The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means.
ECO (https://github.com/evidenceontology/evidenceontology) is released into the public domain under CC0 1.0 Universal (CC0 1.0). Anyone is free to copy, modify, or distribute the work, even for commercial purposes, without asking permission. Please see the Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/) for an easy-to-read description of CC0 1.0 or the full legal code (https://creativecommons.org/publicdomain/zero/1.0/legalcode) for more detailed information. To get a sense of why ECO is CC0 as opposed to licensed under CC-BY, please read this thoughtful discussion (https://github.com/OBOFoundry/OBOFoundry.github.io/issues/285) on the OBO Foundry GitHub site.
A mapping of an evidence term to a Gene Ontology evidence code.
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
The 'term requester' can credit the person, organization or project who request the ontology term.,The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition.
GO biological process terms should be used in the GO with/from field
GO cellular component terms should be used in the GO with/from field
Chemical entity IDs should be used in the GO with/from field
Gene IDs should be used in the GO with/from field
GO molecular function terms should be used in the GO with/from field
Protein IDs should be used in the GO with/from field
Protein complex IDs should be used in the GO with/from field
Transcript IDs should be used in the GO with/from field
a core relation that holds between a part and its whole
part of
a core relation that holds between a whole and its part
has part
realized in
realizes
preceded by
precedes
A relation connecting an evidence type to an assertion method where the assertion method describes the type of process employed to evaluate the evidence.
In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI.
A relation that is an inverse of "used_in" relation.
has measurement unit label
A (currently) primitive relation that relates an information artifact to an entity.
is about
m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q
is quality measurement of
inverse of the relation of is quality measurement of
is quality measured as
The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
The inverse property of is_specified_input_of
has_specified_input
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
is_specified_input_of
The inverse property of is_specified_output_of
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
is_specified_output_of
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
A relation between an information content entity and a value specification that specifies its value.
is a relationship between a process and a preceding occurrent that directly caused the later one to occur
A relationship between two material entities that form a complex based on a selective, non-covalent interaction.
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
inheres in
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
bearer of
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
a relation between a process and a continuant, in which the continuant is somehow involved in the process
has participant
A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
is concretized as
A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
concretizes
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
function of
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
quality of
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
role of
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
has function
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
has quality
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
has role
a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives from
a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
derives into
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
location of
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
located in
immediately preceded by
immediately precedes
temporal relation
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
has measurement value
A relation between a value specification and a number that quantifies it.
A relation between a value specification and a literal.
has specified value
entity
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
independent continuant
spatial region
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
disposition
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
realizable entity
quality
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
specifically dependent continuant
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
site
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
generically dependent continuant
function
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
continuant fiat boundary
immaterial entity
An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways.
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia.
A chemical entity constituting the smallest component of an element having the chemical properties of the element.
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.
A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis.
Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores.
Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image.
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
cell
A cell in vitro that is or has been maintained or propagated as part of a cell culture.
A lymphocyte of B lineage that is capable of B cell mediated immunity.
A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.
The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
neuron
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
A leukocyte with a single non-segmented nucleus in the mature form.
A cell that is part of the nervous system.
A complex of two or more molecular entities that are not covalently bound.
A type of information that is used to support an assertion.
A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator.
inference from background scientific knowledge
A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature.
A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state.
A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient.
If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology.
A type of protein assay evidence where the catalytic activity of an enzyme is determined.
A type of evidence that is the output of a scientific procedure performed to make a discovery, test a hypothesis, or demonstrate a known fact.
A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell.
The 10 previously identified GlnR-regulated genes were all confirmed to be under GlnR control during nitrogen stress (i.e. differential expression in the wild type compared to the DeltaglnR mutant), but in addition a total of 392 genes were significantly up-regulated and 291 significantly down regulated (Additional file 1: Table S1). This indicates that GlnR mediates (directly or indirectly) the expression of over 680 genes.
A type of experimental evidence that is based on characterization of gene expression.
Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process.
A type of expression pattern evidence where abundance of a transcript is analyzed.
In the BL21(DE3)(pJS429) cells, the levels of ClpP2s and VapC10 remained unchanged over a 2-hour period of translation arrest, but the VapB10 level showed to be decreased with a half-life (Figure 7C) similar to that observed in the strain BL21(DE3)(pJS883) (Figure 7B). These indicate that ClpXP2s could degrade VapB10 regardless of the presence or absence of VapC10.
A type of expression pattern evidence resulting from protein abundance quantification techniques.
A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products.
In addition, complementation of the ompR mutation in strain AR6 with plasmid pBR3 resulted in an increase in beta-galactosidase activity (1303 +- 80 Miller units), indicating that the His-tagged OmpR protein, expressed from the gene introduced in trans, was able to positively regulate flhDC expression.
Trans-complementation of fimR on pDL276 (pHR6) in strain DeltafimR harboring pfim(445 b)-cat restored wild-type pfim expression (Figure S1). Taken together, pfim is negatively regulated by FimR.
A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
Indeed, the GroEL protein appears to be more abundant in the LM3 wild type strain compared to the LM3-2 mutant strain, suggesting the involvement of the CcpA protein in the positive regulation of its expression.
A type of experimental phenotypic evidence in which an observable phenotypic difference results from a change or mutation in DNA.
Note that mutations need not be negative. Changes to DNA sequence (mutations) may be detrimental, have no impact, or be beneficial.
The allele that encodes the phenotype most common in a particular natural population is referred to as the wild type allele, while any other form of that allele is known as the mutant form.
A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene.
loss-of-function mutant phenotype evidence
A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest.
analysis of overexpression/ectopic expression phenotype
A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background.
A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed.
A type of direct assay evidence based on the inhibition of the molecular function of a protein.
A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule.
Molecules interacted with might include protein, nucleic acid, ion, or complex.
A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex.
A type of physical interaction evidence that depends on the strength of the interaction between two entities.
A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex.
A type of protein binding evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a 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.
OBSOLETE. A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences.
This term has been made obsolete with the clean up of experimental genomic evidence branch.
obsolete nucleic acid hybridization evidence
The secondary structure of VapC10 (Figure S2), predicted with the 3DJIGSAW prediction tool [36] and the DALI server [37], exhibited homology with several well studied VapC toxins, such as the first PIN domain structure for the protein PAE2754 from the archae bacterium Pyrobaculum aerophilum (30).
A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes.
For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field.
A CRP box-like sequence was found in the promoter-proximate region of sycO-ypkA-yopJ [4], indicating the direct association of CRP with the sycO-ypkA-yopJ promoter region.
To identify further CopR target genes, the binding motif TGAAGATTTnnTGAAGATTT was used to search for similar sequences in the whole C. glutamicum genome using the ERGO (TM) bioinformatics suite (Integrated Genomics, Illinois, USA) allowing four mutations, no deletions and no insertions. 46 hits were found, but only in six cases the putative CopR binding site was located in intergenic regions up to 200 bp upstream of the start codon of the neighbouring gene (cg1336, cg2976, cg3187, cg3337, cg3357 and cg0414).
A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence.
A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database.
match to InterPro member signature evidence
A type of BLAST evidence that is used in a manual assertion.
A type of protein BLAST evidence that is used in a manual assertion.
protein BLAST evidence used in manual assertion
BLAST search criteria for ISS assignment in PAMGO_GAT
A type of nucleotide BLAST evidence that is used in a manual assertion.
nucleotide BLAST evidence used in manual assertion
A type of author statement in which the author makes a statement that is not supported by information in that particular publication, but rather can be traced to a reference cited by that publication.
author statement supported by traceable reference
A type of author statement that is not associated with results presented or a cited reference.
author statement without traceable support
A type of curator inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources.
An assertion of "no evidence data found" carries the assumption that a more-or-less exhaustive search has been conducted.
The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
A type of functional complementation evidence resulting from the introduction of nucleic acids, which are not permanently incorporated into the genome, to temporarily prevent, or "rescue" an organism from a condition.
OBSOLETE. A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins.
A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
A type of evidence resulting from comparing likeness of distinct biological entities.
A type of mutant phenotype evidence resulting from an altered gene product which possesses a new molecular function or a new pattern of gene expression.
gain-of-function mutant phenotype evidence
gain-of-function mutant phenotypic evidence
A type of similarity based on biomolecular sequence.
A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes.
A type of protein expression evidence that accounts for the position of RNA translation to a protein product ranging in scale from differing tissues to regions of an anatomical structure.
spatial pattern of protein expression evidence
A type of transcript expression evidence that accounts for the position of transcription ranging in scale from the position of genes on the chromosome to differing tissues to regions of an anatomical structure.
spatial pattern of transcript expression evidence
A type of expression pattern evidence that is based on the expression pattern of a reporter gene.
A type of experimental phenotypic evidence based on an authors phenotypic description of a species (or higher-level group), which explicitly references an observation made of a voucher specimen (a specimen with a permanent museum catalog).
voucher specimen phenotypic analysis evidence
A type of similarity based on genotype without respect to expression.
A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology.
A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation.
suppressor/enhancer interaction evidence
'traditional' genetic interactions (e.g. suppressors, synthetic lethals)
suppressor/enhancer interaction phenotypic evidence
A type of automatically integrated combinatorial evidence that is used in an automatic assertion.
Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments.
automatically integrated combinatorial evidence used in automatic assertion
In the hns slyA double mutant, hlyE expression was twofold greater than in the parent, and slightly higher than the hns single mutant, suggesting that slyA has a small negative effect on hlyE expressionin the absence of H-NS.
A type of mutant phenotype evidence resulting from an experiment typically constructed to determine if two different genes have an observable genetic interaction (functional connection) as the result of a mutation occurring in the alleles of the two genes of interest.
This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000097, ECO:0000062, ECO:0000104, etc.)
A type of genetic interaction evidence resulting from the suppression of one allelic effect by an allele at another genetic locus.
Epistasis' can be used in different contexts in different areas of genetics. It is sometimes used to mean 'genetic interaction', whereas other times it may be specific to mutations that block the effects of other mutations.
epistatic interaction phenotypic evidence
A type of similarity based on the expression of a genotype in an environment.
Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms.
S. lividans AdpA directly regulates at least the six AdpA-dependent genes listed above and identified by microarrays and qRT-PCR analysis.
To identify the regulon of the response regulator CopR, the transcriptome of the DeltacopRS deletion mutant was compared to that of the wild type using DNA microarrays. For cells grown in standard CGXII medium (1.25 microM CuSO4), no significant gene expression differences were observed, indicating that the CopRS two-component system is not active under this condition (data not shown).
A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks.
differential gene expression evidence from microarray experiment
A type of experimental evidence that is based on an observable characteristic trait, which is the result of the expression of an organisms genotype in an environment.
Observable characteristic traits can be morphology, development, behavior, biochemical or physiological properties, etc.
A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements.
A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned.
A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface.
cRNA to DNA expression microarray evidence
A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures.
A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
functional complementation in heterologous system
functional complementation in heterologous system evidence
A type of bait-prey hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED).
A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures.
A type of bait-prey hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain.
A type of in vitro methylation assay evidence where methylation-sensitive restriction enzymes are utilized to compare differential methylation between two samples by first shearing DNA, followed by end-blunting, ligation of linkers, methylation sensitive restriction, PCR using linker primers, dye labeling and relative quantification of methylated DNA fragments by two-colored array hybridization to a CpG island microarray for visual assessment.
Color is indicative of methylation status - be it hypo- (pseudo-green), hyper- (pseudo-red), or equal methylation (pseudo-yellow).
differential methylation hybridization evidence
A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification.
If performing GO annotation, the interacting protein is referenced in the evidence_with column.
A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures.
OBSOLETE. A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product.
A type of protein fragment functional complementation evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquitin (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough to reconstitute.TAIR:TED
split-ubiquitin functional complementation evidence
A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles.
A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
The interacting protein is referenced in the evidence_with column.
A type of in vitro methylation assay evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
The product is the amplification of existing sequences - i.e. more DNA that can be further processed e.g. sequenced, DNA fingerprinting.
methylation-specific polymerase chain reaction evidence
A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity.
The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane.
A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bound compound.
"Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand.
Comparative phylogenomics along with MLST (multilocus sequence typing) and whole genome sequecing has shown that ribotype 078 lineage is different than other C. difficile lineages [22].
A type of similarity that indicates common ancestry.
A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
OBSOLETE. A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand.
This term has been made obsolete because PCR is not evidence. The children have been appropriately placed under other parents.
obsolete polymerase chain reaction evidence
A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence.
transmembrane domain prediction evidence
A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes.
Genomic cluster analyses include synteny and operon structure.
A type of protein binding evidence where an antibody specific for a target protein is used to precipitate the target protein along with any other molecules (e.g. protein, nucleic acid) that are bound to the target protein.
Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding.
A type of in vitro methylation assay evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers, followed by restrained PCR amplification of sequences methylated at both ends and resolving the PCR products in a denaturing polyacrylamide-sequencing gel to generate fingerprints that consist of multiple anonymous bands that represent the DNA methylome of the cell.
The bands can be individually isolated and characterized which leads to the identification of hypo- and hypermethylation events.
amplification of intermethylated sites evidence
A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues.
A type of curator inference that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system.
The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak.
biological system reconstruction evidence
A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks.
restriction landmark genome scanning evidence
restriction landmark genomic scanning evidence
A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy.
A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies.
immunolocalization of epitope-tagged protein
epitope-tagged protein immunolocalization evidence
A type of DNA detection assay evidence evidence where gene sequence or variation is determined or detected by fluorescently-labeled DNA fragments hybridized to sequence-specific oligonucleotides immobilized on an array.
single nucleotide polymorphism array evidence
The children of 'biological assay evidence' have been moved under 'direct assay evidence', and this term has been deprecated with no children left.
A type of cell growth assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect.
Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter.
Each of the promoter-proximal regions of qrr2 - 4 was subjected to EMSA with the purified His-OpaR protein (Fig. 6b). The results showed that His-OpaR was able to bind to each of the three DNA fragments tested in a dose-dependent manner in vitro.
A type of affinity evidence based on an electrophoretic mobility shift of macromolecules, where proteins, nucleic acids, or both, are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect interactions/complexes between proteins and/or nucleic acid.
EMSA: electrophoretic mobility shift assay
EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid.
electrophoretic mobility shift assay evidence
A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface.
cDNA to DNA expression microarray evidence
OBSOLETE. A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached.
A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions.
A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information.
A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules.
A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface.
microarray RNA expression level evidence
transcript levels (e.g. microarray data)
REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that.
DNA to cDNA expression microarray evidence
A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels.
Northern blot analysis indicated that there was one major band of 1.5-kb (which was used for the stability determination) and two other minor bands of approximately 3.0- and 6.0-kb, which constituted less than 5% of the total signal (Fig. 1C), suggesting that other genes may be cotranscribed along with SMU.1882.
A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples.
Taken together, the results of the RT-PCR analyses and the reporter fusion assays indicate that expression of SMU.1882 is up regulated in the presence of CovR.
The RT-PCR assay indicated that the sycO, ypkA and yopJ genes (designated as pCD12, pCD13 and pCD14 in Y. pestis 91001 [19], respectively) were transcribed as a single primary RNA (Fig. 1), and thereby these three genes constituted a single operon in Y. pestis Microtus strain 201.
Using reverse transcription-PCR, we found that primers designed to span the intergenic regions between zur and the znuC homolog, as well as znuC and znuB homolog each generated a PCR product (Figure 2A). This indicated that these genes were transcribed on the same mRNA.
A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression.
reverse transcription polymerase chain reaction transcription evidence
The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate.
reverse transcription polymerase chain reaction evidence
fur RPAs were performed on RNA isolated from each strain, and an increase in fur expression was seen for G27, 26695, and the Fur swap strain under iron-depletion shock conditions while little to no increase was seen under iron-limited growth conditions (Fig. 4D and data not shown). This data shows that Fur autoregulation is consistent in each strain and further supports the notion that the AA difference in Fur is not responsible for the difference in sodB regulation between G27 and 26695.
A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography.
When we determined the proteolysis role of Lons in VapBC10 proteins by Western blot analysis using the strains BL21(DE3)(pJS882) and BL21(DE3)(pJS427), the levels of VapB10 and VapC10 remained stable over the course of translation inhibition (Figure 7D and E). Thus, Lon could not degrade VapBC10 proteins, consistent with our drop growth evidence (Figure 6B).
A type of protein expression evidence where proteins are separated using gel electrophoresis, blotted onto a membrane, and probed with an antibody that can be detected via light or radioactive emission.
protein expression level evidence based on western blot
Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies.
qualitative western immunoblotting evidence
A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein.
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns.
Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition.
A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'.
Subtractive hybridization is used for isolation and identification of transcripts involving the removal of any sequences present in the control from the test probe to detect only transcripts present in the sample. The method is PCR-based for the comparison of two cDNA libraries.
In contrast, when RpoQ was overexpressed in either the wild type or the DeltalitR mutant, both were essentially nonmotile (Fig. 7), suggesting that quorum signaling regulates motility, at least in part, through an RpoQ mechanism downstream of LitR.
A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
A type of localization evidence where sub-cellular localization of a protein is determined.
A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties.
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria.
GFP fusion protein localization evidence
green fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria.
YFP fusion protein localization evidence
yellow fluorescent protein fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product.
GUS fusion protein localization evidence
beta-glucuronidase fusion protein localization evidence
A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein.
LacZ fusion protein localization evidence
beta-galactosidase fusion protein localization evidence
A type of direct assay evidence resulting from the activity assessment of transport proteins.
A type of affinity evidence resulting from the binding of a molecule to a nucleic acid.
A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer.
A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate.
A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site.
A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
As shown in Fig. 5, addition of reconstituted RNA polymerase holoenzyme, but not the core enzyme, generated expected size bands of 193-nt and 158-nt when P1882 and Pami, respectively, were used as template (lanes 2 and 7). However, the addition of CovR did not lead to any observable increase in transcription from P1882.
A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis.
in vitro reconstitution assay with recombinant protein
in vitro transcription reconstitution assay evidence
A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system.
in vitro recombinant protein transcription reconstitution assay evidence
A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed.
protein expression in heterologous system
heterologous protein expression evidence
A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture.
A type of protein separation evidence that is followed by direct protein sequencing whereby a protein's amino acid sequence is determined experimentally by Edman degradation or by mass spectrometry.
protein separation and direct sequencing
protein separation followed by direct sequencing evidence
A type of protein separation evidence which then utilizes the screening and identification of small-molecules that bind to proteins.
protein separation and fragment identification
protein separation followed by fragment identification evidence
A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein.
The transporter is a recombinant protein.
A type of direct assay evidence where electrical properties of cells or tissues are studied.
The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart.
A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current.
two-electrode voltage clamp recording evidence
A type of direct assay evidence resulting from the detection and quantification of transcribed RNA.
A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed.
transcriptional activation assay evidence
A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed.
For example, the accumulation of a biosynthetic intermediate.
A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined.
Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions.
A type of mutant phenotype evidence in which traits arising from a mutation are visually examined.
A type of similarity evidence in which the location of the gene within the genome provides insight into the gene's function or evolutionary insight.
This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis.
A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium.
A type of experimental evidence arising from the investigation of an animal model system.
A type of experimental evidence arising from a controlled investigation that uses human subjects.
A type of direct assay evidence resulting from a process performed outside the living organism, where the components of an organism have been isolated from their usual biological context, to permit a more detailed or more convenient analysis in an artificial setting.
Use ECO:0001563 (cell growth assay evidence) in place of this term.
obsolete in vitro culture assay evidence
A type of direct assay evidence resulting from studies in which cytoplasmic and/or nuclear cellular components from resting, nonstimulated cells, are isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components for the purpose of in vitro protein synthesis, transcription, DNA replication, etc.
A type of protein inhibition evidence and enzymatic acitivty evidence where the protein under study is an enzyme.
A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment
Such alignments may be pairwise alignments or multiple alignments.
A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors.
Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor.
A putative rho-independent terminator sequence (GCCTGACTACATAGATGTCAGGC) was identified at position 402-bp downstream of SMU.1882 by TransTerm (transterm.dev.java.net) program.
A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model.
Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN.
An assertion method that does not involve human review.
An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically.
A type of documented statement evidence that is based on an assertion by the author of a paper, which is read by a curator.
A type of inferential evidence that is based on a conclusion drawn by a curator.
A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST).
A type of BLAST evidence in which nucleotide sequences are aligned.
Blast search of S. meliloti genome for homologues of X. campestris Ohr protein revealed two paralogues, SMa2389 and SMc00040, showing 52 and 57% identity respectively with Ohr of X. campestris.
A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned.
A type of BLAST evidence that is used in an automatic assertion.
BLAST evidence used in automatic assertion
A type of nucleotide BLAST evidence that is used in an automatic assertion.
nucleotide BLAST evidence used in automatic assertion
A type of protein BLAST evidence that is used in an automatic assertion.
protein BLAST evidence used in automatic assertion
A type of evidence in which at least two distinct types of evidence have been integrated.
A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence.
A type of combinatorial analysis that is used in an automatic assertion.
combinatorial evidence used in automatic assertion
A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene.
This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones.
biological aspect of descendant evidence
A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event.
Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence.
rapid divergence from ancestral sequence evidence
A type of phylogenetic evidence characterized by the absence of key sequence residues.
The loss of certain residues important for function can indicate that a sequence lacks a particular function.
phylogenetic determination of loss of key residues evidence
A means by which a statement is made about an entity.
An assertion method that involves human review.
A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information.
A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides.
A type of experimental evidence where the order of molecules that constitute a biopolymer is determined.
A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique.
Typically thousands to millions of reads are produced in parallel.
high throughput nucleotide sequencing assay evidence
A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage.
In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging.
A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand.
454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA. The target strand is usually prepared by fragmentation, adaptor ligation, and amplification by emulsion PCR.
A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation.
SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag. Samples are prepared by fragmentation of a sample library, adaptor ligation, emulsion PCR, and attachment of resultant beads to glass slides.
A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged.
Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light. The ddNTPs lack an OH group so the next dNTP cannot be attached, causing chain termination.
A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence.
Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq).
A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection.
ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results.
chromatin immunoprecipitation-PCR evidence
To confirm the in vivo binding of FimR to pfim, and to determine the impact of Mn2+ and Fe2+ on the binding activity of FimR, chromatin immunoprecipitation (ChIP) assay-quantitative real time PCR (qPCR) with anti-FimR antibody was employed as detailed in the materials and methods. The strongest binding of FimR to pfim was detected in cells grown in the presence of 50 microM MnCl2 and 50 microM FeSO4 (Figure 5, lane IV), whereas minimal amounts of MnCl2 (0.01 microM) and FeSO4 (0.1 microM) led to the weakest binding (Figure 5, lane I).
A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection.
chromatin immunoprecipitation-qPCR evidence
A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins.
ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used.
chromatin immunoprecipitation-seq evidence
A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions.
A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp.
chromatin immunoprecipitation-chip evidence
A type of DNA detection assay evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes or fluorescent probes for detection and quantification of specific sequences in a DNA sample.
real time polymerase chain reaction evidence
Quantitative PCR enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample. The dye is activated upon binding double-stranded DNA. Although qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173). qPCR can be used to quantitatively determine levels of gene expression.
quantitative polymerase chain reaction evidence
A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, DNA processing, and quantitation that serves to analyze the spatial organization of chromatin in a cell and quantify the number of interactions between genomic loci that are nearby in 3-D space.
chromosome conformation capture-based evidence
Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C.
A type of chromosome conformation-based evidence that is derived by 1) quantifying interactions between a single pair of genomic loci and not multiple interactions and 2) performing polymerase chain reaction (PCR) in the final product quantitation step.
chromosome conformation capture evidence
chromosome conformation capture-PCR evidence
3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation.
A type of chromosome conformation-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray.
circularized chromosome conformation capture evidence
4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation.
A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation.
carbon-copy chromosome conformation capture evidence
5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation.
OBSOLETE. A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step.
See 3C evidence. 3C evidence was initially developed using PCR.
obsolete chromosome conformation capture-PCR evidence
A type of 3C evidence evidence that 1) quantifies interactions between a single pair of genomic loci (not multiple interactions) and 2) performs quantitative polymerase chain reaction (qPCR) in the quantitation step.
chromosome conformation capture-qPCR evidence
A type of chromosome conformation-based evidence that is derived by performing immunoprecipitation enrichment of the biotin labelled ligated fragments events prior to sequencing of the library and mapping it to the genome.
Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step.
A type of chromosome conformation-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with multiplexed high-throughput (HT) sequencing.
chromosome conformation capture sequencing evidence
3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation.
A type of experimental phenotypic evidence resulting from the disruption of a structural feature.
anatomical perturbation phenotypic evidence
A type of experimental phenotypic evidence resulting from modification to the surroundings or conditions in which an organism lives or operates.
Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth.
environmental perturbation phenotypic evidence
A type of anatomical perturbation phenotypic evidence resulting from the surgical removal of tissue or subcellular components.
A type of anatomical perturbation phenotypic evidence resulting from the addition of tissue to an organism through a graft procedure.
A type of combinatorial analysis that is used in a manual assertion.
combinatorial evidence used in manual assertion
A type of automatically integrated combinatorial evidence that is used in a manual assertion.
inferred from reviewed computational analysis
computational combinatorial evidence used in manual assertion
automatically integrated combinatorial evidence used in manual assertion
OBSOLETE. A type of computational combinatorial analysis that is used in an automatic assertion.
obsolete computational combinatorial evidence used in automatic assertion
A type of sequence alignment evidence that is used in a manual assertion.
sequence alignment evidence used in manual assertion
A type of sequence alignment evidence that is used in an automatic assertion.
sequence alignment evidence used in automatic assertion
A type of sequence similarity evidence that is used in an automatic assertion.
sequence similarity evidence used in automatic assertion
Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
A type of sequence similarity evidence that is used in a manual assertion.
inferred from sequence or structural similarity
sequence similarity evidence used in manual assertion
A type of similarity evidence that is used in an automatic assertion.
similarity evidence used in automatic assertion
A type of similarity evidence that is used in a manual assertion.
similarity evidence used in manual assertion
A type of genetic similarity evidence that is used in a manual assertion.
genetic similarity evidence used in manual assertion
A type of genetic similarity evidence that is used in an automatic assertion.
genetic similarity evidence used in automatic assertion
A type of match to sequence model evidence that is used in a manual assertion.
match to sequence model evidence used in manual assertion
A type of match to sequence model evidence that is used in an automatic assertion.
match to sequence model evidence used in automatic assertion
Gene Ontology annotation through association of InterPro records with GO terms.
A type of motif similarity evidence that is used in a manual assertion.
motif similarity evidence used in manual assertion
A type of motif similarity evidence that is used in an automatic assertion.
motif similarity evidence used in automatic assertion
A type of match to InterPro member signature evidence that is used in an automatic assertion.
match to InterPro member signature evidence used in automatic assertion
A type of match to InterPro member signature evidence that is used in a manual assertion.
match to InterPro member signature evidence used in manual assertion
A type of targeting sequence prediction that is used in an automatic assertion.
targeting sequence prediction evidence used in automatic assertion
A type of targeting sequence prediction that is used in a manual assertion.
targeting sequence prediction evidence used in manual assertion
A type of transmembrane domain prediction that is used in an automatic assertion.
transmembrane domain prediction evidence used in automatic assertion
A type of transmembrane domain prediction that is used in a manual assertion.
transmembrane domain prediction evidence used in manual assertion
A type of sequence orthology evidence that is used in an automatic assertion.
sequence orthology evidence used in automatic assertion
Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
A type of sequence orthology evidence that is used in a manual assertion.
sequence orthology evidence used in manual assertion
A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate.
ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein.
enzyme-linked immunoabsorbent assay evidence
A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation.
A type of experimental evidence that is used in a manual assertion.
experimental evidence used in manual assertion
A type of expression pattern evidence that is used in a manual assertion.
expression pattern evidence used in manual assertion
This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000273, ECO:0000276, ECO:0000285, etc.)
obsolete array experiment evidence used in manual assertion
A type of Affymetrix GeneChip evidence that is used in a manual assertion.
Affymetrix GeneChip evidence used in manual assertion
A type of cDNA to DNA expression microarray evidence that is used in a manual assertion.
cDNA to DNA expression microarray evidence used in manual assertion
A type of differential methylation hybridization evidence that is used in a manual assertion.
CpG island microarray evidence used in manual assertion
differential methylation hybridization evidence used in manual assertion
A type of expression microarray evidence that is used in a manual assertion.
expression microarray evidence used in manual assertion
A type of cRNA to DNA expression microarray evidence that is used in a manual assertion.
genomic microarray evidence used in manual assertion
cRNA to DNA expression microarray evidence used in manual assertion
A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion.
Nimblegen array evidence used in manual assertion
A type of array-based sequence capture evidence that is used in a manual assertion.
oligonucleotide microarray evidence used in manual assertion
array-based sequence capture evidence used in manual assertion
A type of qualitative western immunoblotting evidence that is used in a manual assertion.
protein expression level evidence based on western blot used in manual assertion
qualitative western immunoblotting evidence used in manual assertion
A type of expression library screen evidence that is used in a manual assertion.
expression library screen evidence used in manual assertion
A type of heterologous protein expression analysis that is used in a manual assertion.
heterologous protein expression evidence used in manual assertion
A type of protein expression spatial pattern analysis that is used in a manual assertion.
spatial pattern of protein expression evidence used in manual assertion
A type of protein expression analysis that is used in a manual assertion.
protein expression level evidence used in manual assertion
protein expression evidence used in manual assertion
A type of DNA to cDNA expression microarray evidence that is used in a manual assertion.
DNA to cDNA expression microarray evidence used in manual assertion
A type of differential hybridization experiment that is used in a manual assertion.
differential hybridization evidence used in manual assertion
A type of RNA protection assay that is used in a manual assertion.
RNA protection assay evidence used in manual assertion
A type of spatial pattern of transcript expression analysis that is used in a manual assertion.
spatial pattern of transcript expression evidence used in manual assertion
A type of subtractive hybridization experiment that is used in a manual assertion.
subtractive hybridization evidence used in manual assertion
A type of transcript expression evidence that is used in a manual assertion.
transcriptomics evidence used in manual assertion
transcript expression evidence used in manual assertion
A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell.
Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method.
A total of 160 SELEX fragments were cloned and sequenced, which were classified into 29 CRP-binding sequences, including 13 previously identified loci and 16 newly identified sites (Table S2). When the CRP-binding sequences are located upstream or near promoters of the flanking genes, these genes are predicted to be under the control of CRP.
A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein.
systematic evolution of ligands by exponential amplification evidence
systematic evolution of ligands by exponential enrichment
Bacterial one-hybrid assays confirmed the interaction between MtrA and the regulatory sequence of the dnaA initiator gene.
A type of bait-prey hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes.
A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules.
differential gene expression evidence from RNA-seq experiment
Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked.
In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest.
A type of cleavage arrested development that arises after treatment with cytochalasin.
Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments.
A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker.
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript".
green fluorescent protein immunolocalization evidence
A type of immunolocalization evidence that was generated using LacZ protein as a marker.
LacZ protein immunolocalization evidence
This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript".
beta-galactosidase protein immunolocalization evidence
A type of author statement that is used in a manual assertion.
author inference used in manual assertion
author statement used in manual assertion
A type of author statement without traceable support that is used in a manual assertion.
author statement without traceable support used in manual assertion
A type of author statement supported by traceable reference that is used in a manual assertion.
author statement supported by traceable reference used in manual assertion
A type of curator inference that is used in a manual assertion.
curator inference used in manual assertion
A type of inference from background scientific knowledge that is used in a manual assertion.
inference from background scientific knowledge used in manual assertion
An inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources that is used in an manual assertion.
no evidence data found used in manual assertion
A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene.
First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations.
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system.
Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed.
cap analysis of gene expression evidence
A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching.
NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA.
nano-cap analysis of gene expression evidence
A type of documented statement evidence that is based on work performed by a person or group prior to a use by a different person or group.
A type of imported information that is used in a manual assertion.
imported information used in manual assertion
A type of imported information that is used in an automatic assertion.
imported information used in automatic assertion
A type of direct assay evidence that is used in a manual assertion.
direct assay evidence used in manual assertion
A type of mutant phenotype evidence that is used in a manual assertion.
mutant phenotype evidence used in manual assertion
A type of genetic interaction experiment evidence that is used in a manual assertion.
genetic interaction evidence used in manual assertion
A type of genomic context evidence that is used in a manual assertion.
genomic context evidence used in manual assertion
A type of biological aspect of ancestor evidence that is used in a manual assertion.
inferred from biological aspect of ancestor
biological aspect of ancestor evidence used in manual assertion
A type of biological aspect of descendant evidence that is used in a manual assertion.
inferred from biological aspect of descendant
biological aspect of descendant evidence used in manual assertion
A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion.
phylogenetic determination of loss of key residues evidence used in manual assertion
A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion.
rapid divergence from ancestral sequence evidence used in manual assertion
Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
imported manually asserted information used in automatic assertion
A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
imported automatically asserted information used in automatic assertion
In the images shown in Figure 9, the MelR focus is 15 x 33 nm across the shortest and longest axes of the oval in the complex with the shortened arm (right hand panel), compared to 9 x 12 nm in the other complex (centre panel). The simplest explanation for these observations, that is consistent with the location of sites in the DNA fragment (Figure 9), is that one type of complex contains 3 MelR molecules bound at sites 2, 1 and 1' (centre panel), whilst the other contains 4 MelR molecules bound at sites 2, 1, 1' and R (right panel).
A type of direct assay evidence in which an image is created and analyzed.
A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase.
A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript.
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features.
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child.
whole transcript splice pattern evidence
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript.
This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child.
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion.
whole transcript splice pattern evidence used in manual assertion
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion.
coding sequence splice pattern evidence used in manual assertion
A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion.
coding sequence splice pattern evidence used in automatic assertion
A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion.
whole transcript splice pattern evidence used in automatic assertion
A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility.
Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size.
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence
A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined.
An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system.
A type of direct assay evidence where the quantity of a substance used as part of an assay is measured.
Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme.
A type of cell proliferation assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed usually by means of a fluorescent marker and flow cytometric analysis.
We analyzed the electrophoretic pattern of cytosolic proteins extracted from LM3 and LM3-2 cells, grown under standard conditions up to mid-exponential phase (Fig. 1). The presence of differentially expressed proteins in the two strains, together with results of previous studies [28,29] demonstrated the role of CcpA as global regulator in L. plantarum.
A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field.
Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch.
A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous.
pulsed-field gel electrophoresis evidence
A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide.
The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape.
two-dimensional agarose gel electrophoresis evidence
A type of experimental evidence in which a plasmid that is capable of being replicated is introduced into cells, cells are grown without selection for several generations, and retention of the plasmid is determined.
minichromosome maintenance assay evidence
Loss per generation is determined by comparing colony numbers on selective and non-selective media.
A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody.
specific protein inhibition by antibody evidence
A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence.
Support of intron positions by RNA-seq alignment evidence
RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data.
support of intron positions by RNA-sequencing alignment evidence
A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript.
Full support of intron positions by RNA-seq alignment evidence
Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not.
full support of intron positions by RNA-sequencing alignment evidence
A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript.
Partial support of intron positions by RNA-seq alignment evidence
Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample.
partial support of intron positions by RNA-sequencing alignment evidence
A type of sequence alignment evidence resulting from the comparison of a single exon transcript to a collection / database of known single exon genes.
single exon transcript confirmation via alignment evidence
A type of support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
Support of intron positions by RNA-seq alignment evidence used in manual assertion
support of intron positions by RNA-sequencing alignment evidence used in manual assertion
A type of support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
Support of intron positions by RNA-seq alignment evidence used in automatic assertion
support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
A type of full support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
Full support of intron positions by RNA-seq alignment evidence used in automatic assertion
full support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
A type of full support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
Full support of intron positions by RNA-seq alignment evidence used in manual assertion
full support of intron positions by RNA-sequencing alignment evidence used in manual assertion
A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
Partial support of intron positions by RNA-seq alignment evidence used in automatic assertion
partial support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
A type of partial support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion.
Partial support of intron positions by RNA-seq alignment evidence used in manual assertion
partial support of intron positions by RNA-sequencing alignment evidence used in manual assertion
A type of evidence that is used in an manual assertion.
A type of physical interaction evidence that is used in a manual assertion.
physical interaction evidence used in manual assertion
A type of gene neighbors evidence that is used in a manual assertion.
gene neighbors evidence used in manual assertion
A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony.
Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID:7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci.
A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression.
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact)
A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression.
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact)
A type of experimental evidence resulting from the prediction of drug-target interactions by computational means.
biological target-disease association via drug evidence
A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means.
Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true.
A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is computationally derived.
evidence based on computational logical inference
A type of evidence based on computational logical inference that is used in automatic assertion.
evidence based on computational logical inference used in automatic assertion
computational inference used in automatic assertion
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion.
evidence based on logical inference from manual annotation used in automatic assertion
A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion.
evidence based on logical inference from automatic annotation used in automatic assertion
A type of evidence that is used in an automatic assertion.
Gene Ontology annotation based on Enzyme Commission mapping.
Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins.
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping.
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt.
Automatic Gene Ontology annotation based on Rhea mapping.
A type of cell proliferation assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation.
A type of cell-based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells.
[3H]arachidonic acid release assay evidence
A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids.
[3H]-thymidine incorporation assay evidence
A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells).
A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells.
A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells.
A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host.
A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where a cell permeable compound, resazurin (the active ingredient of alamarBlue), is reduced to fluorescent resorufin.
A type of anatomical perturbation phenotypic evidence resulting from the transplantation of an organ or tissue from one individual of the same species with a different genotype.
allograft transplantation experiment evidence
allograft transplantation phenotypic evidence
A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules.
A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic.
A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning.
A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies.
A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets.
A type of immunological assay evidence resulting from the inhibitory effect of polyclonal antibodies (antibodies secreted by different B cell lineages), which while not reacting with a specific antigen, serve to prevent other antibodies from doing so.
A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present.
A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes.
cell proliferation marker detection assay evidence
5-bromo-2'-deoxyuridine incorporation assay evidence
bromodeoxyuridine incorporation assay evidence
A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis.
A type of cell-based assay evidence resulting from the quantification of a sample of cells.
A type of cell-based assay evidence resulting from the quantification of cell permeability.
A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split.
carboxyfluorescein diacetate succinimidyl ester staining evidence
A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH.
chemiluminescence-linked immunoassay evidence
A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product.
A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions.
A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location.
A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish.
A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact.
A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration.
A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal.
A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation.
A type of mutant phenotypic evidence resulting from a mutation causing a change to a protein sequence that produces a constitutively active mutant protein (CAM), that remains active in the absence of upstream signals.
constitutively active mutant protein evidence
To confirm this intriguing observation, we cross-linked AdpA and DNA in the presence of increasing amounts of ATP (figure 2b(iii)). In this assay, ATP prevented the formation of AdpA - DNA complexes in a concentration-dependent manner, an outcome consistent with the results obtained by SPR analysis.
A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification
The crystal structures of E. coli MarR and Enterococcus faecalis SlyA-like proteins show their cross-sections are ~70 angstroms, suggesting they would protect ~20 bp of DNA (Alekshun et al., 2001; Wu et al., 2003). This suggests the presence of two SlyA dimers at the SlyA I site and at least three dimers at the SlyA II site.
A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern.
A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections.
A type of apoptotic assay evidence resulting from the identification of an accumulation of cytochrome C in the cytoplasm after its release from the mitochondria, an early event in apoptosis.
A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence.
4',6-diamidino-2-phenylindole staining evidence
In contrast, and in full agreement with the previous results of Wade et al. (17), the longer deletion in the TB23 fragment, that removes MelR binding site 2, results in a sharp reduction in the repression of the melR promoter by MelR.
A type of mutant phenotype evidence resulting from a mutation in which there is the removal of one or more contiguous nucleotides that may result in altered function or other measurable properties.
As a child of 'experimental phenotypic evidence', this is not to be confused with the biological processes deletion mutation / deletion deficiency in which DNA is lost during DNA replication.
Contrast with knockout phenotypic evidence in which any number of changes to the DNA result in elimination of the function of the gene in question.
The length of the DNA deleted can range from a single nucleotide to enough material that could include multiple genes.
A type of apoptotic assay evidence resulting from the visualization via gel electrophoresis of the fragmented DNA (DNA ladder) which is the result of apoptotic DNA fragmentation.
A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments.
A type of mutant phenotype evidence resulting from a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes.
dominant-negative mutant phenotypic evidence
A type of Edman degradation evidence that is used in a manual assertion.
Edman degradation evidence used in manual assertion
A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds.
A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters.
A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well.
A type of nucleic acid localization evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids.
fluorescence in situ hybridization evidence
A type of dynamic fluorescence quenching evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm.
fluorescence resonance energy transfer evidence
A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded.
A type of histology evidence resulting from the identification of chemical components in cells and tissues.
A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues.
No OD increases with the mutant and the wild type were measured with DMSO provided as electron acceptor at 2 and 10 mM; however, HPLC analyses of cultures with 2 mM DMSO revealed that DMSO was completely consumed in wild type cultures, whereas no DMSO consumption was evident in the mutant cultures (Figure 3).
A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure.
high-performance liquid chromatography evidence
A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins.
A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample.
A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections.
OBSOLETE. A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation.
This term was made obsolete for a couple of reasons: the def. doesn’t make sense as the suggested means of mutagenesis fail to introduce exogenous DNA (it is a child of genetic transformation evidence) and the def. is too much like random mutagenesis evidence.
A type of acetylation assay evidence used in an in vitro experiment.
A type of cleavage assay evidence used in an in vitro experiment.
A type of deubiquitination assay evidence used in an in vitro experiment.
in vitro deubiquitination assay evidence
A type of deacetylation assay evidence used in an in vitro experiment.
A type of defarnesylation assay evidence used in an in vitro experiment.
A type of demethylation assay evidence used in an in vitro experiment.
A type of desumoylation assay evidence used in an in vitro experiment.
A type of farnesylation assay evidence used in an in vitro experiment.
A type of methylation assay evidence used in an in vitro experiment.
A type of palmitoylation assay evidence used in an in vitro experiment.
A type of phosphatase assay evidence used in an in vitro experiment.
A type of protein kinase assay evidence used in an in vitro experiment.
A type of polyADP-ribosylation assay evidence used in an in vitro experiment.
in vitro polyADP-ribosylation assay evidence
A type of sumoylation assay evidence used in an in vitro experiment.
A type of transcription assay evidence used in an in vitro experiment.
A type of translation assay evidence used in an in vitro experiment.
A type of ubiquitination assay evidenceused in an in vitro experiment.
A type of acetylation assay evidence used in an in vivo experiment.
A type of cleavage assay evidence used in an in vivo experiment.
A type of deacetylation assay evidence used in an in vivo experiment.
A type of defarnesylation assay evidence used in an in vivo experiment.
A type of demethylation assay evidence used in an in vivo experiment.
A type of deubiquitination assay evidence used in an in vivo experiment.
A type of desumoylation assay evidence used in an in vivo experiment.
A type of farnesylation assay evidence used in an in vivo experiment.
A type of methylation assay evidence used in an in vivo experiment.
A type of palmitoylation assay evidence used in an in vivo experiment.
A type of phosphatase assay evidence used in an in vivo experiment.
A type of protein kinase assay evidence used in an in vivo experiment.
A type of sumoylation assay evidence used in an in vivo experiment.
A type of transcription assay evidence used in an in vivo experiment.
A type of translation assay evidence used in an in vivo experiment.
A type of ubiquitination assay evidence used in an in vivo experiment.
A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence.
A type of genetic transformation evidence resulting from a change in the DNA that results in the elimination of the function of the gene, allowing for functional analysis.
A change in the DNA may result from any number of processes such (deletion, insertion, frame shift, etc.) Additionally, the gene may be made inoperative via homologous recombination, site-specific nucleases, zinc finger nucleases, transcription activator-like effector nucleases (TALENs), or CRISPR (Clustered regularly interspaced short palindromic repeats).
Contrast with deletion mutation phenotypic evidence in which DNA is deleted which may result in altering the function of the resulting protein(s).
A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid.
A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells.
luminescence-based mammalian interactome mapping assay evidence
A type of experimental evidence that is visible to the naked eye cf. microscopy evidence which requires the aid of a microscope.
A type of bait-prey hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene.
The MS analyses showed that two VapB10 peaks (836.437, 1584.789 m/z) and three VapC10-His6 peaks (1049.526, 1299.733 and 1455.853 m/z) were detected in MS-DIGEST program, indicating that both VapB10 and VapC10-His6 had the expected peptide masses (Figure S3). These results suggest that VapB10 binds to VapC10-His6 forming the TA complex VapBC10 in vivo, which may cause the counteraction of the VapC10-induced growth arrest (Figure 2).
A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles.
A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions.
A type of direct assay evidence resulting from the use of a microscope.
Microscopy may include any of the following: optical, electron, scanning probe, or X-ray.
A type of cell-based assay evidence to measure cell motility in which a "wound" is created in a cell monolayer and the migration of the cells is captured by imaging at regular intervals during cell migration to close the wound.
A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells.
A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells and measures cell viability / metabolic activity.
3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte).
multiplex bead-based immunoassay evidence
A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits.
A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death.
A type of magnetic resonance evidence in which atomic nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting electromagnetic signal is captured.
A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases.
A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of fluorescently labeled nucleotide analog(s) into the DNA.
nucleotide analog incorporation assay evidence
A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid.
A type of direct assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis.
A type of affinity evidence resulting from the appending of affinity tags on proteins so that they may be purified from their biological source using an affinity technique.
phosphopeptide affinity enrichment evidence
A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample.
A type of protein binding evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites.
A type of mutant phenotype evidence resulting from the change in a single nucleotide.
A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated.
A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore.
A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged.
A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions.
A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein.
A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes.
A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant.
A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system.
A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror.
A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences.
A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid or solid by its ability to alter the transmission of light at specific wavelengths.
Electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR) demonstrated that AdpAHis6 specifically bound the oriC fragment (283-bp) containing the in silico-predicted A-boxes in a concentration-dependent manner (figures 1b and 2a), but not the remaining part of oriC (data not shown).
Further confirmation of the specific interaction was obtained by conducting the competing surface plasmon resonance (SPR) assay with the unlabeled DNA fragments. As shown in Additional file 3, a significantly lower response was observed when either the unlabeled S2 or S5 was added together with MtrA, which indicated that they could compete the binding of MtrA with the promoter DNA on the chip.
Our SPR analysis revealed that also housekeeping genes required for ribosome function (rplR) and beta subunit RNA polymerase (rpoB) belong to the LexA regulon, a feature of the SOS network not yet observed in bacteria.
A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction.
Plasmons are generated by an incident light beam.
A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin.
syngeneic transplantation experiment evidence
A type of enzymatic activity assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein.
Tumor necrosis factor - alpha converting enzyme activity assay
A type of cytochemistry evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern.
A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification.
A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate.
tryptic phosphopeptide mapping assay evidence
A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs.
TdT-mediated dUTP-biotin nick end labeling assay
terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence
A type of direct assay evidence resulting from the analysis of a urine sample.
A type of cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye.
metabolic cell proliferation assay evidence
A type of anatomical perturbation phenotypic evidence resulting from the transplantation, implantation, or infusion of live cells, tissues, or organs between individuals of different species.
A type of 3D cell culture evidence that is used in a manual assertion.
3D cell culture evidence used in manual assertion
A type of 51Cr release assay evidence that is used in a manual assertion.
51Cr release assay evidence used in manual assertion
A type of 7-aminoactinomycin staining evidence that is used in a manual assertion.
7-aminoactinomycin staining evidence used in manual assertion
A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion.
[3H]-thymidine incorporation assay evidence used in manual assertion
A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion.
[3H]arachidonic acid release assay evidence used in manual assertion
A type of adhesion assay evidence that is used in a manual assertion.
adhesion assay evidence used in manual assertion
A type of adoptive cell transfer evidence that is used in a manual assertion.
adoptive cell transfer evidence used in manual assertion
A type of alamarBlue assay evidence that is used in a manual assertion.
alamarBlue assay evidence used in manual assertion
A type of allograft transplantation phenotypic evidence that is used in a manual assertion.
allograft transplantation evidence used in manual assertion
allograft transplantation phenotypic evidence used in manual assertion
A type of anion-exchange chromatography evidence that is used in a manual assertion.
anion-exchange chromatography evidence used in manual assertion
A type of annexin-V staining evidence that is used in a manual assertion.
annexin-V staining evidence used in manual assertion
A type of cognitive assay phenotypic evidence used that is used in a manual assertion.
behavioral assay evidence used in manual assertion
cognitive assay phenotypic evidence used in manual assertion
A type of blocking monoclonal antibody evidence that is used in a manual assertion.
blocking monoclonal antibody evidence used in manual assertion
A type of blocking peptide evidence that is used in a manual assertion.
blocking peptide evidence used in manual assertion
A type of blocking polyclonal antibody evidence tthat is used in a manual assertion.
blocking polyclonal antibody evidence used in manual assertion
A type of blood test evidence that is used in a manual assertion.
blood test evidence used in manual assertion
A type of Boyden chamber assay evidence that is used in a manual assertion.
Boyden chamber assay evidence used in manual assertion
A type of bromodeoxyuridine incorporation assay evidence used in manual assertion.
bromodeoxyuridine incorporation assay evidence used in manual assertion
A type of caspase assay evidence that is used in a manual assertion.
caspase assay evidence used in manual assertion
A type of cell counting evidence that is used in a manual assertion.
cell counting evidence used in manual assertion
A type of cell permeability assay evidence that is used in a manual assertion.
cell permeability assay evidence used in manual assertion
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion.
carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion
A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion.
chemiluminescence-linked immunoassay evidence used in manual assertion
A type of chimeric protein phenotypic evidence that is used in a manual assertion.
chimeric protein evidence used in manual assertion
chimeric protein phenotypic evidence used in manual assertion
A type of co-electrophoresis evidence that is used in a manual assertion.
co-electrophoresis evidence used in manual assertion
A type of co-localization evidence that is used in a manual assertion.
co-localization evidence used in manual assertion
A type of co-sedimentation assay evidence that is used in a manual assertion.
co-sedimentation assay evidence used in manual assertion
A type of colony counting evidence that is used in a manual assertion.
colony counting evidence used in manual assertion
A type of comet assay evidence that is used in a manual assertion.
comet assay evidence used in manual assertion
A type of conditional knockin evidence that is used in a manual assertion.
conditional knockin evidence used in manual assertion
A type of conditional knockout evidence that is used in a manual assertion.
conditional knockout evidence used in manual assertion
A type of constitutively active mutant protein evidence that is used a in manual assertion.
constitutively active mutant protein evidence used in manual assertion
A type of cross-linking evidence that is used in a manual assertion.
cross-linking evidence used in manual assertion
A type of crystallography evidence that is used in a manual assertion.
crystallography evidence used in manual assertion
A type of cytochemistry evidence that is used in a manual assertion.
cytochemistry evidence used in manual assertion
A type of cytochrome C release assay evidence that is used in a manual assertion.
cytochrome C release assay evidence used in manual assertion
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion.
4',6-diamidino-2-phenylindole staining evidence used in manual assertion
A type of deletion mutation phenotypic evidence that is used in a manual assertion.
deletion mutation evidence used in manual assertion
deletion mutation phenotypic evidence used in manual assertion
A type of DNA laddering assay evidence that is used in a manual assertion.
DNA laddering assay evidence used in manual assertion
A type of RNA dot blot assay evidence that is used in a manual assertion.
RNA dot blot assay evidence used in manual assertion
A type of dominant-negative mutant phenotypic evidence that is used in a manual assertion.
dominant-negative mutant evidence used in manual assertion
dominant-negative mutant phenotypic evidence used in manual assertion
A type of eTag assay evidence that is used in a manual assertion.
eTag assay evidence used in manual assertion
A type of filter binding assay evidence that is used in a manual assertion.
filter binding assay evidence used in manual assertion
A type of fluorescence in situ hybridization evidence that is used in a manual assertion.
fluorescence in situ hybridization evidence used in manual assertion
A type of fluorescence resonance energy transfer evidence that is used in a manual assertion.
fluorescence resonance energy transfer evidence used in manual assertion
A type of gel-filtration evidence that is used in a manual assertion.
gel-filtration evidence used in manual assertion
A type of histochemistry evidence that is used in a manual assertion.
histochemistry evidence used in manual assertion
A type of immunocytochemistry evidence that is used in a manual assertion.
immunocytochemistry evidence used in manual assertion
A type of histology evidence that is used in a manual assertion.
histology evidence used in manual assertion
A type of immunodepletion evidence that is used in a manual assertion.
immunodepletion evidence used in manual assertion
A type of immunohistochemistry evidence that is used in a manual assertion.
immunohistochemistry evidence used in manual assertion
A type of in vitro acetylation assay evidence that is used in a manual assertion.
in vitro acetylation assay evidence used in manual assertion
A type of in vitro cleavage assay evidence that is used in a manual assertion.
in vitro cleavage assay evidence used in manual assertion
A type of in vitro deacetylation assay evidence that is used in a manual assertion.
in vitro deacetylation assay evidence used in manual assertion
A type of in vitro defarnesylation assay evidence that is used in a manual assertion.
in vitro defarnesylation assay evidence used in manual assertion
A type of in vitro demethylation assay evidence that is used in a manual assertion.
in vitro demethylation assay evidence used in manual assertion
A type of in vitro desumoylation assay evidence that is used in a manual assertion.
in vitro desumoylation assay evidence used in manual assertion
A type of in vitro deubiquitination assay evidence that is used in a manual assertion.
in vitro deubiquitination assay evidence used in manual assertion
A type of in vitro farnesylation assay evidence that is used in a manual assertion.
in vitro farnesylation assay evidence used in manual assertion
A type of in vitro methylation assay evidence that is used in a manual assertion.
in vitro methylation assay evidence used in manual assertion
A type of in vitro palmitoylation assay evidence that is used in a manual assertion.
in vitro palmitoylation assay evidence used in manual assertion
A type of in vitro phosphatase assay evidence that is used in a manual assertion.
in vitro phosphatase assay evidence used in manual assertion
A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion.
in vitro polyADP-ribosylation assay evidence used in manual assertion
A type of in vitro protein kinase assay evidence that is used in a manual assertion.
in vitro protein kinase assay evidence used in manual assertion
A type of in vitro sumoylation assay evidence that is used in a manual assertion.
in vitro sumoylation assay evidence used in manual assertion
A type of in vitro transcription assay evidence that is used in a manual assertion.
in vitro transcription assay evidence used in manual assertion
A type of in vitro translation assay evidence that is used in a manual assertion.
in vitro translation assay evidence used in manual assertion
A type of in vitro ubiquitination assay evidence that is used in a manual assertion.
in vitro ubiquitination assay evidence used in manual assertion
A type of in vivo acetylation assay evidence that is used in manual assertion.
in vivo acetylation assay evidence used in manual assertion
A type of in vivo cleavage assay evidence that is used in a manual assertion.
in vivo cleavage assay evidence used in manual assertion
A type of in vivo deacetylation assay evidence that is used in a manual assertion.
in vivo deacetylation assay evidence used in manual assertion
A type of in vivo defarnesylation assay evidence that is used in a manual assertion.
in vivo defarnesylation assay evidence used in manual assertion
A type of in vivo demethylation assay evidence that is used in a manual assertion.
in vivo demethylation assay evidence used in manual assertion
A type of in vivo desumoylation assay evidence that is used in a manual assertion.
in vivo desumoylation assay evidence used in manual assertion
A type of in vivo deubiquitination assay evidence that is used in a manual assertion.
in vivo deubiquitination assay evidence used in manual assertion
A type of in vivo farnesylation assay evidence that is used in a manual assertion.
in vivo farnesylation assay evidence used in manual assertion
A type of in vivo methylation assay evidence that is used in a manual assertion.
in vivo methylation assay evidence used in manual assertion
A type of in vivo palmitoylation assay evidence that is used in a manual assertion.
in vivo palmitoylation assay evidence used in manual assertion
A type of in vivo phosphatase assay evidence that is used in a manual assertion.
in vivo phosphatase assay evidence used in manual assertion
A type of in vivo protein kinase assay evidence that is used in a manual assertion.
in vivo protein kinase assay evidence used in manual assertion
A type of in vivo sumoylation assay evidence that is used in a manual assertion.
in vivo sumoylation assay evidence used in manual assertion
A type of in vivo transcription assay evidence that is used in a manual assertion.
in vivo transcription assay evidence used in manual assertion
A type of in vivo translation assay evidence that is used in a manual assertion.
in vivo translation assay evidence used in manual assertion
A type of in vivo ubiquitination assay evidence that is used in a manual assertion.
in vivo ubiquitination assay evidence used in manual assertion
OBSOLETE. A type of induced mutation evidence that is used in a manual assertion.
obsolete induced mutation evidence used in manual assertion
A type of knockin evidence that is used in a manual assertion.
knockin evidence used in manual assertion
A type of knockout evidence that is used in a manual assertion.
knockout evidence used in manual assertion
A type of lipid binding assay evidence that is used in a manual assertion.
lipid binding assay evidence used in manual assertion
A type of LUMIER assay evidence that is used in a manual assertion.
luminescence-based mammalian interactome mapping assay evidence used in manual assertion
A type of macroscopy evidence that is used in a manual assertion.
macroscopy evidence used in manual assertion
A type of mammalian 2-hybrid assay evidence that is used in a manual assertion.
mammalian 2-hybrid assay evidence used in manual assertion
A type of mass spectrometry evidence that is used in a manual assertion.
mass spectrometry evidence used in manual assertion
A type of medical imaging evidence that is used in a manual assertion.
medical imaging evidence used in manual assertion
A type of microscopy evidence that is used in a manual assertion.
microscopy evidence used in manual assertion
A type of motility wound healing assay evidence that is used in a manual assertion.
wound healing assay evidence used in manual assertion
motility wound healing assay evidence used in manual assertion
A type of MTS assay evidence that is used in a manual assertion.
MTS assay evidence used in manual assertion
A type of MTT assay evidence that is used in a manual assertion.
MTT assay evidence used in manual assertion
A type of multiplex bead-based immunoassay evidence that is used in a manual assertion.
multiplex bead-based immunoassay evidence used in manual assertion
A type of natural variation mutant evidence that is used in a manual assertion.
natural variation mutant evidence used in manual assertion
A type of nuclear magnetic resonance evidence that is used in a manual assertion.
nuclear magnetic resonance evidence used in manual assertion
A type of nuclear fragmentation evidence that is used in a manual assertion.
nuclear fragmentation evidence used in manual assertion
A type of nuclease protection assay evidence that is used in a manual assertion.
nuclease protection assay evidence used in manual assertion
A type of nucleotide analog incorporation assay evidence that is used in a manual assertion.
nucleotide analog incorporation assay evidence used in manual assertion
A type of phage display evidence that is used in a manual assertion.
phage display evidence used in manual assertion
A type of phosphoamino acid analysis evidence that is used in a manual assertion.
phosphoamino acid analysis evidence used in manual assertion
A type of peptide affinity enrichment evidence that is used in a manual assertion.
peptide affinity enrichment evidence used in manual assertion
A type of peptide array evidence that is used in a manual assertion.
peptide array evidence used in manual assertion
A type of physical examination evidence that is used in a manual assertion.
physical examination evidence used in manual assertion
A type of point mutation phenotypic evidence that is used in a manual assertion.
point mutation evidence used in manual assertion
point mutation phenotypic evidence used in manual assertion
A type of propidium iodide staining evidence that is used in a manual assertion.
propidium iodide staining evidence used in manual assertion
A type of protein detection by fluorescence evidence that is used in a manual assertion.
fluorescence evidence used in manual assertion
A type of protein dot blot assay evidence that is used in a manual assertion.
protein dot blot assay evidence used in manual assertion
A type of protein microarray evidence that is used in a manual assertion.
protein microarray evidence used in manual assertion
A type of protein sequencing assay evidence that is used in a manual assertion.
protein sequencing assay evidence used in manual assertion
A type of quantitative mass spectrometry evidence that is used in a manual assertion.
quantitative mass spectrometry evidence used in manual assertion
A type of radioisotope assay evidence that is used in a manual assertion.
radioisotope assay evidence used in manual assertion
A type of radioimmunoassay evidence that is used in a manual assertion.
radioimmunoassay evidence used in manual assertion
A type of imaging assay evidence that is used in a manual assertion.
imaging assay evidence used in manual assertion
A type of restriction fragment detection evidence that is used in a manual assertion.
restriction fragment detection evidence used in manual assertion
A type of spectrophotometry evidence that is used in a manual assertion.
spectrophotometry evidence used in manual assertion
A type of syngeneic transplantation experiment evidence that is used in a manual assertion.
syngeneic transplantation experiment evidence used in manual assertion
A type of xenotransplantation phenotypic evidence that is used in a manual assertion.
xenotransplantation experiment evidence used in manual assertion
xenotransplantation phenotypic evidence used in manual assertion
A type of WST-1 assay evidence that is used in a manual assertion.
WST-1 assay evidence used in manual assertion
A type of urine test evidence that is used in a manual assertion.
urine test evidence used in manual assertion
A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion.
TdT-mediated dUTP-biotin nick end labeling assay evidence
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion
A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion.
tryptic phosphopeptide mapping assay evidence used in manual assertion
A type of transgenic organism evidence that is used in a manual assertion.
transgenic organism evidence used in manual assertion
A type of tissue microarray evidence that is used in a manual assertion.
tissue microarray evidence used in manual assertion
A type of TACE activity assay evidence that is used in a manual assertion.
Tumor necrosis factor - alpha converting enzyme activity assay evidence
TACE activity assay evidence used in manual assertion
A type of surface plasmon resonance evidence that is used in a manual assertion.
surface plasmon resonance evidence used in manual assertion
A type of restriction landmark genome scanning evidence that is used in a manual assertion.
restriction landmark genomic scanning evidence used in manual assertion
A type of resonant mirror biosensor evidence that is used in a manual assertion.
resonant mirror biosensor evidence used in manual assertion
A type of high-performance liquid chromatography evidence that is used in a manual assertion.
high-performance liquid chromatography evidence used in manual assertion
A type of ectopic expression evidence that is used in a manual assertion.
ectopic expression evidence used in manual assertion
A type of molecule detection assay evidence resulting from the detection and quantification of a small molecule (a low molecular weight (typically < 900 daltons) organic compound), such as lipids, sugars, animo acids, drugs, etc.
A type of direct assay evidence in which the sub-cellular location of a protein or nucleic acid sequence is determined.
A type of localization evidence based on localization of a specific segment of DNA or RNA within tissue by the application of a complementary strand of nucleic acid to which a reporter molecule (i.e. either radio-, fluorescent- or antigen-labeled probe) is attached and quantified using either autoradiography, fluorescence microscopy, or immunohistochemistry.
A type of direct assay evidence where acetylated residues are detected in a protein.
A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected.
A type of direct assay evidence where the removal of acetyl groups are detected in a protein.
A type of direct assay evidence where the removal of farnesyl groups from a protein is detected.
A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected.
A type of direct assay evidence where the removal of sumo groups from a protein is detected.
A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected.
A type of direct assay evidence where farnesylated residues in proteins are detected.
A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected.
A type of direct assay evidence where palmitoylated residues in a protein are detected.
A type of direct assay evidence where the removal of phosphatase groups from a protein is detected.
A type of direct assay evidence where ADP-ribosylated residues in proteins are detected.
A type of enzymatic activity assay evidence that measures transfer of a phosphate to a peptide or protein substrate by a protein kinase.
A type of direct assay evidence where sumoylated residues on a protein are detected.
A type of single cell RNA-sequencing evidence that is used in automatic assertion.
single-cell RNA-sequencing evidence used in automatic assertion
A type of RNA-sequencing evidence that uses a single cell as the source of the RNA.
A type of direct assay evidence where de novo protein synthesis is detected.
A type of direct assay evidence where ubiquitinated residues on a protein are detected.
However, as shown in Fig. 5A, the recombinant mycobacterial cells became sensitive to the anti-TB drugs isoniazid and streptomycin, as evidenced by their inhibited growth in the presence of 25 mug/mL of isoniazid or 0.5 mug/mL of streptomycin in the medium.
Similar growth profiles of these strains were observed in liquid media with the corresponding inducers (data not shown). These indicate that the expression of vapC10 alone led to growth arrest of E. coli, and the simultaneous expression of vapB10 could neutralize this growth-inhibition effect, suggesting that vapC10 encodes a TA toxin and vapB10 encodes the cognate antitoxin.
A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured.
A type of direct assay evidence resulting from the study of cells.
The real-time RT-PCR validated that Zur repressed the first gene of each of the three operons, znuA, znuCB and ykgM-rpmJ2 (Additional file 5).
A type of reverse transcription polymerase chain reaction evidence that combines reverse transcription polymerase chain reaction and real time polymerase chain reaction to quantitatively assay for the detection of RNA levels.
real-time quantitative reverse transcription PCR evidence
real-time reverse transcription polymerase chain reaction evidence
quantitative reverse transcription polymerase chain reaction evidence
A type of quantitative reverse transcription polymerase chain reaction evidence used in manual assertion.
quantitative reverse transcription polymerase chain reaction evidence used in manual assertion
A type of quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion.
quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion.
A type of colony diameter phenotype evidence that is used in manual assertion.
colony diameter phenotype evidence used in manual assertion
A type of single cell RNA-sequencing evidence that is used in manual assertion.
single-cell RNA-sequencing evidence used in manual assertion
A type of colony size phenotypic evidence resulting from measurement of a microbial colony's diameter.
A type of colony diameter phenotype evidence that is used in automatic assertion
colony diameter phenotype evidence used in automatic assertion
A type of direct assay evidence in which a broad variety of physiological processes are measured when two separate membranes merge into a single contiguous membrane.
Measurements can include but are not limited to: synaptic transmission, fertilization, and viral entry.
A type of membrane fusion assay evidence that is used in automatic assertion.
membrane fusion assay evidence used in automatic assertion
A type of membrane fusion assay evidence that is used in manual assertion.
membrane fusion assay evidence used in manual assertion
A type of membrane fusion assay evidence based on the fusion of spheroplasts.
A spheroplast is a Gram-negative bacterium cell in which the cell wall has been almost completely removed.
A type of spheroplast fusion assay evidence used in automatic assertion.
spheroplast fusion assay evidence used in automatic assertion
A type of spheroplast fusion assay evidence that is used in manual assertion.
spheroplast fusion assay evidence used in manual assertion
A type of mass spectrometry evidence where liquid chromatography is used to separate particles in solution, followed by fragmentation and measurement of the mass-to-charge ratio of the resulting particles to identify the amount and type of material entities present in a sample.
liquid chromatography coupled with tandem mass spectrometry evidence
A type of liquid chromatography coupled with tandem mass spectrometry evidence that is used in an automatic assertion.
liquid chromatography coupled with tandem mass spectrometry evidence used in automatic assertion
A type of liquid chromatography coupled with tandem mass spectrometry evidence that is used in a manual assertion.
liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion
A type of anti-sense experiment evidence where gene expression is disrupted through the introduction of double-stranded RNA molecules, 20-25 base pairs in length, which operate within the RNA interference pathway.
small interfering RNA knockdown evidence
A type of small interfering RNA knockdown evidence that is used in an automatic assertion.
small interfering RNA knockdown evidence used in automatic assertion
A type of small interfering RNA knockdown evidence that is used in a manual assertion.
small interfering RNA knockdown evidence used in manual assertion
A type of mass spectrometry evidence where a combination of magnetic and/or electric fields are utilized to capture charged particles in tandem with mass spectrometry.
A type of ion trap mass spectrometry evidence that is used in an automatic assertion.
ion trap mass spectrometry evidence used in automatic assertion
A type of ion trap mass spectrometry evidence that is used in a manual assertion.
ion trap mass spectrometry evidence used in manual assertion
AFM revealed loop structures stabilized by multiple EspR dimer of dimers suggesting the presence of several distant EspR binding sites in the espACD upstream region.
A type of microscopy evidence where a mechanical probe is applied to a sample (i.e. a type of scanning probe microscopy) which can result in production of an image (with resolution in the order of fractions of a nanometer), force measurement, or sample manipulation.
Atomic force microscopy can be used for force measurement (force spectroscopy), imaging (rendering a three-dimensional shape (topography), and manipulation of the sample.
A type of atomic force microscopy evidence that is used in an automatic assertion.
atomic force microscopy evidence used in automatic assertion
A type of atomic force microscopy evidence that is used in a manual assertion.
atomic force microscopy evidence used in manual assertion
A type of experimental evidence employed to study the associations between multiple ribosomes and mRNA that utilizes density gradient centrifugation to separate out the lysate of cells of interest with the objective of isolating polysomes/polyribosomes which are complexes of an mRNA molecule and two or more ribosomes that act to translate mRNA. The optical density of the fractions is then determined.
Once isolated, gel electrophoresis, immunoblot, and other protein profiling techniques can be applied to garner more information.
A type of polysome profiling evidence that is used in an automatic assertion.
polysome profiling evidence used in automatic assertion
A type of polysome profiling evidence that is used in a manual assertion.
polysome profiling evidence used in manual assertion
A type of nucleotide sequencing assay evidence in which DNA sequence variations within a specific set of genes (typically housekeeping genes) are used to characterizes strains by their unique allelic profiles.
A type of multilocus sequence typing evidence that is used in an automatic assertion.
multilocus sequence typing evidence used in automatic assertion
A type of multilocus sequence typing evidence that is used in a manual assertion
multilocus sequence typing evidence used in manual assertion
A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
protein-oligonucleotide microarray binding evidence
A type of cell-based assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death.
A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing.
Secreted Embryonic Alkaline Phosphatase reporter assay
Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane.
alkaline phosphatase reporter gene assay evidence
For each of the three genes, there was a significant increase of beta-galactosidase activity in Deltazur compared to WT when they grew in TMH with the addition of zinc. Thus, Zur repressed the promoter activities of znuC, znuA and ykgM.
A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium.
The assay is often performed using a plasmid borne construction on a lacZ strain.
beta-galactosidase reporter gene assay evidence
A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic.
The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present.
chloramphenicol acetyltransferase reporter gene assay evidence
A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection.
beta-glucuronidase reporter gene assay evidence
A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence.
A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data.
chromatin immunoprecipitation- exonuclease evidence
A type of electrophoretic mobility shift that is used in a manual assertion.
electrophoretic mobility shift assay evidence used in manual assertion
A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion.
reverse transcription polymerase chain reaction evidence used in manual assertion
A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins.
Biotinylation is commonly used for labeling and beads are commonly used as the matrix. Bound protein will remain attached to the beads. Results can be detected through gel electrophoresis and then sequenced by mass-spectrometry. This technique can be used to demonstrate binding of a purified protein, or to purify the binding protein from crude extract or protein mixture.
Subsequent DNase I footprinting experiments (Fig. 5d) indicated that His-PhoP protected a single region located from 102 to 47 bp upstream of rovA. This footprint was considered the PhoP site.
The subsequent DNase I footprinting experiments (Figure 3a) showed that His-OmpR-P protected a single region within the ompR promoter. Therefore, OmpR stimulated its own gene at the transcriptional level, which was mediated through the binding of OmpR-P to its own promoter.
To precisely determine the PhoP-binding sites of target genes, DNase I footprinting assay was performed on 17 PhoP-dependent promoter DNA regions (both coding and noncoding strands) (Additional file 6). DNase I footprinting results confirmed the direct binding of His-PhoP to these promoter regions in vitro.
We therefore pursued DNase I footprinting assays on several of the Crp-associated sequences that gave an unusual downshift in our initial EMSA trials, in an effort to identify a consensus binding sequence (see Fig. S2 in the supplemental material). We mapped sites upstream of crp itself, SCO4561 and SCO2977, and identified a consensus binding sequence [GTG(N)6GNCAC]; derivatives of this motif could be found in all of the secondary metabolism-associated target sequences, although notably, one-half of the palindrome seemed to be better conserved than the other [GTG(N)6GNGAN] (Fig. 2C; Table 1).
A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions.
In DNAse footingprinting amplified DNA combined with TF and DNAse is electrophoresed for fragment comparison with a non-TF control sample. TF-bound fragments do not appear in the gel. Such fragments can be isolated, purified, and sequenced. This technique is often used to identify the binding motif of a TF resolving the protected region to 50-100 bp which can be further examined for TF-binding sites.
Since these FA analyses are conducted with 300 nM scOhrR, this suggests that oxidation leads to at least a 100-fold reduction in DNA-binding affinity.
A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules.
The degree of polarization of a fluorophore is inversely related to its molecular rotation. When the fluorophore is bound to a small molecule, the rate at which it tumbles can decrease significantly from when it is bound tightly to a large protein. If the fluorophore is attached to the larger protein in a binding pair, the difference in polarization between bound and unbound states will be smaller and less accurate. The degree of binding is calculated by using the difference in anisotropy of the partially bound, free, and fully bound states measured by titrating the two binding partners. Fluorescence polarixation assays are homogeneous.
A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing.
The reported sequences should always be verified for presence in the genome sequence.
genomic systematic evolution of ligands by exponential amplification evidence
A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum.
Chemical shifts in the spectrum indicating binding can be detected from analysis of a protein spectrum in the presence or absence of its cognate DNA binding site.
heteronuclear single quantum coherence spectroscopy evidence
A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA.
Methidiumpropyl-EDTA Fe(II) footprinting
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence
A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts.
copper-phenanthroline footprinting evidence
A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light.
green fluorescent protein transcript localization evidence
green fluorescent protein promoter fusion
green fluorescent protein reporter gene assay evidence
A type of bait-prey hybrid interaction evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions.
The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing.
glutathione S-transferase pull-down assay evidence
A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel.
The primer extension assay (Fig. 6a) defined the transcription start sites the three sRNA genes qrr2 - 4, and this assay also indicated that the promoter activity of all the thee qrr genes was under the positive control of OpaR.
The primer extension assay detected two transcriptional start sites located at 343 and 78 bp upstream of rovA (Fig. 2); therefore, two promoters (named P2 and P1, respectively) were transcribed for rovA.
A type of transcript expression evidence used to determine expression levels of mRNA where a labeled synthetic oligonucleotide primer is annealed to mRNA downstream of the presumed transcription start site of a gene. The mRNA is extended with reverse transcriptase, producing cDNA which is electrophoresed, and the band size is enables determination of the 5' end of the mRNA (i.e. the transcription start site).
The most commonly used radiolabel is 32P.
5' RACE analysis was employed to localize the espR promoter using RNA extracted from Mtb H37Rv grown to mid-log phase. The espR transcript starts with a poly-G (7) sequence 144 bp upstream of the translational start codon.
The 5'-end of the espA mRNA was located 66 bp upstream of the translation start codon using 5' RACE (Fig. S3).
Using 5' rapid amplification of cDNA ends (RACE), we mapped the transcriptional start sites of rpoQ and VF_A1016 (Fig. 4A). Neither start site was detected in the DeltarpoQ mutant, supporting the idea that transcription of rpoQ and VF_A1016 requires RpoQ (data not shown).
A type of nucleotide sequencing assay evidence in which RT-PCR (cDNA synthesis) is first used to produce a cDNA copy of a region of the RNA transcript being investigated followed by PCR to capture either the unknown 5' or 3' end of the transcript for sequencing, depending on whether 5' RACE-PCR or 3' RACE-PCR are being undertaken.
5' and 3' RACE-PCR utilize different protocols to amplify an unknown end using the known sequence of the center of the transcript. For cDNA synthesis, 5' RACE-PCR uses an anti-sense oligonucleotide primer (gene specific primer (GSP)) that recognizes a known sequence in the middle of the gene of interest and the reverse transcriptase to add base pairs to the 3' end of the primer. Next, terminal deoxynucleotidyl transferase (TdT) is used to add a string of identical nucleotides to the 3' end of the cDNA. A PCR reaction is then carried out, using a second anti-sense gene specific primer (GSP2) that binds to the known sequence, and a sense (forward) universal primer (UP) that binds the homopolymeric tail added to the 3' ends of the cDNAs to amplify a cDNA product from the 5' end. In contrast, 3' RACE-PCR utilizes the naturally occurring 3' polyA tail of the transcript and uses an Oligo-dT-adaptor primer (a primer with a short sequence of deoxy-thymine nucleotides) that complements the polyA tail and adds a special adaptor sequence to the 5' end of each cDNA. PCR is then used to amplify 3' cDNA from a known region using a sense GSP, and an anti-sense primer complementary to the adaptor sequence.
RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression.
rapid amplification of cDNA ends polymerase chain reaction evidence
A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter.
A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules.
X-ray crystallography can be used for a crystal used to probe at the tridimensional structure of proteins. In some cases, it is possible to co-crystallize the protein bound to its DNA binding site, providing detail on the particular arrangement of the two components.
A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site.
The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII.
DNA adenine methyltransferase identification evidence
A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction.
When ITC is used to study TF, the temperature of two identical cells containing a known concentration of TF is monitored. After the ligand is added to the cells in precisely measured aliquots, the temperature difference in each cell is observed to determine target binding. This value can be used to compute the energetics of the reaction and hence, binding affinity of the TF for the DNA fragment. The thermodynamic profile that is measured includes the values of binding constant (K(a)), stoichiometry (n), and the enthalpy of binding (DeltaH(b)).
isothermal titration calorimetry evidence
A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts.
A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel.
methylation interference footprinting evidence
A type of inference of sequence features from visual inspection that is used in a manual assertion.
inference of sequence features from visual inspection used in manual assertion
A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis.
ferric uptake regulator titration assay evidence
A type of experimental evidence in which the colonization or adhesion capacity is measured.
Has to do with the ability of a symbiont (any organism living in close association with a host, including both beneficial and parasitic relationships) to bind to a host.
A type of host colonization assay evidence that is used in an automatic assertion.
host colonization assay evidence used in automatic assertion
A type of host colonization assay evidence that is used in a manual assertion.
host colonization assay evidence used in manual assertion
A type of host colonization assay evidence in which the infection capacity is measured by assessing changes in the host.
Has to do with the outcome of a bacterial or viral / host interaction, be it a measure of cell death, cytotoxicity, invasion, etc.
A type of infection assay evidence that is used in an automatic assertion.
infection assay evidence used in automatic assertion
A type of infection assay evidence that is used in a manual assertion.
infection assay evidence used in manual assertion
A type of expression pattern evidence in which single-stranded DNA or RNA (probe) are annealed to complementary DNA or RNA in a portion or section of tissue.
A type of in situ hybridization evidence that is used in an automatic assertion.
in situ hybridization evidence used in automatic assertion
A type of in situ hybridization evidence that is used in a manual assertion.
in situ hybridization evidence used in manual assertion
A type of nucleic acid localization evidence and in situ hybridization evidence resulting from the use of colorimetric probes to detect complementary sequences of nucleic acids.
colorimetric in situ hybridization evidence
A type of colorimetric in situ hybridization evidence that is used in an automatic assertion.
colorimetric in situ hybridization evidence used in automatic assertion
A type of colorimetric in situ hybridization evidence that is used in a manual assertion.
colorimetric in situ hybridization evidence used in manual assertion
A type of random mutagenesis phenotypic evidence resulting from the random mutation of a specifically targeted region of DNA.
random mutagenesis of specific target DNA evidence
A type of random mutagenesis of specific target DNA evidence that is used in an automatic assertion.
random mutagenesis of specific target DNA evidence used in automatic assertion
A type of random mutagenesis of specific target DNA evidence that is used in a manual assertion.
random mutagenesis of specific target DNA evidence used in manual assertion
A type of cell-based assay evidence in which optical density is used to measure some aspect of a population of cells. Examples of aspects that can affect optical density measurements include, but are not limited to, cell number and cell shape.
cell population optical density evidence
A type of cell population optical density evidence that is used in an automatic assertion.
cell population optical density evidence used in automatic assertion
A type of cell population optical density evidence that is used in a manual assertion.
cell population optical density evidence used in manual assertion
A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully.
A type of cell-based assay evidence resulting from the measurement of the number of cells, which is a reflection of the balance between cell division and cell loss through cell differentiation or cell death.
A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label.
DNA synthesis cell proliferation assay evidence
A type of cell viability assay evidence resulting from the analysis of ATP concentration (by measuring light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen.
A type of cell-based assay evidence resulting from the ability of an agent to induce cellular necrosis or apoptosis and the subsequent analysis of cell death mechanism.
Use children of ECO:0001565 (cell-based assay evidence) in place of this term.
obsolete in vitro cell based assay evidence
A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image.
A type of cell-based assay evidence resulting from the evaluation of chemotactic ability (i.e. the movement, or lack of movement, in response to a chemical stimulus) of prokaryotic or eukaryotic cells.
A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA.
A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures.
Electron micrographs showed that all the cells are rod-shaped and those of the parent strain Ye9 and the envZ mutant strain EZ10 are flagellated, but the ompR mutant cells lack flagella.
A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image.
A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis.
A type of polyADP-ribosylation assay evidence used in an in vivo experiment.
in vivo polyADP-ribosylation assay evidence
A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion.
in vivo polyADP-ribosylation assay evidence used in manual assertion
A type of direct assay evidence derived by studying an organ, tissues, or cells taken from an organism and studied in an external environment with the minimum alteration of natural conditions.
A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape.
Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes.
two-dimensional polyacrylamide gel electrophoresis evidence
A type of experimental evidence resulting from the use of a spectrometer.
A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression.
Regular expression is a computational tool used for determining whether a given genome contains a DNA region resembling a transcription factor binding motif. For example A/T=W indicates A or T may be present in a column of the alignment. (PMID:20708667).
regular expression motif search evidence
A type of point mutation phenotypic evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another.
A type of point mutation phenotypic evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon.
A type of point mutation phenotypic evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence.
A type of mutant phenotype evidence resulting from a mutation in which there is an insertion of one or more contiguous nucleotides.
A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides.
A type of mutant phenotype evidence resulting from any mutation that causes an insertion or deletion of nucleotides in a DNA sequence that is not divisible by three and therefore changes the codon reading frame and the translated amino acids.
A type of mutant phenotype evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated.
repeat expansion mutation phenotypic evidence
A type of mutant phenotype evidence resulting from a mutation in which there is a change in nucleotides at a splice site.
splice site mutation phenotypic evidence
A type of mutant phenotype evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome.
translocation mutation phenotypic evidence
A type of experimental evidence resulting from the detection and analysis of molecular markers.
A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins.
A type of molecule detection assay evidence resulting from the detection of specific RNAs.
A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA.
A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels.
Differences in the optical path lengths between a surface layer and a buried silica layer can be measured very precisely allowing optical height information to be converted to accumulated mass on the surface. For the purpose of TF-binding site identification, IRIS is coupled with DNA-arrays with immobilized potential binding regions exposed to the protein of interest and eluted. Protein-bound fragments exhibit changes in reflectance that can be used to gauge binding quantitatively.
interferometric reflectance imaging sensor evidence
A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA.
A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane.
A type of DNA dot blot assay evidence that is used in a manual assertion.
DNA dot blot assay evidence used in manual assertion
A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology.
MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
If the AGAA sequence is mutated CTCC (Pxyn2aM, see Table 1), no DNA-protein complex is formed under either repressing or inducing conditions (Figure 1). This result indicates that this part of the xyn2 promoter is essential for binding a transcription factor under repressing conditions.
To identify key residues required for specific GlnR binding we mutated the highly conserved AC-n9-AC and AT-n9-AC DNA binding motifs. Figure 4 shows that the highly conserved adenosine residues in the motif are critical as GlnR binding is abolished when these residues are mutated.
We also tested a hyaS promoter in which one (highest score) of the three putative AdpA-binding sites was mutated (at position -134 to -129, see Additional file 3: Figure S1a): the affinity of AdpA for this promoter region was reduced and one protein-DNA complex disappeared (Additional file 3: Figure S1b). These results suggest that one dimer of AdpA binds the adjacent sites -129 and -123 of S. lividans hyaS promoter and another dimer binds the -100 site resulting in the formation of the two DNA-AdpA complexes depicted in Figure 2.
A type of mutant phenotype phenotype evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence.
Site-directed mutagenesis is often performed in tandem with EMSA. It is often implemented only in conserved motif positions or serially through all positions of a site.
site-directed mutagenesis phenotypic evidence
A type of mutant phenotype evidence where a mutagenic product or process is used to alter the nucleotide sequence and thus induce genetic mutation. Examples include, but are not limited to mutagenic compounds, irradiation, PCR w/ degenerate primers, etc.
Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination.
A type of random mutagenesis phenotypic evidence that is used in a manual assertion.
random mutagenesis evidence used in manual assertion
A sequence alignment of the phlA gene promoter region from strain 2P24 with other well-studied 2,4-DAPG producing Pseudomonas strains revealed a very well conserved palindromic sequence GAAACN5GTTTC (Fig. S1).
In order to identify a potential regulatory motif for KstR2, we used the promoter regions of the kstR2 orthologues as a training set for the motif identification program MEME (Bailey & Elkan, 1994). This identified a potential regulatory sequence that contains a 14 bp inverted palindromic motif AnCAAGnnCTTGnT (Fig. 2).
We mapped sites upstream of crp itself, SCO4561 and SCO2977, and identified a consensus binding sequence [GTG(N)6GNCAC]; derivatives of this motif could be found in all of the secondary metabolism-associated target sequences, although notably, one-half of the palindrome seemed to be better conserved than the other [GTG(N)6GNGAN] (Fig. 2C; Table 1).
A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs.
Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs.
A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match.
This technique is used to identify transcription factor binding sites by searching a bacterial genome for DNA regions resembling a given TF-binding motif. PMID:17085555.
A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'.
The name derives to experimental footprinting techniques where transcription factor (TF)-binding sites are identified by sequencing the region of DNA protected from biochemical agents by the bound TF. This technique is used to identify or verify transcription factor-binding motifs, most commonly in the Eukaryota (PMID:11997340).
A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes.
This technique is used to predict transcription factor binding sites in gene promoter regions by identifying conserved DNA regions across multiple genomes. PMID:22305460. Orthology is a typical comparative criterion used.
comparative genomics motif search evidence
A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences.
Machine learning algorithms include, but are not limited to artificial neural networks, random-forest, k-means clustering, hidden Markov models. This suite of methods can be used to identify or verify transcription factor-binding sites in genomic sequences (PMID:15703297).
machine learning prediction of motif instance evidence
A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis.
This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID:15604457).
position-specific scoring matrix motif search evidence
A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene.
obsolete computationally derived logical inference
obsolete computationally derived logical inference used in automatic assertion
obsolete computationally derived logical inference from automatic assertion used in automatic assertion
obsolete computationally derived logical inference from manual assertion used in automatic assertion
A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion.
Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof.
biological system reconstruction evidence by experimental evidence from single species used in manual assertion
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion.
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments.
biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion
A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion.
Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments.
biological system reconstruction evidence based on orthology evidence used in manual assertion
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species.
biological system reconstruction evidence based on orthology evidence
A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion.
biological system reconstruction evidence based on paralogy evidence used in manual assertion
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion.
Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion
A type of biological system reconstruction based solely on background scientific knowledge of that biological system.
The available knowledge is usually a combination of partial or weak experimental evidence where either some components are missing or no physical interaction evidence can be found but the system is inferred by similarity to related systems in taxonomically-disparate organisms with experimental evidence. Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components.
biological system reconstruction evidence based on inference from background scientific knowledge
A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex.
Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species.
biological system reconstruction evidence based on homology evidence
A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species.
biological system reconstruction evidence based on paralogy evidence
A type of biological system reconstruction evidence that uses experimental evidence as support.
biological system reconstruction evidence by experimental evidence
A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment.
biological system reconstruction evidence by experimental evidence from mixed species
A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species.
biological system reconstruction evidence by experimental evidence from single species
A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied.
A type of multiple sequence alignment evidence that is used in a manual assertion.
multiple sequence alignment evidence used in manual assertion
A type of multiple sequence alignment evidence that is used in an automatic assertion.
multiple sequence alignment evidence used in automatic assertion
A type of motif discovery evidence that is used in a manual assertion.
motif discovery evidence used in manual assertion
A type of motif discovery evidence that is used in an automatic assertion.
motif discovery evidence used in automatic assertion
A type of pairwise sequence alignment evidence that is used in a manual assertion.
pairwise sequence alignment evidence used in manual assertion
A type of pairwise sequence alignment evidence that is used in an automatic evidence.
pairwise sequence alignment evidence used in automatic assertion
A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate.
A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording.
A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane.
obsolete single channel conductance evidence
A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels.
obsolete steady state activation curve evidence
obsolete steady state inactivation curve evidence
A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course.
A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell.
current clamp voltage recording evidence
current clamp voltage recording protocol
A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage.
whole-cell voltage clamp recording evidence
whole-cell voltage clamp recording protocol
A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction.
cell-attached patch-clamp recording evidence
cell-attached single-channel recording evidence
cell-attached single-channel recording protocol
A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution.
cell-detached inside-out patch-clamp recording evidence
cell-detached inside-out single-channel recording evidence
cell-detached inside-out single-channel recording protocol
A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane.
reconstituted bilayer single-channel patch recording evidence
reconstituted bilayer single-channel patch recording protocol
A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage.
voltage clamp current recording evidence
voltage clamp current recording protocol
A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head.
electroencephalography recording evidence
electroencephalography recording protocol
A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures.
A type of immunogold labelling evidence that is used in a manual assertion.
immunogold labelling evidence used in manual assertion
A type of flow cytometry evidence that is used in a manual assertion.
flow cytometry evidence used in manual assertion
A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion.
ELISA evidence|enzyme-linked immunosorbent assay evidence
enzyme-linked immunoabsorbent assay evidence used in manual assertion
A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch).
cell-detached outside-out patch-clamp evidence
cell-detached outside-out single-channel recording evidence
A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway.
cut-open oocyte voltage clamp recording evidence
A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch).
macropatch voltage clamp recording evidence
A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies.
There are significant differences in data analysis and data evaluation if to compare a HTP mass-spec and a regular mass-spec. The regular mass spec method is quite a reliable technique for identifying a protein molecular weight and analysing its post-modifications, other mass-spec applications might require the additional quality controls and more stringent data evaluation. More complex sample mixture is processed, more quality questions should be addressed, such as a sample contamination and sensitivity of the mass spectrometer while using HTP mass-spec. For HTP mass-spec, the analysis of the small data sets allows to manually assign the spectra to proteins or peptides, but for large data sets only the statistical tools can be used instead.
high throughput mass spectrometry evidence
A type of high throughput mass spectrometry evidence that is used in a manual assertion.
high throughput mass spectrometry evidence used in manual assertion
A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis.
A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times.
A type confocal microscopy evidence that is used in a manual assertion.
confocal microscopy evidence used in manual assertion
A type of wide-field microscopy evidence that is used in a manual assertion.
wide-field microscopy evidence used in manual assertion
A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles.
immunogold labelling electron microscopy assay evidence
A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion.
immunogold labelling electron microscopy assay evidence used in manual assertion
A type of direct assay evidence that involves the use of antibodies to detect biomolecules.
A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody.
immunoperoxidase immunolocalization evidence
A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion.
immunoperoxidase immunolocalization evidence used in manual assertion
A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody.
Immunoperoxidase labelling electron microscopy
immunoperoxidase immunolocalization electron microscopy evidence
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion.
immunoperoxidase labelling electron microscopy evidence
immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion
A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
The optical filter is used to select the wavelength of excitation light. The detection camera is typically a CCD camera. Both topographical and dynamic information of a sample are obtained.
wide-field fluorescence microscopy evidence
A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
immunofluorescence wide-field microscopy evidence
The endogenous protein expression and localization for WalR and WalK was also checked using confocal immunofluorescence microscopy. WalR could be localized to the cytoplasm of B. anthracis but WalK could not be detected once again (data not shown).
A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection.
This allows visualization of sub cellular distribution of biomolecules of interest.
immunofluorescence confocal microscopy evidence
A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion.
immunofluorescence confocal microscopy evidence used in manual assertion
A type of mass spectrometry evidence where one or more protein analyses are performed.
A type of cell proliferation assay evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics.
Disk diffusion assays were used to determine if ohr and ohrR mutations affected resistance to ROS. The ohr mutant was less resistant than its parental strain when challenged with organic peroxides as shown by the zones of growth inhibition: 4.1 +- 0.2 cm for CuOOH and 3.1 +- 0.1 cm for tBOOH versus to 2.3 +- 0.2 and 2.5 +- 0.3 cm for wild type strain.
A type of zone of inhibition evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism.
A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by observing the rotational behavior of the cells tethered to a coverslip by their flagella.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another.
A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the rate of accumulation of the cells into a capillary.
To determine the presence of negative chemotaxis, a repellent is added to the organismal suspension (but not in the capillary) and the organisms that fled into the capillary are measured.
To determine the presence of positive chemotaxis, an attractant is placed in the capillary and the presence of positive chemotaxis is determined based on the amount of organism that accumulated in the capillary.
A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion.
biological system reconstruction evidence based on homology evidence used in manual assertion
OBSOLETE. A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease.
obsolete inference from experimental data evidence
OBSOLETE. A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined.
Changes can include any gene mutation/knockout, over-expression or ectopic expression of wild-type or mutant genes, anti-sense experiments, RNAi experiments, specific protein inhibitors.
obsolete inference from phenotype manipulation evidence
A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments.
inferred by association of genotype from phenotype
Used for 1) polymorphism or segregation of genetic markers (SNPs, mutations, RFLPs, microsatellites); 2) polymorphism or segregation of physical markers (FISH, centromeric or heterochromatic regions, chromosomal banding patterns); 3) detection of polymorphisms in inbred stock.
inference by association of genotype from phenotype
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion
A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion.
alkaline phosphatase reporter gene assay evidence used in manual assertion
A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion.
LacZ transcript localization evidence used in manual assertion
beta-galactosidase reporter gene assay evidence used in manual assertion
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion.
chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion
A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion.
chromatin immunoprecipitation-chip evidence used in automatic assertion
A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion.
chromatin immunoprecipitation- exonuclease evidence used in automatic assertion
A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion.
chromatin immunoprecipitation-PCR evidence used in manual assertion
A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion.
chromatin immunoprecipitation-seq evidence used in automatic assertion
A type of comparative genomics motif search evidence that is used in a manual assertion.
comparative genomics motif search evidence used in manual assertion
A type of comparative genomics motif search evidence that is used in an automatic assertion.
comparative genomics motif search evidence used in automatic assertion
A type of consensus search evidence that is used in a manual assertion.
consensus search evidence used in manual assertion
A type of consensus search evidence that is used in an automatic assertion.
consensus search evidence used in automatic assertion
A type of copper-phenanthroline footprinting evidence that is used in a manual assertion.
1,10-phenanthroline-copper footprinting evidence
copper-phenanthroline footprinting evidence used in manual assertion
A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion.
DNA adenine methyltransferase identification evidence used in manual assertion
A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion.
DNA adenine methyltransferase identification evidence used in automatic assertion
A type of DNA affinity chromatography evidence that is used in a manual assertion.
DNA affinity chromatography evidence used in manual assertion
A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion.
cDNA to DNA expression microarray evidence used in automatic assertion
A type of DNAse footprinting evidence that is used in a manual assertion.
DNAse footprinting evidence used in manual assertion
A type of fluorescence anisotropy evidence that is used in a manual assertion.
fluorescence anisotropy evidence used in manual assertion
A type of ferric uptake regulator titration assay evidence that is used in a manual assertion.
ferric uptake regulator titration assay evidence used in manual assertion
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion.
genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion
A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion
A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion.
green fluorescent protein transcript localization evidence used in manual assertion
green fluorescent protein reporter gene assay evidence used in manual assertion
A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion.
green fluorescent protein transcript localization evidence used in automatic assertion
green fluorescent protein reporter gene assay evidence used in automatic assertion
A type of cell growth regulation assay evidence that is used in a manual assertion.
cell growth regulation assay evidence used in manual assertion
A type of cell growth regulation assay evidence that is used in an automatic assertion.
cell growth regulation assay evidence used in automatic assertion
A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion.
glutathione S-transferase pull-down assay evidence used in manual assertion
A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion.
beta-glucuronidase reporter gene assay evidence used in manual assertion
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion.
heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
A type of hydroxyl-radical footprinting evidence that is used in a manual assertion.
hydroxyl-radical footprinting evidence used in manual assertion
A type of immunoprecipitation evidence that is used in a manual assertion.
immunoprecipitation evidence used in manual assertion
A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion.
spectral reflectance imaging biosensor evidence
interferometric reflectance imaging sensor evidence used in manual assertion
A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion.
interferometric reflectance imaging sensor evidence used in automatic assertion
A type of isothermal titration calorimetry evidence that is used in a manual assertion.
isothermal titration calorimetry evidence used in manual assertion
A type of luciferase reporter gene assay evidence that is used in a manual assertion.
luciferase reporter gene assay evidence used in manual assertion
A type of machine learning prediction of motif instance evidence that is used in a manual assertion.
machine learning prediction of motif instance evidence used in manual assertion
A type of machine learning prediction of motif instance evidence that is used in an automatic assertion.
machine learning prediction of motif instance evidence used in automatic assertion
A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion.
matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion.
Methidiumpropyl-EDTA Fe(II) footprinting evidence
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion
A type of northern blot evidence that is used in a manual assertion.
northern blot evidence used in manual assertion
A type of phylogenetic footprinting evidence that is used in a manual assertion.
phylogenetic footprinting evidence used in manual assertion
A type of phylogenetic footprinting evidence that is used in an automatic assertion.
phylogenetic footprinting evidence used in automatic assertion
A type of methylation interference footprinting evidence that is used in a manual assertion.
premethylation interference footprinting evidence used in manual assertion
methylation interference footprinting evidence used in manual assertion
A type of primer extension assay evidence that is used in a manual assertion.
primer extension assay evidence used in manual assertion
A type of position-specific scoring matrix motif search evidence that is used in a manual assertion.
position-specific scoring matrix motif search evidence used in manual assertion
A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion.
position-specific scoring matrix motif search evidence used in automatic assertion
A type of quantitative polymerase chain reaction evidence that is used in a manual assertion.
quantitative polymerase chain reaction evidence used in manual assertion
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion.
rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion
A type of regular expression motif search evidence that is used in a manual assertion.
regular expression motif search evidence used in manual assertion
A type of regular expression motif search evidence that is used in an automatic assertion.
regular expression motif search evidence used in automatic assertion
A type of S1 nuclease protection assay evidence that is used in a manual assertion.
S1 nuclease protection assay evidence used in manual assertion
A type of site-directed phenotypic mutagenesis evidence that is used in a manual assertion.
site-directed mutagenesis evidence used in manual assertion
site-directed mutagenesis phenotypic evidence used in manual assertion
A type of survival rate analysis evidence that is used in a manual assertion.
survival rate analysis evidence used in manual assertion
A type of ultraviolet light footprinting evidence that is used in a manual assertion.
ultraviolet light footprinting evidence used in manual assertion
A type of x-ray crystallography evidence that is used in a manual assertion.
x-ray crystallography evidence used in manual assertion
A type of x-ray crystallography evidence that is used in an automatic assertion.
x-ray crystallography evidence used in automatic assertion
A type of xylE reporter gene assay evidence that is used in a manual assertion.
xylE reporter gene assay evidence used in manual assertion
A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
ad-hoc qualitative phenotype observation evidence
A type of ad-hoc qualitative phenotype observation that is used in a manual assertion.
ad-hoc qualitative phenotype observation evidence used in manual assertion
A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor.
ad-hoc quantitative phenotype observation evidence
A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion.
ad-hoc quantitative phenotype observation evidence used in manual assertion
A type of direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response.
For chemicals, bacteriocins, or phage, the indicator culture is typically present in a soft-agar layer on top of nutrient agar and a small quantity of each dilution is spotted onto the soft agar overlay.
dilution assay evidence
A type of enzyme assay evidence that is used in a manual assertion.
enzymatic activity assay evidence used in manual assertion
A type of cell transfection experiment evidence that is used in a manual assertion.
cell transfection experiment evidence used in manual assertion
A motility assay at 37 degrees C revealed a non-motile phenotype for all strains, as expected (data not shown).
A type of direct assay evidence where the motility of a cell or cells is determined.
A type of immunofluorescence evidence that is used in a manual assertion.
immunofluorescence evidence used in manual assertion
A type of yeast 2-hybrid evidence that is used in a manual assertion.
yeast 2-hybrid evidence used in manual assertion
A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications.
A type of Cya fusion reporter assay evidence that is used in a manual assertion.
Cya fusion reporter assay evidence used in manual assertion
A type of electron microscopy evidence that is used in a manual assertion.
electron microscopy evidence used in manual assertion
A type of super-resolution microscopy evidence that is used in a manual assertion.
super-resolution microscopy evidence used in manual assertion
A type of fractionation evidence that is used in a manual assertion.
fractionation evidence used in manual assertion
A type of electrophysiology assay evidence that is used in a manual assertion.
electrophysiology assay evidence used in manual assertion
A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion.
chromatin immunoprecipitation-chip evidence used in manual assertion
A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion.
chromatin immunoprecipitation- exonuclease evidence used in manual assertion
A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion.
chromatin immunoprecipitation-seq evidence used in manual assertion
A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry.
ultraviolet light cross-linking RNA binding evidence
A type of mRNA interactome capture evidence that is used in a manual assertion.
mRNA interactome capture evidence used in manual assertion
A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels.
A type of patch-clamp recording evidence that is used in a manual assertion.
patch-clamp recording evidence used in manual assertion
A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell.
whole-cell patch-clamp recording evidence
A type of whole-cell patch-clamp recording evidence that is used in a manual assertion.
whole-cell patch-clamp recording evidence used in manual assertion
A type of author statement supported by traceable reference in which the traceable reference is a clinical study.
traceable author statement from published clinical study
author statement supported from referenced clinical study
A type of author statement supported from referenced clinical study that is used in a manual assertion.
Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used when evidence for an HPO annotation is information extracted from articles in the medical literature.
author statement supported from referenced clinical study used in manual assertion
A type of curator inference that is based on the individual clinical experience of a clinician
inference based on individual clinical experience
A type of inference based on individual clinical experience that is used in a manual assertion.
Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used for annotating disorders with a limited amount of published data, and is accompanied by a reference to the individual or center performing the annotation.
inference based on individual clinical experience used in manual assertion
A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development.
A type of biofilm formation assay evidence that is used in a manual assertion.
biofilm formation assay evidence used in manual assertion
A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes.
A type of microtiter plate biofilm assay evidence that is used in a manual assertion.
microtiter plate biofilm assay evidence used in manual assertion
A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate.
Tilting of the plate positions the air-liquid interface on a clear portion to improve visability.
A type of air-liquid interface assay evidence that is used in a manual assertion.
air-liquid interface assay evidence used in manual assertion
A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate. The plate serves to supply nutrients and the semipermeable membrane can be relocated to fresh plates.
The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells.
A type of colony biofilm assay evidence that is used in a manual assertion.
colony biofilm assay evidence used in manual assertion
A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out.
A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion.
Kadouri drip-fed biofilm assay evidence used in manual assertion
A type of co-immunoprecipitation evidence that is used in a manual assertion.
co-immunoprecipitation evidence used in manual assertion
A type of immunolocalization evidence that is used in a manual assertion.
immunolocalization evidence used in manual assertion
A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators.
A type of optogenetic evidence that is used in a manual assertion.
optogenetic evidence used in manual assertion
A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor.
Examples include sensors for ion concentration and potential difference across a membrane.
A type of fluorescent sensor evidence that is used in a manual assertion.
fluorescent sensor evidence used in manual assertion
A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor.
genetically encoded fluorescent sensor evidence
A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion.
genetically encoded fluorescent sensor evidence used in manual assertion
A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors.
electrophysiology - optical assay evidence
Examples include genetically encoded sensors that detect potential difference across plasma membrane.
genetically encoded fluorescent electrophysiology assay evidence
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion.
genetically encoded fluorescent electrophysiology assay evidence used in manual assertion
A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor.
Examples include the genetically encoded calcium indicator GCaMP.
genetically encoded fluorescent ion concentration sensor assay evidence
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion.
genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion
A type of cell fractionation evidence that is used in a manual assertion.
cell fractionation evidence used in manual assertion
A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons.
A type of extracellular recording evidence that is used in a manual assertion.
extracellular recording evidence used in manual assertion
A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron.
single-unit extracellular recording evidence
A type of single-unit extracellular recording evidence that is used in a manual assertion.
single-unit extracellular recording evidence used in manual assertion
A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes.
local field potential recording evidence
A type of field potential recording evidence that is used in a manual assertion.
field potential recording evidence used in manual assertion
A type of genetic transformation evidence that is used in a manual assertion
genetic transformation evidence used in manual assertion
A type of anti-sense experiment evidence that is used in a manual assertion.
anti-sense experiment evidence used in manual assertion
A type of morpholino experiment evidence that is used in a manual assertion.
morpholino experiment evidence used in manual assertion
A type of RNAi evidence that is used in a manual assertion.
A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist.
pharmacological assay evidence used in manual assertion
A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
Some relevant articles include: PMID:23340846, doi:10.1038/nmeth0607-523
A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel.
inferred from high throughput experiment
high throughput evidence used in manual assertion
A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel.
high throughput evidence used in automatic assertion
A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology)
A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
high throughput cell biology evidence used in manual assertion
A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel.
high throughput cell biology evidence used in automatic assertion
A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens.
wide-field epifluorescence microscopy evidence
immunofluorescence wide-field microscopy evidence used in manual assertion
A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter.
wide-field fluorescence microscopy evidence used in manual assertion
A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product.
over expression analysis evidence used in manual assertion
A type of cell-free assay evidence that is used in a manual assertion.
cell-free assay evidence used in manual assertion
obsolete in vitro cell based assay evidence used in manual assertion
A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
FRAP is a fluorescence microscopy-based technique.
fluorescence recovery after photobleaching evidence
A type of fluorescence evidence that is used in a manual assertion where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse.
fluorescence recovery after photobleaching evidence used in manual assertion
A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
RNA sequencing assay evidence used in manual assertion
RNA-seq evidence used in manual assertion
RNAseq evidence used in manual assertion
RNA sequencing|differential gene expression evidence from RNA-seq experiment
RNA-sequencing evidence used in manual assertion
A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules.
RNA sequencing assay evidence used in automatic assertion
RNA-seq evidence used in automatic assertion
RNAseq evidence used in automatic assertion
RNA-sequencing evidence used in automatic assertion
A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
immunolabelling electron microscopy evidence
immuno-labelling electron microscopy evidence
A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues.
immuno-labelling electron microscopy evidence used in manual assertion
A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
immunofluorescence super resolution microscopy evidence
A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue.
immunofluorescence super resolution microscopy evidence used in manual assertion
A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex.
co-purification evidence used in manual assertion
A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities.
affinity evidence used in manual assertion
A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex.
protein binding evidence used in manual assertion
A type of bait-prey hybrid interaction evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein.
bait-prey hybrid interaction evidence used in manual assertion
A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody.
immunological assay evidence used in manual assertion
A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors.
yeast one-hybrid evidence used in manual assertion
A type of split-ubiquitin functional complementation evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein.
split-ubiquitin functional complementation evidence used in manual assertion
A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes.
far-Western blotting evidence used in manual assertion
A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound.
affinity chromatography evidence used in manual assertion
A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid.
nucleic acid binding evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer.
ribohomopolymer binding assay evidence used in manual assertion
A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site.
protein:ion binding evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins.
Southwestern blot evidence used in manual assertion
A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins.
Northwestern blot evidence used in manual assertion
A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand.
systematic evolution of ligands by exponential amplification evidence used in manual assertion
A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey).
bacterial one-hybrid evidence used in manual assertion
A type of protein-oligonucleotide microarray binding evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites.
protein-oligonucleotide microarray binding evidence used in manual assertion
A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background.
functional complementation evidence used in manual assertion
A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or "rescue" an organism from a condition.
transgenic rescue experiment evidence used in manual assertion
A type of transient rescue experiment evidence that is used in a manual assertion.
transient rescue experiment evidence used in manual assertion
A type of suppressor/enhancer interaction phenotypic evidence that is used in a manual assertion.
suppressor/enhancer interaction evidence used in manual assertion
suppressor/enhancer interaction phenotypic evidence used in manual assertion
A type of double mutant phenotypic evidence that is used in a manual assertion.
double mutant phenotype evidence used in manual assertion
double mutant phenotypic evidence used in manual assertion
A type of epistatic interaction phenotypic evidence that is used in a manual assertion.
epistatic interaction evidence used in manual assertion
epistatic interaction phenotypic evidence used in manual assertion
A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene.
functional complementation in heterologous system evidence used in manual assertion
A type of mutant phenotype evidence resulting from altered gene function at higher temperatures.
temperature-sensitive mutant phenotype evidence
temperature-sensitive mutant phenotypic evidence
A type of temperature-sensitive mutant phenotypic evidence that is used in a manual assertion.
temperature-sensitive mutant phenotype evidence used in manual assertion
temperature-sensitive mutant phenotypic evidence used in manual assertion
A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself.
recessive mutant phenotype evidence used in manual assertion
A type of computational evidence where the active site of the molecular system is described with highly accurate quantum theory, while the contribution of the rest of the system is described with molecular mechanical force field.
quantum mechanics/molecular mechanics simulation evidence
A type of quantum mechanics/molecular mechanics simulation evidence that is used in an automatic assertion.
quantum mechanics/molecular mechanics simulation evidence used in automatic assertion
A type of quantum mechanics/molecular mechanics simulation evidence that is used in manual assertion.
quantum mechanics/molecular mechanics simulation evidence used in manual assertion
A type of computational evidence where the energy of a molecular system is predicted as a function of its conformation.
A type of molecular mechanics simulation evidence that is used in an automatic assertion.
molecular mechanics simulation evidence used in automatic assertion
A type of molecular mechanics simulation evidence that is used in manual assertion.
molecular mechanics simulation evidence used in manual assertion
A type of computational evidence where the behavior of matter and light on the atomic and subatomic scale is described.
A type of quantum mechanics simulation evidence that is used in an automatic assertion.
quantum mechanics simulation evidence used in automatic assertion
A type of quantum mechanics simulation evidence that is used in manual assertion.
quantum mechanics simulation evidence used in manual assertion
A type of quantum mechanics simulation evidence that results from the calculation of ground-state electronic structure of atoms, molecules and solid state materials.
density functional theory simulation evidence
A type of density functional theory simulation evidence that is used in manual assertion.
density functional theory simulation evidence used in manual assertion
A type of density functional theory simulation evidence that is used in an automatic assertion.
density functional theory simulation evidence used in automatic assertion
A type of evidence in which information is recorded in some documentation system, for example, but not limited to a publication, survey, or medical record.
A type of documented statement evidence in which information is stated by a health care professional, for example, but not limited to a doctor, nurse, or psychologist.
A type of documented statement evidence in which information is provided by an individual through means including, but not limited to, paper form, electronic form, or verbal communication, and is captured in a documented record.
self-reported individual's statement evidence
A type of self-reported individual's statement evidence in which information is provided by a patient in a clinical setting.
Pablo Botas for Foundation 29, Dx29 project
self-reported patient statement evidence
A type of documented statement evidence that is used in a manual assertion.
documented statement evidence used in manual assertion
A type of documented statement evidence that is used in an automatic assertion.
documented statement evidence used in automatic assertion
A type of self-reported individual's statement evidence that is used in a manual assertion.
self-reported individual's statement evidence used in manual assertion
A type of self-reported individual's statement evidence that is used in an automatic assertion.
self-reported individual's statement evidence used in automatic assertion
A type of self-reported patient statement evidence that is used in a manual assertion.
self-reported patient statement evidence used in manual assertion
A type of self-reported patient statement evidence that is used in an automatic assertion.
self-reported patient statement evidence used in automatic assertion
A type of medical practitioner statement evidence that is used in a manual assertion.
medical practitioner statement evidence used in manual assertion
A type of medical practitioner statement evidence that is used in an automatic assertion.
medical practitioner statement evidence used in automatic assertion
A type of nuclear magnetic resonance evidence used for quantification of metabolites or for the determination of chemical structure or composition.
nuclear magnetic resonance spectroscopy evidence
A type of nuclear magnetic resonance spectroscopy evidence that is used in an automatic assertion.
nuclear magnetic resonance spectroscopy evidence used in automatic assertion
A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion.
nuclear magnetic resonance spectroscopy evidence used in manual assertion
A type of nuclear magnetic resonance evidence used to image anatomy and physiological processes.
nuclear magnetic resonance imaging evidence
A type of nuclear magnetic resonance imaging evidence that is used in an automatic assertion.
nuclear magnetic resonance imaging evidence used in automatic assertion
A type of nuclear magnetic resonance imaging evidence that is used in a manual assertion.
nuclear magnetic resonance imaging evidence used in manual assertion
A type of qualitative western immunoblotting evidence where detection of the signal is carried out through digital imaging and the signal is normalized with methods such as standard curves built from reference housekeeping proteins or total transferred protein measurements.
quantitative western immunoblotting evidence
A type of quantitative western immunoblotting evidence that is used in a manual assertion.
quantitative western immunoblotting evidence used in manual assertion
A type of quantitatative western immunoblotting evidence that is used in an automatic assertion.
quantitative western immunoblotting evidence used in automatic assertion
A type of support of intron positions by RNA-sequencing alignment evidence where RNA-seq alignments from a mixture of samples support all of the intron positions (exon pairs) predicted for a transcript.
mixed support of intron positions by RNA-seq alignment evidence
Mixed support entails that all exon pairs represented in the transcript are supported, but require a combination of evidence from multiple samples. For example, for a transcript containing five exons, if liver RNA-seq reads support the first two introns and brain RNA-seq supports the last three introns, then neither sample meets the criteria for full support (ECO:0000343) but the combination of samples qualifies as Mixed support. Mixed support may result from differential expression, or low expression levels that benefit from combining data.
mixed support of intron positions by RNA-sequencing alignment evidence
A type of mixed support of intron positions by RNA-sequencing alignment evidence that is used in an automatic assertion.
mixed support of intron positions by RNA-seq alignment evidence used in automatic assertion
mixed support of intron positions by RNA-sequencing alignment evidence used in automatic assertion
A type of mixed support of intron positions by RNA-sequencing alignment evidence that is used in a manual assertion
mixed support of intron positions by RNA-seq alignment evidence used in manual assertion
mixed support of intron positions by RNA-sequencing alignment evidence used in manual assertion
A type of nuclear magnetic resonance spectroscopy evidence resulting from measuring the change in a certain type of NMR spectrum as a result of the spontenaous exchange of hydrogen and deuterium nuclei between the sample and the solvent.
nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence
A type of nuclear magnetic resonance spectroscopy evidence in which the electromagnetic singal being measured comes from the perturbation of hydrogen nuclei resulting in a one dimensional spectrum.
proton-based nuclear magnetic resonance evidence
A type of spectrometry evidence derived from irradiating a sample with light (either visible, infrared or ultraviolet wavelengths) and observing the difference of absorption of left-handed and right-handed light by the sample by comparing the extent of circular polarization in the incident and the emitted light.
A type of circular dichroism evidence where the source of radiation is radially accelerated particles, most often moving on a circular path in a synchrotron, typically providing lower wavelengths and therefore higher signal-to-noise ratio compared to regular circular dichroism measurements.
synchrotron radiation circular dichroism evidence
A type of circular dichroism evidence whose spectrum is in the range of 190-230 nm, providing information mainly about amide bonds and through which the relative proportion of secondary structure elements of a protein can be estimated.
A type of circular dichroism evidence whose spectrum is in the range of 250-350 nm , providing information mainly about aromatic residues, i.e. phenylalanine, tyrosine and tryptophan, through which it provides information on the tertiary structure of a protein.
A type of electron microscopy evidence where the sample being studied has been cooled to cryogenic temperatures (typically below -153 degrees Celsius) prior to the experiment.
A type of light scattering evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight and structural transitions by irradiating the sample with an X-ray beam and the scattered intensity is probed at small angles (typically in the range of 0.1-10 degrees) by a detector.
A type of structure determination evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by irradiating the sample with a particle beam and the scattered intensity is probed at a certain angle by a detector.
A type of particle scattering evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight and structural transitions by irradiating the sample with a beam of thermal neutrons and the scattered intensity is probed at small angles (typically in the range of 0.1-10 degrees) by a detector.
A type of inferential evidence where an assertion is derived by the authors of a scientific publication from another assertion and/or primary data via logical inference or other rational means.
A type of combinatorial experimental and author inference evidence where the experimental results and author inference are contained in a single publication.
combinatorial experimental and author inference evidence contained in single publication
A type of X-ray cystallography evidence in which a structural model is built lacking coordinates for some residues indicating high flexibility or structural disorder in that area of the molecule.
X-ray crystallography-based structural model with missing residue coordinates
A type of X-ray cystallography evidence in which a structural model is built that contains high relative B-factor values indicating flexibility in that area of the molecule.
X-ray crystallography-based structural model with high relative B-factor values
A type of cryogenic electron microscopy evidence in which a structural model is built lacking coordinates for some residues indicating high flexibility or structural disorder in that area of the molecule.
cryogenic electron microscopy-based structural model with missing residue coordinates
A type of cryogenic electron microscopy evidence in which a structural model is built that contains high relative B-factor values indicating flexibility in that area of the molecule.
cryogenic electron microscopy-based structural model with high relative B-factor values
A type of spectrophotometry evidence resulting from the evaluation of a molecule in a fluid or solid state by its ability to alter the transmission of infrared light, where the raw data collected is transformed into the specturm by Fourier transform.
Fourier-transform infrared spectroscopy evidence
A type of direct assay evidence derived from measuring the amount of heat absorbed or released by a sample to monitor chemical reactions, phase transitions or other processes affecting the physical state or chemical composition.
A type of heat capacity-based evidence where the heat required to increase the temperature of the sample is continuously monitored and compared to the heat required to increase the temperature of a reference (having a largely identical composition compared to the sample, such as the empty buffer compared to a protein solution) over a range of temperatures.
differential scanning calorimetry evidence
Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer–small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF–TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples.
A type of immunodetection assay evidence that involves the use of antibodies that are selective to conformations of the epitope to which they bind in order to provide information on conformations present in a target molecule.
selective antibody-based structural conformation evidence
A type of mass spectrometry evidence derived from measuring changes in mass associated with the isotopic exchange between amide hydrogens of the protein backbone and its surrounding solvent, providing information on the structural state, the dynamics and the intrinsic chemical properties of the underlying amino acid sequence.
protein hydrogen-deuterium exchange mass spectrometry evidence
A type of nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence that is used in a manual assertion.
nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
A type of nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence that is used in an automatic assertion.
nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in automatic assertion
A type of proton-based nuclear magnetic resonance evidence that is used in a manual assertion.
proton-based nuclear magnetic resonance evidence used in manual assertion
A type of proton-based nuclear magnetic resonance evidence that is used in an automatic assertion.
proton-based nuclear magnetic resonance evidence used in automatic assertion
A type of circular dichroism evidence that is used in a manual assertion.
circular dichroism evidence used in manual assertion
A type of circular dichroism evidence that is used in an automatic assertion.
circular dichroism evidence used in automatic assertion
A type of synchrotron radiation circular dichroism evidence that is used in a manual assertion.
synchrotron radiation circular dichroism evidence used in manual assertion
A type of synchrotron radiation circular dichroism evidence that is used in an automatic assertion.
synchrotron radiation circular dichroism evidence used in automatic assertion
A type of far-UV circular dichroism evidence that is used in a manual assertion.
far-UV circular dichroism evidence used in manual assertion
A type of far-UV circular dichroism evidence that is used in an automatic assertion.
far-UV circular dichroism evidence used in automatic assertion
A type of near-UV circular dichroism evidence that is used in a manual assertion.
near-UV circular dichroism evidence used in manual assertion
A type of near-UV circular dichroism evidence that is used in an automatic assertion.
near-UV circular dichroism evidence used in automatic assertion
A type of cryogenic electron microscopy evidence that is used in a manual assertion.
cryogenic electron microscopy evidence used in manual assertion
A type of cryogenic electron microscopy evidence that is used in an automatic assertion.
cryogenic electron microscopy evidence used in automatic assertion
A type of small-angle X-ray scattering evidence that is used in a manual assertion.
small-angle X-ray scattering evidence used in manual assertion
A type of small-angle X-ray scattering evidence that is used in an automatic assertion.
small-angle X-ray scattering evidence used in automatic assertion
A type of particle scattering evidence that is used in a manual assertion.
particle scattering evidence used in manual assertion
A type of particle scattering evidence that is used in an automatic assertion.
particle scattering evidence used in automatic assertion
A type of small-angle neutron scattering evidence that is used in a manual assertion.
small-angle neutron scattering evidence used in manual assertion
A type of small-angle neutron scattering evidence that is used in an automatic assertion.
small-angle neutron scattering evidence used in automatic assertion
A type of author inference that is used in a manual assertion.
A type of author inference that is used in an automatic assertion.
author inference used in automatic assertion
A type of combinatorial experimental and author inference evidence contained in single publication that is used in a manual assertion.
combinatorial experimental and author inference evidence contained in single publication used in manual assertion
A type of combinatorial experimental and author inference evidence contained in single publication that is used in an automatic assertion.
combinatorial experimental and author inference evidence contained in single publication used in automatic assertion
A type of X-ray crystallography-based structural model with missing residue coordinates that is used in a manual assertion.
X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
A type of X-ray crystallography-based structural model with missing residue coordinates that is used in an automatic assertion.
X-ray crystallography-based structural model with missing residue coordinates used in automatic assertion
A type of X-ray crystallography-based structural model with high relative B-factor values that is used in a manual assertion.
X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
A type of X-ray crystallography-based structural model with high relative B-factor values that is used in an automatic assertion.
X-ray crystallography-based structural model with high relative B-factor values used in automatic assertion
A type of cryogenic electron microscopy-based structural model with missing residue coordinates that is used in a manual assertion.
cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
A type of cryogenic electron microscopy-based structural model with missing residue coordinates that is used in an automatic assertion.
cryogenic electron microscopy-based structural model with missing residue coordinates used in automatic assertion
A type of cryogenic electron microscopy-based structural model with high relative B-factor values that is used in a manual assertion.
cryogenic electron microscopy-based structural model with high relative B-factor values used in manual assertion
A type of cryogenic electron microscopy-based structural model with high relative B-factor values that is used in an automatic assertion.
cryogenic electron microscopy-based structural model with high relative B-factor values used in automatic assertion
A type of Fourier-transform infrared spectroscopy evidence that is used in a manual assertion.
Fourier-transform infrared spectroscopy evidence used in manual assertion
A type of Fourier-transform infrared spectroscopy evidence that is used in an automatic assertion.
Fourier-transform infrared spectroscopy evidence used in automatic assertion
A type of heat capacity-based evidence that is used in a manual assertion.
heat capacity-based evidence used in manual assertion
A type of heat capacity-based evidence that is used in an automatic assertion.
heat capacity-based evidence used in automatic assertion
A type of differential scanning calorimetry evidence that is used in a manual assertion.
differential scanning calorimetry evidence used in manual assertion
A type of differential scanning calorimetry evidence that is used in an automatic assertion.
differential scanning calorimetry evidence used in automatic assertion
A type of selective antibody-based structural conformation evidence that is used in a manual assertion.
selective antibody-based structural conformation evidence used in manual assertion
A type of selective antibody-based structural conformation evidence that is used in an automatic assertion.
selective antibody-based structural conformation evidence used in automatic assertion
A type of protein hydrogen-deuterium exchange mass spectrometry evidence that is used in a manual assertion.
protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
A type of protein hydrogen-deuterium exchange mass spectrometry evidence that is used in an automatic assertion.
protein hydrogen-deuterium exchange mass spectrometry evidence used in automatic assertion
A type of reporter gene assay evidence based on the fusion of the galK gene to a specific promoter for the expression of the enzyme galactokinase.
galactokinase reporter gene assay evidence
A type of RNA-sequencing evidence based on sequencing of the 3' ends of cDNA molecules that are selected by presence of a polyadenylated tail.
polyadenylated transcript 3'-end-sequencing evidence
A type of colony morphology phenotypic evidence based on the presence or absence of a visually apparent boundary formed between colonies of multiple isolates or strains of the same microbial species growing on a solid surface such as that of an agar culture medium.
A type of galactokinase reporter gene assay evidence that is used in a manual assertion.
galactokinase reporter gene assay evidence used in manual assertion
A type of galactokinase reporter gene assay evidence that is used in an automatic assertion.
galactokinase reporter gene assay evidence used in automatic assertion
A type of polyadenylated transcript 3'-end-sequencing evidence that is used in a manual assertion.
polyadenylated transcript 3'-end-sequencing evidence used in manual assertion
A type of polyadenylated transcript 3'-end-sequencing evidence that is used in an automatic assertion.
polyadenylated transcript 3'-end-sequencing evidence used in automatic assertion
A type of colony boundary assay evidence that is used in a manual assertion.
colony boundary assay evidence used in manual assertion
A type of colony boundary assay evidence that is used in an automatic assertion.
colony boundary assay evidence used in automatic assertion
A type of molecule detection assay evidence where the hydrodynamic behaviour of macromolecules is used to study their size, shape and interactions, by spinning the sample solution at high centrifugal field (up to above 100000 rpm and 1000000 g), and monitoring the evolution of sample concentration profile versus the axis of rotation.
A type of physical interaction evidence based on the measurement of the change in the degree of polarization of a fluorophore upon binding to a molecular partner.
A type of bait-prey interaction evidence resulting from an affinity purification in-vitro technique used to detect physical interactions between two or more proteins, where a molecule of interest - a "bait" - is immobilized and incubated with a protein source containing putative "prey" proteins.
A type of electron microscopy evidence where a heavy metal is evaporated onto surface adsorbed molecules and macromolecular assemblies allowing high-contrast visualization of both individual macromolecules and the surface structure of macromolecular assemblies.
rotary shadowing electron microscopy evidence
A type of mass spectrometry evidence resulting from the ionization of polar functional groups producing multiple charged ions followed by the detection of ion cyclotron frequencies within a magnetic field, making it suitable for the study of large molecules (>2 kDa).
electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence
A type of experimental evidence in which particles in strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting eletromagnetic signal is captured.
A type of magnetic resonance evidence in which unpaired electrons in a strong constant magnetic field are perturbed by a weak oscillating magnetic field and the resulting electromagnetic signal is captured.
electron paramagnetic resonance evidence
A type of electron paramagnetic resonance evidence where the signal is obtained by labeling the protein in specific sites with a functional group (most often a nitroxide) containing an unpaired electron using site-directed mutagenesis.
site-directed spin-labelling electron paramagnetic resonance evidence
A type of direct assay evidence where the removal of glycan groups from a substrate (RNA, DNA, or protein) is detected.
A type of physical interaction evidence that is based on the detection of a protein-protein interaction between a bait and prey protein by reconstitution of a reporter protein serving as a detectable entity (usually an enzyme or a fluorescent protein), the two halves of which are each attached separately to the bait and prey.
protein fragment functional complementation evidence
A type of protein fragment functional complementaion evidence where the interaction between bait and prey assemble a functional beta galactosidase enzyme.
beta galactosidase functional complementation evidence
A type of protein fragment functional complementaion evidence where the interaction between bait and prey assemble a transcriptional activation complex consisting of the GAL4 DNA-binding domain and the transactivation domain from the herpes simplex virus protein VP16.
GAL4-VP16 functional complementation evidence
A type of spectrophotometry evidence used to determine a structural fingerprint of the molecule in solution by probing its vibrational modes via the inelastic scattering of photons (called Raman scattering).
A type of temperature-induced protein unfolding evidence that assess thermal denaturation temperature and protein stability under different experimental conditions, e.g. buffer pH or ionic strength, redox potential, usually by means of intrinsic fluorescence or thermofluor.
A type of physical interaction evidence resulting from measuring the change of the fluorescent activity of a molecule as a function of binding to a non-fluorescent partner and its movement in a microspcopic thermal gradient affecting the intensity of fluorescence.
A type of gel electrophoresis evidence resulting from the use of non-denaturing conditions so that the proteins being measured are in their native structural states.
native protein gel electrophoresis evidence
A type of direct assay evidence where the optical properties of a solution is measured in the visible light spectrum, assessing the haziness or cloudiness as a result of the properties of the solutes or the changes in their material states.
A type of affinity evidence derived from an experimental setup where the binding properties of a ligand are assessed by measuring the competition with another ligand with already known binding properties.
A type of structure determination evidence obtained by monitoring structural changes of a protein as a response to changes of an environmental parameter, such as pH or temperature, or the concentration of a denaturant, such as urea.
A type of protein unfolding evidence where the unfolding of the protein is triggered by increasing concentrations of urea.
A type of protein unfolding evidence where the unfolding of the protein is triggered by changes in pH.
A type of protein unfolding evidence where the unfolding of the protein is triggered by changes in temperature.
temperature-induced protein unfolding evidence
A type of cell-based assay evidence resulting from the analysis of cells irreversibly binding to each other.
A type of affinity evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to RNA.
A type of microscopy evidence that is obtained by using the fluorescence of the studied sample instead of or in addition to the scattering, reflection, attenuation or absorption of light.
A type of direct assay evidence where the viscosity of a solution is measured to quantify the material properties of the solution, or the changes of these properties in response to changing composition or environmental factors.
A type of physical interaction evidence derived from the decrease (quenching) of fluorescence as a result of the interaction between a fluorescence donor and acceptor in their excited state.
A type of physical interaction evidence derived from the decrease (quenching) of fluorescence as a result of the intramolecular interaction between a fluorescence donor and acceptor creating a non-fluorescent ground state.
A type of analytical ultracentrifugation evidence that is used in a manual assertion.
analytical ultracentrifugation evidence used in manual assertion
A type of analytical ultracentrifugation evidence that is used in an automatic assertion.
analytical ultracentrifugation evidence used in automatic assertion
A type of fluorescence polarization evidence that is used in a manual assertion.
fluorescence polarization evidence used in manual assertion
A type of fluorescence polarization evidence that is used in an automatic assertion.
fluorescence polarization evidence used in automatic assertion
A type of bait-prey protein pull-down evidence that is used in a manual assertion.
bait-prey protein pull-down evidence used in manual assertion
A type of bait-prey protein pull-down evidence that is used in an automatic assertion.
bait-prey protein pull-down evidence used in automatic assertion
A type of rotary shadowing electron microscopy evidence that is used in a manual assertion.
rotary shadowing electron microscopy evidence used in manual assertion
A type of rotary shadowing electron microscopy evidence that is used in an automatic assertion.
rotary shadowing electron microscopy evidence used in automatic assertion
A type of electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence that is used in a manual assertion.
electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
A type of electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence that is used in an automatic assertion.
electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in automatic assertion
A type of magnetic resonance evidence that is used in a manual assertion.
magnetic resonance evidence used in manual assertion
A type of magnetic resonance evidence that is used in an automatic assertion.
magnetic resonance evidence used in automatic assertion
A type of electron paramagnetic resonance evidence that is used in a manual assertion.
electron paramagnetic resonance evidence used in manual assertion
A type of electron paramagnetic resonance evidence that is used in an automatic assertion.
electron paramagnetic resonance evidence used in automatic assertion
A type of site-directed spin-labelling electron paramagnetic resonance evidence that is used in a manual assertion.
site-directed spin-labelling electron paramagnetic resonance evidence used in manual assertion
A type of site-directed spin-labelling electron paramagnetic resonance evidence that is used in an automatic assertion.
site-directed spin-labelling electron paramagnetic resonance evidence used in automatic assertion
A type of deglycosylation assay evidence that is used in a manual assertion.
deglycosylation assay evidence used in manual assertion
A type of deglycosylation assay evidence that is used in an automatic assertion.
deglycosylation assay evidence used in automatic assertion
A type of protein fragment functional complementation evidence that is used in a manual assertion.
protein fragment functional complementation evidence used in manual assertion
A type of protein fragment functional complementation evidence that is used in an automatic assertion.
protein fragment functional complementation evidence used in automatic assertion
A type of beta galactosidase functional complementation evidence that is used in a manual assertion.
beta galactosidase functional complementation evidence used in manual assertion
A type of beta galactosidase functional complementation evidence that is used in an automatic assertion.
beta galactosidase functional complementation evidence used in automatic assertion
A type of GAL4-VP16 functional complementation evidence that is used in a manual assertion.
GAL4-VP16 functional complementation evidence used in manual assertion
A type of GAL4-VP16 functional complementation evidence that is used in an automatic assertion.
GAL4-VP16 functional complementation evidence used in automatic assertion
A type of Raman spectroscopy evidence that is used in a manual assertion.
Raman spectroscopy evidence used in manual assertion
A type of Raman spectroscopy evidence that is used in an automatic assertion.
Raman spectroscopy evidence used in automatic assertion
A type of protein thermal shift assay evidence that is used in a manual assertion.
protein thermal shift assay evidence used in manual assertion
A type of protein thermal shift assay evidence that is used in an automatic assertion.
protein thermal shift assay evidence used in automatic assertion
A type of microscale thermophoresis evidence that is used in a manual assertion.
microscale thermophoresis evidence used in manual assertion
A type of microscale thermophoresis evidence that is used in an automatic assertion.
microscale thermophoresis evidence used in automatic assertion
A type of native protein gel electrophoresis evidence that is used in a manual assertion.
native protein gel electrophoresis evidence used in manual assertion
A type of native protein gel electrophoresis evidence that is used in an automatic assertion.
native protein gel electrophoresis evidence used in automatic assertion
A type of turbidity measurement evidence that is used in a manual assertion.
turbidity measurement evidence used in manual assertion
A type of turbidity measurement evidence that is used in an automatic assertion.
turbidity measurement evidence used in automatic assertion
A type of competitive binding evidence that is used in a manual assertion.
competitive binding evidence used in manual assertion
A type of competitive binding evidence that is used in an automatic assertion.
competitive binding evidence used in automatic assertion
A type of protein unfolding evidence that is used in a manual assertion.
protein unfolding evidence used in manual assertion
A type of protein unfolding evidence that is used in an automatic assertion.
protein unfolding evidence used in automatic assertion
A type of urea-induced protein unfolding evidence that is used in a manual assertion.
urea-induced protein unfolding evidence used in manual assertion
A type of urea-induced protein unfolding evidence that is used in an automatic assertion.
urea-induced protein unfolding evidence used in automatic assertion
A type of pH-induced protein unfolding evidence that is used in a manual assertion.
pH-induced protein unfolding evidence used in manual assertion
A type of pH-induced protein unfolding evidence that is used in an automatic assertion.
pH-induced protein unfolding evidence used in automatic assertion
A type of temperature-induced protein unfolding evidence that is used in a manual assertion.
temperature-induced protein unfolding evidence used in manual assertion
A type of temperature-induced protein unfolding evidence that is used in an automatic assertion.
temperature-induced protein unfolding evidence used in automatic assertion
A type of cell aggregation evidence that is used in a manual assertion.
cell aggregation evidence used in manual assertion
A type of cell aggregation evidence that is used in an automatic assertion.
cell aggregation evidence used in automatic assertion
A type of RNA-protein binding evidence that is used in a manual assertion.
RNA-protein binding evidence used in manual assertion
A type of RNA-protein binding evidence that is used in an automatic assertion.
RNA-protein binding evidence used in automatic assertion
A type of fluorescence microscopy evidence that is used in a manual assertion.
fluorescence microscopy evidence used in manual assertion
A type of fluorescence microscopy evidence that is used in an automatic assertion.
fluorescence microscopy evidence used in automatic assertion
A type of viscosity measurement evidence that is used in a manual assertion.
viscosity measurement evidence used in manual assertion
A type of viscosity measurement evidence that is used in an automatic assertion.
viscosity measurement evidence used in automatic assertion
A type of dynamic fluorescence quenching evidence that is used in a manual assertion.
dynamic fluorescence quenching evidence used in manual assertion
A type of dynamic fluorescence quenching evidence that is used in an automatic assertion.
dynamic fluorescence quenching evidence used in automatic assertion
A type of static fluorescence quenching evidence that is used in a manual assertion.
static fluorescence quenching evidence used in manual assertion
A type of static fluorescence quenching evidence that is used in an automatic assertion.
static fluorescence quenching evidence used in automatic assertion
A type of staining evidence where Congo red is used to stain cellular structures including amyloid fibrils and aggregates, cell walls of plants and fungi, and for the outer membrane of Gram-negative bacteria.
A type of Congo red staining evidence where the Congo red dye produces an apple-green birefringence when it specifically binds to cross-β-sheets of amyloids which is detectable via cross-polarized light.
A type of fluorescence evidence used to assess the formation of amyloid fibrils indicated by an increase in Thioflavin T fluorescence intensity and a characteristic red shift in the emission spectrum upon binding to amyloids.
thioflavin T based fluorescence spectroscopy evidence
A type of protein thermal shift assay evidence where thermal unfolding is monitored by measuring the fluorescence intensity upon interaction with its environment.
differential scanning fluorimetry evidence
A type of fluorescence evidence that measures fluctuations in fluorescence intensity used to detect biophysical properties of single molecules such as diffusion coefficients and hydrodynamic radii.
fluorescence correlation spectroscopy evidence
A type of fluorescence evidence used to study protein conformation by measuring the emissions of aromatic amino acids, specifically tryptophan, tyrosine and, to a minor extent, phenylalanine residues.
intrinsic fluorescence-based protein conformation evidence
A type of fluorescence evidence used to study binding kinetics by rapidly mixing two interaction components and then "stopping" the reaction in the observation chamber.
stopped-flow fluorescence spectroscopy evidence
A type of fluorescence evidence where the rates of fast chemical reactions in a solution are measured by the intensity of light absorbed or fluoresced by allowing the reaction mixture to come to an equilibrium, and then perturbing the equilibrium by a rapid temperature rise followed by relaxation of the system to the new equilibrium.
A type of computational structure modeling evidence used to build molecular models of intrinsically disordered proteins to capture the dynamic behaviour of their polypeptide chains. Such tools include EOM, ASTEROIDS and ENSEMBLE.
A type of computational evidence used to study the physical movements of atoms and molecules with empirical molecular mechanics force fields.
A type of structure determination evidence in which a computational tool is used to generate a model of structure(s) for a molecule.
computational structure modeling evidence
A type of macroscopy evidence in which non-numerical observed characteristics or features are captured as text descriptions or categorical assignments.
A type of macroscopy evidence in which measurement techniques result in numerical data.
A type of direct assay evidence that reflects the presence, absence, and/or amount of spore formation.
A type of sporulation assay evidence that reflects the presence, absence, and/or amount of asexual spore formation.
A type of sporulation assay evidence that reflects the presence, absence, and/or amount of sexual spore formation.
A type of experimental evidence in which the extent of penetration into a host-surrogate material consisting of a synthetic or other non-living substance is measured.
host-surrogate penetration assay evidence
A type of host colonization assay evidence in which the extent of penetration into host tissue is measured.
A type of radioligand binding assay evidence in which iodine-125 label is used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand.
iodine-125-labeled ligand binding evidence
A type of molecule detection assay evidence in which the detection of the interaction between molecules is done without the use of labels and is instead based on the phase shift-wavelength correlation created between interference patterns off of two unique surfaces on the tip of a biosensor, where the ligand is immobilized onto a bio compatible biosensor while the analyte is in solution.
A type of protein binding evidence in which the use of "bait" molecules or proteins allows the purification or identification of a binding partner, the "prey".
A type of Congo red staining evidence that is used in a manual assertion.
Congo red staining evidence used in manual assertion
A type of Congo red staining evidence that is used in an automatic assertion.
Congo red staining evidence used in automatic assertion
A type of Congo red birefringence evidence that is used in a manual assertion.
Congo red birefringence evidence used in manual assertion
A type of Congo red birefringence evidence that is used in an automatic assertion.
Congo red birefringence evidence used in automatic assertion
A type of thioflavin T based fluorescence spectroscopy evidence that is used in a manual assertion.
thioflavin T based fluorescence spectroscopy evidence used in manual assertion
A type of thioflavin T based fluorescence spectroscopy evidence that is used in an automatic assertion.
thioflavin T based fluorescence spectroscopy evidence used in automatic assertion
A type of differential scanning fluorimetry evidence that is used in a manual assertion.
differential scanning fluorimetry evidence used in manual assertion
A type of differential scanning fluorimetry evidence that is used in an automatic assertion.
differential scanning fluorimetry evidence used in automatic assertion
A type of fluorescence correlation spectroscopy evidence that is used in a manual assertion.
fluorescence correlation spectroscopy evidence used in manual assertion
A type of fluorescence correlation spectroscopy evidence that is used in an automatic assertion.
fluorescence correlation spectroscopy evidence used in automatic assertion
A type of intrinsic fluorescence-based protein conformation evidence that is used in a manual assertion.
intrinsic fluorescence-based protein conformation evidence used in manual assertion
A type of intrinsic fluorescence-based protein conformation evidence that is used in an automatic assertion.
intrinsic fluorescence-based protein conformation evidence used in automatic assertion
A type of stopped-flow fluorescence spectroscopy evidence that is used in a manual assertion.
stopped-flow fluorescence spectroscopy evidence used in manual assertion
A type of stopped-flow fluorescence spectroscopy evidence that is used in an automatic assertion.
stopped-flow fluorescence spectroscopy evidence used in automatic assertion
A type of temperature jump relaxation evidence that is used in a manual assertion.
temperature jump relaxation evidence used in manual assertion
A type of temperature jump relaxation evidence that is used in an automatic assertion.
temperature jump relaxation evidence used in automatic assertion
A type of computational structure modeling evidence that is used in a manual assertion.
computational structure modeling evidence used in manual assertion
A type of computational structure modeling evidence that is used in an automatic assertion.
computational structure modeling evidence used in automatic assertion
A type of structural ensemble generation evidence that is used in a manual assertion.
structural ensemble generation evidence used in manual assertion
A type of structural ensemble generation evidence that is used in an automatic assertion.
structural ensemble generation evidence used in automatic assertion
A type of molecular dynamics evidence that is used in a manual assertion.
molecular dynamics evidence used in manual assertion
A type of molecular dynamics evidence that is used in an automatic assertion.
molecular dynamics evidence used in automatic assertion
A type of qualitative macroscopy evidence that is used in a manual assertion.
qualitative macroscopy evidence used in manual assertion
A type of qualitative macroscopy evidence that is used in an automatic assertion.
qualitative macroscopy evidence used in automatic assertion
A type of quantitative macroscopy evidence that is used in a manual assertion.
quantitative macroscopy evidence used in manual assertion
A type of quantitative macroscopy evidence that is used in an automatic assertion.
quantitative macroscopy evidence used in automatic assertion
A type of sporulation assay evidence that is used in a manual assertion.
sporulation assay evidence used in manual assertion
A type of sporulation assay evidence that is used in an automatic assertion.
sporulation assay evidence used in automatic assertion
A type of asexual sporulation assay evidence that is used in a manual assertion.
asexual sporulation assay evidence used in manual assertion
A type of asexual sporulation assay evidence that is used in an automatic assertion.
asexual sporulation assay evidence used in automatic assertion
A type of sexual sporulation assay evidence that is used in a manual assertion.
sexual sporulation assay evidence used in manual assertion
A type of sexual sporulation assay evidence that is used in an automatic assertion.
sexual sporulation assay evidence used in automatic assertion
A type of host-surrogate penetration assay evidence that is used in a manual assertion.
host-surrogate penetration assay evidence used in manual assertion
A type of host-surrogate penetration assay evidence that is used in an automatic assertion.
host-surrogate penetration assay evidence used in automatic assertion
A type of host penetration assay evidence that is used in a manual assertion.
host penetration assay evidence used in manual assertion
A type of host penetration assay evidence that is used in an automatic assertion.
host penetration assay evidence used in automatic assertion
A type of iodine-125-labeled ligand binding evidence that is used in a manual assertion.
iodine-125-labeled ligand binding evidence used in manual assertion
A type of iodine-125-labeled ligand binding evidence that is used in an automatic assertion.
iodine-125-labeled ligand binding evidence used in automatic assertion
A type of bio-layer interferometry evidence that is used in a manual assertion.
bio-layer interferometry evidence used in manual assertion
A type of bio-layer interferometry evidence that is used in an automatic assertion.
bio-layer interferometry evidence used in automatic assertion
A type of bait-prey interaction evidence that is used in a manual assertion.
bait-prey interaction evidence used in manual assertion
A type of bait-prey interaction evidence that is used in an automatic assertion.
bait-prey interaction evidence used in automatic assertion
A type of self-reported individual's statement evidence in which a person reports their ancestry and that information is taken at face value.
A type of self-reported ancestry evidence that is used in a manual assertion.
self-reported ancestry evidence used in manual assertion
A type of self-reported ancestry evidence that is used in an automatic assertion.
self-reported ancestry evidence used in automatic assertion
A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene.
high throughput mutant phenotype evidence
high throughput mutant phenotypic evidence
A type of high throughput mutant phenotypic evidence that is used in a manual assertion.
high throughput mutant phenotype evidence used in manual assertion
inferred from high throughput mutant phenotype
When using the HMP evidence code, the guidelines for IMP should be adhered to (http://geneontology.org/page/imp-inferred-mutant-phenotype)
high throughput mutant phenotypic evidence used in manual assertion
A type of high throughput evidence resulting from the high throughput analysis of the effect that a given gene has on another gene or genes, and products.
high throughput genetic interaction evidence
high throughput genetic interaction phenotypic evidence
A type of high throughput genetic interaction phenotypic evidence that is used in a manual assertion.
high throughput genetic interaction evidence used in manual assertion
inferred from high throughput genetic interaction
When using the HGI evidence code, the guidelines for IGI should be adhered to (http://geneontology.org/page/igi-inferred-genetic-interaction)
high throughput genetic interaction phenotypic evidence used in manual assertion
A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature.
A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature.
inferred from high throughput direct assay
When using the HDA evidence code, the guidelines for IDA should be adhered to (http://geneontology.org/page/ida-inferred-direct-assay)
high throughput direct assay evidence used in manual assertion
A type of high throughput evidence derived from the high throughput characterization of gene expression.
high throughput expression pattern evidence
A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression.
inferred from high throughput expression pattern
When using the HEP evidence code, the guidelines for EXP should be adhered to (http://geneontology.org/page/iep-inferred-expression-pattern)
high throughput expression pattern evidence used in manual assertion
A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand.
radioactive ligand binding assay evidence
radiometric ligand-binding assay evidence
A type of radioligand binding assay evidence that is used in a manual assertion.
radioligand binding assay evidence used in manual assertion
A type of combinatorial evidence in which the author draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments.
combinatorial evidence from author knowledge and experimental evidence
combinatorial experimental and author inference evidence
A type of combinatorial evidence in which the curator draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments.
combinatorial evidence from curator knowledge and experimental evidence
combinatorial experimental and curator inference evidence
A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion.
combinatorial evidence from author knowledge and experimental evidence used in manual assertion
combinatorial experimental and author inference evidence used in manual assertion
A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion.
combinatorial evidence from curator knowledge and experimental evidence used in manual assertion
combinatorial experimental and curator inference evidence used in manual assertion
A type of substance quantification evidence where an electrical gradient potential is applied to analyze an analyte of interest, resulting in a measurement amount of electrical current across the potential range applied.
A type of voltammetry evidence that is used in a manual assertion.
voltammetry evidence used in manual assertion
A type of fluorescence evidence where a molecule tagged with a fluorescent protein is exposed to ultraviolet or blue light to shift the spectral emission properties for visualization.
A type of photoconversion evidence that is used in a manual assertion.
photoconversion evidence used in manual assertion
A type of immunological assay evidence that involves observation of visible clumping of antibody and antigen into a complex.
A type of agglutination test evidence that is used in a manual assertion.
agglutination test evidence used in manual assertion
A type of agglutination test evidence that involves observaiton of visible clumping of antibody and antigen into a complex on a slide.
A type of slide agglutination test evidence that is used in a manual assertion.
slide agglutination test evidence used in manual assertion
A type of agglutination test evidence that results in detection of nonagglutinating antibodies or complement proteins on red blood cells in vivo.
A type of direct Coombs test evidence that is used in a manual assertion.
direct Coombs test evidence used in manual assertion
A type of agglutination test evidence that results in screening of antibodies against red blood cell antigens (other than the A and B antigens) that are unbound in a patient's serum in vitro.
A type of indirect Coombs test evidence that is used in a manual assertion.
indirect Coombs test evidence used in manual assertion
A type of agglutination test evidence where some bacteria and viruses cross-link red blood cells and clump together.
A type of direct hemagglutination assay evidence that is used in a manual assertion.
direct hemagglutination assay evidence used in manual assertion
A type of agglutination test evidence where antiviral antibodies in a patient's serum or in a lab-produced antiserum neutralize the virus and block it from agglutinating the red blood cells.
viral hemagglutination inhibition assay evidence
A type of viral hemagglutination inhibition assay evidence that is used in a manual assertion.
viral hemagglutination inhibition assay evidence used in manual assertion
A type of immunological assay evidence that results in the detection of presence of specific antibodies in the patient's serum based on the use of complement, a biologically labile serum factor.
A type of compement fixation assay evidence that is used in a manual assertion.
compement fixation assay evidence used in manual assertion
A type of immunogical assay evidence that results in detection of specific neutralizing antibodies in a sample.
A type of neutralization test assay evidence that is used in a manual assertion.
neutralization test assay evidence used in manual assertion
A type of transport assay evidence where the rate of copper transport is estimated.
A type of copper transport assay evidence that is used in a manual assertion.
copper transport assay evidence used in manual assertion
A type of staining evidence that involves the use of the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride to evaluate the respiratory activity of cells.
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence
A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in a manual assertion.
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in manual assertion
A type of cell growth assay evidence resulting in direct quantification of infectious virons and antiviral substances through the counting of discrete plaques (infectious units and cellular dead zones) in cell culture.
A type of plaque assay evidence that is used in a manual assertion.
plaque assay evidence used in manual assertion
A type of fluorescence microscopy evidence where the light source is mounted above the specimen and the excitation light passes through the microscope objective lens on its way toward the specimen.
A type of epifluorescence microscopy evidence that is used in a manual assertion.
epifluorescence microscopy evidence used in manual assertion
A type of electron microscopy evidence where a beam of electrons are transmitted through an ultra thin specimen forming an image which is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera.
conventional transmission electron microscopy(CTEM)
transmission electron microscopy evidence
A type of transmission electron microscopy evidence that is used in a manual assertion.
transmission electron microscopy evidence used in manual assertion
With a general growth of the recombinant mycobacterial strains resulting in minimal change, the cell morphology was further examined using the scanning electron microscopy (SEM) technique. As shown in Fig. 5B, the cell lengthened when 20 ng/mL tetracycline was added to the medium to induce expression of the antisense mtrA mRNA (right panel).
A type of electron microscopy evidence where a focused beam of high-energy electrons is used to generate a variety of signals at the surface of solid specimens.
A type of scanning electron microscopy evidence that is used in a manual assertion.
scanning electron microscopy evidence used in manual assertion
A type of microscopy evidence where a serial images are taken at regular time points to capture the dynamics of what is being observed.
A type of time-lapsed microscopy evidence that is used in a manual assertion.
time-lapsed microscopy evidence used in manual assertion
A type of microscopy evidence where a transparent specimen is illuminated with visible light and small phase shifts in the light passing through the specimen are used to produce an image.
A type of phase contrast microscopy evidence that is used in a manual assertion.
phase contrast microscopy evidence used in manual assertion
A type of microscopy evidence where a sample is illuminated with transmitted white light from below and observed from above.
transmitted light brightfied mircoscopy evidence
A type of transmitted light brightfied mircoscopy evidence that is used in a manual assertion.
transmitted light brightfied mircoscopy evidence used in manual assertion
A type of microscopy evidence that results in a bright image without glare and minimum heating of the specimen by employing both field and an aperture iris diaphragm for illumination.
koehler illumination microscopy evidence
A type of koehler illumination microscopy evidence that is used in a manual assertion.
koehler illumination microscopy evidence used in manual assertion
A type of microscopy evidence that results in visualization of living cells and transparent specimens by taking advantage of differences in the light refraction of different parts of the specimen.
Nomarski interference contrast microscopy
differential interference contrast microscopy evidence
A type of differential interference contrast microscopy evidence that is used in a manual assertion.
differential interference contrast microscopy evidence used in manual assertion
A type of confocal microscopy evidence that results in creation of a continuous confocal multi-colour mosaic from thousands of individually captured images.
extended field laser confocal microscopy evidence
A type of extended field laser confocal microscopy evidence that is used in a manual assertion.
extended field laser confocal microscopy evidence used in manual assertion
A type of confocal microscopy evidence that results in an image that is built up pixel-by-pixel by collecting the emitted photons from the fluorophores in the sample by passing a laser beam through a light source aperture which is then focused by an objective lens into a small area on the surface of the sample.
confocal laser scanning fluorescence microscopy
fluorescence confocal scanning laser microscopy
scanning confocal fluorescence microscopy
confocal laser scanning microscopy evidence
A type of confocal laser scanning microscopy evidence that is used in a manual assertion.
confocal laser scanning microscopy evidence used in manual assertion
A type of structure determination evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by illuminating the sample with a laser beam and the scattered intensity is probed at a certain angle by a detector.
A type of light scattering evidence that is used in a manual assertion.
light scattering evidence used in manual assertion
A type of light scattering evidence derived by analyzing the fluctuations in the internsity of the scattered light by the particles in motion.
A type of dynamic light scattering assay evidence that is used in a manual assertion.
dynamic light scattering assay evidence used in manual assertion
A type of light scattering evidence derived by measuring the average intensity of scattered light by the particles at multiple angles.
A type of static light scattering assay evidence that is used in a manual assertion.
static light scattering assay evidence used in manual assertion
A type of colony morphology phenotypic evidence resulting from the formation of papillae (microcolonies) that protrude outwards from the main colony by mutant cells.
colony papillation assay phenotypic evidence
A type of colony papillation assay phenotypic evidence that is used in a manual assertion.
colony papillation assay evidence used in manual assertion
colony papillation assay phenotypic evidence used in manual assertion
A type of staining evidence that is derived from the use of gentian violet as a general biological stain and an acid-base indicator.
A type of crystal violet staining evidence that is used in a manual assertion.
crystal violet staining evidence used in manual assertion
A type of biofilm formation assay evidence derived from in vitro cultivation and evaluation of bacterial biofilms under hydrodynamic conditions of flow.
A type of flow cell biofilm assay evidence that is used in a manual assertion.
flow cell biofilm assay evidence used in manual assertion
A type of bait-prey hybrid interaction evidence that involves the detection of protein-protein interaction by fusing the protein target (the "bait") to RNA polymerase and fusing protein or peptide library to be analyzed (the "prey") to DNA-binding domain.
A type of bacterial 2-hybrid assay evidence that is used in a manual assertion.
bacterial 2-hybrid assay evidence used in manual assertion
A type of experimental phenotypic evidence that results from the comparison of phenotype profiles (the physical and biochemical traits of organisms in particular environments) across multiple strains; that is, a meta-analysis of a set of phenotypic patterns from many tests in response to a series of changing genetic and/or environmental factors.
A phenome is defined as the SET of physical and biochemical traits, or, as the SET of all phenotypes expressed, i.e. a phenome is defined as the sum total of all phenotypic traits.
D.S. notes: I think this term is meant to be used for high throughput experiments where a large number of mutants is screened for their ability to grow in a large number of conditions. The individual mutants can then clustered based on the similarity of their phenotypic profiles-whether they grew or didn't grow across all the conditions. The goal being to try to identify genes whose products function in the same biological pathways based on their having similar phenotypes across multiple conditions.
A type of phenomic profiling assay evidence that is used in a manual assertion.
phenomic profiling assay evidence used in manual assertion
A type of experimental phenotypic evidence resulting from studying the physical characteristics of an assemblage of microorganisms growing on a solid surface such as the surface of an agar culture medium.
A type of colony morphology phenotypic evidence that is used in a manual assertion.
colony morphology evidence used in manual assertion
colony morphology phenotypic evidence used in manual assertion
A type of colony morphology evidence resulting from studying the colony pigmentation.
A type of colony color phenotypic evidence that is used in a manual assertion.
colony color evidence used in manual assertion
colony color phenotypic evidence used in manual assertion
A type of colony morphology phenotypic evidence resulting from measuring the area or diameter of the colony.
A type of colony size phenotypic evidence that is used in an manual assertion.
colony size evidence used in manual assertion
colony size phenotypic evidence used in manual assertion
A type of cell growth assay evidence resulting from assessing the sensitivity or resistance of bacteria or fungi to an antimicrobial agent or chemical by measuring the size of the zone of inhibition that results when the test organism is grown on a solid surface in the presence of the antimicrobial agent or chemical.
A type of zone of inhibition evidence that is used in a manual assertion.
zone of inhibition evidence used in manual assertion
A type of zone of inhibition evidence resulting from testing the antimicrobial susceptibility by using predefined, continuous, and exponential gradient of antibiotic concentrations immobilized along a rectangular plastic test strip.
A type of Etest evidence that is used in a manual assertion.
A type of expression pattern evidence in which translation is measured by the positions of ribosomes active in a cell, identified through deep sequencing of ribosome-protected mRNA fragments.
A type of ribosome profiling evidence that is used in a manual assertion.
ribosome profiling evidence used in manual assertion
A type of loss-of-function mutant phenotype evidence that is used in a manual assertion.
loss-of-function mutant phenotype evidence used in manual assertion
A type of structural similarity evidence that is used in a manual assertion.
structural similarity evidence used in manual assertion
A type of gain-of-function mutant phenotypic evidence that is used in a manual assertion.
gain-of-function mutant phenotype evidence used in manual assertion
gain-of-function mutant phenotypic evidence used in manual assertion
A type of voucher specimen phenotypic analysis evidence that is used in a manual assertion.
voucher specimen analysis evidence used in manual assertion
voucher specimen phenotypic analysis evidence used in manual assertion
A type of positional similarity evidence that is used in a manual assertion.
positional similarity evidence used in manual assertion
A type of quantitative trait analysis evidence that is used in a manual assertion.
quantitative trait analysis evidence used in manual assertion
A type of compositional similarity evidence that is used in a manual assertion.
compositional similarity evidence used in manual assertion
A type of developmental similarity evidence that is used in a manual assertion.
developmental similarity evidence used in manual assertion
A type of morphological similarity evidence that is used in a manual assertion.
morphological similarity evidence used in manual assertion
A type of gene expression similarity evidence that is used in a manual assertion.
gene expression similarity evidence used in manual assertion
A type of methylation-specific polymerase chain reaction evidence that is used in a manual assertion.
methylation-specific polymerase chain reaction evidence used in manual assertion
A type of southern hybridization evidence that is used in a manual assertion.
southern hybridization evidence used in manual assertion
A type of intermethylated site amplification evidence that is used in a manual assertion.
intermethylated site amplification evidence used in manual assertion
A type of epitope-tagged protein immunolocalization evidence that is used in a manual assertion.
epitope-tagged protein immunolocalization evidence used in manual assertion
A type of co-fractionation evidence that is used in a manual assertion.
co-fractionation evidence used in manual assertion
A type of green fluorescent protein fusion protein localization evidence that is used in a manual assertion.
green fluorescent protein fusion protein localization evidence used in manual assertion
A type of yellow fluorescent protein fusion protein localization evidence that is used in a manual assertion.
yellow fluorescent protein fusion protein localization evidence used in manual assertion
A type of beta-glucuronidase fusion protein localization evidence that is used in a manual assertion.
beta-glucuronidase fusion protein localization evidence used in manual assertion
A type of beta-galactosidase fusion protein localization evidence that is used in a manual assertion.
beta-galactosidase fusion protein localization evidence used in manual assertion
A type of thin layer chromatography evidence that is used in a manual assertion.
thin layer chromatography evidence used in manual assertion
A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in a manual assertion.
in vitro recombinant protein transcription reconstitution assay evidence used in manual assertion
A type of protein separation followed by direct sequencing evidence that is used in a manual assertion.
protein separation followed by direct sequencing evidence used in manual assertion
A type of protein separation followed by fragment identification evidence that is used in a manual assertion.
protein separation followed by fragment identification evidence used in manual assertion
A type of heterologous system uptake evidence that is used in a manual assertion.
heterologous system uptake evidence used in manual assertion
A type of two-electrode voltage clamp recording evidence that is used in a manual assertion.
two-electrode voltage clamp recording evidence used in manual assertion
A type of biochemical trait analysis evidence that is used in a manual assertion.
biochemical trait analysis evidence used in manual assertion
A type of mutant physiological response evidence that is used in a manual assertion.
mutant physiological response evidence used in manual assertion
A type of mutant visible phenotype evidence that is used in a manual assertion.
mutant visible phenotype evidence used in manual assertion
A type of in vivo assay evidence that is used in a manual assertion.
in vivo assay evidence used in manual assertion
A type of animal model system study evidence that is used in a manual assertion.
animal model system study evidence used in manual assertion
A type of clinical study evidence that is used in a manual assertion.
clinical study evidence used in manual assertion
A type of in vitro assay evidence that is used in a manual assertion.
in vitro assay evidence used in manual assertion
A type of enzyme inhibition evidence that is used in a manual assertion.
enzyme inhibition evidence used in manual assertion
A type of Illumina sequencing evidence that is used in a manual assertion.
Illumina sequencing evidence used in manual assertion
A type of 454 pyrosequencing evidence that is used in a manual assertion.
454 pyrosequencing evidence used in manual assertion
A type of SOLiD sequencing evidence that is used in a manual assertion.
SOLiD sequencing evidence used in manual assertion
A type of chain termination sequencing evidence that is used in a manual assertion.
chain termination sequencing evidence used in manual assertion
A type of chromatin immunoprecipitation-qPCR evidence that is used in a manual assertion.
chromatin immunoprecipitation-qPCR evidence used in manual assertion
A type of 4C evidence that is used in a manual assertion.
circularized chromosome conformation capture evidence used in manual assertion
A type of 5C evidence that is used in a manual assertion.
carbon-copy chromosome conformation capture evidence used in manual assertion
A type of 3C-qPCR evidence that is used in a manual assertion.
chromosome conformation capture-qPCR evidence used in manual assertion
3C-qPCR evidence used in manual assertion
A type of Hi-C evidence that is used in a manual assertion.
A type of 3C-seq evidence that is used in a manual assertion.
chromosome conformation capture sequencing evidence used in manual assertion
3C-seq evidence used in manual assertion
A type of environmental perturbation phenotypic evidence that is used in a manual assertion.
environmental perturbation evidence used in manual assertion
environmental perturbation phenotypic evidence used in manual assertion
A type of tissue ablation phenotypic evidence that is used in a manual assertion.
tissue ablation evidence used in manual assertion
tissue ablation phenotypic evidence used in manual assertion
A type of tissue grafting phenotypic evidence that is used in a manual assertion.
tissue grafting evidence used in manual assertion
tissue grafting phenotypic evidence used in manual assertion
A type of cytochalasin experiment evidence that is used in a manual assertion.
cytochalasin experiment evidence used in manual assertion
A type of green fluorescent protein immunolocalization evidence that is used in a manual assertion.
green fluorescent protein immunolocalization evidence used in manual assertion
A type of beta-galactosidase protein immunolocalization evidence that is used in a manual assertion.
beta-galactosidase protein immunolocalization evidence used in manual assertion
A type of cap analysis of gene expression evidence that is used in a manual assertion.
cap analysis of gene expression evidence used in manual assertion
A type of nano-cap analysis of gene expression evidence that is used in a manual assertion.
nano-cap analysis of gene expression evidence used in manual assertion
A type of particle size and count assay evidence that is used in a manual assertion.
particle size and count assay evidence used in manual assertion
A type of competitive growth assay evidence that is used in a manual assertion.
competitive growth assay evidence used in manual assertion
A type of pulsed-field gel electrophoresis evidence that is used in a manual assertion.
pulsed-field gel electrophoresis evidence used in manual assertion
A type of two-dimensional agarose gel electrophoresis evidence that is used in a manual assertion.
two-dimensional agarose gel electrophoresis evidence used in manual assertion
A type of plasmid maintenance assay evidence that is used in a manual assertion.
plasmid maintenance assay evidence used in manual assertion
A type of specific protein inhibition by antibody evidence that is used in a manual assertion.
specific protein inhibition by antibody evidence used in manual assertion
A type of single exon transcript confirmation via alignment evidence that is used in a manual assertion.
single exon transcript confirmation via alignment evidence used in manual assertion
A type of phylogenetic distribution evidence that is used in a manual assertion.
phylogenetic distribution evidence used in manual assertion
A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in a manual assertion.
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) used in manual assertion
A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in a manual assertion.
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) used in manual assertion
A type of biological target-disease association via drug that is used in a manual assertion.
biological target-disease association via drug evidence used in manual assertion
A type of cell staining evidence that is used in a manual assertion.
cell staining evidence used in manual assertion
OBSOLETE. A type of visual sequence inspection evidence that is used in a manual assertion.
obsolete visual sequence inspection evidence used in manual assertion
A type of ATP bioluminescence assay evidence that is used in a manual assertion.
ATP bioluminescence assay evidence used in manual assertion
A type of missense mutation phenotypic evidence that is used in a manual assertion.
missense mutation evidence used in manual assertion
missense mutation pohenotypic evidence used in manual assertion
A type of nonsense mutation phenotypic evidence that is used in a manual assertion.
nonsense mutation evidence used in manual assertion
nonsense mutation phenotypic evidence used in manual assertion
A type of silent mutation evidence that is used in a manual assertion.
silent mutation evidence used in manual assertion
A type of insertion mutation phenotypic evidence that is used in a manual assertion.
insertion mutation evidence used in manual assertion
insertion mutation phenotypic evidence used in manual assertion
A type of duplication mutation evidence that is used in a manual assertion.
duplication mutation evidence used in manual assertion
A type of frameshift mutation phenotypic evidence that is used in a manual assertion.
frameshift mutation evidence used in manual assertion
frameshift mutation phenotypic evidence used in manual assertion
A type of repeat expansion mutation phenotypic evidence that is used in a manual assertion.
repeat expansion mutation evidence used in manual assertion
repeat expansion mutation phenotypic evidence used in manual assertion
A type of splice site mutation phenotypic evidence that is used in a manual assertion.
splice site mutation evidence used in manual assertion
splice site mutation phenotypic evidence used in manual assertion
A type of translocation mutation phenotypic evidence that is used in a manual assertion.
translocation mutation evidence used in manual assertion
translocation mutation phenotypic evidence used in manual assertion
A type of in-gel protein kinase assay evidence that is used in a manual assertion.
in-gel protein kinase assay evidence used in manual assertion
A type of macroscopic current trace evidence that is used in a manual assertion.
macroscopic current trace evidence used in manual assertion
A type of current density evidence that is used in a manual assertion.
current density evidence used in manual assertion
A type of sustained current evidence that is used in a manual assertion.
sustained current evidence used in manual assertion
A type of use dependence of inactivation evidence that is used in a manual assertion.
use dependence of inactivation evidence used in manual assertion
A type of current clamp recording evidence that is used in a manual assertion.
current clamp recording evidence used in manual assertion
A type of whole-cell voltage clamp recording evidence that is used in a manual assertion.
whole-cell voltage clamp recording evidence used in manual assertion
A type of cell-attached single-channel recording evidence that is used in a manual assertion.
cell-attached single-channel recording evidence used in manual assertion
A type of cell-detached inside-out single-channel recording evidence that is used in a manual assertion.
cell-detached inside-out single-channel recording evidence used in manual assertion
A type of reconstituted bilayer single-channel patch recording evidence that is used in a manual assertion.
reconstituted bilayer single-channel patch recording evidence used in manual assertion
A type of electroencephalography recording evidence that is used in a manual assertion.
electroencephalography recording evidence used in manual assertion
A type of cell-detached outside-out single-channel recording evidence that is used in a manual assertion.
cell-detached outside-out single-channel recording evidence used in manual assertion
A type of cut-open oocyte voltage clamp recording evidence that is used in a manual assertion.
cut-open oocyte voltage clamp recording evidence used in manual assertion
A type of macropatch voltage clamp recording evidence that is used in a manual assertion.
macropatch voltage clamp recording evidence used in manual assertion
A type of protein mass spectrometry evidence that is used in a manual assertion.
protein mass spectrometry evidence used in manual assertion
A type of cross-streak test evidence that is used in a manual assertion.
cross-streak test evidence used in manual assertion
A type of tethered cell assay evidence that is used in a manual assertion.
tethered cell assay evidence used in manual assertion
A type of tumble frequency assay evidence that is used in a manual assertion.
tumble frequency assay evidence used in manual assertion
A type of capillary assay evidence that is used in a manual assertion.
capillary assay evidence used in manual assertion
OBSOLETE. A type of inference from experimental data evidence that is used in a manual assertion.
obsolete inference from experimental data evidence used in manual assertion
OBSOLETE. A type of inference from phenotype manipulation evidence that is used in a manual assertion.
obsolete inference from phenotype manipulation evidence used in manual assertion
A type of inference by association of genotype from phenotype that is used in a manual assertion.
inference by association of genotype from phenotype used in manual assertion
A type of motility assay evidence that is used in a manual assertion.
motility assay evidence used in manual assertion
A type of loss-of-function mutant phenotype evidence that is used in an automatic assertion.
loss-of-function mutant phenotype evidence used in automatic assertion
A type of structural similarity evidence that is used in an automatic assertion.
structural similarity evidence used in automatic assertion
A type of gain-of-function mutant phenotypic evidence that is used in an automatic assertion.
gain-of-function mutant phenotype evidence used in automatic assertion
gain-of-function mutant phenotypic evidence used in automatic assertion
A type of voucher specimen phenotypic analysis evidence that is used in an automatic assertion.
voucher specimen analysis evidence used in automatic assertion
voucher specimen phenotypic analysis evidence used in automatic assertion
A type of positional similarity evidence that is used in an automatic assertion.
positional similarity evidence used in automatic assertion
A type of quantitative trait analysis evidence that is used in an automatic assertion.
quantitative trait analysis evidence used in automatic assertion
A type of compositional similarity evidence that is used in an automatic assertion.
compositional similarity evidence used in automatic assertion
A type of developmental similarity evidence that is used in an automatic assertion.
developmental similarity evidence used in automatic assertion
A type of morphological similarity evidence that is used in an automatic assertion.
morphological similarity evidence used in automatic assertion
A type of gene expression similarity evidence that is used in an automatic assertion.
gene expression similarity evidence used in automatic assertion
A type of methylation-specific polymerase chain reaction evidence that is used in an automatic assertion.
methylation-specific polymerase chain reaction evidence used in automatic assertion
A type of southern hybridization evidence that is used in an automatic assertion.
southern hybridization evidence used in automatic assertion
A type of intermethylated site amplification evidence that is used in an automatic assertion.
intermethylated site amplification evidence used in automatic assertion
A type of epitope-tagged protein immunolocalization evidence that is used in an automatic assertion.
epitope-tagged protein immunolocalization evidence used in automatic assertion
A type of co-fractionation evidence that is used in an automatic assertion.
co-fractionation evidence used in automatic assertion
A type of green fluorescent protein fusion protein localization evidence that is used in an automatic assertion.
green fluorescent protein fusion protein localization evidence used in automatic assertion
A type of yellow fluorescent protein fusion protein localization evidence that is used in an automatic assertion.
yellow fluorescent protein fusion protein localization evidence used in automatic assertion
A type of beta-glucuronidase fusion protein localization evidence that is used in an automatic assertion.
beta-glucuronidase fusion protein localization evidence used in automatic assertion
A type of beta-galactosidase fusion protein localization evidence that is used in an automatic assertion.
beta-galactosidase fusion protein localization evidence used in automatic assertion
A type of thin layer chromatography evidence that is used in an automatic assertion.
thin layer chromatography evidence used in automatic assertion
A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in an automatic assertion.
in vitro recombinant protein transcription reconstitution assay evidence used in automatic assertion
A type of protein separation followed by direct sequencing evidence that is used in an automatic assertion.
protein separation followed by direct sequencing evidence used in automatic assertion
A type of protein separation followed by fragment identification evidence that is used in an automatic assertion.
protein separation followed by fragment identification evidence used in automatic assertion
A type of heterologous system uptake evidence that is used in an automatic assertion.
heterologous system uptake evidence used in automatic assertion
A type of two-electrode voltage clamp recording evidence that is used in an automatic assertion.
two-electrode voltage clamp recording evidence used in automatic assertion
A type of biochemical trait analysis evidence that is used in an automatic assertion.
biochemical trait analysis evidence used in automatic assertion
A type of mutant physiological response evidence that is used in an automatic assertion.
mutant physiological response evidence used in automatic assertion
A type of mutant visible phenotype evidence that is used in an automatic assertion.
mutant visible phenotype evidence used in automatic assertion
A type of in vivo assay evidence that is used in an automatic assertion.
in vivo assay evidence used in automatic assertion
A type of animal model system study evidence that is used in an automatic assertion.
animal model system study evidence used in automatic assertion
A type of clinical study evidence that is used in an automatic assertion.
clinical study evidence used in automatic assertion
A type of in vitro assay evidence that is used in an automatic assertion.
in vitro assay evidence used in automatic assertion
A type of enzyme inhibition evidence that is used in an automatic assertion.
enzyme inhibition evidence used in automatic assertion
A type of Illumina sequencing evidence that is used in an automatic assertion.
Illumina sequencing evidence used in automatic assertion
A type of 454 pyrosequencing evidence that is used in an automatic assertion.
454 pyrosequencing evidence used in automatic assertion
A type of SOLiD sequencing evidence that is used in an automatic assertion.
SOLiD sequencing evidence used in automatic assertion
A type of chain termination sequencing evidence that is used in an automatic assertion.
chain termination sequencing evidence used in automatic assertion
A type of chromatin immunoprecipitation-qPCR evidence that is used in an automatic assertion.
chromatin immunoprecipitation-qPCR evidence used in automatic assertion
A type of 4C evidence that is used in an automatic assertion.
circularized chromosome conformation capture evidence used in automatic assertion
A type of 5C evidence that is used in an automatic assertion.
carbon-copy chromosome conformation capture evidence used in automatic assertion
A type of 3C-qPCR evidence that is used in an automatic assertion.
chromosome conformation capture-qPCR evidence used in automatic assertion
3C-qPCR evidence used in automatic assertion
A type of Hi-C evidence that is used in an automatic assertion.
Hi-C evidence used in automatic assertion
A type of 3C-seq evidence that is used in an automatic assertion.
chromosome conformation capture sequencing evidence used in automatic assertion
3C-seq evidence used in automatic assertion
A type of environmental perturbation phenotypic evidence that is used in an automatic assertion.
environmental perturbation evidence used in automatic assertion
environmental perturbation phenotypic evidence used in automatic assertion
A type of tissue ablation phenotypic evidence that is used in an automatic assertion.
tissue ablation evidence used in automatic assertion
tissue ablation phenotypic evidence used in automatic assertion
A type of tissue grafting phenotypic evidence that is used in an automatic assertion.
tissue grafting evidence used in automatic assertion
tissue grafting phenotypic evidence used in automatic assertion
A type of cytochalasin experiment evidence that is used in an automatic assertion.
cytochalasin experiment evidence used in automatic assertion
A type of green fluorescent protein immunolocalization evidence that is used in an automatic assertion.
green fluorescent protein immunolocalization evidence used in automatic assertion
A type of beta-galactosidase protein immunolocalization evidence that is used in an automatic assertion.
beta-galactosidase protein immunolocalization evidence used in automatic assertion
A type of cap analysis of gene expression evidence that is used in an automatic assertion.
cap analysis of gene expression evidence used in automatic assertion
A type of nano-cap analysis of gene expression evidence that is used in an automatic assertion.
nano-cap analysis of gene expression evidence used in automatic assertion
A type of particle size and count assay evidence that is used in an automatic assertion.
particle size and count assay evidence used in automatic assertion
A type of competitive growth assay evidence that is used in an automatic assertion.
competitive growth assay evidence used in automatic assertion
A type of pulsed-field gel electrophoresis evidence that is used in an automatic assertion.
pulsed-field gel electrophoresis evidence used in automatic assertion
A type of two-dimensional agarose gel electrophoresis evidence that is used in an automatic assertion.
two-dimensional agarose gel electrophoresis evidence used in automatic assertion
A type of plasmid maintenance assay evidence that is used in an automatic assertion.
plasmid maintenance assay evidence used in automatic assertion
A type of specific protein inhibition by antibody evidence that is used in an automatic assertion.
specific protein inhibition by antibody evidence used in automatic assertion
A type of single exon transcript confirmation via alignment evidence that is used in an automatic assertion.
single exon transcript confirmation via alignment evidence used in automatic assertion
A type of phylogenetic distribution evidence that is used in an automatic assertion.
phylogenetic distribution evidence used in automatic assertion
A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in an automatic assertion.
differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) used in automatic assertion
A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in an automatic assertion.
differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) used in automatic assertion
A type of biological target-disease association via drug that is used in an automatic assertion.
biological target-disease association via drug evidence used in automatic assertion
A type of cell staining evidence that is used in an automatic assertion.
cell staining evidence used in automatic assertion
OBSOLETE. A type of visual sequence inspection evidence that is used in an automatic assertion.
obsolete visual sequence inspection evidence used in automatic assertion
A type of ATP bioluminescence assay evidence that is used in an automatic assertion.
ATP bioluminescence assay evidence used in automatic assertion
A type of missense mutation phenotypic evidence that is used in an automatic assertion.
missense mutation evidence used in automatic assertion
missense mutation phenotypic evidence used in automatic assertion
A type of nonsense mutation phenotypic evidence that is used in an automatic assertion.
nonsense mutation evidence used in automatic assertion
nonsense mutation phenotypic evidence used in automatic assertion
A type of silent mutation evidence that is used in an automatic assertion.
silent mutation evidence used in automatic assertion
A type of insertion mutation phenotypic evidence that is used in an automatic assertion.
insertion mutation evidence used in automatic assertion
insertion mutation phenotypic evidence used in automatic assertion
A type of duplication mutation evidence that is used in an automatic assertion.
duplication mutation evidence used in automatic assertion
A type of frameshift mutation phenotypic evidence that is used in an automatic assertion.
frameshift mutation evidence used in automatic assertion
frameshift mutation phenotypic evidence used in automatic assertion
A type of repeat expansion mutation phenotypic evidence that is used in an automatic assertion.
repeat expansion mutation evidence used in automatic assertion
repeat expansion mutation phenotypic evidence used in automatic assertion
A type of splice site mutation phenotypic evidence that is used in an automatic assertion.
splice site mutation evidence used in automatic assertion
splice site mutation phenotypic evidence used in automatic assertion
A type of translocation mutation phenotypic evidence that is used in an automatic assertion.
translocation mutation evidence used in automatic assertion
translocation mutation phenotypic evidence used in automatic assertion
A type of in-gel protein kinase assay evidence that is used in an automatic assertion.
in-gel protein kinase assay evidence used in automatic assertion
A type of macroscopic current trace evidence that is used in an automatic assertion.
macroscopic current trace evidence used in automatic assertion
A type of current density evidence that is used in an automatic assertion.
current density evidence used in automatic assertion
A type of sustained current evidence that is used in an automatic assertion.
sustained current evidence used in automatic assertion
A type of use dependence of inactivation evidence that is used in an automatic assertion.
use dependence of inactivation evidence used in automatic assertion
A type of current clamp recording evidence that is used in an automatic assertion.
current clamp recording evidence used in automatic assertion
A type of whole-cell voltage clamp recording evidence that is used in an automatic assertion.
whole-cell voltage clamp recording evidence used in automatic assertion
A type of cell-attached single-channel recording evidence that is used in an automatic assertion.
cell-attached single-channel recording evidence used in automatic assertion
A type of cell-detached inside-out single-channel recording evidence that is used in an automatic assertion.
cell-detached inside-out single-channel recording evidence used in automatic assertion
A type of reconstituted bilayer single-channel patch recording evidence that is used in an automatic assertion.
reconstituted bilayer single-channel patch recording evidence used in automatic assertion
A type of electroencephalography recording evidence that is used in an automatic assertion.
electroencephalography recording evidence used in automatic assertion
A type of cell-detached outside-out single-channel recording evidence that is used in an automatic assertion.
cell-detached outside-out single-channel recording evidence used in automatic assertion
A type of cut-open oocyte voltage clamp recording evidence that is used in an automatic assertion.
cut-open oocyte voltage clamp recording evidence used in automatic assertion
A type of macropatch voltage clamp recording evidence that is used in an automatic assertion.
macropatch voltage clamp recording evidence used in automatic assertion
A type of protein mass spectrometry evidence that is used in an automatic assertion.
protein mass spectrometry evidence used in automatic assertion
A type of cross-streak test evidence that is used in an automatic assertion.
cross-streak test evidence used in automatic assertion
A type of tethered cell assay evidence that is used in an automatic assertion.
tethered cell assay evidence used in automatic assertion
A type of tumble frequency assay evidence that is used in an automatic assertion.
tumble frequency assay evidence used in automatic assertion
A type of capillary assay evidence that is used in an automatic assertion.
capillary assay evidence used in automatic assertion
OBSOLETE. A type of inference from experimental data evidence that is used in an automatic assertion.
obsolete inference from experimental data evidence used in automatic assertion
OBSOLETE. A type of inference from phenotype manipulation evidence that is used in an automatic assertion.
obsolete inference from phenotype manipulation evidence used in automatic assertion
A type of inference by association of genotype from phenotype that is used in an automatic assertion.
inference by association of genotype from phenotype used in automatic assertion
A type of motility assay evidence that is used in an automatic assertion.
motility assay evidence used in automatic assertion
A type of experimental evidence that is used in an automatic assertion.
experimental evidence used in automatic assertion
A type of expression pattern evidence that is used in an automatic assertion.
expression pattern evidence used in automatic assertion
A type of Affymetrix GeneChip evidence that is used in an automatic assertion.
Affymetrix GeneChip evidence used in automatic assertion
A type of cRNA to DNA expression microarray evidence that is used in an automatic assertion.
cRNA to DNA expression microarray evidence used in automatic assertion
A type of expression microarray evidence that is used in an automatic assertion.
expression microarray evidence used in automatic assertion
A type of differential methylation hybridization evidence that is used in an automatic assertion.
differential methylation hybridization evidence used in automatic assertion
A type of transcript expression evidence that is used in an automatic assertion.
transcriptomics evidence used in automatic assertion
transcript expression evidence used in automatic assertion
A type of Nimblegen array evidence that is used in an automatic assertion.
Nimblegen array evidence used in automatic assertion
A type of array-based sequence capture evidence that is used in an automatic assertion.
array-based sequence capture evidence used in automatic assertion
A type of qualitative western immunoblotting evidence that is used in an automatic assertion.
protein expression level evidence based on western blot used in automatic assertion
qualitative western immunoblotting evidence used in automatic assertion
A type of direct assay evidence that is used in an automatic assertion.
direct assay evidence used in automatic assertion
A type of protein expression evidence that is used in an automatic assertion.
protein expression level evidence used in automatic assertion
protein expression evidence used in automatic assertion
A type of expression library screen evidence that is used in an automatic assertion.
expression library screen evidence used in automatic assertion
A type of heterologous protein expression evidence that is used in an automatic assertion.
heterologous protein expression evidence used in automatic assertion
A type of spatial pattern of protein expression evidence that is used in an automatic assertion.
spatial pattern of protein expression evidence used in automatic assertion
A type of DNA to cDNA expression microarray evidence that is used in an automatic assertion.
DNA to cDNA expression microarray evidence used in automatic assertion
A type of differential hybridization evidence that is used in an automatic assertion.
differential hybridization evidence used in automatic assertion
A type of RNA protection assay evidence that is used in an automatic assertion.
RNA protection assay evidence used in automatic assertion
A type of nuclease protection assay evidence that is used in an automatic assertion.
nuclease protection assay evidence used in automatic assertion
A type of spatial pattern of transcript expression evidence that is used in an automatic assertion.
spatial pattern of transcript expression evidence used in automatic assertion
A type of subtractive hybridization evidence that is used in an automatic assertion.
subtractive hybridization evidence used in automatic assertion
A type of author statement that is used in an automatic assertion.
author statement used in automatic assertion
A type of author statement without traceable support that is used in an automatic assertion.
non-traceable author statement used in automatic assertion
author statement without traceable support used in automatic assertion
A type of author statement supported by traceable reference that is used in an automatic assertion.
traceable author statement used in automatic assertion
author statement supported by traceable reference used in automatic assertion
A type of curator inference that is used in an automatic assertion.
curator inference used in automatic assertion
Gene Ontology annotation based on Swiss-Prot keyword mapping.
Gene Ontology annotation based on UniProtKB Subcellular Location vocabulary mapping.
A type of inference from background scientific knowledge that is used in an automatic assertion.
inference from background scientific knowledge used in automatic assertion
An inference that results when research finds no evidence information in the scientific literature, at reference databases, or from other resources that is used in an automatic assertion.
no evidence data found used in automatic assertion
A type of mutant phenotype evidence that is used in an automatic assertion.
mutant phenotype evidence used in automatic assertion
A type of genetic interaction evidence that is used in an automatic assertion.
genetic interaction evidence used in automatic assertion
A type of genomic context evidence that is used in an automatic assertion.
genomic context evidence used in automatic assertion
A type of biological aspect of ancestor evidence that is used in an automatic assertion.
biological aspect of ancestor evidence used in automatic assertion
A type of biological aspect of descendant evidence that is used in an automatic assertion.
biological aspect of descendant evidence used in automatic assertion
A type of phylogenetic determination of loss of key residues evidence that is used in an automatic assertion.
phylogenetic determination of loss of key residues evidence used in automatic assertion
A type of rapid divergence from ancestral sequence evidence that is used in an automatic assertion.
rapid divergence from ancestral sequence evidence used in automatic assertion
A type of physical interaction evidence that is used in an automatic assertion.
physical interaction evidence used in automatic assertion
A type of gene neighbors evidence that is used in an automatic assertion.
gene neighbors evidence used in automatic assertion
A type of Edman degradation evidence that is used in an automatic assertion.
Edman degradation evidence used in automatic assertion
A type of 3D cell culture evidence that is used in an automatic assertion.
3D cell culture evidence used in automatic assertion
A type of 51Cr release assay evidence that is used in an automatic assertion.
51Cr release assay evidence used in automatic assertion
A type of 7-aminoactinomycin staining evidence that is used in an automatic assertion.
7-aminoactinomycin staining evidence used in automatic assertion
A type of [3H]-thymidine incorporation assay evidence that is used in an automatic assertion.
[3H]-thymidine incorporation assay evidence used in automatic assertion
A type of [3H]arachidonic acid release assay evidence that is used in an automatic assertion.
[3H]arachidonic acid release assay evidence used in automatic assertion
A type of adhesion assay evidence that is used in an automatic assertion.
adhesion assay evidence used in automatic assertion
A type of adoptive cell transfer evidence that is used in an automatic assertion.
adoptive cell transfer evidence used in automatic assertion
A type of alamarBlue assay evidence that is used in an automatic assertion.
alamarBlue assay evidence used in automatic assertion
A type of allograft transplantation phenotypic evidence that is used in an automatic assertion.
allograft transplantation evidence used in automatic assertion
allograft transplantation phenotypic evidence used in automatic assertion
A type of anion-exchange chromatography evidence that is used in an automatic assertion.
anion-exchange chromatography evidence used in automatic assertion
A type of annexin-V staining evidence that is used in an automatic assertion.
annexin-V staining evidence used in automatic assertion
A type of cognitive assay phenotypic evidence that is used in an automatic assertion.
behavioral assay evidence used in automatic assertion
cognitive assay phenotypic evidence used in automatic assertion
A type of blocking monoclonal antibody evidence that is used in an automatic assertion.
blocking monoclonal antibody evidence used in automatic assertion
A type of immunological assay evidence that is used in an automatic assertion.
immunological assay evidence used in automatic assertion
A type of blocking peptide evidence that is used in an automatic assertion.
blocking peptide evidence used in automatic assertion
A type of blocking polyclonal antibody evidence that is used in an automatic assertion.
blocking polyclonal antibody evidence used in automatic assertion
A type of blood test evidence that is used in an automatic assertion.
blood test evidence used in automatic assertion
A type of Boyden chamber assay evidence that is used in an automatic assertion.
Boyden chamber assay evidence used in automatic assertion
A type of bromodeoxyuridine incorporation assay evidence that is used in an automatic assertion.
bromodeoxyuridine incorporation assay evidence used in automatic assertion
A type of nucleotide analog incorporation assay evidence that is used in an automatic assertion.
nucleotide analog incorporation assay evidence used in automatic assertion
A type of caspase assay evidence that is used in an automatic assertion.
caspase assay evidence used in automatic assertion
A type of cell counting evidence that is used in an automatic assertion.
cell counting evidence used in automatic assertion
A type of cell permeability assay evidence that is used in an automatic assertion.
cell permeability assay evidence used in automatic assertion
A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in an automatic assertion.
carboxyfluorescein diacetate succinimidyl ester staining evidence used in automatic assertion
A type of chemiluminescence-linked immunoassay evidence that is used in an automatic assertion.
chemiluminescence-linked immunoassay evidence used in automatic assertion
A type of chimeric protein phenotypic evidence that is used in an automatic assertion.
chimeric protein evidence used in automatic assertion
chimeric protein phenotypic evidence used in automatic assertion
A type of co-electrophoresis evidence that is used in an automatic assertion.
co-electrophoresis evidence used in automatic assertion
A type of co-localization evidence that is used in an automatic assertion.
co-localization evidence used in automatic assertion
A type of imaging assay evidence that is used in an automatic assertion.
imaging assay evidence used in automatic assertion
A type of co-sedimentation assay evidence that is used in an automatic assertion.
co-sedimentation assay evidence used in automatic assertion
A type of colony counting evidence that is used in an automatic assertion.
colony counting evidence used in automatic assertion
A type of comet assay evidence that is used in an automatic assertion.
comet assay evidence used in automatic assertion
A type of conditional knockin evidence that is used in an automatic assertion.
conditional knockin evidence used in automatic assertion
A type of knockin evidence that is used in an automatic assertion.
knockin evidence used in automatic assertion
A type of conditional knockout evidence that is used in an automatic assertion.
conditional knockout evidence used in automatic assertion
A type of knockout evidence that is used in an automatic assertion.
knockout evidence used in automatic assertion
A type of constitutively active mutant protein evidence that is used in an automatic assertion.
constitutively active mutant protein evidence used in automatic assertion
A type of cross-linking evidence that is used in an automatic assertion.
cross-linking evidence used in automatic assertion
A type of protein binding evidence that is used in an automatic assertion.
protein binding evidence used in automatic assertion
A type of crystallography evidence that is used in an automatic assertion.
crystallography evidence used in automatic assertion
A type of cytochemistry evidence that is used in an automatic assertion.
cytochemistry evidence used in automatic assertion
A type of histochemistry evidence that is used in an automatic assertion.
histochemistry evidence used in automatic assertion
A type of cytochrome C release assay evidence that is used in an automatic assertion.
cytochrome C release assay evidence used in automatic assertion
A type of 4',6-diamidino-2-phenylindole staining evidence that is used in an automatic assertion.
4',6-diamidino-2-phenylindole staining evidence used in automatic assertion
A type of deletion mutation phenotypic evidence that is used in an automatic assertion.
deletion mutation evidence used in automatic assertion
deletion mutation phenotypic evidence used in automatic assertion
A type of DNA laddering assay evidence that is used in an automatic assertion.
DNA laddering assay evidence used in automatic assertion
A type of RNA dot blot assay evidence that is used in an automatic assertion.
RNA dot blot assay evidence used in automatic assertion
A type of dominant-negative mutant phenotypic evidence that is used in an automatic assertion.
dominant-negative mutant evidence used in automatic assertion
dominant-negative mutant phenotypic evidence used in automatic assertion
A type of eTag assay evidence that is used in an automatic assertion.
eTag assay evidence used in automatic assertion
A type of affinity evidence that is used in an automatic assertion.
affinity evidence used in automatic assertion
A type of filter binding assay evidence that is used in an automatic assertion.
filter binding assay evidence used in automatic assertion
A type of fluorescence in situ hybridization evidence that is used in an automatic assertion.
fluorescence in situ hybridization evidence used in automatic assertion
A type of fluorescence resonance energy transfer evidence that is used in an automatic assertion.
fluorescence resonance energy transfer evidence used in automatic assertion
A type of gel-filtration evidence that is used in an automatic assertion.
gel-filtration evidence used in automatic assertion
A type of histology evidence that is used in an automatic assertion.
histology evidence used in automatic assertion
A type of immunocytochemistry evidence that is used in an automatic assertion.
immunocytochemistry evidence used in automatic assertion
A type of immunodepletion evidence that is used in an automatic assertion.
immunodepletion evidence used in automatic assertion
A type of immunohistochemistry evidence that is used in an automatic assertion.
immunohistochemistry evidence used in automatic assertion
A type of in vitro acetylation assay evidence that is used in an automatic assertion.
in vitro acetylation assay evidence used in automatic assertion
A type of in vitro cleavage assay evidence that is used in an automatic assertion.
in vitro cleavage assay evidence used in automatic assertion
A type of in vitro deacetylation assay evidence that is used in an automatic assertion.
in vitro deacetylation assay evidence used in automatic assertion
A type of in vitro defarnesylation assay evidence that is used in an automatic assertion.
in vitro defarnesylation assay evidence used in automatic assertion
A type of in vitro demethylation assay evidence that is used in an automatic assertion.
in vitro demethylation assay evidence used in automatic assertion
A type of in vitro desumoylation assay evidence that is used in an automatic assertion.
in vitro desumoylation assay evidence used in automatic assertion
A type of in vitro deubiquitination assay evidence that is used in an automatic assertion.
in vitro deubiquitination assay evidence used in automatic assertion
A type of in vitro farnesylation assay evidence that is used in an automatic assertion.
in vitro farnesylation assay evidence used in automatic assertion
A type of in vitro methylation assay evidence that is used in an automatic assertion.
in vitro methylation assay evidence used in automatic assertion
A type of in vitro palmitoylation assay evidence that is used in an automatic assertion.
in vitro palmitoylation assay evidence used in automatic assertion
A type of in vitro phosphatase assay evidence that is used in an automatic assertion.
in vitro phosphatase assay evidence used in automatic assertion
A type of in vitro polyADP-ribosylation assay evidence that is used in an automatic assertion.
in vitro polyADP-ribosylation assay evidence used in automatic assertion
A type of in vitro protein kinase assay evidence that is used in an automatic assertion.
in vitro protein kinase assay evidence used in automatic assertion
A type of in vitro sumoylation assay evidence that is used in an automatic assertion.
in vitro sumoylation assay evidence used in automatic assertion
A type of in vitro transcription assay evidence that is used in an automatic assertion.
in vitro transcription assay evidence used in automatic assertion
A type of in vitro translation assay evidence that is used in an automatic assertion.
in vitro translation assay evidence used in automatic assertion
A type of in vitro ubiquitination assay evidence that is used in an automatic assertion.
in vitro ubiquitination assay evidence used in automatic assertion
A type of in vivo acetylation assay evidence that is used in an automatic assertion.
in vivo acetylation assay evidence used in automatic assertion
A type of in vivo cleavage assay evidence that is used in an automatic assertion.
in vivo cleavage assay evidence used in automatic assertion
A type of in vivo deacetylation assay evidence that is used in an automatic assertion.
in vivo deacetylation assay evidence used in automatic assertion
A type of in vivo defarnesylation assay evidence that is used in an automatic assertion.
in vivo defarnesylation assay evidence used in automatic assertion
A type of in vivo demethylation assay evidence that is used in an automatic assertion.
in vivo demethylation assay evidence used in automatic assertion
A type of in vivo desumoylation assay evidence that is used in an automatic assertion.
in vivo desumoylation assay evidence used in automatic assertion
A type of in vivo deubiquitination assay evidence that is used in an automatic assertion.
in vivo deubiquitination assay evidence used in automatic assertion
A type of in vivo farnesylation assay evidence that is used in an automatic assertion.
in vivo farnesylation assay evidence used in automatic assertion
A type of in vivo methylation assay evidence that is used in an automatic assertion.
in vivo methylation assay evidence used in automatic assertion
A type of in vivo palmitoylation assay evidence that is used in an automatic assertion.
in vivo palmitoylation assay evidence used in automatic assertion
A type of in vivo phosphatase assay evidence that is used in an automatic assertion.
in vivo phosphatase assay evidence used in automatic assertion
A type of in vivo protein kinase assay evidence that is used in an automatic assertion.
in vivo protein kinase assay evidence used in automatic assertion
A type of in vivo sumoylation assay evidence that is used in an automatic assertion.
in vivo sumoylation assay evidence used in automatic assertion
A type of in vivo transcription assay evidence that is used in an automatic assertion.
in vivo transcription assay evidence used in automatic assertion
A type of in vivo translation assay evidence that is used in an automatic assertion.
in vivo translation assay evidence used in automatic assertion
A type of in vivo ubiquitination assay evidence that is used in an automatic assertion.
in vivo ubiquitination assay evidence used in automatic assertion
OBSOLETE. A type of induced mutation evidence that is used in an automatic assertion.
obsolete induced mutation evidence used in automatic assertion
A type of genetic transformation evidence that is used in an automatic assertion.
genetic transformation evidence used in automatic assertion
A type of lipid binding assay evidence that is used in an automatic assertion.
lipid binding assay evidence used in automatic assertion
A type of luminescence-based mammalian interactome mapping assay evidence that is used in an automatic assertion.
luminescence-based mammalian interactome mapping assay evidence used in automatic assertion
A type of macroscopy evidence that is used in an automatic assertion.
macroscopy evidence used in automatic assertion
A type of mammalian 2-hybrid assay evidence that is used in an automatic assertion.
mammalian 2-hybrid assay evidence used in automatic assertion
A type of bait-prey hybrid interaction evidence that is used in an automatic assertion.
bait-prey hybrid interaction evidence used in automatic assertion
A type of mass spectrometry evidence that is used in an automatic assertion.
mass spectrometry evidence used in automatic assertion
A type of medical imaging evidence that is used in an automatic assertion.
medical imaging evidence used in automatic assertion
A type of microscopy evidence that is used in an automatic assertion.
microscopy evidence used in automatic assertion
A type of motility wound healing assay evidence that is used in an automatic assertion.
motility wound healing assay evidence used in automatic assertion
A type of MTS assay evidence that is used in an automatic assertion.
MTS assay evidence used in automatic assertion
A type of MTT assay evidence that is used in an automatic assertion.
MTT assay evidence used in automatic assertion
A type of multiplex bead-based immunoassay evidence that is used in an automatic assertion.
multiplex bead-based immunoassay evidence used in automatic assertion
A type of natural variation mutant evidence that is used in an automatic assertion.
natural variation mutant evidence used in automatic assertion
A type of nuclear magnetic resonance evidence that is used in an automatic assertion.
nuclear magnetic resonance evidence used in automatic assertion
A type of nuclear fragmentation evidence that is used in an automatic assertion.
nuclear fragmentation evidence used in automatic assertion
A type of phage display evidence that is used in an automatic assertion.
phage display evidence used in automatic assertion
A type of phosphoamino acid analysis evidence that is used in an automatic assertion.
phosphoamino acid analysis evidence used in automatic assertion
A type of peptide affinity enrichment evidence that is used in an automatic assertion.
peptide affinity enrichment evidence used in automatic assertion
A type of peptide array evidence that is used in an automatic assertion.
peptide array evidence used in automatic assertion
A type of physical examination evidence that is used in an automatic assertion.
physical examination evidence used in automatic assertion
A type of point mutation phenotypic evidence that is used in an automatic assertion.
point mutation evidence used in automatic assertion
point mutation phenotypic evidence used in automatic assertion
A type of propidium iodide staining evidence that is used in an automatic assertion.
propidium iodide staining evidence used in automatic assertion
A type of fluorescence evidence that is used in an automatic assertion.
fluorescence evidence used in automatic assertion
A type of protein dot blot assay evidence that is used in an automatic assertion.
protein dot blot assay evidence used in automatic assertion
A type of protein microarray evidence that is used in an automatic assertion.
protein microarray evidence used in automatic assertion
A type of protein sequencing assay evidence that is used in an automatic assertion.
protein sequencing assay evidence used in automatic assertion
A type of quantitative mass spectrometry evidence that is used in an automatic assertion.
quantitative mass spectrometry evidence used in automatic assertion
A type of radioisotope assay evidence that is used in an automatic assertion.
radioisotope assay evidence used in automatic assertion
A type of radioimmunoassay evidence that is used in an automatic assertion.
radioimmunoassay evidence used in automatic assertion
A type of restriction fragment detection evidence that is used in an automatic assertion.
restriction fragment detection evidence used in automatic assertion
A type of spectrophotometry evidence that is used in an automatic assertion.
spectrophotometry evidence used in automatic assertion
A type of syngeneic transplantation experiment evidence that is used in an automatic assertion.
syngeneic transplantation experiment evidence used in automatic assertion
A type of xenotransplantation phenotypic evidence that is used in an automatic assertion.
xenotransplantation experiment evidence used in automatic assertion
xenotransplantation phenotypic evidence used in automatic assertion
A type of WST-1 assay evidence that is used in an automatic assertion.
WST-1 assay evidence used in automatic assertion
A type of urine test evidence that is used in an automatic assertion.
urine test evidence used in automatic assertion
A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence that is used in an automatic assertion.
terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in automatic assertion
A type of tryptic phosphopeptide mapping assay evidence that is used in an automatic assertion.
tryptic phosphopeptide mapping assay evidence used in automatic assertion
A type of transgenic organism evidence that is used in an automatic assertion.
transgenic organism evidence used in automatic assertion
A type of tissue microarray evidence that is used in an automatic assertion.
tissue microarray evidence used in automatic assertion
A type of TACE activity assay evidence that is used in an automatic assertion.
TACE activity assay evidence used in automatic assertion
A type of enzyme assay evidence that is used in an automatic assertion.
enzymatic activity assay evidence used in automatic assertion
A type of surface plasmon resonance evidence that is used in an automatic assertion.
surface plasmon resonance evidence used in automatic assertion
A type of restriction landmark genomic scanning evidence that is used in an automatic assertion.
restriction landmark genomic scanning evidence used in automatic assertion
A type of resonant mirror biosensor evidence that is used in an automatic assertion.
resonant mirror biosensor evidence used in automatic assertion
A type of high-performance liquid chromatography evidence that is used in an automatic assertion.
high-performance liquid chromatography evidence used in automatic assertion
A type of ectopic expression evidence that is used in an automatic assertion.
ectopic expression evidence used in automatic assertion
A type of electrophoretic mobility shift assay evidence that is used in an automatic assertion.
electrophoretic mobility shift assay evidence used in automatic assertion
A type of reverse transcription polymerase chain reaction evidence that is used in an automatic assertion.
reverse transcription polymerase chain reaction evidence used in automatic assertion
A type of in vivo polyADP-ribosylation assay evidence that is used in an automatic assertion.
in vivo polyADP-ribosylation assay evidence used in automatic assertion
A type of DNA dot blot assay evidence that is used in an automatic assertion.
DNA dot blot assay evidence used in automatic assertion
A type of random mutagenesis phenotypic evidence that is used in an automatic assertion.
random mutagenesis evidence used in automatic assertion
A type of biological system reconstruction evidence by experimental evidence from single species that is used in an automatic assertion.
biological system reconstruction evidence by experimental evidence from single species used in automatic assertion
A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in an automatic assertion.
biological system reconstruction evidence by experimental evidence from mixed species used in automatic assertion
A type of biological system reconstruction evidence based on orthology evidence that is used in an automatic assertion.
biological system reconstruction evidence based on orthology evidence used in automatic assertion
A type of biological system reconstruction evidence based on homology evidence that is used in an automatic assertion.
biological system reconstruction evidence based on homology evidence used in automatic assertion
A type of biological system reconstruction evidence based on paralogy evidence that is used in an automatic assertion.
biological system reconstruction evidence based on paralogy evidence used in automatic assertion
A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in an automatic assertion.
biological system reconstruction evidence based on inference from background scientific knowledge used in automatic assertion
A type of immunogold labelling evidence that is used in an automatic assertion.
immunogold labelling evidence used in automatic assertion
A type of immunolocalization evidence that is used in an automatic assertion.
immunolocalization evidence used in automatic assertion
A type of flow cytometry evidence that is used in an automatic assertion.
flow cytometry evidence used in automatic assertion
A type of enzyme-linked immunoabsorbent assay evidence that is used in an automatic assertion.
enzyme-linked immunoabsorbent assay evidence used in automatic assertion
A type of high throughput mass spectrometry evidence that is used in an automatic assertion.
high throughput mass spectrometry evidence used in automatic assertion
A type of confocal microscopy evidence that is used in an automatic assertion.
confocal microscopy evidence used in automatic assertion
A type of wide-field microscopy evidence that is used in an automatic assertion.
wide-field microscopy evidence used in automatic assertion
A type of immunogold labelling electron microscopy assay evidence that is used in an automatic assertion.
immunogold labelling electron microscopy assay evidence used in automatic assertion
A type of electron microscopy evidence that is used in an automatic assertion.
electron microscopy evidence used in automatic assertion
A type of immunoperoxidase immunolocalization evidence that is used in an automatic assertion.
immunoperoxidase immunolocalization evidence used in automatic assertion
A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in an automatic assertion.
immunoperoxidase immunolocalization electron microscopy evidence used in automatic assertion
A type of immunofluorescence confocal microscopy evidence that is used in an automatic assertion.
immunofluorescence confocal microscopy evidence used in automatic assertion
A type of immunofluorescence evidence that is used in an automatic assertion.
immunofluorescence evidence used in automatic assertion
A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in an automatic assertion.
two-dimensional polyacrylamide gel electrophoresis evidence used in automatic assertion
A type of alkaline phosphatase reporter gene assay evidence that is used in an automatic assertion.
alkaline phosphatase reporter gene assay evidence used in automatic assertion
A type of beta-galactosidase reporter gene assay evidence that is used in an automatic assertion.
LacZ transcript localization evidence used in automatic assertion
beta-galactosidase reporter gene assay evidence used in automatic assertion
A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in an automatic assertion.
chloramphenicol acetyltransferase reporter gene assay evidence used in automatic assertion
A type of chromatin immunoprecipitation-PCR evidence that is used in an automatic assertion.
chromatin immunoprecipitation-PCR evidence used in automatic assertion
A type of immunoprecipitation evidence that is used in an automatic assertion.
immunoprecipitation evidence used in automatic assertion
A type of copper-phenanthroline footprinting evidence that is used in an automatic assertion.
copper-phenanthroline footprinting evidence used in automatic assertion
A type of nucleic acid binding evidence that is used in an automatic assertion.
nucleic acid binding evidence used in automatic assertion
A type of DNA affinity chromatography evidence that is used in an automatic assertion.
DNA affinity chromatography evidence used in automatic assertion
A type of DNAse footprinting evidence that is used in an automatic assertion.
DNAse footprinting evidence used in automatic assertion
A type of fluorescence anisotropy evidence that is used in an automatic assertion.
fluorescence anisotropy evidence used in automatic assertion
A type of ferric uptake regulator titration assay evidence that is used in an automatic assertion.
ferric uptake regulator titration assay evidence used in automatic assertion
A type of systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion.
systematic evolution of ligands by exponential amplification evidence used in automatic assertion
A type of glutathione S-transferase pull-down assay evidence that is used in an automatic assertion.
glutathione S-transferase pull-down assay evidence used in automatic assertion
A type of beta-glucuronidase reporter gene assay evidence that is used in an automatic assertion.
beta-glucuronidase reporter gene assay evidence used in automatic assertion
A type of heteronuclear single quantum coherence spectroscopy evidence that is used in an automatic assertion.
heteronuclear single quantum coherence spectroscopy evidence used in automatic assertion
A type of hydroxyl-radical footprinting evidence that is used in an automatic assertion.
hydroxyl-radical footprinting evidence used in automatic assertion
A type of isothermal titration calorimetry evidence that is used in an automatic assertion.
isothermal titration calorimetry evidence used in automatic assertion
A type of luciferase reporter gene assay evidence that is used in an automatic assertion.
luciferase reporter gene assay evidence used in automatic assertion
A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in an automatic assertion.
methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in automatic assertion
A type of northern blot evidence that is used in an automatic assertion.
northern blot evidence used in automatic assertion
A type of methylation interference footprinting evidence that is used in an automatic assertion.
premethylation interference footprinting evidence used in automatic assertion
methylation interference footprinting evidence used in automatic assertion
A type of primer extension assay evidence that is used in an automatic assertion.
primer extension assay evidence used in automatic assertion
A type of quantitative polymerase chain reaction evidence that is used in an automatic assertion.
quantitative polymerase chain reaction evidence used in automatic assertion
A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in an automatic assertion.
rapid amplification of cDNA ends polymerase chain reaction evidence used in automatic assertion
A type of S1 nuclease protection assay evidence that is used in an automatic assertion.
S1 nuclease protection assay evidence used in automatic assertion
A type of site-directed mutagenesis phenotypic evidence that is used in an automatic assertion.
site-directed mutagenesis evidence used in automatic assertion
site-directed mutagenesis phenotypic evidence used in automatic assertion
A type of survival rate analysis evidence that is used in an automatic assertion.
survival rate analysis evidence used in automatic assertion
A type of ultraviolet light footprinting evidence that is used in an automatic assertion.
ultraviolet light footprinting evidence used in automatic assertion
A type of xylE reporter gene assay evidence that is used in an automatic assertion.
xylE reporter gene assay evidence used in automatic assertion
A type of ad-hoc qualitative phenotype observation evidence that is used in an automatic assertion.
ad-hoc qualitative phenotype observation evidence used in automatic assertion
A type of ad-hoc quantitative phenotype observation evidence that is used in an automatic assertion.
ad-hoc quantitative phenotype observation evidence used in automatic assertion
A type of cell transfection experiment evidence that is used in an automatic assertion.
cell transfection experiment evidence used in automatic assertion
A type of yeast 2-hybrid evidence that is used in an automatic assertion.
yeast 2-hybrid evidence used in automatic assertion
A type of Cya fusion reporter assay evidence that is used in an automatic assertion.
Cya fusion reporter assay evidence used in automatic assertion
A type of super-resolution microscopy evidence that is used in an automatic assertion.
super-resolution microscopy evidence used in automatic assertion
A type of fractionation evidence that is used in an automatic assertion.
fractionation evidence used in automatic assertion
A type of electrophysiology assay evidence that is used in an automatic assertion.
electrophysiology assay evidence used in automatic assertion
A type of mRNA interactome capture evidence that is used in an automatic assertion.
mRNA interactome capture evidence used in automatic assertion
A type of patch-clamp recording evidence that is used in an automatic assertion.
patch-clamp recording evidence used in automatic assertion
A type of whole-cell patch-clamp recording evidence that is used in an automatic assertion.
whole-cell patch-clamp recording evidence used in automatic assertion
A type of author statement supported from referenced clinical study that is used in an automatic assertion.
traceable author statement from published clinical study used in automatic assertion
author statement supported from referenced clinical study used in automatic assertion
A type of inference based on individual clinical experience that is used in an automatic assertion.
inference based on individual clinical experience used in automatic assertion
A type of biofilm formation assay evidence that is used in an automatic assertion.
biofilm formation assay evidence used in automatic assertion
A type of microtiter plate biofilm assay evidence that is used in an automatic assertion.
microtiter plate biofilm assay evidence used in automatic assertion
A type of air-liquid interface assay evidence that is used in an automatic assertion.
air-liquid interface assay evidence used in automatic assertion
A type of colony biofilm assay evidence that is used in an automatic assertion.
colony biofilm assay evidence used in automatic assertion
A type of Kadouri drip-fed biofilm assay evidence that is used in an automatic assertion.
Kadouri drip-fed biofilm assay evidence used in automatic assertion
A type of co-immunoprecipitation evidence that is used in an automatic assertion.
co-immunoprecipitation evidence used in automatic assertion
A type of optogenetic evidence that is used in an automatic assertion.
optogenetic evidence used in automatic assertion
A type of fluorescent sensor evidence that is used in an automatic assertion.
fluorescent sensor evidence used in automatic assertion
A type of genetically encoded fluorescent sensor evidence that is used in an automatic assertion.
genetically encoded fluorescent sensor evidence used in automatic assertion
A type of genetically encoded fluorescent electrophysiology assay evidence that is used in an automatic assertion.
genetically encoded fluorescent electrophysiology assay evidence used in automatic assertion
A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in an automatic assertion.
genetically encoded fluorescent ion concentration sensor assay evidence used in automatic assertion
A type of cell fractionation evidence that is used in an automatic assertion.
cell fractionation evidence used in automatic assertion
A type of extracellular recording evidence that is used in an automatic assertion.
extracellular recording evidence used in automatic assertion
A type of single-unit extracellular recording evidence that is used in an automatic assertion.
single-unit extracellular recording evidence used in automatic assertion
A type of field potential recording evidence that is used in an automatic assertion.
field potential recording evidence used in automatic assertion
A type of anti-sense experiment evidence that is used in an automatic assertion.
anti-sense experiment evidence used in automatic assertion
A type of morpholino experiment evidence that is used in an automatic assertion.
morpholino experiment evidence used in automatic assertion
A type of RNAi evidence that is used in an automatic assertion.
RNAi evidence used in automatic assertion
A type of pharmacological assay evidence that is used in an automatic assertion.
pharmacological assay evidence used in automatic assertion
A type of immunofluorescence wide-field microscopy evidence that is used in an automatic assertion.
immunofluorescence wide-field microscopy evidence used in automatic assertion
A type of wide-field fluorescence microscopy evidence that is used in an automatic assertion.
wide-field fluorescence microscopy evidence used in automatic assertion
A type of over expression analysis evidence that is used in an automatic assertion.
over expression analysis evidence used in automatic assertion
A type of cell-free assay evidence that is used in an automatic assertion.
cell-free assay evidence used in automatic assertion
A type of fluorescence recovery after photobleaching evidence that is used in an automatic assertion.
fluorescence recovery after photobleaching evidence used in automatic assertion
A type of immuno-labelling electron microscopy evidence that is used in an automatic assertion.
immuno-labelling electron microscopy evidence used in automatic assertion
A type of immunofluorescence super resolution microscopy evidence that is used in an automatic assertion.
immunofluorescence super resolution microscopy evidence used in automatic assertion
A type of co-purification evidence that is used in an automatic assertion.
co-purification evidence used in automatic assertion
A type of yeast one-hybrid evidence that is used in an automatic assertion.
yeast one-hybrid evidence used in automatic assertion
A type of split-ubiquitin functional complementation evidence that is used in an automatic assertion.
split-ubiquitin functional complementation evidence used in automatic assertion
A type of far-Western blotting evidence that is used in an automatic assertion.
far-Western blotting evidence used in automatic assertion
A type of affinity chromatography evidence that is used in an automatic assertion.
affinity chromatography evidence used in automatic assertion
A type of ribohomopolymer binding assay evidence that is used in an automatic assertion.
ribohomopolymer binding assay evidence used in automatic assertion
A type of protein:ion binding evidence that is used in an automatic assertion.
protein:ion binding evidence used in automatic assertion
A type of Southwestern blot evidence that is used in an automatic assertion.
Southwestern blot evidence used in automatic assertion
A type of Northwestern blot evidence that is used in an automatic assertion.
Northwestern blot evidence used in automatic assertion
A type of bacterial one-hybrid evidence that is used in an automatic assertion.
bacterial one-hybrid evidence used in automatic assertion
A type of protein-oligonucleotide microarray binding evidence that is used in an automatic assertion.
protein-oligonucleotide microarray binding evidence used in automatic assertion
A type of functional complementation evidence that is used in an automatic assertion.
functional complementation evidence used in automatic assertion
A type of transgenic rescue experiment evidence that is used in an automatic assertion.
transgenic rescue experiment evidence used in automatic assertion
A type of transient rescue experiment evidence that is used in an automatic assertion.
transient rescue experiment evidence used in automatic assertion
A type of suppressor/enhancer interaction phenotypic evidence that is used in an automatic assertion.
suppressor/enhancer interaction evidence used in automatic assertion
suppressor/enhancer interaction phenotypic evidence used in automatic assertion
A type of double mutant phenotypic evidence that is used in an automatic assertion.
double mutant phenotype evidence used in automatic assertion
double mutant phenotypic evidence used in automatic assertion
A type of epistatic interaction phenotypic evidence that is used in an automatic assertion.
epistatic interaction evidence used in automatic assertion
epistatic interaction phenotypic evidence used in automatic assertion
A type of functional complementation in heterologous system evidence that is used in an automatic assertion.
functional complementation in heterologous system evidence used in automatic assertion
A type of temperature-sensitive mutant phenotypic evidence that is used in an automatic assertion.
temperature-sensitive mutant phenotype evidence used in automatic assertion
temperature-sensitive mutant phenotypic evidence used in automatic assertion
A type of recessive mutant phenotype evidence that is used in an automatic assertion.
recessive mutant phenotype evidence used in automatic assertion
A type of high throughput mutant phenotypic evidence that is used in an automatic assertion.
high throughput mutant phenotype evidence used in automatic assertion
high throughput mutant phenotypic evidence used in automatic assertion
A type of high throughput genetic interaction phenotypic evidence that is used in an automatic assertion.
high throughput genetic interaction evidence used in automatic assertion
high throughput genetic interaction phenotypic evidence used in automatic assertion
A type of high throughput direct assay evidence that is used in an automatic assertion.
high throughput direct assay evidence used in automatic assertion
A type of high throughput expression pattern evidence that is used in an automatic assertion.
high throughput expression pattern evidence used in automatic assertion
A type of radioligand binding assay evidence that is used in an automatic assertion.
radioligand binding assay evidence used in automatic assertion
A type of combinatorial evidence from author knowledge and experimental evidence that is used in an automatic assertion.
combinatorial evidence from author knowledge and experimental evidence used in automatic assertion
combinatorial experimental and author inference evidence used in automatic assertion
A type of combinatorial evidence from curator knowledge and experimental evidence that is used in an automatic assertion.
combinatorial evidence from curator knowledge and experimental evidence used in automatic assertion
combinatorial experimental and curator inference evidence used in automatic assertion
A type of voltammetry evidence that is used in an automatic assertion.
voltammetry evidence used in automatic assertion
A type of photoconversion evidence that is used in an automatic assertion.
photoconversion evidence used in automatic assertion
A type of agglutination test evidence that is used in an automatic assertion.
agglutination test evidence used in automatic assertion
A type of slide agglutination test evidence that is used in an automatic assertion.
slide agglutination test evidence used in automatic assertion
A type of direct Coombs test evidence that is used in an automatic assertion.
direct Coombs test evidence used in automatic assertion
A type of indirect Coombs test evidence that is used in an automatic assertion.
indirect Coombs test evidence used in automatic assertion
A type of direct hemagglutination assay evidence that is used in an automatic assertion.
direct hemagglutination assay evidence used in automatic assertion
A type of viral hemagglutination inhibition assay evidence that is used in an automatic assertion.
viral hemagglutination inhibition assay evidence used in automatic assertion
A type of compement fixation assay evidence that is used in an automatic assertion.
compement fixation assay evidence used in automatic assertion
A type of neutralization test assay evidence that is used in an automatic assertion.
neutralization test assay evidence used in automatic assertion
A type of copper transport assay evidence that is used in an automatic assertion.
copper transport assay evidence used in automatic assertion
A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in an automatic assertion.
5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in automatic assertion
A type of plaque assay evidence that is used in an automatic assertion.
plaque assay evidence used in automatic assertion
A type of epifluorescence microscopy evidence that is used in an automatic assertion.
epifluorescence microscopy evidence used in automatic assertion
A type of transmission electron microscopy evidence that is used in an automatic assertion.
transmission electron microscopy evidence used in automatic assertion
A type of scanning electron microscopy evidence that is used in an automatic assertion.
scanning electron microscopy evidence used in automatic assertion
A type of time-lapsed microscopy evidence that is used in an automatic assertion.
time-lapsed microscopy evidence used in automatic assertion
A type of phase contrast microscopy evidence that is used in an automatic assertion.
phase contrast microscopy evidence used in automatic assertion
A type of transmitted light brightfied mircoscopy evidence that is used in an automatic assertion.
transmitted light brightfied mircoscopy evidence used in automatic assertion
A type of koehler illumination microscopy evidence that is used in an automatic assertion.
koehler illumination microscopy evidence used in automatic assertion
A type of differential interference contrast microscopy evidence that is used in an automatic assertion.
differential interference contrast microscopy evidence used in automatic assertion
A type of extended field laser confocal microscopy evidence that is used in an automatic assertion.
extended field laser confocal microscopy evidence used in automatic assertion
A type of confocal laser scanning microscopy evidence that is used in an automatic assertion.
confocal laser scanning microscopy evidence used in automatic assertion
A type of light scattering evidence that is used in an automatic assertion.
light scattering evidence used in automatic assertion
A type of dynamic light scattering assay evidence that is used in an automatic assertion.
dynamic light scattering assay evidence used in automatic assertion
A type of static light scattering assay evidence that is used in an automatic assertion.
static light scattering assay evidence used in automatic assertion
A type of colony papillation assay phenotypic evidence that is used in an automatic assertion.
colony papillation assay evidence used in automatic assertion
colony papillation assay phenotypic evidence used in automatic assertion
A type of crystal violet staining evidence that is used in an automatic assertion.
crystal violet staining evidence used in automatic assertion
A type of flow cell biofilm assay evidence that is used in an automatic assertion.
flow cell biofilm assay evidence used in automatic assertion
A type of bacterial 2-hybrid assay evidence that is used in an automatic assertion.
bacterial 2-hybrid assay evidence used in automatic assertion
A type of phenomic profiling assay evidence that is used in an automatic assertion.
phenomic profiling assay evidence used in automatic assertion
A type of colony morphology phenotypic evidence that is used in an automatic assertion.
colony morphology evidence used in automatic assertion
colony morphology phenotypic evidence used in automatic assertion
A type of colony color phenotypic evidence that is used in an automatic assertion.
colony color evidence used in automatic assertion
colony color phenotypic evidence used in automatic assertion
A type of colony size phenotypic evidence that is used in an automatic assertion.
colony size evidence used in automatic assertion
colony size phenotypic evidence used in automatic assertion
A type of zone of inhibition evidence that is used in an automatic assertion.
zone of inhibition evidence used in automatic assertion
A type of Etest evidence that is used in an automatic assertion.
Etest evidence used in automatic assertion
A type of ribosome profiling evidence that is used in an automatic assertion.
ribosome profiling evidence used in automatic assertion
A type of evidence based on computational logical inference that is used in a manual assertion.
evidence based on computational logical inference used in manual assertion
computational inference used in manual assertion
A type of transcriptional activation assay evidence that is used in a manual assertion.
transcriptional activation assay evidence used in manual assertion
A type of transcriptional activation assay evidence that is used in an automatic assertion.
transcriptional activation assay evidence used in automatic assertion
A type of experimental phenotypic evidence that is used in a manual assertion.
experimental phenotypic evidence used in manual assertion
A type of experimental phenotypic evidence that is used in an automatic assertion.
experimental phenotypic evidence used in automatic assertion
A type of curator inference from authoritative resource based on information located in a queryable database and is optimized for computers.
A type of curator inference from published work where the reference is to an entry in a compendium that provides summarized information on a subject.
A type of curator inference from encyclopedia where the reference is to a Wikipedia article.
A type of curator inference from encyclopedia where the reference is to an Encyclopedia Britannica article.
A type of curator inference from encyclopedia in which the reference is to an article in the National Library of Medicine's MedLinePlus encyclopedia.
curator inference from MedlinePlus encyclopedia
A type of curator inference from published work in which the entry comes from a collection of words with definitions, usages, pronounciations, and more.
A type of curator inference from dictionary in which the reference is to an entry in the Oxford Dictionaries.
curator inference from Oxford Dictionary
A type of curator inference from dictionary in which the reference is to an entry in the Merriam-Webster Dictionary.
curator inference from Merriam-Webster Dictionary
A type of curator inference from dictionary in which the reference is to an entry in the National Library of Medicine's MedLinePlus dictionary.
curator inference from MedlinePlus dictionary
A type of curator inference from published work reporting on research findings.
curator inference from journal publication
A type of curator inference from published work based on a book, which may be a reference to a URL (for ebooks) or a DOI.
A type of curator inference that is from what is generally considered an authoritative source on the topic, including model organism databases, newspaper articles, books, journal publications, etc.
curator inference from authoritative source
A type of manually integrated combinatorial evidence in which two or more distinct types of computational evidence are integrated manually.
manually integrated combinatorial computational evidence
A type of manually integrated combinatorial computational evidence that is used in a manual assertion.
manually integrated combinatorial computational evidence used in manual assertion
A type of manually integrated combinatorial computational evidence that is used in an automatic assertion.
manually integrated combinatorial computational evidence used in automatic assertion
A type of automatically integrated combinatorial evidence in which two or more distinct types of computational evidence are integrated automatically.
automatically integrated combinatorial computational evidence
A type of automatically integrated combinatorial computational evidence that is used in a manual assertion.
automatically integrated combinatorial computational evidence used in manual assertion
A type of automatically integrated combinatorial computational evidence that is used in an automatic assertion.
automatically integrated combinatorial computational evidence used in automatic assertion
A type of combinatorial evidence in which two or more distinct types of experimental evidence are integrated.
A type of manually integrated combinatorial evidence in which two or more distinct types of experimental evidence are integrated manually.
manually integrated combinatorial experimental evidence
A type of manually integrated combinatorial experimental evidence that is used in a manual assertion.
manually integrated combinatorial experimental evidence used in manual assertion
A type of manually integrated combinatorial experimental evidence that is used in an automatic assertion.
manually integrated combinatorial experimental evidence used in automatic assertion
A type of automatically integrated combinatorial evidence in which two or more distinct types of experimental evidence are integrated automatically.
automatically integrated combinatorial experimental evidence
A type of automatically integrated combinatorial experimental evidence that is used in a manual assertion.
automatically integrated combinatorial experimental evidence used in manual assertion
A type of automatically integrated combinatorial experimental evidence that is used in an automatic assertion.
automatically integrated combinatorial experimental evidence used in automatic assertion
A type of combinatorial evidence in which at least one line of experimental evidence and at least one line of computational evidence have been integrated.
combinatorial computational and experimental evidence
A type of manually integrated combinatorial evidence in which at least one line of experimental evidence and at least one line of computational evidence have been integrated manually.
manually integrated combinatorial computational and experimental evidence
A type of manually integrated combinatorial computational and experimental evidence that is used in a manual assertion.
manually integrated combinatorial computational and experimental evidence used in manual assertion
A type of manually integrated combinatorial computational and experimental evidence that is used in an automatic assertion.
manually integrated combinatorial computational and experimental evidence used in automatic assertion
A type of automatically integrated combinatorial evidence in which at least one line of experimental evidence and at least one line of computational evidence have been integrated automatically.
automatically integrated combinatorial computational and experimental evidence
A type of automatically integrated combinatorial computational and experimental evidence that is used in a manual assertion.
automatically integrated combinatorial computational and experimental evidence used in manual assertion
A type of automatically integrated combinatorial computational and experimental evidence that is used in an automatic assertion.
automatically integrated combinatorial computational and experimental evidence used in automatic assertion
A type of computational evidence that is used in a manual assertion.
computational evidence used in manual assertion
A type of computational evidence that is used in an automatic assertion.
computational evidence used in automatic assertion
A type of evidence in which data are produced, and/or generated, and/or analyzed on a computer.
A type of combinatorial evidence in which at least two distinct types of evidence have been integrated automatically.
automatically integrated combinatorial evidence
A type of combinatorial evidence in which at least two distinct types of evidence have been integrated manually.
manually integrated combinatorial evidence
A type of manually integrated combinatorial evidence that is used in a manual assertion.
manually integrated combinatorial evidence used in manual assertion
A type of manually integrated combinatorial evidence that is used in an automatic assertion.
manually integrated combinatorial evidence used in automatic assertion
A type of combinatorial evidence in which at least two distinct types of computational evidence have been integrated.
A type of combinatorial computational evidence that is used in a manual assertion.
combinatorial computational evidence used in manual assertion
A type of combinatorial computational evidence that is used in an automatic assertion.
combinatorial computational evidence used in automatic assertion
A type of chromatography evidence that is used in a manual assertion.
chromatography evidence used in manual assertion
A type of chromatography evidence that is used in an automatic assertion.
chromatography evidence used in automatic assertion
A type of reporter gene assay evidence that is used in a manual assertion.
reporter gene assay evidence used in manual assertion
A type of protein separation evidence that is used in a manual assertion.
protein separation evidence used in manual assertion
A type of substance quantification evidence that is used in a manual assertion.
substance quantification evidence used in manual assertion
A type of voltage clamp recording evidence that is used in a manual assertion.
voltage clamp recording evidence used in manual assertion
A type of protein kinase assay evidence that is used in a manual assertion.
protein kinase assay evidence used in manual assertion
A type of gel electrophoresis evidence that is used in a manual assertion.
gel electrophoresis evidence used in manual assertion
A type of sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence that is used in a manual assertion.
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
A type of ex vivo assay evidence that is used in a manual assertion.
ex vivo assay evidence used in manual assertion
A type of cleavage assay evidence that is used in a manual assertion.
cleavage assay evidence used in manual assertion
A type of deacetylation assay evidence that is used in a manual assertion.
deacetylation assay evidence used in manual assertion
A type of transcription assay evidence that is used in a manual assertion.
transcription assay evidence used in manual assertion
A type of phosphatase assay evidence that is used in a manual assertion.
phosphatase assay evidence used in manual assertion
A type of cell-based assay evidence that is used in a manual assertion.
cell-based assay evidence used in manual assertion
A type of cell proliferation assay evidence that is used in a manual assertion.
cell proliferation assay evidence used in manual assertion
A type of DNA synthesis cell proliferation assay evidence that is used in a manual assertion.
DNA synthesis cell proliferation assay evidence used in manual assertion
A type of apoptotic assay evidence that is used in a manual assertion.
apoptotic assay evidence used in manual assertion
A type of cell growth assay evidence that is used in a manual assertion.
cell growth assay evidence used in manual assertion
A type of disk diffusion test evidence that is used in a manual assertion.
disk diffusion test evidence used in manual assertion
A type of chemotaxis assay evidence that is used in a manual assertion.
chemotaxis assay evidence used in manual assertion
A type of cytotoxicity assay evidence that is used in a manual assertion.
cytotoxicity assay evidence used in manual assertion
A type of cell viability assay evidence that is used in a manual assertion.
cell viability assay evidence used in manual assertion
A type of methylation assay evidence that is used in a manual assertion.
methylation assay evidence used in manual assertion
OBSOLETE. A type of protein assay evidence that is used in a manual assertion.
obsolete protein assay evidence used in manual assertion
A type of chromatin immunoprecipitation evidence that is used in a manual assertion.
chromatin immunoprecipitation evidence used in manual assertion
A type of protein inhibition evidence that is used in a manual assertion.
protein inhibition evidence used in manual assertion
A type of sumoylation assay evidence that is used in a manual assertion.
sumoylation assay evidence used in manual assertion
A type of transport assay evidence that is used in a manual assertion.
transport assay evidence used in manual assertion
A type of defarnesylation assay evidence that is used in a manual assertion.
defarnesylation assay evidence used in manual assertion
A type of deubiquitination assay evidence that is used in a manual assertion.
deubiquitination assay evidence used in manual assertion
A type of palmitoylation assay evidence that is used in a manual assertion.
palmitoylation assay evidence used in manual assertion
A type of acetylation assay evidence that is used in a manual assertion.
acetylation assay evidence used in manual assertion
A type of demethylation assay evidence that is used in a manual assertion.
demethylation assay evidence used in manual assertion
A type of polyADP-ribosylation assay evidence that is used in a manual assertion.
polyADP-ribosylation assay evidence used in manual assertion
A type of staining evidence that is used in a manual assertion.
staining evidence used in manual assertion
A type of translation assay evidence that is used in a manual assertion.
translation assay evidence used in manual assertion
A type of ubiquitination assay evidence that is used in a manual assertion.
ubiquitination assay evidence used in manual assertion
A type of immunodetection assay evidence that is used in a manual assertion.
immunodetection assay evidence used in manual assertion
A type of desumoylation assay evidence that is used in a manual assertion.
desumoylation assay evidence used in manual assertion
A type of farnesylation assay evidence that is used in a manual assertion.
farnesylation assay evidence used in manual assertion
A type of reconstitution assay evidence that is used in a manual assertion.
reconstitution assay evidence used in manual assertion
A type of in vitro transcription reconstitution assay evidence that is used in a manual assertion.
in vitro transcription reconstitution assay evidence used in manual assertion
A type of localization evidence that is used in a manual assertion.
localization evidence used in manual assertion
A type of protein localization evidence that is used in a manual assertion.
protein localization evidence used in manual assertion
A type of fusion protein localization evidence that is used in a manual assertion.
fusion protein localization evidence used in manual assertion
A type of nucleic acid localization evidence that is used in a manual assertion.
nucleic acid localization evidence used in manual assertion
A type of anatomical perturbation phenotypic evidence that is used in a manual assertion.
anatomical perturbation phenotypic evidence used in manual assertion
A type of cleavage arrested development evidence that is used in a manual assertion.
cleavage arrested development evidence used in manual assertion
A type of spectrometry evidence that is used in a manual assertion.
spectrometry evidence used in manual assertion
A type of sequencing assay evidence that is used in a manual assertion.
sequencing assay evidence used in manual assertion
A type of nucleotide sequencing assay evidence that is used in a manual assertion.
nucleotide sequencing assay evidence used in manual assertion
A type of high throughput nucleotide sequencing assay evidence that is used in a manual assertion.
high throughput nucleotide sequencing assay evidence used in manual assertion
A type of structure determination evidence that is used in a manual assertion.
structure determination evidence used in manual assertion
A type of molecule detection assay evidence that is used in a manual assertion.
molecule detection assay evidence used in manual assertion
A type of DNA detection assay evidence that is used in a manual assertion.
DNA detection assay evidence used in manual assertion
A type of protein detection assay evidence that is used in a manual assertion.
protein detection assay evidence used in manual assertion
A type of RNA detection assay evidence that is used in a manual assertion.
RNA detection assay evidence used in manual assertion
A type of small molecule detection assay evidence that is used in a manual assertion.
small molecule detection assay evidence used in manual assertion
A type of chromosome conformation-based evidence that is used in a manual assertion.
chromosome conformation-based evidence used in manual assertion
A type of 3C evidence that is used in a manual assertion.
A type of combinatorial computational and experimental evidence that is used in a manual assertion.
combinatorial computational and experimental evidence used in manual assertion
A type of combinatorial experimental evidence that is used in a manual assertion.
combinatorial experimental evidence used in manual assertion
A type of biological system reconstruction evidence that is used in a manual assertion.
biological system reconstruction evidence used in manual assertion
A type of biological system reconstruction evidence by experimental evidence that is used in a manual assertion.
biological system reconstruction evidence by experimental evidence used in manual assertion
A type of phenotypic similarity evidence that is used in a manual assertion.
phenotypic similarity evidence used in manual assertion
A type of transcript splice pattern evidence that is used in a manual assertion.
transcript splice pattern evidence used in manual assertion
A type of phylogenetic evidence that is used in a manual assertion.
phylogenetic evidence used in manual assertion
A type of inferential evidence that is used in a manual assertion.
inferential evidence used in manual assertion
A type of curator inference from authoritative source that is used in a manual assertion.
curator inference from authoritative source used in manual assertion
A type of curator inference from encyclopedia that is used in a manual assertion.
curator inference from encyclopedia used in manual assertion
A type of curator inference from Wikipedia that is used in a manual assertion.
curator inference from Wikipedia used in manual assertion
A type of curator inference from MedlinePlus encyclopedia that is used in a manual assertion.
curator inference from MedlinePlus encyclopedia used in manual assertion
A type of curator inference from Britannica that is used in a manual assertion.
curator inference from Britannica used in manual assertion
A type of curator inference from book that is used in a manual assertion.
curator inference from book used in manual assertion
A type of curator inference from journal publication that is used in a manual assertion.
curator inference from journal publication used in manual assertion
A type of curator inference from database that is used in a manual assertion.
curator inference from database used in manual assertion
A type of curator inference from dictionary that is used in a manual assertion.
curator inference from dictionary used in manual assertion
A type of curator inference from MedlinePlus dictionary that is used in a manual assertion.
curator inference from MedlinePlus dictionary used in manual assertion
A type of curator inference from Oxford Dictionary that is used in a manual assertion.
curator inference from Oxford Dictionary used in manual assertion
A type of curator inference from Merriam-Webster Dictionary that is used in a manual assertion.
curator inference from Merriam-Webster Dictionary used in manual assertion
A type of reporter gene assay evidence that is used in an automatic assertion.
reporter gene assay evidence used in automatic assertion
A type of voltage clamp recording evidence that is used in an automatic assertion.
voltage clamp recording evidence used in automatic assertion
A type of protein kinase assay evidence that is used in an automatic assertion.
protein kinase assay evidence used in automatic assertion
A type of transcription assay evidence that is used in an automatic assertion.
transcription assay evidence used in automatic assertion
A type of gel electrophoresis evidence that is used in an automatic assertion.
gel electrophoresis evidence used in automatic assertion
A type of sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence that is used in an automatic assertion.
sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in automatic assertion
A type of deacetylation assay evidence that is used in an automatic assertion.
deacetylation assay evidence used in automatic assertion
A type of phosphatase assay evidence that is used in an automatic assertion.
phosphatase assay evidence used in automatic assertion
A type of cell-based assay evidence that is used in an automatic assertion.
cell-based assay evidence used in automatic assertion
A type of cell viability assay evidence that is used in an automatic assertion.
cell viability assay evidence used in automatic assertion
A type of cell proliferation assay evidence that is used in an automatic assertion.
cell proliferation assay evidence used in automatic assertion
A type of DNA synthesis cell proliferation assay evidence that is used in an automatic assertion.
DNA synthesis cell proliferation assay evidence used in automatic assertion
A type of apoptotic assay evidence that is used in an automatic assertion.
apoptotic assay evidence used in automatic assertion
A type of cell growth assay evidence that is used in an automatic assertion.
cell growth assay evidence used in automatic assertion
A type of disk diffusion test evidence that is used in an automatic assertion.
disk diffusion test evidence used in automatic assertion
A type of chemotaxis assay evidence that is used in an automatic assertion.
chemotaxis assay evidence used in automatic assertion
A type of cytotoxicity assay evidence that is used in an automatic assertion.
cytotoxicity assay evidence used in automatic assertion
A type of cleavage assay evidence that is used in an automatic assertion.
cleavage assay evidence used in automatic assertion
A type of methylation assay evidence that is used in an automatic assertion.
methylation assay evidence used in automatic assertion
OBSOLETE. A type of protein assay evidence that is used in an automatic assertion.
obsolete protein assay evidence used in automatic assertion
A type of protein inhibition evidence that is used in an automatic assertion.
protein inhibition evidence used in automatic assertion
A type of chromatin immunoprecipitation evidence that is used in an automatic assertion.
chromatin immunoprecipitation evidence used in automatic assertion
A type of protein separation evidence that is used in an automatic assertion.
protein separation evidence used in automatic assertion
A type of sumoylation assay evidence that is used in an automatic assertion.
sumoylation assay evidence used in automatic assertion
A type of transport assay evidence that is used in an automatic assertion.
transport assay evidence used in automatic assertion
A type of defarnesylation assay evidence that is used in an automatic assertion.
defarnesylation assay evidence used in automatic assertion
A type of deubiquitination assay evidence that is used in an automatic assertion.
deubiquitination assay evidence used in automatic assertion
A type of palmitoylation assay evidence that is used in an automatic assertion.
palmitoylation assay evidence used in automatic assertion
A type of ex vivo assay evidence that is used in an automatic assertion.
ex vivo assay evidence used in automatic assertion
A type of acetylation assay evidence that is used in an automatic assertion.
acetylation assay evidence used in automatic assertion
A type of demethylation assay evidence that is used in an automatic assertion.
demethylation assay evidence used in automatic assertion
A type of immunodetection assay evidence that is used in an automatic assertion.
immunodetection assay evidence used in automatic assertion
A type of polyADP-ribosylation assay evidence that is used in an automatic assertion.
polyADP-ribosylation assay evidence used in automatic assertion
A type of staining evidence that is used in an automatic assertion.
staining evidence used in automatic assertion
A type of translation assay evidence that is used in an automatic assertion.
translation assay evidence used in automatic assertion
A type of farnesylation assay evidence that is used in an automatic assertion.
farnesylation assay evidence used in automatic assertion
A type of ubiquitination assay evidence that is used in an automatic assertion.
ubiquitination assay evidence used in automatic assertion
A type of desumoylation assay evidence that is used in an automatic assertion.
desumoylation assay evidence used in automatic assertion
A type of reconstitution assay evidence that is used in an automatic assertion.
reconstitution assay evidence used in automatic assertion
A type of in vitro transcription reconstitution assay evidence that is used in an automatic assertion.
in vitro transcription reconstitution assay evidence used in automatic assertion
A type of substance quantification evidence that is used in an automatic assertion.
substance quantification evidence used in automatic assertion
A type of localization evidence that is used in an automatic assertion.
localization evidence used in automatic assertion
A type of protein localization evidence that is used in an automatic assertion.
protein localization evidence used in automatic assertion
A type of fusion protein localization evidence that is used in an automatic assertion.
fusion protein localization evidence used in automatic assertion
A type of nucleic acid localization evidence that is used in an automatic assertion.
nucleic acid localization evidence used in automatic assertion
A type of anatomical perturbation phenotypic evidence that is used in an automatic assertion.
anatomical perturbation phenotypic evidence used in automatic assertion
A type of cleavage arrested development evidence that is used in an automatic assertion.
cleavage arrested development evidence used in automatic assertion
A type of sequencing assay evidence that is used in an automatic assertion.
sequencing assay evidence used in automatic assertion
A type of nucleotide sequencing assay evidence that is used in an automatic assertion.
nucleotide sequencing assay evidence used in automatic assertion
A type of high throughput nucleotide sequencing assay evidence that is used in an automatic assertion.
high throughput nucleotide sequencing assay evidence used in automatic assertion
A type of structure determination evidence that is used in an automatic assertion.
structure determination evidence used in automatic assertion
A type of molecule detection assay evidence that is used in an automatic assertion.
molecule detection assay evidence used in automatic assertion
A type of DNA detection assay evidence that is used in an automatic assertion.
DNA detection assay evidence used in automatic assertion
A type of RNA detection assay evidence that is used in an automatic assertion.
RNA detection assay evidence used in automatic assertion
A type of protein detection assay evidence that is used in an automatic assertion.
protein detection assay evidence used in automatic assertion
A type of small molecule detection assay evidence that is used in an automatic assertion.
small molecule detection assay evidence used in automatic assertion
A type of spectrometry evidence that is used in an automatic assertion.
spectrometry evidence used in automatic assertion
A type of chromosome conformation-based evidence that is used in an automatic assertion.
chromosome conformation-based evidence used in automatic assertion
A type of 3C evidence that is used in an automatic assertion.
A type of phenotypic similarity evidence that is used in an automatic assertion.
phenotypic similarity evidence used in automatic assertion
A type of transcript splice pattern evidence that is used in an automatic assertion.
transcript splice pattern evidence used in automatic assertion
A type of phylogenetic evidence that is used in an automatic assertion.
phylogenetic evidence used in automatic assertion
A type of biological system reconstruction evidence that is used in an automatic assertion.
biological system reconstruction evidence used in automatic assertion
A type of biological system reconstruction evidence by experimental evidence that is used in an automatic assertion.
biological system reconstruction evidence by experimental evidence used in automatic assertion
A type of combinatorial computational and experimental evidence that is used in an automatic assertion.
combinatorial computational and experimental evidence used in automatic assertion
A type of combinatorial experimental evidence that is used in an automatic assertion.
combinatorial experimental evidence used in automatic assertion
A type of inferential evidence that is used in an automatic assertion.
inferential evidence used in automatic assertion
A type of curator inference from authoritative source that is used in an automatic assertion.
curator inference from authoritative source used in automatic assertion
A type of curator inference from encyclopedia that is used in an automatic assertion.
curator inference from encyclopedia used in automatic assertion
A type of curator inference from Wikipedia that is used in an automatic assertion.
curator inference from Wikipedia used in automatic assertion
A type of curator inference from Britannica that is used in an automatic assertion.
curator inference from Britannica used in automatic assertion
A type of curator inference from MedlinePlus encyclopedia that is used in an automatic assertion.
curator inference from MedlinePlus encyclopedia used in automatic assertion
A type of curator inference from book that is used in an automatic assertion.
curator inference from book used in automatic assertion
A type of curator inference from dictionary that is used in an automatic assertion.
curator inference from dictionary used in automatic assertion
A type of curator inference from MedlinePlus dictionary that is used in an automatic assertion.
curator inference from MedlinePlus dictionary used in automatic assertion
A type of curator inference from Merriam-Webster Dictionary that is used in an automatic assertion.
curator inference from Merriam-Webster Dictionary used in automatic assertion
A type of curator inference from Oxford Dictionary that is used in an automatic assertion.
curator inference from Oxford Dictionary used in automatic assertion
A type of curator inference from journal publication that is used in an automatic assertion.
curator inference from journal publication used in automatic assertion
A type of radioisotope assay evidence in which radioisotopic labeling is used to quantify a substance after a biochemical process or extraction from a biological sample.
radioisotope quantification assay evidence
A type of radioisotope quantification assay evidence that is used in an automatic assertion.
radioisotope quantification assay evidence used in automatic assertion
A type of radioisotope quantification assay evidence that is used in a manual assertion.
radioisotope quantification assay evidence used in manual assertion
A type of fluorescence evidence in which fluorescent labeling is used to quantify a substance after a biochemical process or extraction from a biological sample.
fluorescence quantification assay evidence
A type of fluorescence quantification assay evidence that is used in an automatic assertion.
fluorescence quantification assay evidence used in automatic assertion
A type of fluorescence quantification assay evidence that is used in a manual assertion.
fluorescence quantification assay evidence used in manual assertion
A type of inferential evidence in which sequence features are inferred based on visual inspection of the sequence.
This type of inference may be made by either a curator or an author.
inference of sequence features from visual inspection
A type of computational evidence in which computational systems build models based on sample data, known as training data, in order to make predictions or decisions without being explicitly programmed to do so. Such systems are trained on a combination of existing data about an entity, and are applied to the generation of new labels, such as numerical or textual or categorical.
A type of neural network method evidence which leverages a broad suite of neural network models, which use a combination of data attributes of an entity called features as inputs, and map them to outputs through multiple layers of connected hidden units, whose parameters are learned from data.
deep learning neural network method evidence
A type of machine learning method evidence which uses a combination of data attributes to derive knowledge used to create a set of rules. These rules collectively represent the prediction model and are in the form of "IF:THEN" statements. The knowledge applied can be traced back to the rules and the original data.
rule-based machine learning method evidence
A type of machine learning method evidence that is used in a manual assertion.
machine learning method evidence used in manual assertion
A type of machine learning method evidence that is used in an automatic assertion.
machine learning method evidence used in automatic assertion
A type of deep learning neural network method evidence that is used in a manual assertion.
deep learning neural network method evidence used in manual assertion
A type of deep learning neural network method evidence that is used in an automatic assertion.
deep learning neural network method evidence used in automatic assertion
A type of rule-based machine learning method evidence that is used in a manual assertion.
rule-based machine learning method evidence used in manual assertion
A type of rule-based machine learning method evidence that is used in an automatic assertion.
rule-based machine learning method evidence used in automatic assertion
A type of fluorescence in situ hybridization evidence resulting from the use of fluorescent probes to localize and quantify individual RNA molecules in single cells for studying gene expression.
single molecule fluorescence in situ hybridization evidence
A type of machine learning method evidence that uses a supervised learning model with associated algorithms for classification. Support vector machines aim to determine a hyperplane that separates two classes while maximizing the distance from the hyperplane to any given data point in those classes.
A type of computational evidence that employs a string algorithm to identify a string within a larger string or body of text, where a string is a particular series of characters consisting of letters, numbers, symbols, spaces, etc.
A type of string-matching method evidence in which patterns consisting of characters and/or symbols in particular combinations and/or order are used to identify matches in a larger string or body of text.
A type of machine learning method evidence in which the machine learning model consists of nodes connected to each other with edges that are organized into layers, where the edges can transmit signals between nodes such that the system acts similarly to biological neurons.
A type of computational inference where a geographic property of an entity is determined by searching coordinates associated with the entity against polygons with associated geographic properties in the form of shapefiles.
coordinate mapping to geographic property shapefiles
A type of curator inference in which the structure of a possible intermediate molecule made during a biosynthetic process is inferred based on the structure of the final molecule in the process.
inference of intermediate molecular structure from structure of final molecule
A type of single molecule fluorescence in situ hybridization evidence that is used in a manual assertion.
single molecule fluorescence in situ hybridization evidence used in manual assertion
A type of single molecule fluorescence in situ hybridization evidence that is used in an automatic assertion.
single molecule fluorescence in situ hybridization evidence used in automatic assertion
A type of support vector machine evidence that is used in a manual assertion.
support vector machine evidence used in manual assertion
A type of support vector machine evidence that is used in an automatic assertion.
support vector machine evidence used in automatic assertion
A type of string-matching method evidence that is used in a manual assertion.
string-matching method evidence used in manual assertion
A type of string-matching method evidence that is used in an automatic assertion.
string-matching method evidence used in automatic assertion
A type of regular expression method evidence that is used in a manual assertion.
regular expression method evidence used in manual assertion
A type of regular expression method evidence that is used in an automatic assertion.
regular expression method evidence used in automatic assertion
A type of neural network method evidence that is used in a manual assertion.
neural network method evidence used in manual assertion
A type of neural network method evidence that is used in an automatic assertion.
neural network method evidence used in automatic assertion
A type of coordinate mapping to geographic property shapefiles that is used in a manual assertion.
coordinate mapping to geographic property shapefiles used in manual assertion
A type of coordinate mapping to geographic property shapefiles that is used in an automatic assertion.
coordinate mapping to geographic property shapefiles used in automatic assertion
A type of inference of intermediate molecular structure from structure of final molecule that is used in a manual assertion.
inference of intermediate molecular structure from structure of final molecule used in manual assertion
A type of inference of intermediate molecular structure from structure of final molecule that is used in an automatic assertion.
inference of intermediate molecular structure from structure of final molecule used in automatic assertion
The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
transcription cis-regulatory region binding
Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
core promoter sequence-specific DNA binding
transcription regulatory region nucleic acid binding
The cellular synthesis of RNA on a template of RNA.
A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.
negative regulation of cytokine production
positive regulation of cytokine production
Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
regulation of response to biotic stimulus
negative regulation of response to biotic stimulus
positive regulation of response to biotic stimulus
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
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.
Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
nucleobase-containing compound metabolic process
The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
regulation of transcription, DNA-templated
cellular aromatic compound metabolic process
cellular component disassembly involved in execution phase of apoptosis
movement of cell or subcellular component
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
cellular response to DNA damage stimulus
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
positive regulation of cell population proliferation
negative regulation of cell population proliferation
negative regulation of biosynthetic process
positive regulation of biosynthetic process
negative regulation of metabolic process
positive regulation of metabolic process
negative regulation of catabolic process
positive regulation of catabolic process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
regulation of macromolecule biosynthetic process
positive regulation of macromolecule biosynthetic process
negative regulation of macromolecule biosynthetic process
positive regulation of macromolecule metabolic process
negative regulation of macromolecule metabolic process
posttranscriptional regulation of gene expression
positive regulation of organelle organization
negative regulation of organelle organization
cellular component assembly involved in morphogenesis
inorganic molecular entity transmembrane transporter activity
hydrolase activity, acting on ester bonds
regulation of nucleobase-containing compound metabolic process
A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph.
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
Interacting selectively and non-covalently with a specific domain of a protein.
regulation of anatomical structure morphogenesis
passive transmembrane transporter activity
regulation of transmembrane transporter activity
Assembly of actin filaments by the addition of actin monomers to a filament.
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
regulation of cellular metabolic process
negative regulation of cellular metabolic process
positive regulation of cellular metabolic process
regulation of cellular biosynthetic process
negative regulation of cellular biosynthetic process
positive regulation of cellular biosynthetic process
regulation of cellular catabolic process
negative regulation of cellular catabolic process
positive regulation of cellular catabolic process
regulation of cell projection organization
negative regulation of cell projection organization
positive regulation of cell projection organization
negative regulation of translation in response to stress
positive regulation of translation in response to stress
regulation of deoxyribonuclease activity
regulation of endodeoxyribonuclease activity
negative regulation of nuclease activity
positive regulation of nuclease activity
negative regulation of deoxyribonuclease activity
positive regulation of deoxyribonuclease activity
negative regulation of endodeoxyribonuclease activity
positive regulation of endodeoxyribonuclease activity
regulation of response to external stimulus
negative regulation of response to external stimulus
positive regulation of response to external stimulus
regulation of cellular protein metabolic process
negative regulation of cellular protein metabolic process
positive regulation of cellular protein metabolic process
negative regulation of icosanoid secretion
positive regulation of icosanoid secretion
negative regulation of transporter activity
positive regulation of transporter activity
regulation of ion transmembrane transporter activity
negative regulation of ion transmembrane transporter activity
positive regulation of ion transmembrane transporter activity
regulation of tumor necrosis factor production
negative regulation of tumor necrosis factor production
positive regulation of tumor necrosis factor production
negative regulation of organic acid transport
positive regulation of organic acid transport
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
Any process in which a macromolecule is transported to, or maintained in, a specific location.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
regulation of cellular amide metabolic process
negative regulation of cellular amide metabolic process
positive regulation of cellular amide metabolic process
cellular nitrogen compound metabolic process
cellular macromolecule biosynthetic process
nucleobase-containing compound biosynthetic process
nucleobase-containing compound catabolic process
negative regulation of transmembrane transport
positive regulation of transmembrane transport
regulation of ion transmembrane transport
negative regulation of ion transmembrane transport
positive regulation of ion transmembrane transport
post-transcriptional gene silencing by RNA
Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya.
regulation of molecular function, epigenetic
RNA-mediated gene silencing by inhibition of translation
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
regulation of cell population proliferation
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
positive regulation of apoptotic process
negative regulation of apoptotic process
positive regulation of programmed cell death
negative regulation of programmed cell death
positive regulation of catalytic activity
negative regulation of catalytic activity
regulation of translation by machinery localization
regulation of translation in response to stress
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
regulation of cellular component biogenesis
positive regulation of cellular component biogenesis
negative regulation of molecular function
positive regulation of molecular function
cellular macromolecule metabolic process
cellular macromolecule catabolic process
cellular nitrogen compound catabolic process
cellular nitrogen compound biosynthetic process
negative regulation of transcription, DNA-templated
positive regulation of transcription, DNA-templated
negative regulation of translational elongation
positive regulation of translational elongation
negative regulation of nucleobase-containing compound metabolic process
positive regulation of nucleobase-containing compound metabolic process
positive regulation of biological process
negative regulation of biological process
positive regulation of response to stimulus
negative regulation of response to stimulus
positive regulation of developmental growth
negative regulation of developmental growth
anatomical structure formation involved in morphogenesis
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
negative regulation of DNA metabolic process
positive regulation of DNA metabolic process
negative regulation of developmental process
positive regulation of developmental process
regulation of cellular component organization
negative regulation of cellular component organization
positive regulation of cellular component organization
regulation of nitrogen compound metabolic process
negative regulation of nitrogen compound metabolic process
positive regulation of nitrogen compound metabolic process
positive regulation of protein transport
negative regulation of protein transport
regulation of multicellular organismal process
positive regulation of multicellular organismal process
negative regulation of multicellular organismal process
positive regulation of protein metabolic process
negative regulation of protein metabolic process
negative regulation of RNA metabolic process
positive regulation of RNA metabolic process
regulation of cellular component movement
negative regulation of cellular component movement
positive regulation of cellular component movement
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
positive regulation of hydrolase activity
negative regulation of hydrolase activity
regulation of posttranscriptional gene silencing
positive regulation of posttranscriptional gene silencing
negative regulation of posttranscriptional gene silencing
regulation of antisense RNA transcription
negative regulation of antisense RNA transcription
positive regulation of antisense RNA transcription
regulation of macromolecule metabolic process
regulation of cell adhesion molecule production
negative regulation of cell adhesion molecule production
positive regulation of cell adhesion molecule production
developmental growth involved in morphogenesis
apoptotic process involved in morphogenesis
negative regulation of gene silencing by RNA
regulation of establishment of protein localization
siRNA-mediated gene silencing by inhibition of translation
cellular response to organic cyclic compound
cellular response to organonitrogen compound
cellular response to endogenous stimulus
tumor necrosis factor superfamily cytokine production
cellular component organization or biogenesis
regulation of cellular response to stress
regulation of arachidonic acid secretion
positive regulation of arachidonic acid secretion
nucleic acid phosphodiester bond hydrolysis
DNA synthesis involved in DNA replication
plasma membrane bounded cell projection assembly
regulation of plasma membrane bounded cell projection assembly
negative regulation of plasma membrane bounded cell projection assembly
positive regulation of plasma membrane bounded cell projection assembly
regulation of plasma membrane bounded cell projection organization
plasma membrane bounded cell projection organization
catalytic activity, acting on a nucleic acid
regulation of execution phase of apoptosis
negative regulation of execution phase of apoptosis
positive regulation of execution phase of apoptosis
negative regulation of arachidonic acid secretion
organic cyclic compound metabolic process
organic cyclic compound catabolic process
organic cyclic compound biosynthetic process
organonitrogen compound metabolic process
organonitrogen compound biosynthetic process
cellular response to oxygen-containing compound
regulation of apoptotic process involved in morphogenesis
negative regulation of apoptotic process involved in morphogenesis
positive regulation of apoptotic process involved in morphogenesis
regulation of apoptotic DNA fragmentation
negative regulation of apoptotic DNA fragmentation
positive regulation of apoptotic DNA fragmentation
negative regulation of RNA biosynthetic process
positive regulation of RNA biosynthetic process
apoptotic process involved in development
negative regulation of response to wounding
positive regulation of response to wounding
regulation of nucleic acid-templated transcription
negative regulation of nucleic acid-templated transcription
positive regulation of nucleic acid-templated transcription
regulation of tumor necrosis factor superfamily cytokine production
negative regulation of tumor necrosis factor superfamily cytokine production
positive regulation of tumor necrosis factor superfamily cytokine production
negative regulation of DNA catabolic process
positive regulation of DNA catabolic process
negative regulation of protein localization
positive regulation of protein localization
negative regulation of apoptotic process involved in development
positive regulation of apoptotic process involved in development
regulation of apoptotic process involved in development
negative regulation of core promoter binding
positive regulation of core promoter binding
negative regulation of establishment of protein localization
positive regulation of establishment of protein localization
negative regulation of lipid localization
positive regulation of lipid localization
sequence-specific double-stranded DNA binding
regulation of cellular macromolecule biosynthetic process
negative regulation of cellular macromolecule biosynthetic process
negative regulation of fatty acid transport
positive regulation of fatty acid transport
negative regulation of DNA biosynthetic process
positive regulation of DNA biosynthetic process
regulation of transcription regulatory region DNA binding
negative regulation of transcription regulatory region DNA binding
positive regulation of transcription regulatory region DNA binding
regulation of response to DNA damage stimulus
negative regulation of response to DNA damage stimulus
positive regulation of response to DNA damage stimulus
negative regulation of chromosome organization
positive regulation of chromosome organization
A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
measurement unit label
A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
objective specification
A directive information entity that describes an action the bearer will take.
action specification
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
datum label
A quality of an information bearer that imparts the information content
information carrier
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
data item
A generically dependent continuant that is about some thing.
information content entity
A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
scalar measurement datum
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
directive information entity
A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
algorithm
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
curation status specification
An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
image
Data about an ontology part is a data item about a part of an ontology, for example a term
data about an ontology part
A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
plan specification
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
measurement datum
A material entity in which a concretization of an information content entity inheres.
material information bearer
The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
obsolescence reason specification
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
figure
A denotator type indicates how a term should be interpreted from an ontological perspective.
denotator type
A scalar measurement datum that is the result of measurement of mass quality
mass measurement datum
A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population.
infection
A process that realizes a plan which is the concretization of a plan specification.
planned process
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
biological feature identification objective
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
reference substance role
Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
xenotransplantation
Is a material entity that is created or changed during material processing.
processed material
A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
is the transplantation of organs between members of the same species.
allotransplantation
a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response
positive reference substance role
a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
evaluant role
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
assay
a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
culture medium
A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
reagent role
A planned process which results in physical changes in a specified input material
material processing
A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
participant under investigation role
a protocol application to replace an organ or tissue of an organism
transplantation
a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
specimen role
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
sequence feature identification objective
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
molecular feature identification objective
A device manufacture with the intent to provide a porous unsized paper used for filtering.
A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
cell co-culturing
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. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
clonal cDNA library
An assay that produces a picture of an entity.
A microtiter_plate is a flat plate with multiple wells used as small test tubes.
An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics.
chromatin immunoprecipitation
An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material.
Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
cellular feature identification objective
a material processing that digests the fraction of input material that is susceptible to that enzyme
enzymatic cleavage
A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest.
dye role
Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
artificially induced nucleic acid hybridization
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
DNA extraction
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
organism feature identification objective
A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
protocol
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
adding a material entity into a target
A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
analyte role
An assay that determines interactions between proteins, such as protein-protein binding.
protein-protein interaction detection assay
a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
eluate
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
material to be added role
A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
drawing a conclusion based on data
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
histological sample preparation
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9))).
An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q.
An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
light emission function
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
magnify function
A contain function is a function to constrain a material entities location in space
contain function
A heat function is a function that increases the internal kinetic energy of a material
heat function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
material separation function
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
excitation function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
synthesizing function
A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
perturb function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
filter function
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
mechanical function
An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
electricity supply function
An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
ionization function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
cool function
An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
energy supply function
An image acquisition function is a function to acquire an image of a material
image acquisition function
An image creation device is a device which captures a digitized image of an object
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
environment control function
A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
sort function
is double stranded DNA that is the specified output of a polymerase chain reaction
PCR product
a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
nucleic acid template role
A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
cloning vector role
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
polymerase chain reaction
cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
cloning insert role
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity)
reverse transcriptase
an extract is a material entity which results from an extraction process
extract
An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity.
(protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
enzyme
a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
polyacrylamide gel
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
adding material objective
An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
an assay objective to determine the presence or concentration of an analyte in the evaluant
analyte measurement objective
a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
agarose gel
an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
assay objective
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
target of material addition role is a role realized by an entity into which a material is added in a material addition process
target of material addition role
An electrophysiology recording assay where the recording location of the electrode is intracellular
intra cellular electrophysiology recording assay
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
measure function
An electrophysiology recording assay where the recording location of the electrode is extracellular
extracellular electrophysiology recording assay
an objective specifiction that creates an specific output object from input materials.
material transformation objective
An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles.
a planned process that carries out a study design
An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
reverse transcribed polymerase chain reaction
a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
scattered molecular aggregate
A chromatography consumable is a consumable that is used in a chromatography experiment.
A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures.
A sequencing assay which determines information on the sequence of a DNA molecule.
An assay that studies blood and blood producing organs using a variety of techniques and instruments
An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
is an objective to transform a material entity into spatially separated components.
A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals.
differential expression analysis data transformation
a portion of urine collected from an organism
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
A planned process with the objective of collecting a specimen.
A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies.
A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating.
a material obtained from an organism in order to be a representative of the whole
A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
separation into different composition objective
A objective specification to obtain a material entity for potential use as an input during an investigation.
is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
creating a mixture of molecules in solution
is an objective to obtain an output material that contains several input materials.
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
An assay that measures the occurrence of death events in one or more organisms over time
is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
A material entity that has the material sample role
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
study design independent variable
A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
A process in which bonds are created that link one polymer to another
An objective specification maintains some or all of the qualities of a material over time.
a planned process in which an organism is exposed to some stimulus with the intent to invoke an action
DNA that has been produced in an enzymatic amplification process
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
A device in which a measure function inheres.
The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules.
A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
a specimen that was taken from a live organism
An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes.
detection of specific nucleic acid polymers with complementary probes
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
A cytometry assay that monitors a cell population to track how many are killed by other cells.
A cell killing assay that measures if and how many target cells are killed within an organism.
A cytometry assay which measures the degreee to which input cells are replicating.
An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity.
An assay, based on the PCR, that amplifies and simultaneously quantifies a specific DNA molecule based on the use of complementary probes/primers. It enables both detection and quantification (as absolute number of copies or relative amount when normalized to DNA input or additional normalizing genes) of one or more specific sequences in a DNA sample.
real time polymerase chain reaction assay
a specimen that was taken from a dead organism
A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture.
A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest.
X-ray crystallography 3D molecular structure determination assay
An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene.
promoter activity detection by reporter gene assay
A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution.
a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction.
A specimen that has been modified in order to be able to detect it in future experiments
is a material entity bearing the disposition to infect an organism
infectious agent
A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
the part of the execution of an intervention design study which is varied between two or more subjects in the study
A device with a separation function realized in a planed process
A specimen that has been intentionally physically modified.
An assay in which a measurement is made by observing entities located in a live cell.
An assay in which a measurement is made by observing entities located in an organism.
A device that can be used to restrict the location of material entities over time
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels.
cell-cell binding detection by flow cytometry assay
An assay in which a measurement is made by observing entities located in a container.
A study design in which the independent variable is the environmental condition in which the specimen is growing
A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
A microscope that produces an image of an object by targeting it with an electron beam
The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
A planned process that captures an image of an object.
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
A binding assay where the specified output is a binding constant
A device which has a function to emit light.
A perturbation device is a device which is designed to perform a perturb function
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
A device that moves charged particles through a medium by using an electric field induced by electrodes.
A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
high performance liquid chromatography instrument
A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane.
A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
An device that is used to determine the order of nucleotides in nucleic acid sequences.
An electrophoresis system in which an electric field is applied to a gel matrix
A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level.
A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
An device that is used to determine the order of amino acids in protein sequences.
A device that is used to generate X-rays.
A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed.
binding constant
A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration.
3D structure determination of bound molecular complex assay
An assay with the objective to characterize the disposition of two or more material entities to form a complex.
a process that results in the increase of cell numbers
cell culture expansion
a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
gene knock out
a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
gene knock in
a material entity, organism or cell, that is the output of a genetic transformation process.
genetically modified material
a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
transfection
a material transformation objective aims to create genetically modified organism or cell
genetic transformation objective
A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation.
induced mutagenesis
A measurement datum that describes the structural orientation of a material entity in 3D space.
An assay that determines the sequence of an RNA molecule.
A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
genotyping by high throughput sequencing design
A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
genetic population background information
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
epigenetic modification identification objective
A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance
transcription profiling by high throughput sequencing design
A genotyping assay that uses a high througput sequencer
genotyping by high throughput sequencing assay
An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin
A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications.
A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology
DNA methylation profiling by high throughput sequencing assay
An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance.
A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
DNA methylation profiling by array design
A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
genotype information
A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex.
X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex
A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
transcription profiling by RT-PCR design
An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology.
A molecular feature identification objective that aims to characterize the abundance of transcripts
transcription profiling identification objective
A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
post-transcriptional modification design
A transcription profiling assay that uses reverse transcription PCR (RT-PCR).
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
genetic alteration information
A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
protein and DNA interaction identification objective
A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays.
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
genetic characteristics information
A study design that investigates protein binding sites on nucleic acids.
protein binding site identification design
A study design that identifies forms and abundance of transcripts in the genome.
A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology.
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
A transcription profiling assay that uses array technology.
A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner.
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
specimen from organism
Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection.
An assay in which a material's fluorescence is determined.
The process in which a ligand binds to an MHC molecule to form a stable complex
A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
purification
A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
specimen with pre- or post-mortem status
A MHC:ligand binding assay that measures a binding constant.
assay measuring a binding constant of a MHC:ligand complex
A sequence data item that is about the primary structure of DNA
The process of material entities forming complexes.
A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand.
A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material.
An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material.
An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material.
A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity.
A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component
A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy.
A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope).
antibody binding detection by fluorescence quenching
A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and 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.
An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay.
An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest.
An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid.
An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells.
A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE).
nano-cap analysis of gene expression assay
A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome
An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay.
An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain.
An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence
An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity
chromosome organization assay by fluorescence in-situ hybridization
An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
methylation-specific polymerase chain reaction assay
An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences.
amplification of intermethylated sites assay
An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization.
An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041).
cytochalasin-induced inhibition of actin polymerization assay
is an objective specification which aims to discover cellular structure properties
cellular structure feature identification objective
An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies.
a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR).
A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope.
assay measuring biological activity resulting from B cell epitope:antibody binding
A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant.
assay measuring a binding constant of a B cell epitope:antibody complex
A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex.
3D molecular structure determination assay of an antigen:antibody complex
A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex.
X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex
A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process.
paired-end library preparation
An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA.
methylation-sensitive restriction enzyme sequencing assay
A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
A biological or chemical entity that bears a reagent role in virtue of it being intended for application in a scientific technique to participate in (or have molecular parts that participate in) a chemical reaction that facilitates the generation of data about some distinct entity, or the generation of some distinct material specified output.
reagent
An information content entity that is inferred from data.
A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
cell freezing medium
A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation.
multiplex ligation-mediated amplification
A molecular feature identification objective that aims to determine spatial organization of chromatin.
chromosome conformation identification objective
An assay that measures the organization of chromosomes at the genome-wide scale.
Carbon-copy chromosome conformation capture assay
A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site
chromatin immunoprecipitation with exonuclease sequencing assay
A value specification that consists of two parts: a numeral and a unit label
An information content entity that specifies a value within a classification scheme or on a quantitative scale.
a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed
A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target.
competitive binding reference ligand role
An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation
assay using chromatin immunoprecipitation
An assay that counts and/or measures characteristics of cells.
An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules.
A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other.
An analyte assay where binding of the analyte to immobilized matrix is measured.
An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section.
A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex.
3D molecular structure determination assay of a T cell epitope:MHC:TCR complex
An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation.
A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein.
A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex.
3D molecular structure determination assay of a MHC:ligand complex
A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the recongition of the epitope.
assay measuring biological activity resulting from T cell epitope:MHC:TCR binding
A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant.
assay measuring a binding constant of a T cell epitope:MHC:TCR complex
An immune epitope assay that characterizes the structrue of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule.
A material entity that has two or more specimens as its parts.
collection of specimens
An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest.
A container with an environmental control function.
A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA.
rapid amplification of cDNA ends
An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution.
high performance liquid chromotography assay
An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye.
An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied.
A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy.
A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples.
An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies.
An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen.
An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance).
An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations.
A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.
A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell.
A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations.
A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels.
An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface.
An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique.
An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue.
An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry.
An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei.
A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR.
A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes.
A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
measurand role
An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library.
An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes.
A study design that investigates the features of interaction between molecules.
molecular interaction identification design
An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer.
An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR.
An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together.
A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components.
in vitro transcription reconstitution assay
A genetic transformation which reduces the expression of a specific gene or genes in an organism.
An assay that uses polymerase chain reaction technique to amplify DNA.
A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
molecular label role
A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
molecular label
A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription.
cDNA library
A cytometry assay that measures the abundance and/or characteristics of lymphocytes
An assay that has a urine specimen as evaluant.
An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex.
3D molecular structure determination assay
A complex of molecular entitites which is the result of an antibody binding to an antigen.
A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope complex.
A complex of molecular entities which is the result of a MHC molecule binding with a ligand.
A 3D structure determination assay that determines the 3-dimensional configuration of a cell.
A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell.
3D neural cell structure determination assay
An immune epitope assay that characterizes the structrue of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope.
An immune epitope assay that characterizes the structrue of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope.
A binding datum that is expressed using numbers.
An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output.
assay measuring quantitative binding of a MHC:ligand complex
An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output.
assay measuring quantitative binding of an antigen:antibody complex
An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output.
assay measuring quantitative binding of an epitope:MHC:TCR complex
A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
Epstein Barr virus transformed B cell
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
organism
A material entity that has the specimen role.
specimen
A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
organ section
A planned process that produces output data from input data.
data transformation
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
differential expression analysis objective
A data transformation which has the objective of spectrum analysis.
mass spectrometry analysis
An objective specification to transformation input data into output data
data transformation objective
is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process.
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
pool of specimens
A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute.
chemical solution
solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation
solvent role
solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
solute role
An assay that measures DNA damage (DNA breakage) in eucaryotic cells exposed to a challenge by determining the size and shape of DNA migration by detecting fluorescently labeled DNA from a cell placed in an electric field using gel electrophoresis
an organism that is the output of a genetic transformation process
genetically modified organism
A material entity that has been going through a process of being put into solution
dissolved material entity
A material separation in which a desired component of an input material is separated from the remainder
extraction
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
staining
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
polymerization
An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity
enzymatic ligation
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
nucleic acid hybridization
the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
elution
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions.
A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
A cytometer is an instrument for counting and/or measuring characteristics of cells.
A device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal.
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
study design
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
A reference experiment design type is where all samples are compared to a common reference.
is process in which a material substance is added to a cell culture
adding substance to cell culture
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
collecting specimen from organism
A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance.
administering substance in vivo
a material processing in which components of an input material become segregated in space
material component separation
An assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached
An assay that uses visual examination of cells or tissue (or images of them) to make an assessment regarding a quality of the cells or tissue. This assay can include steps of staining, imaging, and judgement.
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
maintaining cell culture
An assay that detects a specified substance
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
artificially induced reverse transcription
A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
cell permeabilization
a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
addition of molecular label
the introduction. alteration or integration of genetic material into a cell or organism
genetic transformation
An assay that determines the 3-dimensional configuration of an input material.
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
preparative chromatography
An assay the uses chemical or biochemical means to infer the sequence of a biomaterial
an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material
specific enzymatic cleavage
a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities
gradient separation
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
electrophoresis
the use of environmental conditions to select for the organism or cells that have a certain trait
selection by survival
A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence
DNA restriction enzyme digestion
the use of enzymes to increase the number of molecules of a biomaterial
enzymatic amplification
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
recombinant vector cloning
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
RNA extraction
a material separation to recover the nucleic acid fraction of an input material
nucleic acid extraction
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
phage display library
a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it
transgenic organism
a material entity bearing the epitope role
epitope
is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding.
epitope binding by adaptive immune receptor
the detrimental process in which an infectious agent colonizes or replicates in a host environment
infection process
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
adaptive immune receptor
is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture
experimental infection of cell culture
is a material entity that has the antigen role
antigen
A T cell epitope assay that measures the binding of T cell receptor to an epitope.
assay measuring binding of a T cell epitope:MHC:TCR complex
Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor.
disposition to be bound by an adaptive immune receptor
a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule.
MHC:epitope complex binding to TCR
The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell.
restricting MHC role
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
disposition to infect an organism
a material that is added to another one in a material combination process
A material entity into which another is being added in a material combinatino process
Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. see OBI_1110120 below
assay antigen role
abnormal, harmful processes caused by or associated with a disease
pathologic process
A MHC ligand assay that detects the binding of a ligand to an MHC molecule.
assay measuring binding of a MHC:ligand complex
A B cell epitope assay that measures the binding of an antibody receptor to an epitope.
assay measuring binding of a B cell epitope:antibody complex
An assay that detects the binding of an epitope to an adaptive immune receptor, or an immune process resulting from such a binding event, or characterizes the structrue of the complex resulting from such a binding event.
A specimen that is derived from some bodily fluid
An analyte assay that measures the abundance of protein
An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died.
A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality which inheres in a continuant.
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
A scalar optical quality which obtains by the magnitude of the light emitted by the bearer.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate.
A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
A quality that inheres in an entire organism or part of an organism.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof.
A protein that is a translation product of the Aspergillus oryzae RIB40 nucS gene or a 1:1 ortholog thereof.
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
A fluid that is composed of blood plasma and erythrocytes.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Anatomical group that has its parts adjacent to one another.
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
Excretion that is the output of a kidney
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A unit which is a standard measure of the amount of matter/energy of a physical object.
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
failed exploratory term
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
metadata complete
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
pending final vetting
placeholder removed
terms merged
term imported
term split
universal
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
defined class
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expression
Terms with this status should eventually replaced with a term from another ontology.
to be replaced with external ontology term
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
requires discussion
A length unit which is equal to 10 [-10] m.
A relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence