI-MI

translation regulation
type: Class
subclass of: causal regulatory mechanism
definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
created by: ppm
creation date: 2017-01-19T15:48:53Z
has_exact_synonym: translation regulation
has_exact_synonym: translational regulation
has_obo_namespace: PSI-MI
id: MI:2248
in_subset: PSI-MI slim

Axiom
annotated source: translation regulation
annotated property: definition
annotated target: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
database_cross_reference: PMID:25428369

Axiom
annotated source: translation regulation
annotated property: has_exact_synonym
annotated target: translation regulation
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: translation regulation
annotated property: has_exact_synonym
annotated target: translational regulation
has_synonym_type: Alternate label curated by PSI-MI

post transcriptional regulation
type: Class
subclass of: causal regulatory mechanism
definition: Any process that control gene expression at the RNA level, between the transcription and the translation of the gene.
created by: ppm
creation date: 2017-01-19T15:54:32Z
has_exact_synonym: post transcriptional regulation
has_exact_synonym: post-transcriptional regulation
has_obo_namespace: PSI-MI
id: MI:2249
in_subset: PSI-MI slim

Axiom
annotated source: post transcriptional regulation
annotated property: definition
annotated target: Any process that control gene expression at the RNA level, between the transcription and the translation of the gene.
database_cross_reference: PMID:25428369

Axiom
annotated source: post transcriptional regulation
annotated property: has_exact_synonym
annotated target: post transcriptional regulation
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: post transcriptional regulation
annotated property: has_exact_synonym
annotated target: post-transcriptional regulation
has_synonym_type: Alternate label curated by PSI-MI

direct causal regulation
type: Class
definition: The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B.
created by: ppm
creation date: 2017-01-19T15:56:00Z
has_exact_synonym: direct
has_exact_synonym: direct causal regulation
has_obo_namespace: PSI-MI
id: MI:2250
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: direct causal regulation
annotated property: definition
annotated target: The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B.
database_cross_reference: PMID:15845847

Axiom
annotated source: direct causal regulation
annotated property: has_exact_synonym
annotated target: direct
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: direct causal regulation
annotated property: has_exact_synonym
annotated target: direct causal regulation
has_synonym_type: Unique short label curated by PSI-MI

transcriptional regulation by direct binding of dbTF to DNA regulatory element
type: Class
definition: Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
created by: ppm
creation date: 2017-01-19T15:57:01Z
has_obo_namespace: PSI-MI
id: MI:2251
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: transcriptional regulation by direct binding of dbTF to DNA regulatory element
annotated property: definition
annotated target: Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
database_cross_reference: PMID:25428369

guanine nucleotide exchange factor reaction
type: Class
subclass of: enzymatic reaction
definition: The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP.
created by: ppm
creation date: 2017-01-19T16:13:36Z
has_exact_synonym: GEF reaction
has_obo_namespace: PSI-MI
id: MI:2252
in_subset: PSI-MI slim

Axiom
annotated source: guanine nucleotide exchange factor reaction
annotated property: definition
annotated target: The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP.
database_cross_reference: PMID:23303910

Axiom
annotated source: guanine nucleotide exchange factor reaction
annotated property: has_exact_synonym
annotated target: GEF reaction
has_synonym_type: Unique short label curated by PSI-MOD

gtpase-activating protein reaction
type: Class
definition: A family of cellular proteins able to increases the activity of a GTPase.
created by: ppm
creation date: 2017-01-19T16:16:04Z
has_exact_synonym: GAP reaction
has_exact_synonym: GTPase-Accelerating Protein reaction
has_exact_synonym: RGS protein reaction
has_obo_namespace: PSI-MI
id: MI:2253
deprecated: true

Axiom
annotated source: gtpase-activating protein reaction
annotated property: definition
annotated target: A family of cellular proteins able to increases the activity of a GTPase.
database_cross_reference: PMID:17173929

Axiom
annotated source: gtpase-activating protein reaction
annotated property: has_exact_synonym
annotated target: GAP reaction
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: gtpase-activating protein reaction
annotated property: has_exact_synonym
annotated target: GTPase-Accelerating Protein reaction
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: gtpase-activating protein reaction
annotated property: has_exact_synonym
annotated target: RGS protein reaction
has_synonym_type: Alternate label curated by PSI-MI

chemical activation reaction
type: Class
definition: The effect of a chemical compound that results in the activation or in an increased activation of a target molecule.
created by: ppm
creation date: 2017-01-19T16:23:55Z
has_exact_synonym: chemical activation reaction
has_obo_namespace: PSI-MI
id: MI:2254
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: chemical activation reaction
annotated property: definition
annotated target: The effect of a chemical compound that results in the activation or in an increased activation of a target molecule.
database_cross_reference: PMID:26467481

Axiom
annotated source: chemical activation reaction
annotated property: has_exact_synonym
annotated target: chemical activation reaction
has_synonym_type: Unique short label curated by PSI-MI

chemical inhibition reaction
type: Class
definition: The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule.
created by: ppm
creation date: 2017-01-19T16:25:05Z
has_exact_synonym: chemical inhibition reaction
has_obo_namespace: PSI-MI
id: MI:2255
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: chemical inhibition reaction
annotated property: definition
annotated target: The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule.
database_cross_reference: PMID:26467481

Axiom
annotated source: chemical inhibition reaction
annotated property: has_exact_synonym
annotated target: chemical inhibition reaction
has_synonym_type: Unique short label curated by PSI-MI

relocalization
type: Class
definition: Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
created by: ppm
creation date: 2017-01-19T16:26:15Z
has_exact_synonym: relocalization
has_obo_namespace: PSI-MI
id: MI:2256
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: relocalization
annotated property: definition
annotated target: Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
database_cross_reference: PMID:26467481

Axiom
annotated source: relocalization
annotated property: has_exact_synonym
annotated target: relocalization
has_synonym_type: Unique short label curated by PSI-MI

small molecule catalysis reaction
type: Class
definition: The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules.
created by: ppm
creation date: 2017-01-19T16:27:34Z
has_exact_synonym: small molecule catalysis reaction
has_obo_namespace: PSI-MI
id: MI:2257
in_subset: PSI-MI slim
deprecated: true

Axiom
annotated source: small molecule catalysis reaction
annotated property: definition
annotated target: The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules.
database_cross_reference: PMID:26467481

Axiom
annotated source: small molecule catalysis reaction
annotated property: has_exact_synonym
annotated target: small molecule catalysis reaction
has_synonym_type: Unique short label curated by PSI-MI

xenobiotic
type: Class
subclass of: small molecule
definition: Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism.
created by: ppm
creation date: 2017-01-19T16:46:33Z
has_exact_synonym: chemical
has_exact_synonym: drug
has_exact_synonym: xenobiotic
has_obo_namespace: PSI-MI
id: MI:2258
in_subset: PSI-MI slim

Axiom
annotated source: xenobiotic
annotated property: definition
annotated target: Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism.
database_cross_reference: PMID:14755292

Axiom
annotated source: xenobiotic
annotated property: has_exact_synonym
annotated target: chemical
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: xenobiotic
annotated property: has_exact_synonym
annotated target: drug
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: xenobiotic
annotated property: has_exact_synonym
annotated target: xenobiotic
has_synonym_type: Unique short label curated by PSI-MI

causal interactor type
type: Class
subclass of: causal interaction
definition: Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements.
created by: ppm
creation date: 2017-01-19T16:51:20Z
has_exact_synonym: causal interactor type
has_obo_namespace: PSI-MI
id: MI:2259

Axiom
annotated source: causal interactor type
annotated property: definition
annotated target: Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements.
database_cross_reference: PMID:26467481

Axiom
annotated source: causal interactor type
annotated property: has_exact_synonym
annotated target: causal interactor type
has_synonym_type: Unique short label curated by PSI-MI

stimulus
type: Class
subclass of: causal interactor type
definition: Any detectable change in the internal or external environment of a cell, tissue, organ, or organism.
created by: ppm
creation date: 2017-01-19T16:52:44Z
has_exact_synonym: stimulus
has_obo_namespace: PSI-MI
id: MI:2260
in_subset: PSI-MI slim

Axiom
annotated source: stimulus
annotated property: definition
annotated target: Any detectable change in the internal or external environment of a cell, tissue, organ, or organism.
database_cross_reference: PMID:14755292

Axiom
annotated source: stimulus
annotated property: has_exact_synonym
annotated target: stimulus
has_synonym_type: Unique short label curated by PSI-MI

phenotype
type: Class
subclass of: causal interactor type
definition: Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function.
created by: ppm
creation date: 2017-01-19T16:54:07Z
has_exact_synonym: phenotype
has_obo_namespace: PSI-MI
id: MI:2261
in_subset: PSI-MI slim

Axiom
annotated source: phenotype
annotated property: definition
annotated target: Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function.
database_cross_reference: PMID:19380745

Axiom
annotated source: phenotype
annotated property: has_exact_synonym
annotated target: phenotype
has_synonym_type: Unique short label curated by PSI-MI

causal regulatory modification
type: Class
subclass of: causal interaction
definition: The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity.
created by: ppm
creation date: 2017-01-19T17:03:04Z
has_exact_synonym: causal regulatory modification
has_obo_namespace: PSI-MI
id: MI:2262
comment: CAUTION: This is a temporary branch. These terms will be soon added in the PSI-MOD ontology and this branch will became obsolete.

Axiom
annotated source: causal regulatory modification
annotated property: definition
annotated target: The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity.
database_cross_reference: PMID:26467481

Axiom
annotated source: causal regulatory modification
annotated property: has_exact_synonym
annotated target: causal regulatory modification
has_synonym_type: Unique short label curated by PSI-MI

s-nitrosylation
type: Class
subclass of: enzymatic reaction
definition: Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine.
created by: ppm
creation date: 2017-01-19T17:11:46Z
has_exact_synonym: s-nitrosylation
has_obo_namespace: PSI-MI
id: MI:2263
in_subset: PSI-MI slim

Axiom
annotated source: s-nitrosylation
annotated property: definition
annotated target: Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine.
database_cross_reference: PMID:15688001

Axiom
annotated source: s-nitrosylation
annotated property: has_exact_synonym
annotated target: s-nitrosylation
has_synonym_type: Unique short label curated by PSI-MI

tyrosinated residue
type: Class
subclass of: causal regulatory modification
definition: A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin.
created by: ppm
creation date: 2017-01-23T10:26:40Z
has_exact_synonym: tyrosinated residue
has_obo_namespace: PSI-MI
id: MI:2264
in_subset: PSI-MI slim

Axiom
annotated source: tyrosinated residue
annotated property: definition
annotated target: A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin.
database_cross_reference: PMID:26467481

Axiom
annotated source: tyrosinated residue
annotated property: has_exact_synonym
annotated target: tyrosinated residue
has_synonym_type: Unique short label curated by PSI-MI

de-acetylated residue
type: Class
subclass of: causal regulatory modification
definition: A protein modification that effectively remove an acyl group from a protein.
created by: ppm
creation date: 2017-01-23T10:30:06Z
has_exact_synonym: de-acetylated residue
has_exact_synonym: deacetylated residue
has_obo_namespace: PSI-MI
id: MI:2265
in_subset: PSI-MI slim

Axiom
annotated source: de-acetylated residue
annotated property: definition
annotated target: A protein modification that effectively remove an acyl group from a protein.
database_cross_reference: PMID:26467481

Axiom
annotated source: de-acetylated residue
annotated property: has_exact_synonym
annotated target: de-acetylated residue
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: de-acetylated residue
annotated property: has_exact_synonym
annotated target: deacetylated residue
has_synonym_type: Alternate label curated by PSI-MI

de-phosphorylated residue
type: Class
subclass of: causal regulatory modification
definition: A protein modification that effectively remove a phosphate group from a protein by hydrolysis.
created by: ppm
creation date: 2017-01-23T10:32:50Z
has_exact_synonym: de-phosphorylated residue
has_exact_synonym: dephosphorylated residue
has_obo_namespace: PSI-MI
id: MI:2266
in_subset: PSI-MI slim

Axiom
annotated source: de-phosphorylated residue
annotated property: definition
annotated target: A protein modification that effectively remove a phosphate group from a protein by hydrolysis.
database_cross_reference: PMID:26467481

Axiom
annotated source: de-phosphorylated residue
annotated property: has_exact_synonym
annotated target: de-phosphorylated residue
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: de-phosphorylated residue
annotated property: has_exact_synonym
annotated target: dephosphorylated residue
has_synonym_type: Alternate label curated by PSI-MI

de-sumoylated residue
type: Class
subclass of: causal regulatory modification
definition: A protein modification that effectively cleaves the G-K bond and releases SUMO proteins.
created by: ppm
creation date: 2017-01-23T10:46:01Z
has_exact_synonym: de-sumoylated residue
has_exact_synonym: desumoylated residue
has_obo_namespace: PSI-MI
id: MI:2267
in_subset: PSI-MI slim

Axiom
annotated source: de-sumoylated residue
annotated property: definition
annotated target: A protein modification that effectively cleaves the G-K bond and releases SUMO proteins.
database_cross_reference: PMID:26467481

Axiom
annotated source: de-sumoylated residue
annotated property: has_exact_synonym
annotated target: de-sumoylated residue
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: de-sumoylated residue
annotated property: has_exact_synonym
annotated target: desumoylated residue
has_synonym_type: Alternate label curated by PSI-MI

de-methylated residue
type: Class
subclass of: causal regulatory modification
definition: A protein modification that effectively removes one or more methyl groups from a protein.
created by: ppm
creation date: 2017-01-23T10:47:33Z
has_exact_synonym: de-methylated residue
has_exact_synonym: demethylated residue
has_obo_namespace: PSI-MI
id: MI:2268
in_subset: PSI-MI slim

Axiom
annotated source: de-methylated residue
annotated property: definition
annotated target: A protein modification that effectively removes one or more methyl groups from a protein.
database_cross_reference: PMID:26467481

Axiom
annotated source: de-methylated residue
annotated property: has_exact_synonym
annotated target: de-methylated residue
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: de-methylated residue
annotated property: has_exact_synonym
annotated target: demethylated residue
has_synonym_type: Alternate label curated by PSI-MI

de-ubiquitinylated residue
type: Class
subclass of: causal regulatory modification
definition: A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins.
created by: ppm
creation date: 2017-01-23T10:48:53Z
has_exact_synonym: de-ubiquitinylated residue
has_exact_synonym: deubiquitinylated residue
has_obo_namespace: PSI-MI
id: MI:2269
in_subset: PSI-MI slim

Axiom
annotated source: de-ubiquitinylated residue
annotated property: definition
annotated target: A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins.
database_cross_reference: PMID:26467481

Axiom
annotated source: de-ubiquitinylated residue
annotated property: has_exact_synonym
annotated target: de-ubiquitinylated residue
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: de-ubiquitinylated residue
annotated property: has_exact_synonym
annotated target: deubiquitinylated residue
has_synonym_type: Alternate label curated by PSI-MI

signalink
type: Class
subclass of: interaction database
definition: SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks. http://signalink.org
created by: ppm
creation date: 2017-01-23T11:41:20Z
database_cross_reference: url:http://signalink.org
has_exact_synonym: SignaLink
has_exact_synonym: signalink
has_obo_namespace: PSI-MI
id: MI:2270
in_subset: PSI-MI slim

Axiom
annotated source: signalink
annotated property: definition
annotated target: SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks. http://signalink.org
database_cross_reference: PMID:23331499

Axiom
annotated source: signalink
annotated property: has_exact_synonym
annotated target: SignaLink
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: signalink
annotated property: has_exact_synonym
annotated target: signalink
has_synonym_type: Unique short label curated by PSI-MI

edam
type: Class
subclass of: experiment database
definition: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. http://edamontology.org/
created by: ppm
creation date: 2017-01-26T15:09:47Z
database_cross_reference: url:http://edamontology.org/
has_exact_synonym: EDAM
has_exact_synonym: EMBRACE Data And Methods
has_exact_synonym: edam
has_obo_namespace: PSI-MI
id: MI:2271
in_subset: PSI-MI slim

Axiom
annotated source: edam
annotated property: definition
annotated target: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. http://edamontology.org/
database_cross_reference: PMID:23479348

Axiom
annotated source: edam
annotated property: has_exact_synonym
annotated target: EDAM
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: edam
annotated property: has_exact_synonym
annotated target: EMBRACE Data And Methods
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: edam
annotated property: has_exact_synonym
annotated target: edam
has_synonym_type: Unique short label curated by PSI-MI

tyrosinylation
type: Class
subclass of: enzymatic reaction
definition: Reversible reaction that add a tyrosine residue to an amino-acid.
created by: ppm
creation date: 2017-01-26T15:21:43Z
database_cross_reference: GO:GO:0018322
has_exact_synonym: tyrosinylation
has_obo_namespace: PSI-MI
id: MI:2272
in_subset: PSI-MI slim

Axiom
annotated source: tyrosinylation
annotated property: has_exact_synonym
annotated target: tyrosinylation
has_synonym_type: Unique short label curated by PSI-MI

tyrosination
type: Class
subclass of: tyrosinylation
definition: Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin.
created by: ppm
creation date: 2017-01-26T15:22:39Z
database_cross_reference: GO:GO:0018166
has_exact_synonym: tyrosination
has_obo_namespace: PSI-MI
id: MI:2273
in_subset: PSI-MI slim

Axiom
annotated source: tyrosination
annotated property: definition
annotated target: Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin.
database_cross_reference: PMID:10842328

Axiom
annotated source: tyrosination
annotated property: has_exact_synonym
annotated target: tyrosination
has_synonym_type: Unique short label curated by PSI-MI

regulator
type: Class
subclass of: biological role
definition: Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity.
created by: ppm
creation date: 2017-01-26T15:29:51Z
has_exact_synonym: modulator
has_exact_synonym: regulator
has_obo_namespace: PSI-MI
id: MI:2274
in_subset: PSI-MI slim

Axiom
annotated source: regulator
annotated property: definition
annotated target: Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity.
database_cross_reference: PMID:14755292

Axiom
annotated source: regulator
annotated property: has_exact_synonym
annotated target: modulator
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: regulator
annotated property: has_exact_synonym
annotated target: regulator
has_synonym_type: Unique short label curated by PSI-MI

regulator target
type: Class
subclass of: biological role
definition: Entity whose concentration, frequency, rate or extent are regulated by the regulator entity.
created by: ppm
creation date: 2017-01-26T15:31:14Z
has_exact_synonym: modulator target
has_exact_synonym: regulator target
has_obo_namespace: PSI-MI
id: MI:2275
in_subset: PSI-MI slim

Axiom
annotated source: regulator target
annotated property: definition
annotated target: Entity whose concentration, frequency, rate or extent are regulated by the regulator entity.
database_cross_reference: PMID:14755292

Axiom
annotated source: regulator target
annotated property: has_exact_synonym
annotated target: modulator target
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: regulator target
annotated property: has_exact_synonym
annotated target: regulator target
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification
type: Class
subclass of: biological feature
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification.
created by: ppm
creation date: 2017-03-06T11:04:25Z
has_exact_synonym: carbohydrate chemical modification
has_obo_namespace: PSI-MI
id: MI:2276

Axiom
annotated source: carbohydrate chemical modification
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification
has_synonym_type: Unique short label curated by PSI-MI

Cr-two hybrid
type: Class
subclass of: two hybrid bait and prey pooling approach
definition: This method uses Cre recombinase as a two-hybrid protein-protein interaction reporter that functions intracellularly to covalently and unidirectionally link interacting bait and prey plasmids via specialized loxP sites that flank the protein-coding sequences. The linked protein-coding sequences serve as interaction-identifying DNA molecules that enable massively multiplexed screening coupled with next-generation DNA sequencing to detect protein-protein interactions.
created by: ppm
creation date: 2017-06-20T15:57:41Z
has_exact_synonym: Cre recombinase two hybrid
has_exact_synonym: cr-2h
has_exact_synonym: cr-two hybrid
has_obo_namespace: PSI-MI
id: MI:2277
in_subset: PSI-MI slim

Axiom
annotated source: Cr-two hybrid
annotated property: has_exact_synonym
annotated target: Cre recombinase two hybrid
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: Cr-two hybrid
annotated property: has_exact_synonym
annotated target: cr-2h
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: Cr-two hybrid
annotated property: has_exact_synonym
annotated target: cr-two hybrid
has_synonym_type: Unique short label curated by PSI-MI

polymer chain length
type: Class
subclass of: participant attribute name
definition: Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers.
created by: ppm
creation date: 2017-07-05T10:27:19Z
has_exact_synonym: polymer chain length
has_obo_namespace: PSI-MI
id: MI:2278
in_subset: PSI-MI slim

Axiom
annotated source: polymer chain length
annotated property: definition
annotated target: Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers.
database_cross_reference: PMID:14755292

Axiom
annotated source: polymer chain length
annotated property: has_exact_synonym
annotated target: polymer chain length
has_synonym_type: Unique short label curated by PSI-MI

complex portal
type: Class
subclass of: interaction database
subclass of: participant database
definition: The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry.
created by: ppm
creation date: 2017-07-28T09:34:45Z
database_cross_reference: search-url:
has_exact_synonym: Complex Portal
has_exact_synonym: complex portal
has_obo_namespace: PSI-MI
id: MI:2279
in_subset: PSI-MI slim

Axiom
annotated source: complex portal
annotated property: definition
annotated target: The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry.
database_cross_reference: PMID:25313161

Axiom
annotated source: complex portal
annotated property: database_cross_reference
annotated target: search-url:
label: http://www.ebi.ac.uk/complexportal/complex/${ac}

Axiom
annotated source: complex portal
annotated property: has_exact_synonym
annotated target: Complex Portal
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: complex portal
annotated property: has_exact_synonym
annotated target: complex portal
has_synonym_type: Unique short label curated by PSI-MI

deamidation reaction
type: Class
subclass of: enzymatic reaction
definition: Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline).
created by: ppm
creation date: 2017-08-08T14:38:29Z
has_exact_synonym: deamidation
has_obo_namespace: PSI-MI
id: MI:2280
in_subset: PSI-MI slim

Axiom
annotated source: deamidation reaction
annotated property: definition
annotated target: Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline).
database_cross_reference: PMID:2703484
database_cross_reference: PMID:3440704

Axiom
annotated source: deamidation reaction
annotated property: has_exact_synonym
annotated target: deamidation
has_synonym_type: Unique short label curated by PSI-MI

deamidation assay
type: Class
subclass of: enzymatic study
definition: Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3.
created by: ppm
creation date: 2017-08-08T14:49:09Z
has_exact_synonym: amidase assay
has_exact_synonym: deamidation
has_obo_namespace: PSI-MI
id: MI:2281
in_subset: PSI-MI slim

Axiom
annotated source: deamidation assay
annotated property: definition
annotated target: Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3.
database_cross_reference: GO:0004040

Axiom
annotated source: deamidation assay
annotated property: has_exact_synonym
annotated target: amidase assay
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: deamidation assay
annotated property: has_exact_synonym
annotated target: deamidation
has_synonym_type: Unique short label curated by PSI-MI

complex-primary
type: Class
subclass of: cross-reference type
definition: Complex object unique primary identifier that is assigned to a complex in the Complex Portal.
created by: ppm
creation date: 2017-08-25T13:31:03Z
has_exact_synonym: complex-primary
has_obo_namespace: PSI-MI
id: MI:2282
in_subset: PSI-MI slim

Axiom
annotated source: complex-primary
annotated property: definition
annotated target: Complex object unique primary identifier that is assigned to a complex in the Complex Portal.
database_cross_reference: PMID:25313161

Axiom
annotated source: complex-primary
annotated property: has_exact_synonym
annotated target: complex-primary
has_synonym_type: Unique short label curated by PSI-MI

southwestern blotting
type: Class
subclass of: far western blotting
definition: Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting.
created by: ppm
creation date: 2017-11-15T15:35:20Z
has_exact_synonym: southwestern blot
has_exact_synonym: southwestern blotting
has_obo_namespace: PSI-MI
id: MI:2283
in_subset: PSI-MI slim

Axiom
annotated source: southwestern blotting
annotated property: definition
annotated target: Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting.
database_cross_reference: PMID:26404144

Axiom
annotated source: southwestern blotting
annotated property: has_exact_synonym
annotated target: southwestern blot
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: southwestern blotting
annotated property: has_exact_synonym
annotated target: southwestern blotting
has_synonym_type: Alternate label curated by PSI-MI

complex component
type: Class
subclass of: cross-reference type
definition: Indicates that the cross-referenced molecule is a component of a containing complex.
created by: ppm
creation date: 2017-12-15T11:08:53Z
has_exact_synonym: complex component
has_exact_synonym: complex-component
has_obo_namespace: PSI-MI
id: MI:2284
in_subset: PSI-MI slim

Axiom
annotated source: complex component
annotated property: definition
annotated target: Indicates that the cross-referenced molecule is a component of a containing complex.
database_cross_reference: PMID:25313161

Axiom
annotated source: complex component
annotated property: has_exact_synonym
annotated target: complex component
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: complex component
annotated property: has_exact_synonym
annotated target: complex-component
has_synonym_type: Alternate label curated by PSI-MI

miRNA interference luciferase reporter assay
type: Class
subclass of: post transcriptional interference
definition: The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs.
created by: pporras
creation date: 2018-05-02T15:22:12Z
has_exact_synonym: miRNA interference luciferase assay
has_obo_namespace: PSI-MI
id: MI:2285
in_subset: PSI-MI slim

Axiom
annotated source: miRNA interference luciferase reporter assay
annotated property: definition
annotated target: The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs.
database_cross_reference: PMID:14697198
database_cross_reference: PMID:21431711

Axiom
annotated source: miRNA interference luciferase reporter assay
annotated property: has_exact_synonym
annotated target: miRNA interference luciferase assay
has_synonym_type: Unique short label curated by PSI-MI

functional association
type: Class
subclass of: interaction type
definition: Binary relationship between biological entities when one of them modulates the other in terms of function, expression, degradation or stability of the other and the relationship between the partners cannot be ascertained as direct, so intermediate steps are implicitly present. This relation specifically does not imply a physical interaction between the entities involved.
created by: pporras
creation date: 2018-06-27T15:24:40Z
has_exact_synonym: functional association
has_obo_namespace: PSI-MI
id: MI:2286
in_subset: PSI-MI slim

Axiom
annotated source: functional association
annotated property: has_exact_synonym
annotated target: functional association
has_synonym_type: Unique short label curated by PSI-MI

identification by structure determination
type: Class
subclass of: experimental participant identification
definition: Identity of the participant was established (or confirmed) by fitting its molecular model to the experimentally determined electron density.
created by: pporras
creation date: 2018-06-28T15:00:41Z
has_exact_synonym: identification by structure determination
has_exact_synonym: structure determination
has_obo_namespace: PSI-MI
id: MI:2287
in_subset: PSI-MI slim

Axiom
annotated source: identification by structure determination
annotated property: definition
annotated target: Identity of the participant was established (or confirmed) by fitting its molecular model to the experimentally determined electron density.
database_cross_reference: PMID:7877166

Axiom
annotated source: identification by structure determination
annotated property: has_exact_synonym
annotated target: identification by structure determination
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: identification by structure determination
annotated property: has_exact_synonym
annotated target: structure determination
has_synonym_type: Unique short label curated by PSI-MI

DAP-seq
type: Class
subclass of: affinity chromatography technology
definition: DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced.
created by: pporras
creation date: 2018-06-28T16:09:45Z
has_exact_synonym: DNA affinity purification sequencing
has_exact_synonym: dap-seq
has_obo_namespace: PSI-MI
id: MI:2288
in_subset: PSI-MI slim

Axiom
annotated source: DAP-seq
annotated property: definition
annotated target: DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced.
database_cross_reference: PMID:27203113

Axiom
annotated source: DAP-seq
annotated property: has_exact_synonym
annotated target: DNA affinity purification sequencing
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: DAP-seq
annotated property: has_exact_synonym
annotated target: dap-seq
has_synonym_type: Unique short label curated by PSI-MI

virotrap
type: Class
subclass of: biochemical
definition: The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots.
created by: pporras
creation date: 2018-09-13T10:18:19Z
has_exact_synonym: viral particle co-purification
has_obo_namespace: PSI-MI
id: MI:2289
in_subset: PSI-MI slim

Axiom
annotated source: virotrap
annotated property: definition
annotated target: The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots.
database_cross_reference: PMID:27122307

Axiom
annotated source: virotrap
annotated property: has_exact_synonym
annotated target: viral particle co-purification
has_synonym_type: Alternate label curated by PSI-MI

optical tweezers
type: Class
subclass of: force spectroscopy
definition: Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
created by: pporras
creation date: 2018-09-13T10:39:59Z
has_obo_namespace: PSI-MI
id: MI:2290
in_subset: PSI-MI slim

Axiom
annotated source: optical tweezers
annotated property: definition
annotated target: Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
database_cross_reference: PMID:17023539
database_cross_reference: PMID:17081984

atomic force microscopy cantilevers
type: Class
subclass of: force spectroscopy
definition: Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip.
created by: pporras
creation date: 2018-09-13T10:49:44Z
has_exact_synonym: afm cantilevers
has_obo_namespace: PSI-MI
id: MI:2291
in_subset: PSI-MI slim

Axiom
annotated source: atomic force microscopy cantilevers
annotated property: definition
annotated target: Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip.
database_cross_reference: PMID:18511917

Axiom
annotated source: atomic force microscopy cantilevers
annotated property: has_exact_synonym
annotated target: afm cantilevers
has_synonym_type: Unique short label curated by PSI-MI

magnetic tweezers
type: Class
subclass of: force spectroscopy
definition: Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
created by: pporras
creation date: 2018-09-13T12:04:16Z
has_exact_synonym: electromagnetic tweezers
has_obo_namespace: PSI-MI
id: MI:2292
in_subset: PSI-MI slim

Axiom
annotated source: magnetic tweezers
annotated property: definition
annotated target: Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
database_cross_reference: PMID:18511917

Axiom
annotated source: magnetic tweezers
annotated property: has_exact_synonym
annotated target: electromagnetic tweezers
has_synonym_type: Alternate label curated by PSI-MI

5' position
type: Class
subclass of: feature range status
definition: Term describing the upstream end of a nucleotide sequence.
created by: pporras
creation date: 2018-09-14T09:15:05Z
has_obo_namespace: PSI-MI
id: MI:2293
in_subset: PSI-MI slim

Axiom
annotated source: 5' position
annotated property: definition
annotated target: Term describing the upstream end of a nucleotide sequence.
database_cross_reference: PMID:14755292

5' range
type: Class
subclass of: feature range status
definition: Term describing the upstream region of a nucleotide sequence, exact coordinates not available.
created by: pporras
creation date: 2018-09-14T09:25:33Z
has_obo_namespace: PSI-MI
id: MI:2294
in_subset: PSI-MI slim

Axiom
annotated source: 5' range
annotated property: definition
annotated target: Term describing the upstream region of a nucleotide sequence, exact coordinates not available.
database_cross_reference: PMID:14755292

3' position
type: Class
subclass of: feature range status
definition: Term describing the downstream end of a nucleotide sequence.
created by: pporras
creation date: 2018-09-14T09:26:47Z
has_obo_namespace: PSI-MI
id: MI:2295
in_subset: PSI-MI slim

Axiom
annotated source: 3' position
annotated property: definition
annotated target: Term describing the downstream end of a nucleotide sequence.
database_cross_reference: PMID:14755292

3' range
type: Class
subclass of: feature range status
definition: Term describing the downstream region of a nucleotide sequence, exact coordinates not available.
created by: pporras
creation date: 2018-09-14T09:27:33Z
has_obo_namespace: PSI-MI
id: MI:2296
in_subset: PSI-MI slim

Axiom
annotated source: 3' range
annotated property: definition
annotated target: Term describing the downstream region of a nucleotide sequence, exact coordinates not available.
database_cross_reference: PMID:14755292

carbohydrate chemical modification causing an interaction
type: Class
subclass of: carbohydrate chemical modification
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact.
created by: pporras
creation date: 2018-09-14T09:45:20Z
has_exact_synonym: carbohydrate chemical modification causing
has_obo_namespace: PSI-MI
id: MI:2297
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification causing an interaction
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification causing an interaction
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification causing
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification with no effect
type: Class
subclass of: carbohydrate chemical modification
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form.
created by: pporras
creation date: 2018-09-14T09:49:02Z
has_exact_synonym: carbohydrate chemical modification not affecting interaction
has_obo_namespace: PSI-MI
id: MI:2298
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification with no effect
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification with no effect
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification not affecting interaction
has_synonym_type: Alternate label curated by PSI-MI

carbohydrate chemical modification decreasing interaction
type: Class
subclass of: carbohydrate chemical modification
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T09:53:05Z
has_exact_synonym: carbohydrate chemical modification decreasing
has_obo_namespace: PSI-MI
id: MI:2299
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification decreasing interaction
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification decreasing interaction
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification decreasing
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification decreasing interaction rate
type: Class
subclass of: carbohydrate chemical modification decreasing interaction
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T09:56:38Z
has_exact_synonym: carbohydrate chemical modification decreasing rate
has_obo_namespace: PSI-MI
id: MI:2300
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification decreasing interaction rate
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification decreasing interaction rate
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification decreasing rate
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification decreasing interaction strength
type: Class
subclass of: carbohydrate chemical modification decreasing interaction
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T09:58:21Z
has_exact_synonym: carbohydrate chemical modification decreasing strength
has_obo_namespace: PSI-MI
id: MI:2301
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification decreasing interaction strength
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification decreasing interaction strength
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification decreasing strength
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification disrupting interaction
type: Class
subclass of: carbohydrate chemical modification decreasing interaction
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T10:03:25Z
has_exact_synonym: carbohydrate chemical modification disrupting
has_obo_namespace: PSI-MI
id: MI:2302
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification disrupting interaction
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification disrupting interaction
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification disrupting
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification disrupting interaction strength
type: Class
subclass of: carbohydrate chemical modification disrupting interaction
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T10:06:44Z
has_exact_synonym: carbohydrate chemical modification disrupting strength
has_obo_namespace: PSI-MI
id: MI:2303
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification disrupting interaction strength
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification disrupting interaction strength
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification disrupting strength
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification disrupting interaction rate
type: Class
subclass of: carbohydrate chemical modification disrupting interaction
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T10:08:37Z
has_exact_synonym: carbohydrate chemical modification disrupting rate
has_obo_namespace: PSI-MI
id: MI:2304
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification disrupting interaction rate
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification disrupting interaction rate
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification disrupting rate
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification increasing interaction
type: Class
subclass of: carbohydrate chemical modification
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T10:11:37Z
has_exact_synonym: carbohydrate chemical modification increasing
has_obo_namespace: PSI-MI
id: MI:2305
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification increasing interaction
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification increasing interaction
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification increasing
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification increasing interaction strength
type: Class
subclass of: carbohydrate chemical modification increasing interaction
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T10:22:03Z
has_exact_synonym: carbohydrate chemical modification increasing strength
has_obo_namespace: PSI-MI
id: MI:2306
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification increasing interaction strength
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification increasing interaction strength
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification increasing strength
has_synonym_type: Unique short label curated by PSI-MI

carbohydrate chemical modification increasing interaction rate
type: Class
subclass of: carbohydrate chemical modification increasing interaction
definition: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
created by: pporras
creation date: 2018-09-14T10:23:21Z
has_exact_synonym: carbohydrate chemical modification increasing rate
has_obo_namespace: PSI-MI
id: MI:2307
in_subset: PSI-MI slim

Axiom
annotated source: carbohydrate chemical modification increasing interaction rate
annotated property: definition
annotated target: Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
database_cross_reference: PMID:14755292

Axiom
annotated source: carbohydrate chemical modification increasing interaction rate
annotated property: has_exact_synonym
annotated target: carbohydrate chemical modification increasing rate
has_synonym_type: Unique short label curated by PSI-MI

attached carbohydrate
type: Class
subclass of: biological feature
definition: Carbohydrate species chemically attached to proteins, or other organic molecules.
created by: pporras
creation date: 2018-09-14T10:26:12Z
has_exact_synonym: attached glycan
has_exact_synonym: glycosylation
has_obo_namespace: PSI-MI
id: MI:2308
in_subset: PSI-MI slim
comment: Specific carbohydrate species can be represented through the MOD ontology and their representation escapes the scope of this CV.

Axiom
annotated source: attached carbohydrate
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate
annotated property: has_exact_synonym
annotated target: attached glycan
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: attached carbohydrate
annotated property: has_exact_synonym
annotated target: glycosylation
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate causing an interaction
type: Class
subclass of: attached carbohydrate
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact.
created by: pporras
creation date: 2018-09-14T10:37:41Z
has_exact_synonym: attached carbohydrate causing
has_exact_synonym: glycosylation causing interaction
has_obo_namespace: PSI-MI
id: MI:2309
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate causing an interaction
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate causing an interaction
annotated property: has_exact_synonym
annotated target: attached carbohydrate causing
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: attached carbohydrate causing an interaction
annotated property: has_exact_synonym
annotated target: glycosylation causing interaction
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate with no effect
type: Class
subclass of: attached carbohydrate
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact.
created by: pporras
creation date: 2018-09-14T10:40:12Z
has_exact_synonym: attached carbohydrate not affecting interaction
has_exact_synonym: glycosylation with no effect
has_obo_namespace: PSI-MI
id: MI:2310
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate with no effect
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate with no effect
annotated property: has_exact_synonym
annotated target: attached carbohydrate not affecting interaction
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: attached carbohydrate with no effect
annotated property: has_exact_synonym
annotated target: glycosylation with no effect
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate decreasing interaction
type: Class
subclass of: attached carbohydrate
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
created by: pporras
creation date: 2018-09-14T10:42:27Z
has_exact_synonym: attached carbohydrate decreasing
has_exact_synonym: glycosylation decreasing interaction
has_obo_namespace: PSI-MI
id: MI:2311
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate decreasing interaction
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate decreasing interaction
annotated property: has_exact_synonym
annotated target: attached carbohydrate decreasing
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: attached carbohydrate decreasing interaction
annotated property: has_exact_synonym
annotated target: glycosylation decreasing interaction
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate increasing interaction
type: Class
subclass of: attached carbohydrate
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
created by: pporras
creation date: 2018-09-14T10:46:39Z
has_exact_synonym: attached carbohydrate increasing
has_exact_synonym: glycosylation increasing interaction
has_obo_namespace: PSI-MI
id: MI:2312
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate increasing interaction
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate increasing interaction
annotated property: has_exact_synonym
annotated target: attached carbohydrate increasing
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: attached carbohydrate increasing interaction
annotated property: has_exact_synonym
annotated target: glycosylation increasing interaction
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate increasing interaction strength
type: Class
subclass of: attached carbohydrate increasing interaction
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule.
created by: pporras
creation date: 2018-09-14T10:47:14Z
has_exact_synonym: attached carbohydrate increasing strength
has_exact_synonym: glycosylation increasing strength
has_obo_namespace: PSI-MI
id: MI:2313
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate increasing interaction strength
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate increasing interaction strength
annotated property: has_exact_synonym
annotated target: attached carbohydrate increasing strength
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: attached carbohydrate increasing interaction strength
annotated property: has_exact_synonym
annotated target: glycosylation increasing strength
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate increasing interaction rate
type: Class
subclass of: attached carbohydrate increasing interaction
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
created by: pporras
creation date: 2018-09-14T10:49:39Z
has_exact_synonym: attached carbohydrate increasing rate
has_exact_synonym: glycosylation increasing rate
has_obo_namespace: PSI-MI
id: MI:2314
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate increasing interaction rate
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate increasing interaction rate
annotated property: has_exact_synonym
annotated target: attached carbohydrate increasing rate
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: attached carbohydrate increasing interaction rate
annotated property: has_exact_synonym
annotated target: glycosylation increasing rate
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate disrupting interaction rate
type: Class
subclass of: attached carbohydrate decreasing interaction
subclass of: attached carbohydrate disrupting interaction
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
created by: pporras
creation date: 2018-09-14T10:50:23Z
has_exact_synonym: attached carbohydrate disrupting rate
has_exact_synonym: glycosylation disrupting rate
has_obo_namespace: PSI-MI
id: MI:2315
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate disrupting interaction rate
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate disrupting interaction rate
annotated property: has_exact_synonym
annotated target: attached carbohydrate disrupting rate
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: attached carbohydrate disrupting interaction rate
annotated property: has_exact_synonym
annotated target: glycosylation disrupting rate
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate disrupting interaction strength
type: Class
subclass of: attached carbohydrate decreasing interaction
subclass of: attached carbohydrate disrupting interaction
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule.
created by: pporras
creation date: 2018-09-14T10:51:06Z
has_exact_synonym: attached carbohydrate disrupting strength
has_exact_synonym: glycosylation disrupting strength
has_obo_namespace: PSI-MI
id: MI:2316
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate disrupting interaction strength
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate disrupting interaction strength
annotated property: has_exact_synonym
annotated target: attached carbohydrate disrupting strength
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: attached carbohydrate disrupting interaction strength
annotated property: has_exact_synonym
annotated target: glycosylation disrupting strength
has_synonym_type: Alternate label curated by PSI-MI

attached carbohydrate disrupting interaction
type: Class
subclass of: attached carbohydrate decreasing interaction
definition: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
created by: pporras
creation date: 2018-09-18T09:11:58Z
has_exact_synonym: attached carbohydrate disrupting
has_exact_synonym: glycosylation disrupting interaction
has_obo_namespace: PSI-MI
id: MI:2317
in_subset: PSI-MI slim

Axiom
annotated source: attached carbohydrate disrupting interaction
annotated property: definition
annotated target: Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
database_cross_reference: PMID:14755292

Axiom
annotated source: attached carbohydrate disrupting interaction
annotated property: has_exact_synonym
annotated target: attached carbohydrate disrupting
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: attached carbohydrate disrupting interaction
annotated property: has_exact_synonym
annotated target: glycosylation disrupting interaction
has_synonym_type: Alternate label curated by PSI-MI

force measurement
type: Class
subclass of: biophysical
definition: A technique that measures forces generated by interactions between molecules.
created by: pporras
creation date: 2018-10-11T13:41:11Z
has_exact_synonym: intermolecular force
has_obo_namespace: PSI-MI
has_related_synonym: molecular force measurement
id: MI:2318
in_subset: PSI-MI slim

Axiom
annotated source: force measurement
annotated property: definition
annotated target: A technique that measures forces generated by interactions between molecules.
database_cross_reference: PMID:14755292

Axiom
annotated source: force measurement
annotated property: has_exact_synonym
annotated target: intermolecular force
has_synonym_type: Alternate label curated by PSI-MI

surface force measurement
type: Class
subclass of: force measurement
definition: A technique that measures interaction force between two surfaces as they are brought together and retracted.
created by: pporras
creation date: 2018-10-11T13:44:53Z
has_obo_namespace: PSI-MI
has_related_synonym: surface adhesion force measurement
id: MI:2319
in_subset: PSI-MI slim

Axiom
annotated source: surface force measurement
annotated property: definition
annotated target: A technique that measures interaction force between two surfaces as they are brought together and retracted.
database_cross_reference: doi:10.1038/262774a0

aruk-ucl
type: Class
subclass of: interaction database
definition: The Alzheimer's Research UK Gene Ontology Project represents a collaboration between University College London, the European Bioinformatics Institute (EBI) and the University of Manchester, funded by Alzheimer's Research UK. This annotation group is a member of the IMEx Consortium. www.ucl.ac.uk/functional-gene-annotation/neurological
created by: pporras
creation date: 2018-10-16T09:26:24Z
has_exact_synonym: Alzheimer's Research UK Gene Ontology Project
has_obo_namespace: PSI-MI
id: MI:2320
in_subset: PSI-MI slim

Axiom
annotated source: aruk-ucl
annotated property: has_exact_synonym
annotated target: Alzheimer's Research UK Gene Ontology Project
has_synonym_type: Alternate label curated by PSI-MI

high-throughput sequencing
type: Class
subclass of: nucleotide sequence identification
definition: High-throughput (a.k.a. "next-generation") sequencing applies to methods that allow for sequencing of genome-scale number of bases.
created by: pporras
creation date: 2018-11-13T14:59:35Z
has_exact_synonym: next-generation sequencing
has_exact_synonym: ngs sequencing
has_obo_namespace: PSI-MI
id: MI:2321
in_subset: PSI-MI slim

Axiom
annotated source: high-throughput sequencing
annotated property: definition
annotated target: High-throughput (a.k.a. "next-generation") sequencing applies to methods that allow for sequencing of genome-scale number of bases.
database_cross_reference: PMID:19900591

Axiom
annotated source: high-throughput sequencing
annotated property: has_exact_synonym
annotated target: next-generation sequencing
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: high-throughput sequencing
annotated property: has_exact_synonym
annotated target: ngs sequencing
has_synonym_type: Unique short label curated by PSI-MI

Illumina dye sequencing
type: Class
subclass of: high-throughput sequencing
definition: This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence.
created by: pporras
creation date: 2018-11-13T15:23:38Z
has_exact_synonym: illumina sequencing
has_exact_synonym: solexa sequencing
has_obo_namespace: PSI-MI
id: MI:2322
in_subset: PSI-MI slim

Axiom
annotated source: Illumina dye sequencing
annotated property: definition
annotated target: This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence.
database_cross_reference: PMID:18987734

Axiom
annotated source: Illumina dye sequencing
annotated property: has_exact_synonym
annotated target: illumina sequencing
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: Illumina dye sequencing
annotated property: has_exact_synonym
annotated target: solexa sequencing
has_synonym_type: Alternate label curated by PSI-MI

kiss
type: Class
subclass of: protein complementation assay
definition: KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges.
created by: pporras
creation date: 2019-04-02T09:58:26Z
has_exact_synonym: KISS
has_exact_synonym: kinase substrate sensor
has_exact_synonym: kiss
has_obo_namespace: PSI-MI
id: MI:2323
in_subset: PSI-MI slim

Axiom
annotated source: kiss
annotated property: definition
annotated target: KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges.
database_cross_reference: PMID:25154561
database_cross_reference: PMID:29855964

Axiom
annotated source: kiss
annotated property: has_exact_synonym
annotated target: KISS
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: kiss
annotated property: has_exact_synonym
annotated target: kinase substrate sensor
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: kiss
annotated property: has_exact_synonym
annotated target: kiss
has_synonym_type: Unique short label curated by PSI-MI

dbsnp
type: Class
subclass of: feature database
definition: dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
created by: pporras
creation date: 2019-04-02T10:52:06Z
database_cross_reference: search-url:
has_exact_synonym: dbSNP
has_exact_synonym: dbsnp
has_obo_namespace: PSI-MI
id: MI:2324
in_subset: PSI-MI slim

Axiom
annotated source: dbsnp
annotated property: definition
annotated target: dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
database_cross_reference: PMID:11125122

Axiom
annotated source: dbsnp
annotated property: database_cross_reference
annotated target: search-url:
label: https://www.ncbi.nlm.nih.gov/snp/${ac}

Axiom
annotated source: dbsnp
annotated property: has_exact_synonym
annotated target: dbSNP
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: dbsnp
annotated property: has_exact_synonym
annotated target: dbsnp
has_synonym_type: Unique short label curated by PSI-MI

nanoluc luciferase protein tag
type: Class
subclass of: luciferase tag
definition: NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris.
created by: pporras
creation date: 2019-04-11T14:07:06Z
has_exact_synonym: NLuc
has_exact_synonym: NanoLuc
has_exact_synonym: nanoluc luciferase
has_exact_synonym: nluc
has_obo_namespace: PSI-MI
id: MI:2325
in_subset: PSI-MI slim

Axiom
annotated source: nanoluc luciferase protein tag
annotated property: definition
annotated target: NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris.
database_cross_reference: PMID:22894855

Axiom
annotated source: nanoluc luciferase protein tag
annotated property: has_exact_synonym
annotated target: NLuc
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: nanoluc luciferase protein tag
annotated property: has_exact_synonym
annotated target: NanoLuc
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: nanoluc luciferase protein tag
annotated property: has_exact_synonym
annotated target: nanoluc luciferase
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: nanoluc luciferase protein tag
annotated property: has_exact_synonym
annotated target: nluc
has_synonym_type: Unique short label curated by PSI-MI

nanoluc-n
type: Class
subclass of: nanoluc luciferase protein tag
definition: The n-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: pporras
creation date: 2019-04-11T14:14:54Z
has_exact_synonym: N-terminal fragment of nanoluc luciferase
has_exact_synonym: nluc-n
has_obo_namespace: PSI-MI
id: MI:2326
in_subset: PSI-MI slim

Axiom
annotated source: nanoluc-n
annotated property: has_exact_synonym
annotated target: N-terminal fragment of nanoluc luciferase
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: nanoluc-n
annotated property: has_exact_synonym
annotated target: nluc-n
has_synonym_type: Unique short label curated by PSI-MI

nanoluc-c
type: Class
subclass of: nanoluc luciferase protein tag
definition: The c-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
created by: pporras
creation date: 2019-04-11T14:16:59Z
has_exact_synonym: C-terminal fragment of nanoluc luciferase
has_exact_synonym: nluc-c
has_obo_namespace: PSI-MI
id: MI:2327
in_subset: PSI-MI slim

Axiom
annotated source: nanoluc-c
annotated property: has_exact_synonym
annotated target: C-terminal fragment of nanoluc luciferase
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: nanoluc-c
annotated property: has_exact_synonym
annotated target: nluc-c
has_synonym_type: Unique short label curated by PSI-MI

snap tag
type: Class
subclass of: tag
definition: The SNAP-tag protein is an engineered version of the ubiquitous mammalian enzyme AGT, encoded in humans by the O-6-methylguanine-DNA methyltransferase (MGMT) gene. The tag is a 182 residues polypeptide with self-labeling activity that accepts O6-benzylguanine derivatives.
created by: pporras
creation date: 2019-04-23T10:19:29Z
has_exact_synonym: SNAP tag
has_exact_synonym: snap tag
has_obo_namespace: PSI-MI
id: MI:2328
in_subset: PSI-MI slim

Axiom
annotated source: snap tag
annotated property: definition
annotated target: The SNAP-tag protein is an engineered version of the ubiquitous mammalian enzyme AGT, encoded in humans by the O-6-methylguanine-DNA methyltransferase (MGMT) gene. The tag is a 182 residues polypeptide with self-labeling activity that accepts O6-benzylguanine derivatives.
database_cross_reference: PMID:12725859

Axiom
annotated source: snap tag
annotated property: has_exact_synonym
annotated target: SNAP tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: snap tag
annotated property: has_exact_synonym
annotated target: snap tag
has_synonym_type: Unique short label curated by PSI-MI

hydrophobic interaction chromatography
type: Class
subclass of: chromatography technology
definition: Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by utilizing a reversible interaction between these proteins and the hydrophobic surface of a HIC matrix.
created by: pporras
creation date: 2019-04-23T13:40:51Z
has_exact_synonym: HIC
has_exact_synonym: hic
has_obo_namespace: PSI-MI
id: MI:2329
in_subset: PSI-MI slim

Axiom
annotated source: hydrophobic interaction chromatography
annotated property: definition
annotated target: Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by utilizing a reversible interaction between these proteins and the hydrophobic surface of a HIC matrix.
database_cross_reference: PMID:27730562

Axiom
annotated source: hydrophobic interaction chromatography
annotated property: has_exact_synonym
annotated target: HIC
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: hydrophobic interaction chromatography
annotated property: has_exact_synonym
annotated target: hic
has_synonym_type: Unique short label curated by PSI-MI

sumo tag
type: Class
subclass of: fusion protein
definition: Covalent attachment of the small ubiquitin-like modifier (SUMO) protein as a fusion protein.
created by: pporras
creation date: 2019-07-11T15:50:31Z
has_exact_synonym: SUMO tag
has_exact_synonym: sumo tag
has_obo_namespace: PSI-MI
id: MI:2330
in_subset: PSI-MI slim

Axiom
annotated source: sumo tag
annotated property: definition
annotated target: Covalent attachment of the small ubiquitin-like modifier (SUMO) protein as a fusion protein.
database_cross_reference: PMID:19107426

Axiom
annotated source: sumo tag
annotated property: has_exact_synonym
annotated target: SUMO tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: sumo tag
annotated property: has_exact_synonym
annotated target: sumo tag
has_synonym_type: Unique short label curated by PSI-MI

phage library
type: Class
subclass of: sample process
definition: A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion.
created by: pporras
creation date: 2019-07-11T15:54:51Z
has_obo_namespace: PSI-MI
id: MI:2331
in_subset: PSI-MI slim

Axiom
annotated source: phage library
annotated property: definition
annotated target: A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion.
database_cross_reference: PMID:9661810

g1 spin label
type: Class
subclass of: spin label
definition: Paramagnetic molecule formed by a gadolinium complex based on 4-mercaptomethyl-dipicolinic acid (4MMDPA) attached to a cysteine side chain.
created by: pporras
creation date: 2019-07-11T16:04:14Z
has_exact_synonym: Gd3+-4MMDPA tag
has_exact_synonym: g1 spin label
has_exact_synonym: g1-spin label
has_obo_namespace: PSI-MI
id: MI:2332

Axiom
annotated source: g1 spin label
annotated property: definition
annotated target: Paramagnetic molecule formed by a gadolinium complex based on 4-mercaptomethyl-dipicolinic acid (4MMDPA) attached to a cysteine side chain.
database_cross_reference: PMID:25438671

Axiom
annotated source: g1 spin label
annotated property: has_exact_synonym
annotated target: Gd3+-4MMDPA tag
has_synonym_type: Alternate label curated by PSI-MI

Axiom
annotated source: g1 spin label
annotated property: has_exact_synonym
annotated target: g1 spin label
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: g1 spin label
annotated property: has_exact_synonym
annotated target: g1-spin label
has_synonym_type: Alternate label curated by PSI-MI

mutation with complex effect
type: Class
subclass of: mutation
definition: A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that has a complex effect over the interaction when compared with the wild-type. A complex effect is such that cannot be described in increasing, decreasing, causing, disrupting or no effect terms.
created by: pporras
creation date: 2019-07-11T16:17:45Z
has_obo_namespace: PSI-MI
id: MI:2333
in_subset: PSI-MI slim

luminescence donor
type: Class
subclass of: experimental role
definition: Fluorophore or luminiscence source which emits electromagnetic radiation of given wavelength.
created by: pporras
creation date: 2019-07-11T16:26:29Z
has_obo_namespace: PSI-MI
id: MI:2334
in_subset: PSI-MI slim

Axiom
annotated source: luminescence donor
annotated property: definition
annotated target: Fluorophore or luminiscence source which emits electromagnetic radiation of given wavelength.
database_cross_reference: PMID:14755292

luminescence acceptor
type: Class
subclass of: experimental role
definition: Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor, then re-emit its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore it self.
created by: pporras
creation date: 2019-07-11T16:26:47Z
has_exact_synonym: luminescence accept
has_obo_namespace: PSI-MI
id: MI:2335
in_subset: PSI-MI slim

Axiom
annotated source: luminescence acceptor
annotated property: definition
annotated target: Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor, then re-emit its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore it self.
database_cross_reference: PMID:14755292

Axiom
annotated source: luminescence acceptor
annotated property: has_exact_synonym
annotated target: luminescence accept
has_synonym_type: Unique short label curated by PSI-MI

luminescence acceptor donor pair
type: Class
subclass of: experimental role
definition: Pair of luminescence donor-fluorophore or fluorophores attached to the same molecule used in a bret or fret experiment to observe the details of conformational changes.
created by: pporras
creation date: 2019-07-11T16:27:09Z
has_exact_synonym: luminescence acceptor-donor pair
has_obo_namespace: PSI-MI
id: MI:2336

Axiom
annotated source: luminescence acceptor donor pair
annotated property: definition
annotated target: Pair of luminescence donor-fluorophore or fluorophores attached to the same molecule used in a bret or fret experiment to observe the details of conformational changes.
database_cross_reference: PMID:14755292

Axiom
annotated source: luminescence acceptor donor pair
annotated property: has_exact_synonym
annotated target: luminescence acceptor-donor pair
has_synonym_type: Alternate label curated by PSI-MI

chemiluminiscence donor
type: Class
subclass of: luminescence donor
definition: Luminiscence source which emits electromagnetic radiation of given wavelength through a chemical process.
created by: pporras
creation date: 2019-07-11T16:37:54Z
has_obo_namespace: PSI-MI
id: MI:2337
in_subset: PSI-MI slim

Axiom
annotated source: chemiluminiscence donor
annotated property: definition
annotated target: Luminiscence source which emits electromagnetic radiation of given wavelength through a chemical process.
database_cross_reference: PMID:14755292

electron tomography
type: Class
subclass of: 3D electron microscopy
definition: Three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images from a tilt series recorded with a transmission electron microscope.
created by: pporras
creation date: 2019-07-17T13:23:36Z
has_exact_synonym: 3D-EM-tomo
has_obo_namespace: PSI-MI
id: MI:2338
in_subset: PSI-MI slim

Axiom
annotated source: electron tomography
annotated property: definition
annotated target: Three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images from a tilt series recorded with a transmission electron microscope.
database_cross_reference: PMID:12160704

Axiom
annotated source: electron tomography
annotated property: has_exact_synonym
annotated target: 3D-EM-tomo
has_synonym_type: Unique short label curated by PSI-MI

electron microscopy 3D single particle reconstruction
type: Class
subclass of: 3D electron microscopy
definition: Three-dimensional (3D) reconstruction of single, transparent objects from a collection of images of randomly oriented particles recorded with a transmission electron microscope.
created by: pporras
creation date: 2019-07-22T13:39:03Z
has_exact_synonym: 3D-EM-single
has_obo_namespace: PSI-MI
id: MI:2339
in_subset: PSI-MI slim

Axiom
annotated source: electron microscopy 3D single particle reconstruction
annotated property: definition
annotated target: Three-dimensional (3D) reconstruction of single, transparent objects from a collection of images of randomly oriented particles recorded with a transmission electron microscope.
database_cross_reference: PMID:12160704

Axiom
annotated source: electron microscopy 3D single particle reconstruction
annotated property: has_exact_synonym
annotated target: 3D-EM-single
has_synonym_type: Unique short label curated by PSI-MI

electron microscopy 3D helical reconstruction
type: Class
subclass of: 3D electron microscopy
definition: Three-dimensional (3D) reconstruction of helical objects from a collection of fiber images recorded with a transmission electron microscope.
created by: pporras
creation date: 2019-07-22T13:40:56Z
has_exact_synonym: 3D-EM-helical
has_obo_namespace: PSI-MI
id: MI:2340
in_subset: PSI-MI slim

Axiom
annotated source: electron microscopy 3D helical reconstruction
annotated property: definition
annotated target: Three-dimensional (3D) reconstruction of helical objects from a collection of fiber images recorded with a transmission electron microscope.
database_cross_reference: PMID:12160704

Axiom
annotated source: electron microscopy 3D helical reconstruction
annotated property: has_exact_synonym
annotated target: 3D-EM-helical
has_synonym_type: Unique short label curated by PSI-MI

luminescence transmitter
type: Class
subclass of: experimental role
definition: Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor and then act as a donor via re-emission of its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore itself.
created by: pporras
creation date: 2019-07-22T13:51:08Z
has_obo_namespace: PSI-MI
id: MI:2341
in_subset: PSI-MI slim

Axiom
annotated source: luminescence transmitter
annotated property: definition
annotated target: Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor and then act as a donor via re-emission of its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore itself.
database_cross_reference: PMID:14755292

partial identity match
type: Class
subclass of: cross-reference type
definition: Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical.
created by: pporras
creation date: 2019-07-30T15:05:43Z
has_exact_synonym: partial match
has_exact_synonym: similar object in an external resource
has_obo_namespace: PSI-MI
id: MI:2342
in_subset: PSI-MI slim

Axiom
annotated source: partial identity match
annotated property: definition
annotated target: Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical.
database_cross_reference: PMID:14755292

Axiom
annotated source: partial identity match
annotated property: has_exact_synonym
annotated target: partial match
has_synonym_type: Unique short label curated by PSI-MI

Axiom
annotated source: partial identity match
annotated property: has_exact_synonym
annotated target: similar object in an external resource
has_synonym_type: Alternate label curated by PSI-MI

genomic coordinates
type: Class
subclass of: participant attribute name
subclass of: feature attribute name
definition: Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies.
created by: pporras
creation date: 2019-07-30T16:06:16Z
has_exact_synonym: genomic coord
has_obo_namespace: PSI-MI
id: MI:2343
in_subset: PSI-MI slim

Axiom
annotated source: genomic coordinates
annotated property: definition
annotated target: Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies.
database_cross_reference: PMID:14755292

Axiom
annotated source: genomic coordinates
annotated property: has_exact_synonym
annotated target: genomic coord
has_synonym_type: Unique short label curated by PSI-MI

rhea
type: Class
subclass of: interaction database
definition: Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. Rhea uses the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to precisely describe reactions participants and their chemical structures. All reactions are balanced for mass and charge and are linked to source literature, metabolic resources and other functional vocabularies such as the enzyme classification of the NC-IUBMB.
created by: pporras
creation date: 2019-10-28T17:31:37Z
database_cross_reference: search-url:
has_exact_synonym: Rhea
has_obo_namespace: PSI-MI
id: MI:2344