TEMP
type: Ontology
imports: chmo.owl
auto-generated-by: OBO-Edit 2.3.1
date: 16:10:2023 11:38
default-namespace: PRIDE
has_obo_format_version: 1.3
saved-by: Yasset Perez-Riverol
comment: I would set treat-xrefs-as-equivalent but there are some weird xrefs that would break that behaviour (PRIDE:PRIDE, value-type:xsd:string, ...)

definition
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

part_of
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: PRIDE

has_units
type: ObjectProperty
has_obo_namespace: PRIDE
id: has_units

part_of
type: ObjectProperty
type: TransitiveProperty
has_obo_namespace: PRIDE
id: part_of

dissociation method
type: Class
subclass of: Protocol step description additional parameter
definition: Fragmentation method used for dissociation or fragmentation
has_obo_namespace: PRIDE
id: MS:1000044

Axiom
annotated source: dissociation method
annotated property: definition
annotated target: Fragmentation method used for dissociation or fragmentation
database_cross_reference: PRIDE:PRIDE

collision energy
type: Class
subclass of: Protocol step description additional parameter
definition: Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion.
has_obo_namespace: PRIDE
id: MS:1000045

Axiom
annotated source: collision energy
annotated property: definition
annotated target: Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion.
database_cross_reference: PRIDE:PRIDE

mass analyzer
type: Class
subclass of: Instrument properties
definition: mass analyzer
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: MS:1000451

Axiom
annotated source: mass analyzer
annotated property: definition
annotated target: mass analyzer
database_cross_reference: PRIDE:PRIDE

label free sample
type: Class
subclass of: Label
definition: A sample that has not been labelled or modified
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: MS:1002038

Axiom
annotated source: label free sample
annotated property: definition
annotated target: A sample that has not been labelled or modified
database_cross_reference: PRIDE:PRIDE

Content Creation date
type: Class
subclass of: File Properties
definition: The date on which data creation began [NCI]
created by: ypriverol
creation date: 2018-08-29T14:52:49Z
has_obo_namespace: PRIDE
id: NCIT:C69199

Axiom
annotated source: Content Creation date
annotated property: definition
annotated target: The date on which data creation began [NCI]
database_cross_reference: PRIDE:PRIDE

Reference additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000000
comment: Root node for terms relating to Reference additional parameters, in the context of ExperimentCollection/Experiment/Reference/additional/CvParam

Protocol step description additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000001
comment: Root node for terms relating to the description of a protocol as ordered steps, in relation to the PRIDE.xml element ExperimentCollection/Experiment/Protocol/ProtocolSteps/StepDescription

ModificationItem additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000002
comment: Root node for terms relating to the description of a ModificationItem (post translational modification or artifactual modification) in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/ModificationItem/additional/cvParam

Peptide item additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000003
comment: Root node for terms relating to the description of a PeptideItem in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/additional/cvParam

Identification additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000004
comment: Root node for terms relating to the description of an Identification in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/additional/cvParam

Gel additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000005
comment: Root node for terms relating to the description of a Gel in relation to the PRIDE.xml element ExperimentCollection/Experiment/TwoDimensionalIdentification/Gel/additional/cvParam

Experiment additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000006
comment: Root node for terms relating to the description of an Experiment in relation to the PRIDE.xml element ExperimentCollection/Experiment/additional/cvParam

SearchEngineVersion
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000007
comment: Version number / identifier for search engine.
deprecated: true

Protein search engine output parameter
type: Class
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000008

Ion mass tolerance
type: Class
subclass of: Protein search engine output parameter
subclass of: Peptide search engine output parameter
has_obo_namespace: PRIDE
id: PRIDE:0000009

PrecursorIon mass tolerance
type: Class
subclass of: Ion mass tolerance
has_obo_namespace: PRIDE
id: PRIDE:0000010

MS2 ion mass tolerance
type: Class
subclass of: Ion mass tolerance
has_obo_namespace: PRIDE
id: PRIDE:0000011

Delta Cn
type: Class
subclass of: Protein search engine output parameter
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Sequest
definition: 1.0 - normalized correlation score.
has_obo_namespace: PRIDE
id: PRIDE:0000012

Axiom
annotated source: Delta Cn
annotated property: definition
annotated target: 1.0 - normalized correlation score.
database_cross_reference: PRIDE:PRIDE

X correlation
type: Class
subclass of: Protein search engine output parameter
subclass of: Peptide search engine output parameter
has_obo_namespace: PRIDE
id: PRIDE:0000013

X correlation (+1)
type: Class
subclass of: X correlation
has_obo_namespace: PRIDE
id: PRIDE:0000014

X correlation (+2)
type: Class
subclass of: X correlation
has_obo_namespace: PRIDE
id: PRIDE:0000015

X correlation (+3)
type: Class
subclass of: X correlation
has_obo_namespace: PRIDE
id: PRIDE:0000016

Sample description additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000017
comment: Root term for parameters in the context of ExperimentCollection/Experiment/mzData/description/admin/sampleDescription/cvParam

Disease free
type: Class
subclass of: Sample description additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000018
comment: Term to describe the fact that the sample derives from an organism which has been positively shown to be free of disease, e.g. as the consequence of a broad-spectrum screen. NOTE: A request has been made to have this concept added to MeSH. Once this has been achieved, this term will be dropped from the PRIDE CV and all uses of the this term will be updated to the appropriate MeSH concept.

Solubilization
type: Class
subclass of: Protocol step description additional parameter
definition: To make something soluble or more soluble, especially in water, by the action of a detergent or other agent.
has_obo_namespace: PRIDE
id: PRIDE:0000019

Axiom
annotated source: Solubilization
annotated property: definition
annotated target: To make something soluble or more soluble, especially in water, by the action of a detergent or other agent.
database_cross_reference: PRIDE:PRIDE

Depletion
type: Class
subclass of: Protocol step description additional parameter
definition: The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components.
has_obo_namespace: PRIDE
id: PRIDE:0000020

Axiom
annotated source: Depletion
annotated property: definition
annotated target: The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components.
database_cross_reference: PRIDE:PRIDE

Fractionation
type: Class
subclass of: Protocol step description additional parameter
definition: Process of classification of an analyte or a group of analytes from a sample according to physical (e.g., size) or chemical (e.g., bonding, reactivity) properties. (from https://doi.org/10.1351/goldbook.FT06825)
has_obo_namespace: PRIDE
id: PRIDE:0000021

Axiom
annotated source: Fractionation
annotated property: definition
annotated target: Process of classification of an analyte or a group of analytes from a sample according to physical (e.g., size) or chemical (e.g., bonding, reactivity) properties. (from https://doi.org/10.1351/goldbook.FT06825)
database_cross_reference: PRIDE:PRIDE

Separation
type: Class
subclass of: Protocol step description additional parameter
definition: To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time.
has_obo_namespace: PRIDE
id: PRIDE:0000022

Axiom
annotated source: Separation
annotated property: definition
annotated target: To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time.
database_cross_reference: PRIDE:PRIDE

Band excision
type: Class
subclass of: Protocol step description additional parameter
definition: The removal of a region of a gel which contains protein(s) of interest.
has_obo_namespace: PRIDE
id: PRIDE:0000023

Axiom
annotated source: Band excision
annotated property: definition
annotated target: The removal of a region of a gel which contains protein(s) of interest.
database_cross_reference: PRIDE:PRIDE

Enzyme digestion
type: Class
subclass of: Protocol step description additional parameter
definition: The fragmentation of proteins into peptides through the use of an enzyme such as trypsin.
has_obo_namespace: PRIDE
id: PRIDE:0000024

Axiom
annotated source: Enzyme digestion
annotated property: definition
annotated target: The fragmentation of proteins into peptides through the use of an enzyme such as trypsin.
database_cross_reference: PRIDE:PRIDE

Reduction
type: Class
subclass of: Protocol step description additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000025

Alkylation
type: Class
subclass of: Protocol step description additional parameter
definition: The transfer of an alkyl group from one molecule to another.
has_obo_namespace: PRIDE
id: PRIDE:0000026

Axiom
annotated source: Alkylation
annotated property: definition
annotated target: The transfer of an alkyl group from one molecule to another.
database_cross_reference: PRIDE:PRIDE

Mass spectrometry
type: Class
subclass of: Protocol step description additional parameter
definition: This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically.
has_obo_namespace: PRIDE
id: PRIDE:0000027

Axiom
annotated source: Mass spectrometry
annotated property: definition
annotated target: This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically.
database_cross_reference: PRIDE:PRIDE

Cv Label
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000028
comment: Valid values for cvLabel entries referencing external database / CV / ontology.

PubMed
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000029
comment: Valid value for the cvLabel entry referencing PubMed.

PRIDE
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000030
comment: Valid value for the cvLabel entry referencing PRIDE

GO
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000031
comment: Valid value for the cvLabel entry referencing GO.

MeSH
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000032
comment: Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH)

NEWT
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000033
comment: Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy.

PSI
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000034
comment: Valid value for the cvLabel entry referencing the PSI ontology

UNIMOD
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000035
comment: Valid value for the cvLabel entry referencing UNIMOD

RESID
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000036
comment: Valid value for the cvLabel entry referencing RESID.

Staining
type: Class
subclass of: Protocol step description additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000037

ISBN
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000038
comment: Valid value for the cvLabel entry referencing ISBN

Organelle isolation
type: Class
subclass of: Protocol step description additional parameter
definition: Any technique which separates differentiated structures from the cell.
has_obo_namespace: PRIDE
id: PRIDE:0000039

Axiom
annotated source: Organelle isolation
annotated property: definition
annotated target: Any technique which separates differentiated structures from the cell.
database_cross_reference: PRIDE:PRIDE

Experiment description
type: Class
subclass of: Experiment additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000040
comment: This CV term should be used in association with a value that is a free-text description of the experiment.

Search database protein sequence
type: Class
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000041

DOI
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000042

FIX
type: Class
subclass of: Cv Label
has_obo_namespace: PRIDE
id: PRIDE:0000043

Search algorithm
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000044

Sequest
type: Class
subclass of: Search algorithm
subclass of: Identification software
has_obo_namespace: PRIDE
id: PRIDE:0000045

Mascot
type: Class
subclass of: Search algorithm
subclass of: Quantification software
subclass of: Identification software
has_obo_namespace: PRIDE
id: PRIDE:0000046

XTandem
type: Class
subclass of: Search algorithm
subclass of: Identification software
has_obo_namespace: PRIDE
id: PRIDE:0000047
comment: Really X

OutputParameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000048
deprecated: true

Peptide search engine output parameter
type: Class
subclass of: Peptide item additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000049

Rank/Sp
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Sequest
definition: Final correlation score rank and preliminary score rank.
has_obo_namespace: PRIDE
id: PRIDE:0000050

Axiom
annotated source: Rank/Sp
annotated property: definition
annotated target: Final correlation score rank and preliminary score rank.
database_cross_reference: PRIDE:PRIDE

(M+H)+
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Sequest
definition: m/z of the singly-charged precursor (precursor mass + mass of hydrogen atom).
has_obo_namespace: PRIDE
id: PRIDE:0000051

Axiom
annotated source: (M+H)+
annotated property: definition
annotated target: m/z of the singly-charged precursor (precursor mass + mass of hydrogen atom).
database_cross_reference: PRIDE:PRIDE

Cn
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Sequest
definition: normalized correlation score.
has_obo_namespace: PRIDE
id: PRIDE:0000052

Axiom
annotated source: Cn
annotated property: definition
annotated target: normalized correlation score.
database_cross_reference: PRIDE:PRIDE

Sequest score
type: Class
subclass of: Protein search engine output parameter
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Sequest
definition: raw correlation score (Sequest).
has_obo_namespace: PRIDE
has_related_synonym: C*10^4
id: PRIDE:0000053

Axiom
annotated source: Sequest score
annotated property: definition
annotated target: raw correlation score (Sequest).
database_cross_reference: PRIDE:PRIDE

Sp
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Sequest
definition: preliminary score.
has_obo_namespace: PRIDE
id: PRIDE:0000054

Axiom
annotated source: Sp
annotated property: definition
annotated target: preliminary score.
database_cross_reference: PRIDE:PRIDE

Ions
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Sequest
definition: the number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide.
has_obo_namespace: PRIDE
id: PRIDE:0000055

Axiom
annotated source: Ions
annotated property: definition
annotated target: the number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide.
database_cross_reference: PRIDE:PRIDE

Bioworks
type: Class
subclass of: Sequest
subclass of: Identification software
has_obo_namespace: PRIDE
id: PRIDE:0000056

Molecular weight
type: Class
subclass of: Protein search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Bioworks
definition: Molecular weight of a protein.
has_obo_namespace: PRIDE
id: PRIDE:0000057

Axiom
annotated source: Molecular weight
annotated property: definition
annotated target: Molecular weight of a protein.
database_cross_reference: PRIDE:PRIDE

z
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Bioworks
has_obo_namespace: PRIDE
id: PRIDE:0000058

File
type: Class
subclass of: Peptide search engine output parameter
has_obo_namespace: PRIDE
id: PRIDE:0000059

Scan
type: Class
subclass of: Peptide search engine output parameter
has_obo_namespace: PRIDE
id: PRIDE:0000060

Coverage
type: Class
subclass of: Protein search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Bioworks
has_obo_namespace: PRIDE
id: PRIDE:0000061

rsp
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Bioworks
has_obo_namespace: PRIDE
id: PRIDE:0000062

Protein description line
type: Class
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000063

Secondary accession
type: Class
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000064

Upstream flanking sequence
type: Class
subclass of: Peptide item additional parameter
definition: Any sequence reported before the start of the peptide.
has_obo_namespace: PRIDE
id: PRIDE:0000065

Axiom
annotated source: Upstream flanking sequence
annotated property: definition
annotated target: Any sequence reported before the start of the peptide.
database_cross_reference: PRIDE:PRIDE

Downstream flanking seqeuence
type: Class
subclass of: Peptide item additional parameter
definition: Any sequence reported after the end of the peptide sequence.
has_obo_namespace: PRIDE
id: PRIDE:0000066

Axiom
annotated source: Downstream flanking seqeuence
annotated property: definition
annotated target: Any sequence reported after the end of the peptide sequence.
database_cross_reference: PRIDE:PRIDE

Reference reporting this experiment
type: Class
subclass of: Reference additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000067

Reference describing sample preparation
type: Class
subclass of: Reference additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000068

Mascot score
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Mascot
definition: Score as defined for the Mascot search algorithm.
has_obo_namespace: PRIDE
id: PRIDE:0000069

Axiom
annotated source: Mascot score
annotated property: definition
annotated target: Score as defined for the Mascot search algorithm.
database_cross_reference: PRIDE:PRIDE

Peptide cleavage
type: Class
subclass of: Enzyme digestion
definition: Cleavage of the peptide bond.
has_obo_namespace: PRIDE
id: PRIDE:0000070

Axiom
annotated source: Peptide cleavage
annotated property: definition
annotated target: Cleavage of the peptide bond.
database_cross_reference: PRIDE:PRIDE

Search engine setting
type: Class
subclass of: Protocol step description additional parameter
subclass of: Peptide item additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000071

Fixed modification setting
type: Class
subclass of: Search engine setting
has_obo_namespace: PRIDE
id: PRIDE:0000072

Variable modification setting
type: Class
subclass of: Search engine setting
has_obo_namespace: PRIDE
id: PRIDE:0000073

Maximum Missed Cleavages Setting
type: Class
subclass of: Search engine setting
has_obo_namespace: PRIDE
id: PRIDE:0000074

Mass value type setting
type: Class
subclass of: Search engine setting
has_obo_namespace: PRIDE
id: PRIDE:0000075

Mass value type setting monoisotopic
type: Class
subclass of: Mass value type setting
has_obo_namespace: PRIDE
id: PRIDE:0000076

Mass value type setting average
type: Class
subclass of: Mass value type setting
has_obo_namespace: PRIDE
id: PRIDE:0000077

Peptide mass tolerance setting
type: Class
subclass of: Search engine setting
has_obo_namespace: PRIDE
id: PRIDE:0000078

Accurate mass mode setting
type: Class
subclass of: Search engine setting
has_obo_namespace: PRIDE
id: PRIDE:0000079

Accurate mass mode setting true
type: Class
subclass of: Accurate mass mode setting
has_obo_namespace: PRIDE
id: PRIDE:0000080

Accurate mass mode setting false
type: Class
subclass of: Accurate mass mode setting
has_obo_namespace: PRIDE
id: PRIDE:0000081

Mass error type setting
type: Class
subclass of: Search engine setting
has_obo_namespace: PRIDE
id: PRIDE:0000082

mass error type setting ppm
type: Class
subclass of: Mass error type setting
has_obo_namespace: PRIDE
id: PRIDE:0000083

mass error type setting mmu
type: Class
subclass of: Mass error type setting
has_obo_namespace: PRIDE
id: PRIDE:0000084

mass error type setting percent
type: Class
subclass of: Mass error type setting
has_obo_namespace: PRIDE
id: PRIDE:0000085

mass error type setting Daltons
type: Class
subclass of: Mass error type setting
has_obo_namespace: PRIDE
id: PRIDE:0000086

Protonated setting
type: Class
subclass of: Search engine setting
has_obo_namespace: PRIDE
id: PRIDE:0000087

Protonated setting MH+
type: Class
subclass of: Protonated setting
has_obo_namespace: PRIDE
id: PRIDE:0000088

Protonated setting Mr
type: Class
subclass of: Protonated setting
has_obo_namespace: PRIDE
id: PRIDE:0000089

Protonated setting M-H-
type: Class
subclass of: Protonated setting
has_obo_namespace: PRIDE
id: PRIDE:0000090

Rank
type: Class
subclass of: Peptide search engine output parameter
has_obo_namespace: PRIDE
id: PRIDE:0000091

All peptides matched
type: Class
subclass of: Peptide search engine output parameter
has_obo_namespace: PRIDE
id: PRIDE:0000092

All peptides matched true
type: Class
subclass of: All peptides matched
has_obo_namespace: PRIDE
id: PRIDE:0000093

All peptides matched false
type: Class
subclass of: All peptides matched
has_obo_namespace: PRIDE
id: PRIDE:0000094

Masses matched
type: Class
subclass of: Peptide search engine output parameter
has_obo_namespace: PRIDE
id: PRIDE:0000095

Reported Chromosome
type: Class
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000096

Project
type: Class
subclass of: Experiment additional parameter
definition: Allows experiments to be grouped or organised under projects. Experiments may be grouped under more than one project.
has_obo_namespace: PRIDE
id: PRIDE:0000097

Axiom
annotated source: Project
annotated property: definition
annotated target: Allows experiments to be grouped or organised under projects. Experiments may be grouped under more than one project.
database_cross_reference: PRIDE:PRIDE

Indistinguishable alternative protein accession
type: Class
subclass of: Identification additional parameter
definition: A qualifier is mandatory when using this term. The qualifier is an alternative protein accession that is indistinguishable from the primary protein accession based upon observed peptide sequences only.
has_obo_namespace: PRIDE
id: PRIDE:0000098

Axiom
annotated source: Indistinguishable alternative protein accession
annotated property: definition
annotated target: A qualifier is mandatory when using this term. The qualifier is an alternative protein accession that is indistinguishable from the primary protein accession based upon observed peptide sequences only.
database_cross_reference: PRIDE:PRIDE

PeptideProphet probability score
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: PeptideProphet
definition: The probability score for this peptide assignment to be correct, as calculated by PeptideProphet.
has_obo_namespace: PRIDE
id: PRIDE:0000099

Axiom
annotated source: PeptideProphet probability score
annotated property: definition
annotated target: The probability score for this peptide assignment to be correct, as calculated by PeptideProphet.
database_cross_reference: PRIDE:PRIDE

ProteinProphet probability score
type: Class
subclass of: Protein search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: ProteinProphet
definition: The probability score for this protein identification to be correct, as calculated by ProteinProphet.
has_obo_namespace: PRIDE
id: PRIDE:0000100

Axiom
annotated source: ProteinProphet probability score
annotated property: definition
annotated target: The probability score for this protein identification to be correct, as calculated by ProteinProphet.
database_cross_reference: PRIDE:PRIDE

PeptideProphet
type: Class
subclass of: Search algorithm
definition: The PeptideProphet algorithm.
has_obo_namespace: PRIDE
id: PRIDE:0000101

Axiom
annotated source: PeptideProphet
annotated property: definition
annotated target: The PeptideProphet algorithm.
database_cross_reference: PRIDE:PRIDE

ProteinProphet
type: Class
subclass of: Search algorithm
definition: The ProteinProphet algorithm.
has_obo_namespace: PRIDE
id: PRIDE:0000102

Axiom
annotated source: ProteinProphet
annotated property: definition
annotated target: The ProteinProphet algorithm.
database_cross_reference: PRIDE:PRIDE

Gel run date
type: Class
subclass of: Gel additional parameter
definition: The date upon which the gel was run. A value is mandatory - must be formatted as xsd:dateTime.
has_obo_namespace: PRIDE
id: PRIDE:0000103

Axiom
annotated source: Gel run date
annotated property: definition
annotated target: The date upon which the gel was run. A value is mandatory - must be formatted as xsd:dateTime.
database_cross_reference: PRIDE:PRIDE

Sample volume loaded
type: Class
subclass of: Gel additional parameter
definition: The volume of sample loaded on to the gel measured in micro litres. Mandatory value must be formatted as xsd:Double.
database_cross_reference: PRIDE:PRIDE
has_obo_namespace: PRIDE
id: PRIDE:0000104

Axiom
annotated source: Sample volume loaded
annotated property: definition
annotated target: The volume of sample loaded on to the gel measured in micro litres. Mandatory value must be formatted as xsd:Double.
database_cross_reference: PRIDE:PRIDE

Width in pixels
type: Class
subclass of: Gel additional parameter
definition: The width of the referenced gel image in pixels. Mandatory value of type xsd:int.
has_obo_namespace: PRIDE
id: PRIDE:0000105

Axiom
annotated source: Width in pixels
annotated property: definition
annotated target: The width of the referenced gel image in pixels. Mandatory value of type xsd:int.
database_cross_reference: PRIDE:PRIDE

Height in pixels
type: Class
subclass of: Gel additional parameter
definition: The height of the referenced gel image in pixels. Mandatory value of type xsd:int.
has_obo_namespace: PRIDE
id: PRIDE:0000106

Axiom
annotated source: Height in pixels
annotated property: definition
annotated target: The height of the referenced gel image in pixels. Mandatory value of type xsd:int.
database_cross_reference: PRIDE:PRIDE

Gel spot parameter
type: Class
subclass of: Identification additional parameter
definition: Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification.
has_obo_namespace: PRIDE
id: PRIDE:0000107

Axiom
annotated source: Gel spot parameter
annotated property: definition
annotated target: Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification.
database_cross_reference: PRIDE:PRIDE

Gel spot intensity
type: Class
subclass of: Gel spot parameter
definition: The intensity of the spot on the gel. Mandatory value of type xsd:double.
has_obo_namespace: PRIDE
id: PRIDE:0000108

Axiom
annotated source: Gel spot intensity
annotated property: definition
annotated target: The intensity of the spot on the gel. Mandatory value of type xsd:double.
database_cross_reference: PRIDE:PRIDE

Gel spot area
type: Class
subclass of: Gel spot parameter
definition: The area of the spot on the gel measured in millimetres squared. Mandatory value of type xsd:double.
has_obo_namespace: PRIDE
id: PRIDE:0000109

Axiom
annotated source: Gel spot area
annotated property: definition
annotated target: The area of the spot on the gel measured in millimetres squared. Mandatory value of type xsd:double.
database_cross_reference: PRIDE:PRIDE

Gel spot volume
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Spot normalized volume
definition: The volume of the spot on the gel measured in millimetres cubed. Mandatory value of type xsd:double.
has_obo_namespace: PRIDE
id: PRIDE:0000110

Axiom
annotated source: Gel spot volume
annotated property: definition
annotated target: The volume of the spot on the gel measured in millimetres cubed. Mandatory value of type xsd:double.
database_cross_reference: PRIDE:PRIDE

Reference describing data analysis
type: Class
subclass of: Reference additional parameter
definition: A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment.
has_obo_namespace: PRIDE
id: PRIDE:0000111

Axiom
annotated source: Reference describing data analysis
annotated property: definition
annotated target: A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment.
database_cross_reference: PRIDE:PRIDE

Identified by peptide mass fingerprint
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
definition: The annotated protein identification arises from peptide mass fingerprinting. Peptide identifications may or may not be included.
has_exact_synonym: PMF
has_obo_namespace: PRIDE
id: PRIDE:0000112

Axiom
annotated source: Identified by peptide mass fingerprint
annotated property: definition
annotated target: The annotated protein identification arises from peptide mass fingerprinting. Peptide identifications may or may not be included.
database_cross_reference: PRIDE:PRIDE

Identified by peptide fragmentation
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
definition: The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching.
has_exact_synonym: PFF
has_obo_namespace: PRIDE
id: PRIDE:0000113

Axiom
annotated source: Identified by peptide fragmentation
annotated property: definition
annotated target: The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching.
database_cross_reference: PRIDE:PRIDE

iTRAQ reagent 114
type: Class
subclass of: iTRAQ reagent
has_obo_namespace: PRIDE
id: PRIDE:0000114
comment: The name of the sample labelled with iTRAQ reagent 114.

iTRAQ reagent 115
type: Class
subclass of: iTRAQ reagent
has_obo_namespace: PRIDE
id: PRIDE:0000115
comment: The name of the sample labelled with iTRAQ reagent 115.

iTRAQ reagent 116
type: Class
subclass of: iTRAQ reagent
has_obo_namespace: PRIDE
id: PRIDE:0000116
comment: The name of the sample labelled with iTRAQ reagent 116.

iTRAQ reagent 117
type: Class
subclass of: iTRAQ reagent
has_obo_namespace: PRIDE
id: PRIDE:0000117
comment: The name of the sample labelled with iTRAQ reagent 117.

iTRAQ intensity 114
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000118
comment: The intensity of the sample labelled with iTRAQ reagent 114.

iTRAQ intensity 115
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000119
comment: The intensity of the sample labelled with iTRAQ reagent 115.

iTRAQ intensity 116
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000120
comment: The intensity of the sample labelled with iTRAQ reagent 116.

iTRAQ intensity 117
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000121
comment: The intensity of the sample labelled with iTRAQ reagent 117.

Two Dimensional Polyacrylamide Gel Electrophoresis
type: Class
subclass of: Separation
definition: A type of gel electrophoresis in which proteins are first separated by charge and then by molecular weight, enabling the analysis of complex protein mixtures.
has_obo_namespace: PRIDE
id: PRIDE:0000122

Axiom
annotated source: Two Dimensional Polyacrylamide Gel Electrophoresis
annotated property: definition
annotated target: A type of gel electrophoresis in which proteins are first separated by charge and then by molecular weight, enabling the analysis of complex protein mixtures.
database_cross_reference: PRIDE:PRIDE

Immobilized pH Gradient Electrophoresis
type: Class
subclass of: SDS PAGE
subclass of: Restriction
  on property: part_of
  some values from: Two Dimensional Polyacrylamide Gel Electrophoresis
definition: Electrophoresis using an gel which has a pH gradient along its length.
has_obo_namespace: PRIDE
id: PRIDE:0000123

Axiom
annotated source: Immobilized pH Gradient Electrophoresis
annotated property: definition
annotated target: Electrophoresis using an gel which has a pH gradient along its length.
database_cross_reference: PRIDE:PRIDE

Sodium dodecyl sulfate polyacrylamide gel electrophoresis
type: Class
subclass of: SDS PAGE
subclass of: Restriction
  on property: part_of
  some values from: Two Dimensional Polyacrylamide Gel Electrophoresis
definition: A type of polyacrylamide gel electrophoresis in which the anionic detergent sodium dodecyl sulfate (SDS) is used to denature the sample proteins into linear monomers, rendering their charge proportional to their length so that migration is a function of size. Abbreviated SDS-polyacrylamide gel electrophoresis or SDS-PAGE.
has_obo_namespace: PRIDE
id: PRIDE:0000124

Axiom
annotated source: Sodium dodecyl sulfate polyacrylamide gel electrophoresis
annotated property: definition
annotated target: A type of polyacrylamide gel electrophoresis in which the anionic detergent sodium dodecyl sulfate (SDS) is used to denature the sample proteins into linear monomers, rendering their charge proportional to their length so that migration is a function of size. Abbreviated SDS-polyacrylamide gel electrophoresis or SDS-PAGE.
database_cross_reference: PRIDE:PRIDE

pH low value
type: Class
subclass of: Immobilized pH Gradient Electrophoresis
definition: The lowest pH of an immobilised pH gradient gel.
has_obo_namespace: PRIDE
id: PRIDE:0000125

Axiom
annotated source: pH low value
annotated property: definition
annotated target: The lowest pH of an immobilised pH gradient gel.
database_cross_reference: PRIDE:PRIDE

pH high value
type: Class
subclass of: Immobilized pH Gradient Electrophoresis
definition: The highest pH of an immobilised pH gradient gel.
has_obo_namespace: PRIDE
id: PRIDE:0000126

Axiom
annotated source: pH high value
annotated property: definition
annotated target: The highest pH of an immobilised pH gradient gel.
database_cross_reference: PRIDE:PRIDE

IPG strip length cm
type: Class
subclass of: Immobilized pH Gradient Electrophoresis
definition: The length in centimeters of an immobilised pH gradient gel.
has_obo_namespace: PRIDE
id: PRIDE:0000127
comment: This value associated with this CV term should always be in centimeters.

Axiom
annotated source: IPG strip length cm
annotated property: definition
annotated target: The length in centimeters of an immobilised pH gradient gel.
database_cross_reference: PRIDE:PRIDE

First dimension details
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Immobilized pH Gradient Electrophoresis
definition: Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters.
has_obo_namespace: PRIDE
id: PRIDE:0000128
comment: This CV term should be used in association with a value that is a free-text description of the first dimension details

Axiom
annotated source: First dimension details
annotated property: definition
annotated target: Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters.
database_cross_reference: PRIDE:PRIDE

Second dimension details
type: Class
subclass of: Sodium dodecyl sulfate polyacrylamide gel electrophoresis
definition: Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis.
has_obo_namespace: PRIDE
id: PRIDE:0000129
comment: This CV term should be used in association with a value that is a free-text description of the second dimension details

Axiom
annotated source: Second dimension details
annotated property: definition
annotated target: Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis.
database_cross_reference: PRIDE:PRIDE

Obsoleted parameters
type: Class
definition: Obsoleted terms.
has_obo_namespace: PRIDE
id: PRIDE:0000130
deprecated: true

Axiom
annotated source: Obsoleted parameters
annotated property: definition
annotated target: Obsoleted terms.
database_cross_reference: Curator:Rc

Spot normalized volume
type: Class
subclass of: Gel spot parameter
definition: A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values.
has_obo_namespace: PRIDE
id: PRIDE:0000131

Axiom
annotated source: Spot normalized volume
annotated property: definition
annotated target: A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values.
database_cross_reference: PRIDE:PRIDE

Spot normalized volume method
type: Class
subclass of: Gel spot parameter
definition: The method by which the normalized value for spot volume is derived from the individual gel spot volume values.
has_obo_namespace: PRIDE
id: PRIDE:0000132

Axiom
annotated source: Spot normalized volume method
annotated property: definition
annotated target: The method by which the normalized value for spot volume is derived from the individual gel spot volume values.
database_cross_reference: PRIDE:PRIDE

Isobaric residue K/Q
type: Class
subclass of: Peptide item additional parameter
definition: The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146).
has_obo_namespace: PRIDE
id: PRIDE:0000133

Axiom
annotated source: Isobaric residue K/Q
annotated property: definition
annotated target: The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146).
database_cross_reference: PRIDE:PRIDE

Anticoagulant
type: Class
subclass of: Protocol step description additional parameter
definition: A substance that prevents coagulation; that is, it stops blood from clotting.
has_obo_namespace: PRIDE
id: PRIDE:0000134

Axiom
annotated source: Anticoagulant
annotated property: definition
annotated target: A substance that prevents coagulation; that is, it stops blood from clotting.
database_cross_reference: PRIDE:PRIDE

Mapping date
type: Class
subclass of: Identification additional parameter
definition: Date of last mapping of given identifier to current UniProt accession number.
has_obo_namespace: PRIDE
id: PRIDE:0000135

Axiom
annotated source: Mapping date
annotated property: definition
annotated target: Date of last mapping of given identifier to current UniProt accession number.
database_cross_reference: PRIDE:PRIDE

Mapping status
type: Class
subclass of: Identification additional parameter
definition: Status of last mapping of given identifier to current UniProt accession number. Valid values are 'mappingAllOK', 'not mapped peptide mismatch', 'not mapped accession not found' and 'not mapped taxon not found' .
has_obo_namespace: PRIDE
id: PRIDE:0000136

Axiom
annotated source: Mapping status
annotated property: definition
annotated target: Status of last mapping of given identifier to current UniProt accession number. Valid values are 'mappingAllOK', 'not mapped peptide mismatch', 'not mapped accession not found' and 'not mapped taxon not found' .
database_cross_reference: PRIDE:PRIDE

Mapping history
type: Class
subclass of: Identification additional parameter
definition: Status of last mapping of given identifier to current UniProt accession number. Valid values are 'unchanged since last mapping', 'changed accession' and 'changed version of accession' .
has_obo_namespace: PRIDE
id: PRIDE:0000137

Axiom
annotated source: Mapping history
annotated property: definition
annotated target: Status of last mapping of given identifier to current UniProt accession number. Valid values are 'unchanged since last mapping', 'changed accession' and 'changed version of accession' .
database_cross_reference: PRIDE:PRIDE

Discriminant score
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: PeptideProphet
definition: PeptideProphet discriminant score fval.
has_obo_namespace: PRIDE
id: PRIDE:0000138

Axiom
annotated source: Discriminant score
annotated property: definition
annotated target: PeptideProphet discriminant score fval.
database_cross_reference: PRIDE:PRIDE

Not Mapped SOAP Error
type: Class
subclass of: Mapping status
definition: Error message: SOAP protocol failed.
has_obo_namespace: PRIDE
id: PRIDE:0000139

Axiom
annotated source: Not Mapped SOAP Error
annotated property: definition
annotated target: Error message: SOAP protocol failed.
database_cross_reference: PRIDE:PRIDE

Not Mapped Database Error
type: Class
subclass of: Mapping status
definition: Error message: Error with queried database.
has_obo_namespace: PRIDE
id: PRIDE:0000140

Axiom
annotated source: Not Mapped Database Error
annotated property: definition
annotated target: Error message: Error with queried database.
database_cross_reference: PRIDE:PRIDE

Not Mapped No Mapping Found
type: Class
subclass of: Mapping status
definition: Error message: Unable to match given identifier.
has_obo_namespace: PRIDE
id: PRIDE:0000141

Axiom
annotated source: Not Mapped No Mapping Found
annotated property: definition
annotated target: Error message: Unable to match given identifier.
database_cross_reference: PRIDE:PRIDE

Not Mapped Peptide Mismatch
type: Class
subclass of: Mapping status
definition: Error message: One or more peptide sequences did not match query sequence.
has_obo_namespace: PRIDE
id: PRIDE:0000142

Axiom
annotated source: Not Mapped Peptide Mismatch
annotated property: definition
annotated target: Error message: One or more peptide sequences did not match query sequence.
database_cross_reference: PRIDE:PRIDE

Mapped Taxon Not Found
type: Class
subclass of: Mapping status
definition: Error message: No mapping to proteins from defined taxon.
has_obo_namespace: PRIDE
id: PRIDE:0000143

Axiom
annotated source: Mapped Taxon Not Found
annotated property: definition
annotated target: Error message: No mapping to proteins from defined taxon.
database_cross_reference: PRIDE:PRIDE

Mapped All Ok
type: Class
subclass of: Mapping status
definition: Sucessful completion of operation message.
has_obo_namespace: PRIDE
id: PRIDE:0000144

Axiom
annotated source: Mapped All Ok
annotated property: definition
annotated target: Sucessful completion of operation message.
database_cross_reference: PRIDE:PRIDE

PepSplice
type: Class
subclass of: Search algorithm
subclass of: Identification software
definition: The PepSplice algorithm.
has_obo_namespace: PRIDE
id: PRIDE:0000145

Axiom
annotated source: PepSplice
annotated property: definition
annotated target: The PepSplice algorithm.
database_cross_reference: PRIDE:PRIDE

PepSplice precision
type: Class
subclass of: PepSplice
subclass of: Restriction
  on property: part_of
  some values from: PepSplice
has_obo_namespace: PRIDE
id: PRIDE:0000146

PepSplice False Discovery Rate
type: Class
subclass of: PepSplice
subclass of: Restriction
  on property: part_of
  some values from: PepSplice
has_obo_namespace: PRIDE
id: PRIDE:0000147

PepSplice P-value
type: Class
subclass of: PepSplice
subclass of: Restriction
  on property: part_of
  some values from: PepSplice
definition: A Score based on the hypergeometric model.
has_obo_namespace: PRIDE
id: PRIDE:0000148

Axiom
annotated source: PepSplice P-value
annotated property: definition
annotated target: A Score based on the hypergeometric model.
database_cross_reference: PRIDE:PRIDE

PepSplice Deltascore
type: Class
subclass of: PepSplice
subclass of: Restriction
  on property: part_of
  some values from: PepSplice
definition: The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together.
has_obo_namespace: PRIDE
id: PRIDE:0000149

Axiom
annotated source: PepSplice Deltascore
annotated property: definition
annotated target: The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together.
database_cross_reference: PRIDE:PRIDE

PepSplice Score Count
type: Class
subclass of: PepSplice
subclass of: Restriction
  on property: part_of
  some values from: PepSplice
definition: The score count.
has_obo_namespace: PRIDE
id: PRIDE:0000150

Axiom
annotated source: PepSplice Score Count
annotated property: definition
annotated target: The score count.
database_cross_reference: PRIDE:PRIDE

PepSplice Penalty
type: Class
subclass of: PepSplice
subclass of: Restriction
  on property: part_of
  some values from: PepSplice
definition: The Sum of all penalties for the peptide assignment.
has_obo_namespace: PRIDE
id: PRIDE:0000151

Axiom
annotated source: PepSplice Penalty
annotated property: definition
annotated target: The Sum of all penalties for the peptide assignment.
database_cross_reference: PRIDE:PRIDE

PepSplice Read Direction
type: Class
subclass of: PepSplice
subclass of: Restriction
  on property: part_of
  some values from: PepSplice
definition: The reading direction on the DNA.
has_obo_namespace: PRIDE
id: PRIDE:0000152

Axiom
annotated source: PepSplice Read Direction
annotated property: definition
annotated target: The reading direction on the DNA.
database_cross_reference: PRIDE:PRIDE

PepSplice Forward Read Direction
type: Class
subclass of: PepSplice Read Direction
definition: The reading direction on the DNA is 5' to 3'.
has_obo_namespace: PRIDE
id: PRIDE:0000153

Axiom
annotated source: PepSplice Forward Read Direction
annotated property: definition
annotated target: The reading direction on the DNA is 5' to 3'.
database_cross_reference: PRIDE:PRIDE

PepSplice Reverse Read Direction
type: Class
subclass of: PepSplice
subclass of: PepSplice Read Direction
definition: The reading direction on the DNA 3' to 5'.
has_obo_namespace: PRIDE
id: PRIDE:0000154

Axiom
annotated source: PepSplice Reverse Read Direction
annotated property: definition
annotated target: The reading direction on the DNA 3' to 5'.
database_cross_reference: PRIDE:PRIDE

Unmappable
type: Class
subclass of: Mapping status
definition: unsucessful mapping.
has_obo_namespace: PRIDE
id: PRIDE:0000155

Axiom
annotated source: Unmappable
annotated property: definition
annotated target: unsucessful mapping.
database_cross_reference: PRIDE:PRIDE

Project identifier
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Project
definition: unique identifier of project.
has_exact_synonym: Project ID
has_obo_namespace: PRIDE
id: PRIDE:0000156

Axiom
annotated source: Project identifier
annotated property: definition
annotated target: unique identifier of project.
database_cross_reference: PRIDE:PRIDE

Search type
type: Class
subclass of: Search engine setting
definition: type of search.
has_obo_namespace: PRIDE
id: PRIDE:0000157

Axiom
annotated source: Search type
annotated property: definition
annotated target: type of search.
database_cross_reference: PRIDE:PRIDE

MS search
type: Class
subclass of: Search type
has_obo_namespace: PRIDE
id: PRIDE:0000158

MS/MS search
type: Class
subclass of: Search type
has_obo_namespace: PRIDE
id: PRIDE:0000159

Enzyme
type: Class
subclass of: Search engine setting
definition: type of enzyme used to fragment the protein. The value will equal the name of the enxzyme used e.g. .
has_obo_namespace: PRIDE
id: PRIDE:0000160

Axiom
annotated source: Enzyme
annotated property: definition
annotated target: type of enzyme used to fragment the protein. The value will equal the name of the enxzyme used e.g. .
database_cross_reference: PRIDE:PRIDE

Fragment mass tolerance setting
type: Class
subclass of: Search engine setting
definition: range of acceptable fragment masses accepted by instrument.
has_obo_namespace: PRIDE
id: PRIDE:0000161

Axiom
annotated source: Fragment mass tolerance setting
annotated property: definition
annotated target: range of acceptable fragment masses accepted by instrument.
database_cross_reference: PRIDE:PRIDE

Allowed missed cleavages
type: Class
subclass of: Search engine setting
definition: number of missed cleavage sites taken into account.
has_obo_namespace: PRIDE
id: PRIDE:0000162

Axiom
annotated source: Allowed missed cleavages
annotated property: definition
annotated target: number of missed cleavage sites taken into account.
database_cross_reference: PRIDE:PRIDE

Instrument type
type: Class
subclass of: Search engine setting
definition: name of instrument used in analysis.
has_obo_namespace: PRIDE
id: PRIDE:0000163

Axiom
annotated source: Instrument type
annotated property: definition
annotated target: name of instrument used in analysis.
database_cross_reference: PRIDE:PRIDE

Mapped Without Supporting Peptides
type: Class
subclass of: Mapping status
definition: Sucessful mapping without supporting evidence from peptides.
has_obo_namespace: PRIDE
id: PRIDE:0000164

Axiom
annotated source: Mapped Without Supporting Peptides
annotated property: definition
annotated target: Sucessful mapping without supporting evidence from peptides.
database_cross_reference: PRIDE:PRIDE

Automatic allocation
type: Class
subclass of: Identification additional parameter
definition: PICR tool has allocated the accession number.
has_obo_namespace: PRIDE
id: PRIDE:0000165

Axiom
annotated source: Automatic allocation
annotated property: definition
annotated target: PICR tool has allocated the accession number.
database_cross_reference: PRIDE:PRIDE

Ambiguous modification
type: Class
subclass of: ModificationItem additional parameter
definition: Modification with a MonoDeltaMass, which can not unambiguously be assigned to only one modification and for which several possibilities exist.
has_obo_namespace: PRIDE
id: PRIDE:0000166

Axiom
annotated source: Ambiguous modification
annotated property: definition
annotated target: Modification with a MonoDeltaMass, which can not unambiguously be assigned to only one modification and for which several possibilities exist.
database_cross_reference: PRIDE:PRIDE

Novel locus information
type: Class
subclass of: Identification additional parameter
definition: Detailed information about a genomic locus identified by whole genome searches.
has_obo_namespace: PRIDE
id: PRIDE:0000167

Axiom
annotated source: Novel locus information
annotated property: definition
annotated target: Detailed information about a genomic locus identified by whole genome searches.
database_cross_reference: PRIDE:PRIDE

Nucleic acid sequence
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000168

Start position of the nucleic acid sequence on the chromosome
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000169

Stop position of the nucleic acid sequence on the chromosome
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000170

funding reference
type: Class
subclass of: Reference additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000171

Search database protein sequence length
type: Class
subclass of: Identification additional parameter
definition: Value of average of all individual peptide identifications for this protein.
has_obo_namespace: PRIDE
id: PRIDE:0000172

Axiom
annotated source: Search database protein sequence length
annotated property: definition
annotated target: Value of average of all individual peptide identifications for this protein.
database_cross_reference: PRIDE:PRIDE

MeanOfPeptideScores
type: Class
subclass of: Identification additional parameter
definition: Value of average of all individual peptide scores.
has_obo_namespace: PRIDE
id: PRIDE:0000173

Axiom
annotated source: MeanOfPeptideScores
annotated property: definition
annotated target: Value of average of all individual peptide scores.
database_cross_reference: PRIDE:PRIDE

Isoelectric point
type: Class
subclass of: Protein search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Bioworks
definition: Isoelectric point of a protein.
has_exact_synonym: pI
has_obo_namespace: PRIDE
id: PRIDE:0000174

Axiom
annotated source: Isoelectric point
annotated property: definition
annotated target: Isoelectric point of a protein.
database_cross_reference: PRIDE:PRIDE

XML generation software
type: Class
subclass of: Experiment additional parameter
definition: The software which was used to generate the PRIDE XML file.
has_obo_namespace: PRIDE
id: PRIDE:0000175

Axiom
annotated source: XML generation software
annotated property: definition
annotated target: The software which was used to generate the PRIDE XML file.
database_cross_reference: PRIDE:PRIDE

X!Tandem Hyperscore
type: Class
subclass of: Peptide search engine output parameter
definition: The X!Tandem hyperscore for the peptide.
has_obo_namespace: PRIDE
id: PRIDE:0000176

Axiom
annotated source: X!Tandem Hyperscore
annotated property: definition
annotated target: The X!Tandem hyperscore for the peptide.
database_cross_reference: PRIDE:PRIDE

Spectrum Mill peptide score
type: Class
subclass of: Peptide search engine output parameter
definition: The Spectrum Mill score for the peptide.
has_obo_namespace: PRIDE
id: PRIDE:0000177

Axiom
annotated source: Spectrum Mill peptide score
annotated property: definition
annotated target: The Spectrum Mill score for the peptide.
database_cross_reference: PRIDE:PRIDE

Peptide selection
type: Class
subclass of: Protocol step description additional parameter
definition: A protocol step to select for a particular type of peptides.
has_obo_namespace: PRIDE
id: PRIDE:0000178

Axiom
annotated source: Peptide selection
annotated property: definition
annotated target: A protocol step to select for a particular type of peptides.
database_cross_reference: PRIDE:PRIDE

dotproduct
type: Class
subclass of: XTandem
definition: X|Tandem dot product score.
has_obo_namespace: PRIDE
id: PRIDE:0000179

Axiom
annotated source: dotproduct
annotated property: definition
annotated target: X|Tandem dot product score.
database_cross_reference: PRIDE:PRIDE

delta
type: Class
subclass of: XTandem
definition: X|Tandem delta score.
has_obo_namespace: PRIDE
id: PRIDE:0000180

Axiom
annotated source: delta
annotated property: definition
annotated target: X|Tandem delta score.
database_cross_reference: PRIDE:PRIDE

deltastar
type: Class
subclass of: XTandem
definition: X|Tandem delta star score.
has_obo_namespace: PRIDE
id: PRIDE:0000181

Axiom
annotated source: deltastar
annotated property: definition
annotated target: X|Tandem delta star score.
database_cross_reference: PRIDE:PRIDE

zscore
type: Class
subclass of: XTandem
definition: X|Tandem Z score.
has_obo_namespace: PRIDE
id: PRIDE:0000182

Axiom
annotated source: zscore
annotated property: definition
annotated target: X|Tandem Z score.
database_cross_reference: PRIDE:PRIDE

expect
type: Class
subclass of: XTandem
definition: X|Tandem expectancy score.
has_obo_namespace: PRIDE
id: PRIDE:0000183

Axiom
annotated source: expect
annotated property: definition
annotated target: X|Tandem expectancy score.
database_cross_reference: PRIDE:PRIDE

Query number
type: Class
subclass of: Mascot
definition: Search parameter that allows users to find query results from old data.
has_obo_namespace: PRIDE
id: PRIDE:0000184

Axiom
annotated source: Query number
annotated property: definition
annotated target: Search parameter that allows users to find query results from old data.
database_cross_reference: PRIDE:PRIDE

OMSSA E-value
type: Class
subclass of: Peptide search engine output parameter
definition: E-value parameter from OMSSA.
has_obo_namespace: PRIDE
id: PRIDE:0000185

Axiom
annotated source: OMSSA E-value
annotated property: definition
annotated target: E-value parameter from OMSSA.
database_cross_reference: PRIDE:PRIDE

OMSSA P-value
type: Class
subclass of: Peptide search engine output parameter
definition: P-value parameter from OMSSA.
has_obo_namespace: PRIDE
id: PRIDE:0000186

Axiom
annotated source: OMSSA P-value
annotated property: definition
annotated target: P-value parameter from OMSSA.
database_cross_reference: PRIDE:PRIDE

Fragment Ion Annotation
type: Class
subclass of: Peptide item additional parameter
definition: Fragment ion annotation of the peptide.
has_exact_synonym: product ion property
has_obo_namespace: PRIDE
id: PRIDE:0000187

Axiom
annotated source: Fragment Ion Annotation
annotated property: definition
annotated target: Fragment ion annotation of the peptide.
database_cross_reference: PRIDE:PRIDE

product ion m/z
type: Class
subclass of: Fragment Ion Annotation
definition: Mass.
has_exact_synonym: fragment ion mass
has_obo_namespace: PRIDE
id: PRIDE:0000188

Axiom
annotated source: product ion m/z
annotated property: definition
annotated target: Mass.
database_cross_reference: PRIDE:PRIDE

product ion intensity
type: Class
subclass of: Fragment Ion Annotation
definition: Intensity.
has_exact_synonym: fragment ion intensity
has_obo_namespace: PRIDE
id: PRIDE:0000189

Axiom
annotated source: product ion intensity
annotated property: definition
annotated target: Intensity.
database_cross_reference: PRIDE:PRIDE

product ion mass error
type: Class
subclass of: Fragment Ion Annotation
definition: Mass error.
has_exact_synonym: fragment ion mass error
has_obo_namespace: PRIDE
id: PRIDE:0000190

Axiom
annotated source: product ion mass error
annotated property: definition
annotated target: Mass error.
database_cross_reference: PRIDE:PRIDE

product ion retention time error
type: Class
subclass of: Fragment Ion Annotation
definition: Retention time error in minutes.
has_exact_synonym: fragment ion retention time error
has_obo_namespace: PRIDE
id: PRIDE:0000191

Axiom
annotated source: product ion retention time error
annotated property: definition
annotated target: Retention time error in minutes.
database_cross_reference: PRIDE:PRIDE

product ion type
type: Class
subclass of: Fragment Ion Annotation
definition: Product ion type.
has_exact_synonym: fragment ion type
has_obo_namespace: PRIDE
id: PRIDE:0000192

Axiom
annotated source: product ion type
annotated property: definition
annotated target: Product ion type.
database_cross_reference: PRIDE:PRIDE

y ion
type: Class
subclass of: product ion type
definition: Y ion type.
has_exact_synonym: y fragment ion
has_obo_namespace: PRIDE
id: PRIDE:0000193

Axiom
annotated source: y ion
annotated property: definition
annotated target: Y ion type.
database_cross_reference: PRIDE:PRIDE

b ion
type: Class
subclass of: product ion type
definition: B ion type.
has_exact_synonym: b fragment ion
has_obo_namespace: PRIDE
id: PRIDE:0000194

Axiom
annotated source: b ion
annotated property: definition
annotated target: B ion type.
database_cross_reference: PRIDE:PRIDE

b ion -NH3
type: Class
subclass of: b ion
definition: B ion type with a neutral loss of an ammonia group.
has_exact_synonym: b fragment ion -NH3
has_obo_namespace: PRIDE
id: PRIDE:0000195

Axiom
annotated source: b ion -NH3
annotated property: definition
annotated target: B ion type with a neutral loss of an ammonia group.
database_cross_reference: PRIDE:PRIDE

b ion -H2O
type: Class
subclass of: b ion
definition: B ion type with a neutral loss of a water molecule.
has_exact_synonym: b fragment ion -H2O
has_obo_namespace: PRIDE
id: PRIDE:0000196

Axiom
annotated source: b ion -H2O
annotated property: definition
annotated target: B ion type with a neutral loss of a water molecule.
database_cross_reference: PRIDE:PRIDE

y ion -H2O
type: Class
subclass of: y ion
definition: Y ion type with the neutral loss of a molecule water.
has_exact_synonym: y fragment ion -H2O
has_obo_namespace: PRIDE
id: PRIDE:0000197

Axiom
annotated source: y ion -H2O
annotated property: definition
annotated target: Y ion type with the neutral loss of a molecule water.
database_cross_reference: PRIDE:PRIDE

y ion -NH3
type: Class
subclass of: y ion
definition: Y ion type with the neutral loss of an ammonia group.
has_exact_synonym: y fragment ion -NH3
has_obo_namespace: PRIDE
id: PRIDE:0000198

Axiom
annotated source: y ion -NH3
annotated property: definition
annotated target: Y ion type with the neutral loss of an ammonia group.
database_cross_reference: PRIDE:PRIDE

in source ion
type: Class
subclass of: product ion type
definition: Ion resulting from in-source fragmentation.
has_exact_synonym: in source fragment ion
has_exact_synonym: in-source ion
has_obo_namespace: PRIDE
id: PRIDE:0000199

Axiom
annotated source: in source ion
annotated property: definition
annotated target: Ion resulting from in-source fragmentation.
database_cross_reference: PRIDE:PRIDE

non-identified ion
type: Class
subclass of: product ion type
definition: Fragment ion that could not be assigned to a predicted fragment ion mass.
has_exact_synonym: unidentified ion
has_obo_namespace: PRIDE
id: PRIDE:0000200

Axiom
annotated source: non-identified ion
annotated property: definition
annotated target: Fragment ion that could not be assigned to a predicted fragment ion mass.
database_cross_reference: PRIDE:PRIDE

co-eluting ion
type: Class
subclass of: product ion type
definition: Fragment ion that was matched to another, co-eluting peptide precursor.
has_obo_namespace: PRIDE
id: PRIDE:0000201

Axiom
annotated source: co-eluting ion
annotated property: definition
annotated target: Fragment ion that was matched to another, co-eluting peptide precursor.
database_cross_reference: PRIDE:PRIDE

Parent Ion Annotation
type: Class
subclass of: Peptide item additional parameter
definition: Parent ion annotation of the peptide.
has_obo_namespace: PRIDE
id: PRIDE:0000202

Axiom
annotated source: Parent Ion Annotation
annotated property: definition
annotated target: Parent ion annotation of the peptide.
database_cross_reference: PRIDE:PRIDE

parent ion retention time
type: Class
subclass of: Parent Ion Annotation
definition: Retention time in minutes.
has_obo_namespace: PRIDE
id: PRIDE:0000203

Axiom
annotated source: parent ion retention time
annotated property: definition
annotated target: Retention time in minutes.
database_cross_reference: PRIDE:PRIDE

product ion charge
type: Class
subclass of: Fragment Ion Annotation
definition: Charge state.
has_exact_synonym: fragment ion charge
has_obo_namespace: PRIDE
id: PRIDE:0000204

Axiom
annotated source: product ion charge
annotated property: definition
annotated target: Charge state.
database_cross_reference: PRIDE:PRIDE

Heavy stable isotope label
type: Class
definition: A general term for any stable isotope method.
has_obo_namespace: PRIDE
id: PRIDE:0000205
deprecated: true

Axiom
annotated source: Heavy stable isotope label
annotated property: definition
annotated target: A general term for any stable isotope method.
database_cross_reference: PRIDE:PRIDE

Heavy stable isotope label residue
type: Class
definition: The precise amino acid that has been modified.
has_obo_namespace: PRIDE
id: PRIDE:0000206
deprecated: true

Axiom
annotated source: Heavy stable isotope label residue
annotated property: definition
annotated target: The precise amino acid that has been modified.
database_cross_reference: PRIDE:PRIDE

Light stable isotope label
type: Class
definition: A general term for any stable isotope method.
has_obo_namespace: PRIDE
id: PRIDE:0000207
deprecated: true

Axiom
annotated source: Light stable isotope label
annotated property: definition
annotated target: A general term for any stable isotope method.
database_cross_reference: PRIDE:PRIDE

Light stable isotope label residue
type: Class
definition: The precise amino acid that has been modified.
has_obo_namespace: PRIDE
id: PRIDE:0000208
deprecated: true

Axiom
annotated source: Light stable isotope label residue
annotated property: definition
annotated target: The precise amino acid that has been modified.
database_cross_reference: PRIDE:PRIDE

Peptide pair id
type: Class
subclass of: Peptide item additional parameter
definition: Facilitate mapping between peptide pairs (usually heavy/light) to which the stable isotope ratio below relates.
has_obo_namespace: PRIDE
id: PRIDE:0000209

Axiom
annotated source: Peptide pair id
annotated property: definition
annotated target: Facilitate mapping between peptide pairs (usually heavy/light) to which the stable isotope ratio below relates.
database_cross_reference: PRIDE:PRIDE

Stable isotope ratio
type: Class
subclass of: Peptide item additional parameter
definition: Ratio of peptide pair the sequence/sample is the numerator in the ratio.
has_obo_namespace: PRIDE
id: PRIDE:0000210

Axiom
annotated source: Stable isotope ratio
annotated property: definition
annotated target: Ratio of peptide pair the sequence/sample is the numerator in the ratio.
database_cross_reference: PRIDE:PRIDE

Quantitative sample reference
type: Class
subclass of: Peptide item additional parameter
definition: This links back to the value given to the heavy/light stable isotope label to relate the peptide ratio back to the sample.
has_obo_namespace: PRIDE
id: PRIDE:0000211

Axiom
annotated source: Quantitative sample reference
annotated property: definition
annotated target: This links back to the value given to the heavy/light stable isotope label to relate the peptide ratio back to the sample.
database_cross_reference: PRIDE:PRIDE

Mascot expect value
type: Class
subclass of: Mascot
definition: Expect value as defined for the Mascot search algorithm.
has_obo_namespace: PRIDE
id: PRIDE:0000212

Axiom
annotated source: Mascot expect value
annotated property: definition
annotated target: Expect value as defined for the Mascot search algorithm.
database_cross_reference: PRIDE:PRIDE

Inspect
type: Class
subclass of: Search algorithm
subclass of: Identification software
definition: The Inspect search algorithm.
has_obo_namespace: PRIDE
id: PRIDE:0000213

Axiom
annotated source: Inspect
annotated property: definition
annotated target: The Inspect search algorithm.
database_cross_reference: PRIDE:PRIDE

Inspect MQScore
type: Class
subclass of: Inspect
definition: Quality score of a match.
has_obo_namespace: PRIDE
id: PRIDE:0000214

Axiom
annotated source: Inspect MQScore
annotated property: definition
annotated target: Quality score of a match.
database_cross_reference: PRIDE:PRIDE

Inspect p-value
type: Class
subclass of: Inspect
definition: Probability that the top match is correct.
has_obo_namespace: PRIDE
id: PRIDE:0000215

Axiom
annotated source: Inspect p-value
annotated property: definition
annotated target: Probability that the top match is correct.
database_cross_reference: PRIDE:PRIDE

ProteomExchange project accession number
type: Class
subclass of: Experiment additional parameter
definition: ProteomExchange accession number of the project where the PRIDE experiment is included.
has_obo_namespace: PRIDE
id: PRIDE:0000216

Axiom
annotated source: ProteomExchange project accession number
annotated property: definition
annotated target: ProteomExchange accession number of the project where the PRIDE experiment is included.
database_cross_reference: PRIDE:PRIDE

ProteomExchange project hash
type: Class
subclass of: Experiment additional parameter
definition: Hash in Tranche of the whole ProteomExchange project where the PRIDE experiment is included.
has_obo_namespace: PRIDE
id: PRIDE:0000217

Axiom
annotated source: ProteomExchange project hash
annotated property: definition
annotated target: Hash in Tranche of the whole ProteomExchange project where the PRIDE experiment is included.
database_cross_reference: PRIDE:PRIDE

Original MS data file format
type: Class
subclass of: Experiment additional parameter
definition: Original format of the file containing MS data.
has_obo_namespace: PRIDE
id: PRIDE:0000218

Axiom
annotated source: Original MS data file format
annotated property: definition
annotated target: Original format of the file containing MS data.
database_cross_reference: PRIDE:PRIDE

Date of search
type: Class
subclass of: Experiment additional parameter
definition: Date when the search was performed.
has_obo_namespace: PRIDE
id: PRIDE:0000219

Axiom
annotated source: Date of search
annotated property: definition
annotated target: Date when the search was performed.
database_cross_reference: PRIDE:PRIDE

Calculated Mass To Charge Ratio
type: Class
subclass of: Peptide item additional parameter
definition: m/z value converted from the MH+ value, according to this formula: CalculatedMZ = (precursorMH+ - HYDROGEN_MASS + (precursorCharge * HYDROGEN_MASS))/ precursorCharge.
has_obo_namespace: PRIDE
id: PRIDE:0000220

Axiom
annotated source: Calculated Mass To Charge Ratio
annotated property: definition
annotated target: m/z value converted from the MH+ value, according to this formula: CalculatedMZ = (precursorMH+ - HYDROGEN_MASS + (precursorCharge * HYDROGEN_MASS))/ precursorCharge.
database_cross_reference: PRIDE:PRIDE

parent ion retention time error
type: Class
subclass of: Parent Ion Annotation
definition: Retention time error in minutes.
has_obo_namespace: PRIDE
id: PRIDE:0000221

Axiom
annotated source: parent ion retention time error
annotated property: definition
annotated target: Retention time error in minutes.
database_cross_reference: PRIDE:PRIDE

spectrum iTRAQ ratio
type: Class
subclass of: Peptide item additional parameter
definition: average iTRAQ ratio sample over control.
has_obo_namespace: PRIDE
id: PRIDE:0000222
deprecated: true

Axiom
annotated source: spectrum iTRAQ ratio
annotated property: definition
annotated target: average iTRAQ ratio sample over control.
database_cross_reference: PRIDE:PRIDE

peptide iTRAQ ratio average
type: Class
subclass of: Peptide item additional parameter
definition: Average spectrum iTRAQ ratio (=geometric mean) for the peptide.
has_obo_namespace: PRIDE
id: PRIDE:0000223
deprecated: true

Axiom
annotated source: peptide iTRAQ ratio average
annotated property: definition
annotated target: Average spectrum iTRAQ ratio (=geometric mean) for the peptide.
database_cross_reference: PRIDE:PRIDE

protein iTRAQ ratio average
type: Class
subclass of: Identification additional parameter
definition: Average spectrum iTRAQ ratio (=geometric mean) for the protein.
has_obo_namespace: PRIDE
id: PRIDE:0000224
deprecated: true

Axiom
annotated source: protein iTRAQ ratio average
annotated property: definition
annotated target: Average spectrum iTRAQ ratio (=geometric mean) for the protein.
database_cross_reference: PRIDE:PRIDE

protein iTRAQ ratio number of contributing spectra
type: Class
subclass of: Identification additional parameter
definition: Number of quantified spectra contributing to the protein iTRAQ ratio.
has_obo_namespace: PRIDE
id: PRIDE:0000225
deprecated: true

Axiom
annotated source: protein iTRAQ ratio number of contributing spectra
annotated property: definition
annotated target: Number of quantified spectra contributing to the protein iTRAQ ratio.
database_cross_reference: PRIDE:PRIDE

protein iTRAQ ratio standard deviation
type: Class
subclass of: Identification additional parameter
definition: Geometric sample standard deviation of the protein iTRAQ ratio.
has_obo_namespace: PRIDE
id: PRIDE:0000226
deprecated: true

Axiom
annotated source: protein iTRAQ ratio standard deviation
annotated property: definition
annotated target: Geometric sample standard deviation of the protein iTRAQ ratio.
database_cross_reference: PRIDE:PRIDE

x ion
type: Class
subclass of: product ion type
definition: X ion type.
has_exact_synonym: x fragment ion
has_obo_namespace: PRIDE
id: PRIDE:0000227

Axiom
annotated source: x ion
annotated property: definition
annotated target: X ion type.
database_cross_reference: PRIDE:PRIDE

x ion -H2O
type: Class
subclass of: x ion
definition: X ion type with the neutral loss of a molecule water.
has_exact_synonym: x fragment ion -H2O
has_obo_namespace: PRIDE
id: PRIDE:0000228

Axiom
annotated source: x ion -H2O
annotated property: definition
annotated target: X ion type with the neutral loss of a molecule water.
database_cross_reference: PRIDE:PRIDE

x ion -NH3
type: Class
subclass of: x ion
definition: X ion type with the neutral loss of an ammonia group.
has_exact_synonym: x fragment ion -NH3
has_obo_namespace: PRIDE
id: PRIDE:0000229

Axiom
annotated source: x ion -NH3
annotated property: definition
annotated target: X ion type with the neutral loss of an ammonia group.
database_cross_reference: PRIDE:PRIDE

z ion
type: Class
subclass of: product ion type
definition: Z ion type.
has_exact_synonym: z fragment ion
has_obo_namespace: PRIDE
id: PRIDE:0000230

Axiom
annotated source: z ion
annotated property: definition
annotated target: Z ion type.
database_cross_reference: PRIDE:PRIDE

z ion -H2O
type: Class
subclass of: z ion
definition: Z ion type with the neutral loss of a molecule water.
has_exact_synonym: z fragment ion -H2O
has_obo_namespace: PRIDE
id: PRIDE:0000231

Axiom
annotated source: z ion -H2O
annotated property: definition
annotated target: Z ion type with the neutral loss of a molecule water.
database_cross_reference: PRIDE:PRIDE

z ion -NH3
type: Class
subclass of: z ion
definition: Z ion type with the neutral loss of an ammonia group.
has_exact_synonym: z fragment ion -NH3
has_obo_namespace: PRIDE
id: PRIDE:0000232

Axiom
annotated source: z ion -NH3
annotated property: definition
annotated target: Z ion type with the neutral loss of an ammonia group.
database_cross_reference: PRIDE:PRIDE

a ion
type: Class
subclass of: product ion type
definition: A ion type.
has_exact_synonym: a fragment ion
has_obo_namespace: PRIDE
id: PRIDE:0000233

Axiom
annotated source: a ion
annotated property: definition
annotated target: A ion type.
database_cross_reference: PRIDE:PRIDE

a ion -H2O
type: Class
subclass of: a ion
definition: A ion type with the neutral loss of a molecule water.
has_exact_synonym: a fragment ion -H2O
has_obo_namespace: PRIDE
id: PRIDE:0000234

Axiom
annotated source: a ion -H2O
annotated property: definition
annotated target: A ion type with the neutral loss of a molecule water.
database_cross_reference: PRIDE:PRIDE

a ion -NH3
type: Class
subclass of: a ion
definition: A ion type with the neutral loss of an ammonia group.
has_exact_synonym: a fragment ion -NH3
has_obo_namespace: PRIDE
id: PRIDE:0000235

Axiom
annotated source: a ion -NH3
annotated property: definition
annotated target: A ion type with the neutral loss of an ammonia group.
database_cross_reference: PRIDE:PRIDE

c ion
type: Class
subclass of: product ion type
definition: C ion type.
has_exact_synonym: c fragment ion
has_obo_namespace: PRIDE
id: PRIDE:0000236

Axiom
annotated source: c ion
annotated property: definition
annotated target: C ion type.
database_cross_reference: PRIDE:PRIDE

c ion -H2O
type: Class
subclass of: c ion
definition: C ion type with the neutral loss of a molecule water.
has_exact_synonym: c fragment ion -H2O
has_obo_namespace: PRIDE
id: PRIDE:0000237

Axiom
annotated source: c ion -H2O
annotated property: definition
annotated target: C ion type with the neutral loss of a molecule water.
database_cross_reference: PRIDE:PRIDE

c ion -NH3
type: Class
subclass of: c ion
definition: C ion type with the neutral loss of an ammonia group.
has_exact_synonym: c fragment ion -NH3
has_obo_namespace: PRIDE
id: PRIDE:0000238

Axiom
annotated source: c ion -NH3
annotated property: definition
annotated target: C ion type with the neutral loss of an ammonia group.
database_cross_reference: PRIDE:PRIDE

immonium ion
type: Class
subclass of: product ion type
definition: Immonium ion type.
has_obo_namespace: PRIDE
id: PRIDE:0000239

Axiom
annotated source: immonium ion
annotated property: definition
annotated target: Immonium ion type.
database_cross_reference: PRIDE:PRIDE

immonium A
type: Class
subclass of: immonium ion
definition: Immonium ion type for alanine.
has_obo_namespace: PRIDE
id: PRIDE:0000240

Axiom
annotated source: immonium A
annotated property: definition
annotated target: Immonium ion type for alanine.
database_cross_reference: PRIDE:PRIDE

immonium C
type: Class
subclass of: immonium ion
definition: Immonium ion type for cysteine.
has_obo_namespace: PRIDE
id: PRIDE:0000241

Axiom
annotated source: immonium C
annotated property: definition
annotated target: Immonium ion type for cysteine.
database_cross_reference: PRIDE:PRIDE

immonium D
type: Class
subclass of: immonium ion
definition: Immonium ion type for aspartic acid.
has_obo_namespace: PRIDE
id: PRIDE:0000242

Axiom
annotated source: immonium D
annotated property: definition
annotated target: Immonium ion type for aspartic acid.
database_cross_reference: PRIDE:PRIDE

immonium E
type: Class
subclass of: immonium ion
definition: Immonium ion type for glutamic acid.
has_obo_namespace: PRIDE
id: PRIDE:0000243

Axiom
annotated source: immonium E
annotated property: definition
annotated target: Immonium ion type for glutamic acid.
database_cross_reference: PRIDE:PRIDE

immonium F
type: Class
subclass of: immonium ion
definition: Immonium ion type for phenylalanine.
has_obo_namespace: PRIDE
id: PRIDE:0000244

Axiom
annotated source: immonium F
annotated property: definition
annotated target: Immonium ion type for phenylalanine.
database_cross_reference: PRIDE:PRIDE

immonium G
type: Class
subclass of: immonium ion
definition: Immonium ion type for glycine.
has_obo_namespace: PRIDE
id: PRIDE:0000245

Axiom
annotated source: immonium G
annotated property: definition
annotated target: Immonium ion type for glycine.
database_cross_reference: PRIDE:PRIDE

immonium H
type: Class
subclass of: immonium ion
definition: Immonium ion type for histidine.
has_obo_namespace: PRIDE
id: PRIDE:0000246

Axiom
annotated source: immonium H
annotated property: definition
annotated target: Immonium ion type for histidine.
database_cross_reference: PRIDE:PRIDE

immonium I
type: Class
subclass of: immonium ion
definition: Immonium ion type for isoleucine.
has_obo_namespace: PRIDE
id: PRIDE:0000247

Axiom
annotated source: immonium I
annotated property: definition
annotated target: Immonium ion type for isoleucine.
database_cross_reference: PRIDE:PRIDE

immonium K
type: Class
subclass of: immonium ion
definition: Immonium ion type for lysine.
has_obo_namespace: PRIDE
id: PRIDE:0000248

Axiom
annotated source: immonium K
annotated property: definition
annotated target: Immonium ion type for lysine.
database_cross_reference: PRIDE:PRIDE

immonium L
type: Class
subclass of: immonium ion
definition: Immonium ion type for leucine.
has_obo_namespace: PRIDE
id: PRIDE:0000249

Axiom
annotated source: immonium L
annotated property: definition
annotated target: Immonium ion type for leucine.
database_cross_reference: PRIDE:PRIDE

immonium M
type: Class
subclass of: immonium ion
definition: Immonium ion type for methionine.
has_obo_namespace: PRIDE
id: PRIDE:0000250

Axiom
annotated source: immonium M
annotated property: definition
annotated target: Immonium ion type for methionine.
database_cross_reference: PRIDE:PRIDE

immonium N
type: Class
subclass of: immonium ion
definition: Immonium ion type for asparagine.
has_obo_namespace: PRIDE
id: PRIDE:0000251

Axiom
annotated source: immonium N
annotated property: definition
annotated target: Immonium ion type for asparagine.
database_cross_reference: PRIDE:PRIDE

immonium P
type: Class
subclass of: immonium ion
definition: Immonium ion type for proline.
has_obo_namespace: PRIDE
id: PRIDE:0000252

Axiom
annotated source: immonium P
annotated property: definition
annotated target: Immonium ion type for proline.
database_cross_reference: PRIDE:PRIDE

immonium Q
type: Class
subclass of: immonium ion
definition: Immonium ion type for glutamine.
has_obo_namespace: PRIDE
id: PRIDE:0000253

Axiom
annotated source: immonium Q
annotated property: definition
annotated target: Immonium ion type for glutamine.
database_cross_reference: PRIDE:PRIDE

immonium R
type: Class
subclass of: immonium ion
definition: Immonium ion type for arginine.
has_obo_namespace: PRIDE
id: PRIDE:0000254

Axiom
annotated source: immonium R
annotated property: definition
annotated target: Immonium ion type for arginine.
database_cross_reference: PRIDE:PRIDE

immonium S
type: Class
subclass of: immonium ion
definition: Immonium ion type for serine.
has_obo_namespace: PRIDE
id: PRIDE:0000255

Axiom
annotated source: immonium S
annotated property: definition
annotated target: Immonium ion type for serine.
database_cross_reference: PRIDE:PRIDE

immonium T
type: Class
subclass of: immonium ion
definition: Immonium ion type for threnine.
has_obo_namespace: PRIDE
id: PRIDE:0000256

Axiom
annotated source: immonium T
annotated property: definition
annotated target: Immonium ion type for threnine.
database_cross_reference: PRIDE:PRIDE

immonium V
type: Class
subclass of: immonium ion
definition: Immonium ion type for valine.
has_obo_namespace: PRIDE
id: PRIDE:0000257

Axiom
annotated source: immonium V
annotated property: definition
annotated target: Immonium ion type for valine.
database_cross_reference: PRIDE:PRIDE

immonium W
type: Class
subclass of: immonium ion
definition: Immonium ion type for tryptophan.
has_obo_namespace: PRIDE
id: PRIDE:0000258

Axiom
annotated source: immonium W
annotated property: definition
annotated target: Immonium ion type for tryptophan.
database_cross_reference: PRIDE:PRIDE

immonium Y
type: Class
subclass of: immonium ion
definition: Immonium ion type for tyrosine.
has_obo_namespace: PRIDE
id: PRIDE:0000259

Axiom
annotated source: immonium Y
annotated property: definition
annotated target: Immonium ion type for tyrosine.
database_cross_reference: PRIDE:PRIDE

precursor ion type
type: Class
subclass of: Parent Ion Annotation
definition: precursor ion type.
has_exact_synonym: parent ion type
has_obo_namespace: PRIDE
id: PRIDE:0000260

Axiom
annotated source: precursor ion type
annotated property: definition
annotated target: precursor ion type.
database_cross_reference: PRIDE:PRIDE

precursor ion -H2O
type: Class
subclass of: precursor ion
definition: Precursor ion type with the neutral loss of a molecule water.
has_exact_synonym: parent ion -H2O
has_obo_namespace: PRIDE
id: PRIDE:0000261

Axiom
annotated source: precursor ion -H2O
annotated property: definition
annotated target: Precursor ion type with the neutral loss of a molecule water.
database_cross_reference: PRIDE:PRIDE

precursor ion -NH3
type: Class
subclass of: precursor ion
definition: Precursor ion type with the neutral loss of an ammonia group.
has_exact_synonym: parent ion -NH3
has_obo_namespace: PRIDE
id: PRIDE:0000262

Axiom
annotated source: precursor ion -NH3
annotated property: definition
annotated target: Precursor ion type with the neutral loss of an ammonia group.
database_cross_reference: PRIDE:PRIDE

precursor ion
type: Class
subclass of: precursor ion type
definition: Precursor ion.
has_exact_synonym: parent ion
has_obo_namespace: PRIDE
id: PRIDE:0000263

Axiom
annotated source: precursor ion
annotated property: definition
annotated target: Precursor ion.
database_cross_reference: PRIDE:PRIDE

iTRAQ reagent 113
type: Class
subclass of: iTRAQ reagent
has_obo_namespace: PRIDE
id: PRIDE:0000264
comment: The name of the sample labelled with iTRAQ reagent 113

iTRAQ reagent 118
type: Class
subclass of: iTRAQ reagent
has_obo_namespace: PRIDE
id: PRIDE:0000265
comment: The name of the sample labelled with iTRAQ reagent 118

iTRAQ reagent 119
type: Class
subclass of: iTRAQ reagent
has_obo_namespace: PRIDE
id: PRIDE:0000266
comment: The name of the sample labelled with iTRAQ reagent 119

iTRAQ reagent 121
type: Class
subclass of: iTRAQ reagent
has_obo_namespace: PRIDE
id: PRIDE:0000267
comment: The name of the sample labelled with iTRAQ reagent 121

iTRAQ intensity 113
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000268
comment: The intensity of the sample labelled with iTRAQ reagent 113

iTRAQ intensity 118
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000269
comment: The intensity of the sample labelled with iTRAQ reagent 118

iTRAQ intensity 119
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000270
comment: The intensity of the sample labelled with iTRAQ reagent 119

iTRAQ intensity 121
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000271
comment: The intensity of the sample labelled with iTRAQ reagent 121

Project secondary name
type: Class
subclass of: Experiment additional parameter
definition: Allows experiments inside the same project to be grouped or organised as subprojects. This will not be displayed in the PRIDE web page.
has_obo_namespace: PRIDE
id: PRIDE:0000272

Axiom
annotated source: Project secondary name
annotated property: definition
annotated target: Allows experiments inside the same project to be grouped or organised as subprojects. This will not be displayed in the PRIDE web page.
database_cross_reference: PRIDE:PRIDE

SloMo score threshold for valid modification location
type: Class
subclass of: Search algorithm
has_obo_namespace: PRIDE
id: PRIDE:0000273

MaxQuant percentage threshold for valid modification location
type: Class
subclass of: Search algorithm
has_obo_namespace: PRIDE
id: PRIDE:0000274

SloMo score
type: Class
subclass of: Search algorithm
has_obo_namespace: PRIDE
id: PRIDE:0000275

MaxQuant percentage
type: Class
subclass of: Search algorithm
has_obo_namespace: PRIDE
id: PRIDE:0000276

Valid location
type: Class
subclass of: ModificationItem additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000277

Processing method additional parameter
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000278

In silico enzyme digestion
type: Class
subclass of: Processing method additional parameter
definition: Enzyme that is selected as a parameter of the search engine.
has_obo_namespace: PRIDE
id: PRIDE:0000279

Axiom
annotated source: In silico enzyme digestion
annotated property: definition
annotated target: Enzyme that is selected as a parameter of the search engine.
database_cross_reference: PRIDE:PRIDE

zH ion
type: Class
subclass of: z ion
definition: Z ion type with one extra proton
has_exact_synonym: zH fragment ion
has_obo_namespace: PRIDE
id: PRIDE:0000280

Axiom
annotated source: zH ion
annotated property: definition
annotated target: Z ion type with one extra proton
database_cross_reference: PRIDE:PRIDE

zHH ion
type: Class
subclass of: z ion
definition: Z ion type with two extra protons
has_exact_synonym: zHH fragment ion
has_obo_namespace: PRIDE
id: PRIDE:0000281

Axiom
annotated source: zHH ion
annotated property: definition
annotated target: Z ion type with two extra protons
database_cross_reference: PRIDE:PRIDE

Fixed modification
type: Class
subclass of: ModificationItem additional parameter
definition: Fixed type of post-translational modification.
has_obo_namespace: PRIDE
id: PRIDE:0000282

Axiom
annotated source: Fixed modification
annotated property: definition
annotated target: Fixed type of post-translational modification.
database_cross_reference: PRIDE:PRIDE

Variable modification
type: Class
subclass of: ModificationItem additional parameter
definition: Variable type of post-translational modification.
has_obo_namespace: PRIDE
id: PRIDE:0000283

Axiom
annotated source: Variable modification
annotated property: definition
annotated target: Variable type of post-translational modification.
database_cross_reference: PRIDE:PRIDE

Sf
type: Class
subclass of: Peptide search engine output parameter
subclass of: Restriction
  on property: part_of
  some values from: Sequest
definition: The Sf score for each peptide is calculated by a neural network algorithm that incorporates teh Xcorr, DeltaCn, Sp, RSp, peptide mass, charge state, and the number of matched peptides for the search. The protein Sf score is the sum of peptide Sf scores for all the peptides associated with that protein.
has_obo_namespace: PRIDE
id: PRIDE:0000284

Axiom
annotated source: Sf
annotated property: definition
annotated target: The Sf score for each peptide is calculated by a neural network algorithm that incorporates teh Xcorr, DeltaCn, Sp, RSp, peptide mass, charge state, and the number of matched peptides for the search. The protein Sf score is the sum of peptide Sf scores for all the peptides associated with that protein.
database_cross_reference: PRIDE:PRIDE

TMT reagent 126
type: Class
subclass of: TMT reagent
has_obo_namespace: PRIDE
id: PRIDE:0000285
comment: The name of the sample labelled with TMT reagent 126

TMT reagent 127
type: Class
subclass of: TMT reagent
has_obo_namespace: PRIDE
id: PRIDE:0000286
comment: The name of the sample labelled with TMT reagent 127

TMT reagent 128
type: Class
subclass of: TMT reagent
has_obo_namespace: PRIDE
id: PRIDE:0000287
comment: The name of the sample labelled with TMT reagent 128

TMT reagent 129
type: Class
subclass of: TMT reagent
has_obo_namespace: PRIDE
id: PRIDE:0000288
comment: The name of the sample labelled with TMT reagent 129

TMT reagent 130
type: Class
subclass of: TMT reagent
has_obo_namespace: PRIDE
id: PRIDE:0000289
comment: The name of the sample labelled with TMT reagent 130

TMT reagent 131
type: Class
subclass of: TMT reagent
has_obo_namespace: PRIDE
id: PRIDE:0000290
comment: The name of the sample labelled with TMT reagent 131

TMT intensity 126
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000291
comment: The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS]

TMT intensity 127
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000292
comment: The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS]

TMT intensity 128
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000293
comment: The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS]

TMT intensity 129
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000294
comment: The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS]

TMT intensity 130
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000295
comment: The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS]

TMT intensity 131
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000296
comment: The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS]

Gene name
type: Class
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000297
comment: Name of the gene that has been identified (if a nucleotide database was used to perform the search)

Modification Position in Protein Sequence
type: Class
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000298
comment: Position of the modification in the protein sequence

Submitted Protein Accession
type: Class
subclass of: Identification additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000299
comment: The original submitted protein accession for this identification. This might have been curated as part of the submission process.

Gel spot identifier
type: Class
subclass of: Gel spot parameter
definition: The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication.
created by: jg
creation date: 2011-05-12T11:32:07Z
has_obo_namespace: PRIDE
id: PRIDE:0000300

Axiom
annotated source: Gel spot identifier
annotated property: definition
annotated target: The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication.
database_cross_reference: PRIDE:PRIDE

Non-significant protein identification
type: Class
subclass of: Identification additional parameter
definition: Identifies a protein identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value).
created by: jg
creation date: 2011-05-12T11:39:59Z
has_obo_namespace: PRIDE
id: PRIDE:0000301

Axiom
annotated source: Non-significant protein identification
annotated property: definition
annotated target: Identifies a protein identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value).
database_cross_reference: PRIDE:PRIDE

Non-significant peptide identification
type: Class
subclass of: Peptide item additional parameter
definition: Identifies a peptide identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value).
created by: jg
creation date: 2011-05-12T11:50:00Z
has_obo_namespace: PRIDE
id: PRIDE:0000302

Axiom
annotated source: Non-significant peptide identification
annotated property: definition
annotated target: Identifies a peptide identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value).
database_cross_reference: PRIDE:PRIDE

Decoy hit
type: Class
subclass of: Identification additional parameter
definition: Indicates that this protein identification comes from the used decoy database.
created by: jg
creation date: 2011-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000303
deprecated: true

Axiom
annotated source: Decoy hit
annotated property: definition
annotated target: Indicates that this protein identification comes from the used decoy database.
database_cross_reference: PRIDE:PRIDE

Gel identifier
type: Class
subclass of: Gel spot parameter
definition: The gel's identifier. This identifier should resemble the one used in, for example, the associated publication.
created by: jg
creation date: 2011-05-25T11:22:05Z
has_obo_namespace: PRIDE
id: PRIDE:0000304

Axiom
annotated source: Gel identifier
annotated property: definition
annotated target: The gel's identifier. This identifier should resemble the one used in, for example, the associated publication.
database_cross_reference: PRIDE:PRIDE

Gel-based experiment
type: Class
subclass of: Bottom-up proteomics
definition: Defines a gel-based proteomics experiment.
created by: jg
creation date: 2011-05-25T05:44:24Z
has_obo_namespace: PRIDE
id: PRIDE:0000305

Axiom
annotated source: Gel-based experiment
annotated property: definition
annotated target: Defines a gel-based proteomics experiment.
database_cross_reference: PRIDE:PRIDE

Imported from NCBI Peptidome
type: Class
subclass of: Experiment additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000306
comment: Experiment.[Curator:ACSORDAS]

Quantification method
type: Class
subclass of: Quantification parameter
created by: jg
creation date: 2011-07-22T09:15:33Z
has_obo_namespace: PRIDE
id: PRIDE:0000307
comment: Defines various quantification methods

Gel-based quantification method
type: Class
subclass of: Quantification method
created by: jg
creation date: 2011-07-22T09:16:24Z
has_obo_namespace: PRIDE
id: PRIDE:0000308
comment: Describes gel-based quantification methods

Gel-free quantification method
type: Class
subclass of: Quantification method
created by: jg
creation date: 2011-07-22T09:17:03Z
has_obo_namespace: PRIDE
id: PRIDE:0000309
comment: Describes gel-free quantification methods

Isotope labeling
type: Class
subclass of: Gel-free quantification method
created by: jg
creation date: 2011-07-22T09:17:34Z
has_obo_namespace: PRIDE
id: PRIDE:0000310
comment: Describes quantification techniques using isotope labeling

Selected Reaction Monitoring
type: Class
subclass of: Gel-free quantification method
created by: jg
creation date: 2011-07-22T09:18:39Z
has_obo_namespace: PRIDE
id: PRIDE:0000311
comment: Describes quantification techniques based on selected / multiple reaction monitoring

Label free
type: Class
subclass of: Gel-free quantification method
created by: jg
creation date: 2011-07-22T09:19:54Z
has_obo_namespace: PRIDE
id: PRIDE:0000312
comment: Describes label free quantification techniques.

iTRAQ
type: Class
subclass of: MS2 based isotope labeling
created by: jg
creation date: 2011-07-22T09:20:23Z
has_obo_namespace: PRIDE
id: PRIDE:0000313
comment: Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level

TMT
type: Class
subclass of: MS2 based isotope labeling
created by: jg
creation date: 2011-07-22T09:23:12Z
has_exact_synonym: Tandem Mass Tag
has_obo_namespace: PRIDE
id: PRIDE:0000314
comment: Tandem Mass Tag is a MS2 based isotope labeling quantification technique

SILAC
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:25:50Z
has_exact_synonym: Stable isotope labeling with amino acids in cell culture
has_obo_namespace: PRIDE
id: PRIDE:0000315
comment: Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification

MS1 based isotope labeling
type: Class
subclass of: Isotope labeling
created by: jg
creation date: 2011-07-22T09:28:05Z
has_obo_namespace: PRIDE
id: PRIDE:0000316
comment: Describes isotope labeling quantification techniques detectable at MS1 level.

MS2 based isotope labeling
type: Class
subclass of: Isotope labeling
created by: jg
creation date: 2011-07-22T09:29:15Z
has_obo_namespace: PRIDE
id: PRIDE:0000317
comment: Describes isotope labeling quantification techniques detectable at MS1 level.

18O
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:30:12Z
has_obo_namespace: PRIDE
id: PRIDE:0000318
comment: The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen.

ICAT
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:31:24Z
has_exact_synonym: Isotope-Coded Affinity Tags
has_obo_namespace: PRIDE
id: PRIDE:0000319
comment: Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements.

AQUA
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:32:46Z
has_obo_namespace: PRIDE
id: PRIDE:0000320
comment: AQUA is an isotope labeling based quantification technique that uses known peptides.

ICPL
type: Class
subclass of: MS1 based isotope labeling
created by: jg
creation date: 2011-07-22T09:34:37Z
has_exact_synonym: Isotope-coded protein label
has_obo_namespace: PRIDE
id: PRIDE:0000321
comment: Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses.

emPAI
type: Class
subclass of: Label free
created by: jg
creation date: 2011-07-22T09:36:57Z
has_exact_synonym: Exponentially Modified Protein Abundance Index
has_obo_namespace: PRIDE
id: PRIDE:0000322
comment: The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantification of the proteins in a mixture based on protein coverage by the peptide matches in a database search result.

TIC
type: Class
subclass of: Label free
created by: jg
creation date: 2011-07-22T09:38:17Z
has_exact_synonym: Total Ion Current
has_obo_namespace: PRIDE
id: PRIDE:0000323
comment: The Total Ion Current (TIC) can be measured or calculated in order to target specific ions.

Quantification reagent
type: Class
subclass of: Sample description additional parameter
subclass of: Quantification parameter
created by: jg
creation date: 2011-07-22T09:43:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000324
comment: A reagent used for quantification.

SILAC heavy
type: Class
subclass of: SILAC reagent
subclass of: SILAC
created by: jg
creation date: 2011-07-22T09:44:18Z
has_obo_namespace: PRIDE
id: PRIDE:0000325
comment: The heavy label used in SILAC experiments.

SILAC light
type: Class
subclass of: SILAC reagent
subclass of: SILAC
created by: jg
creation date: 2011-07-22T09:45:40Z
has_obo_namespace: PRIDE
id: PRIDE:0000326
comment: The light reagent used in SILAC experiments.

SILAC medium
type: Class
subclass of: SILAC reagent
subclass of: SILAC
created by: jg
creation date: 2011-07-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000327
comment: The medium weight reagent used in SILAC experiments.

SILAC reagent
type: Class
subclass of: Reagents used in Labeled Methods
created by: jg
creation date: 2011-07-22T09:48:42Z
has_obo_namespace: PRIDE
id: PRIDE:0000328
comment: Reagent used in SILAC labeling.

iTRAQ reagent
type: Class
subclass of: Reagents used in Labeled Methods
created by: jg
creation date: 2011-07-22T09:49:46Z
has_obo_namespace: PRIDE
id: PRIDE:0000329
comment: Reagent used in iTRAQ experiments.

Arbitrary quantification unit
type: Class
subclass of: Quantification unit
created by: jg
creation date: 2012-03-06T11:32:24Z
has_obo_namespace: PRIDE
id: PRIDE:0000330
comment: A unit describing values that can only be interpreted within the same spectrum but cannot be compared to values found in other spectra and or experiments.

Counts
type: Class
subclass of: Arbitrary quantification unit
created by: jg
creation date: 2012-03-06T11:33:13Z
has_obo_namespace: PRIDE
id: PRIDE:0000331
comment: Quantification values reported as arbitrary counts (most often ion counts).

TMT reagent
type: Class
subclass of: Reagents used in Labeled Methods
created by: jg
creation date: 2011-07-22T10:08:04Z
has_obo_namespace: PRIDE
id: PRIDE:0000337
comment: Reagent used in TMT experiments.

ICAT reagent
type: Class
subclass of: Reagents used in Labeled Methods
created by: jg
creation date: 2011-07-22T10:19:04Z
has_obo_namespace: PRIDE
id: PRIDE:0000344
comment: Reagent used in ICAT experiments.

ICAT light reagent
type: Class
subclass of: ICAT reagent
created by: jg
creation date: 2011-07-22T10:19:38Z
has_obo_namespace: PRIDE
id: PRIDE:0000345

ICAT heavy reagent
type: Class
subclass of: ICAT reagent
created by: jg
creation date: 2011-07-22T10:19:38Z
has_obo_namespace: PRIDE
id: PRIDE:0000346

ICPL reagent
type: Class
subclass of: Reagents used in Labeled Methods
created by: jg
creation date: 2011-07-22T10:22:42Z
has_obo_namespace: PRIDE
id: PRIDE:0000347
comment: Reagent used in ICPL experiments.

ICPL 0 reagent
type: Class
subclass of: ICPL reagent
created by: jg
creation date: 2011-07-22T10:24:42Z
has_obo_namespace: PRIDE
id: PRIDE:0000348

ICPL 4 reagent
type: Class
subclass of: ICPL reagent
created by: jg
creation date: 2011-07-22T10:24:42Z
has_obo_namespace: PRIDE
id: PRIDE:0000349

ICPL 6 reagent
type: Class
subclass of: ICPL reagent
created by: jg
creation date: 2011-07-22T10:24:42Z
has_obo_namespace: PRIDE
id: PRIDE:0000350

ICPL 10 reagent
type: Class
subclass of: ICPL reagent
created by: jg
creation date: 2011-07-22T10:24:42Z
has_obo_namespace: PRIDE
id: PRIDE:0000351

Quantification value
type: Class
subclass of: Quantification parameter
created by: jg
creation date: 2011-07-22T10:26:08Z
has_obo_namespace: PRIDE
id: PRIDE:0000352
comment: Parameters to report quantification values.

Multiplexed quantification value
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
subclass of: Quantification value
created by: jg
creation date: 2011-07-22T10:26:33Z
has_obo_namespace: PRIDE
id: PRIDE:0000353
comment: Parameters describing quantification values for multiplexed samples.

Intensity subsample 1
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T10:27:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000354

Intensity subsample 2
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T10:27:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000355

Intensity subsample 3
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T10:27:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000356

Intensity subsample 4
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T10:27:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000357

Intensity subsample 5
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T10:27:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000358

Intensity subsample 6
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T10:27:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000359

Intensity subsample 7
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T10:27:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000360

Intensity subsample 8
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T10:27:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000361

Other quantification value
type: Class
subclass of: Quantification value
created by: jg
creation date: 2011-07-22T10:55:31Z
has_obo_namespace: PRIDE
id: PRIDE:0000362
comment: Values from other quantification techniques.

emPAI value
type: Class
subclass of: Identification additional parameter
subclass of: Other quantification value
created by: jg
creation date: 2011-07-22T10:55:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000363
comment: The emPAI for the protein.

TIC value
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
subclass of: Other quantification value
created by: jg
creation date: 2011-07-22T10:57:36Z
has_obo_namespace: PRIDE
id: PRIDE:0000364
comment: The Total Ion Count for the given entity.

Multiplexed sample description
type: Class
subclass of: Sample description additional parameter
created by: jg
creation date: 2011-07-22T10:59:57Z
has_obo_namespace: PRIDE
id: PRIDE:0000365
comment: Describes multiples subsamples.

Contains multiple subsamples
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:00:32Z
has_obo_namespace: PRIDE
id: PRIDE:0000366
comment: Identifies samples that are made up of multiplexed subsamples.

Subsample 1 description
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:02:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000367

Subsample 2 description
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:02:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000368

Subsample 3 description
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:02:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000369

Subsample 4 description
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:02:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000370

Subsample 5 description
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:02:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000371

Subsample 6 description
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:02:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000372

Subsample 7 description
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:02:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000373

Subsample 8 description
type: Class
subclass of: Multiplexed sample description
created by: jg
creation date: 2011-07-22T11:02:56Z
has_obo_namespace: PRIDE
id: PRIDE:0000374

Standard deviation subsample 1
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000375

Standard deviation subsample 2
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000376

Standard deviation subsample 3
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000377

Standard deviation subsample 4
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000378

Standard deviation subsample 5
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000379

Standard deviation subsample 6
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000380

Standard deviation subsample 7
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000381

Standard deviation subsample 8
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000382

Standard error subsample 1
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000383

Standard error subsample 2
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000384

Standard error subsample 3
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000385

Standard error subsample 4
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000386

Standard error subsample 5
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000387

Standard error subsample 6
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000388

Standard error subsample 7
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000389

Standard error subsample 8
type: Class
subclass of: Multiplexed quantification value
created by: jg
creation date: 2011-07-22T11:04:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000390

Quantification parameter
type: Class
created by: jg
creation date: 2011-07-26T03:59:31Z
has_obo_namespace: PRIDE
id: PRIDE:0000391
comment: Quantification related parameter.

Quantification unit
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
subclass of: Quantification parameter
created by: jg
creation date: 2011-07-26T04:00:17Z
has_obo_namespace: PRIDE
id: PRIDE:0000392
comment: Unit used to report quantification results.

Relative quantification unit
type: Class
subclass of: Quantification unit
created by: jg
creation date: 2011-07-26T04:01:53Z
has_obo_namespace: PRIDE
id: PRIDE:0000393
comment: Unit to report relative quantification results.

Absolute quantification unit
type: Class
subclass of: Quantification unit
created by: jg
creation date: 2011-07-26T04:02:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000394
comment: Unit used to describe absolute quantification results.

Ratio
type: Class
subclass of: Relative quantification unit
created by: jg
creation date: 2011-07-26T04:12:44Z
has_obo_namespace: PRIDE
id: PRIDE:0000395
comment: Quantification results represent ratios.

Copies per cell
type: Class
subclass of: Absolute quantification unit
created by: jg
creation date: 2011-07-26T04:13:32Z
has_obo_namespace: PRIDE
id: PRIDE:0000396
comment: Quantification results are reported as copies per cell.

Data derived from previous dataset
type: Class
subclass of: Experiment additional parameter
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000397
comment: One dataset is a reanalysis of previously published data

No PTMs are included in the dataset
type: Class
subclass of: Experiment additional parameter
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000398
comment: No post-translational-modifications are been included in the identified peptides of one dataset

Accepted manuscript
type: Class
subclass of: Experiment additional parameter
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000399
comment: A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet.

Reference
type: Class
subclass of: Experiment additional parameter
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000400
comment: Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet.

The allowed value-type for this CV term.
type: Axiom
annotated source: Reference
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Experimental information has been refined since this experiment was originally made publicly available
type: Class
subclass of: Experiment additional parameter
has_obo_namespace: PRIDE
id: PRIDE:0000401
comment: This means that the experimental information available has been improved, for instance precursor charges were added.

Original data
type: Class
subclass of: Experiment additional parameter
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000402
comment: One dataset is not a reanalysis of previously published data

Associated file URI
type: Class
subclass of: Experiment additional parameter
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000403
comment: URI of one external file associated to the PRIDE experiment (maybe through a PX submission).

The allowed value-type for this CV term.
type: Axiom
annotated source: Associated file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Associated raw file URI
type: Class
subclass of: Associated file URI
subclass of: file uri
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000404
comment: URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission).

The allowed value-type for this CV term.
type: Axiom
annotated source: Associated raw file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Submit PRIDE Experiment to IntAct
type: Class
subclass of: Experiment additional parameter
created by: rc
has_obo_namespace: PRIDE
id: PRIDE:0000405
comment: Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (maybe through a PX submission).

ProteomeCentral dataset URI
type: Class
subclass of: Experiment additional parameter
definition: URI associated to one PX submission in ProteomeCentral.
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000406

Axiom
annotated source: ProteomeCentral dataset URI
annotated property: definition
annotated target: URI associated to one PX submission in ProteomeCentral.
database_cross_reference: PRIDE:PRIDE

The allowed value-type for this CV term.
type: Axiom
annotated source: ProteomeCentral dataset URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Result file URI
type: Class
subclass of: Associated file URI
subclass of: file uri
definition: URI of one file labeled as 'Result', associated to one PX submission.
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000407

Axiom
annotated source: Result file URI
annotated property: definition
annotated target: URI of one file labeled as 'Result', associated to one PX submission.
database_cross_reference: PRIDE:PRIDE

The allowed value-type for this CV term.
type: Axiom
annotated source: Result file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Search engine output file URI
type: Class
subclass of: Associated file URI
subclass of: file uri
definition: URI of one search engine output file associated to one PX submission.
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000408

Axiom
annotated source: Search engine output file URI
annotated property: definition
annotated target: URI of one search engine output file associated to one PX submission.
database_cross_reference: PRIDE:PRIDE

The allowed value-type for this CV term.
type: Axiom
annotated source: Search engine output file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Peak list file URI
type: Class
subclass of: Associated file URI
subclass of: file uri
definition: URI of one of one search engine output file associated to one PX submission.
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000409

Axiom
annotated source: Peak list file URI
annotated property: definition
annotated target: URI of one of one search engine output file associated to one PX submission.
database_cross_reference: PRIDE:PRIDE

The allowed value-type for this CV term.
type: Axiom
annotated source: Peak list file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

'Other' type file URI
type: Class
subclass of: Associated file URI
subclass of: file uri
definition: URI of one file labeled as 'Other', associated to one PX submission.
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000410

Axiom
annotated source: 'Other' type file URI
annotated property: definition
annotated target: URI of one file labeled as 'Other', associated to one PX submission.
database_cross_reference: PRIDE:PRIDE

The allowed value-type for this CV term.
type: Axiom
annotated source: 'Other' type file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Dataset FTP location
type: Class
subclass of: Experiment additional parameter
definition: FTP location of one entire PX data set.
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000411

Axiom
annotated source: Dataset FTP location
annotated property: definition
annotated target: FTP location of one entire PX data set.
database_cross_reference: PRIDE:PRIDE

The allowed value-type for this CV term.
type: Axiom
annotated source: Dataset FTP location
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Dataset with no associated published manuscript
type: Class
subclass of: Experiment additional parameter
definition: A dataset which does not have an associated published manuscript.
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000412

Axiom
annotated source: Dataset with no associated published manuscript
annotated property: definition
annotated target: A dataset which does not have an associated published manuscript.
database_cross_reference: PRIDE:PRIDE

Instrument name
type: Class
subclass of: Experiment additional parameter
definition: The value of this term (related to one PRIDE experiment) can be used to provide the name of instruments that are not included in any other CV yet.
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000413

Axiom
annotated source: Instrument name
annotated property: definition
annotated target: The value of this term (related to one PRIDE experiment) can be used to provide the name of instruments that are not included in any other CV yet.
database_cross_reference: PRIDE:PRIDE

The allowed value-type for this CV term.
type: Axiom
annotated source: Instrument name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Peer-reviewed dataset
type: Class
subclass of: Experiment additional parameter
definition: Dataset has been peer-reviewed somehow.
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000414

Axiom
annotated source: Peer-reviewed dataset
annotated property: definition
annotated target: Dataset has been peer-reviewed somehow.
database_cross_reference: PRIDE:PRIDE

Non peer-reviewed dataset
type: Class
subclass of: Experiment additional parameter
definition: Dataset that has not been peer-reviewed by any means.
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000415

Axiom
annotated source: Non peer-reviewed dataset
annotated property: definition
annotated target: Dataset that has not been peer-reviewed by any means.
database_cross_reference: PRIDE:PRIDE

Supported dataset by repository
type: Class
subclass of: Experiment additional parameter
definition: The PX dataset is supported by and is available through the submission repository.
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000416

Axiom
annotated source: Supported dataset by repository
annotated property: definition
annotated target: The PX dataset is supported by and is available through the submission repository.
database_cross_reference: PRIDE:PRIDE

Unsupported dataset by repository
type: Class
subclass of: Experiment additional parameter
definition: The PX dataset is not fully supported by the submission repository.
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000417

Axiom
annotated source: Unsupported dataset by repository
annotated property: definition
annotated target: The PX dataset is not fully supported by the submission repository.
database_cross_reference: PRIDE:PRIDE

Other member of protein ambiguity group
type: Class
subclass of: Identification additional parameter
definition: Accession of another protein that was assigned to the same protein ambiguity group. This term must be repeated to include all protein group members, except for itself.
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000418

Axiom
annotated source: Other member of protein ambiguity group
annotated property: definition
annotated target: Accession of another protein that was assigned to the same protein ambiguity group. This term must be repeated to include all protein group members, except for itself.
database_cross_reference: PRIDE:PRIDE

b ion -H3PO4
type: Class
subclass of: b ion
definition: B ion type with a neutral loss of a phosphate molecule.
has_exact_synonym: b fragment ion -H3PO4
has_obo_namespace: PRIDE
id: PRIDE:0000419

Axiom
annotated source: b ion -H3PO4
annotated property: definition
annotated target: B ion type with a neutral loss of a phosphate molecule.
database_cross_reference: PRIDE:PRIDE

b ion -2H3PO4
type: Class
subclass of: b ion
definition: B ion type with a neutral loss of 2 phosphate molecules.
has_exact_synonym: b fragment ion -2H3PO4
has_obo_namespace: PRIDE
id: PRIDE:0000420

Axiom
annotated source: b ion -2H3PO4
annotated property: definition
annotated target: B ion type with a neutral loss of 2 phosphate molecules.
database_cross_reference: PRIDE:PRIDE

b ion -3H3PO4
type: Class
subclass of: b ion
definition: B ion type with a neutral loss of 3 phosphate molecules.
has_exact_synonym: b fragment ion -3H3PO4
has_obo_namespace: PRIDE
id: PRIDE:0000421

Axiom
annotated source: b ion -3H3PO4
annotated property: definition
annotated target: B ion type with a neutral loss of 3 phosphate molecules.
database_cross_reference: PRIDE:PRIDE

y ion -H3PO4
type: Class
subclass of: y ion
definition: Y ion type with a neutral loss of a phosphate molecule.
has_exact_synonym: y fragment ion -H3PO4
has_obo_namespace: PRIDE
id: PRIDE:0000422

Axiom
annotated source: y ion -H3PO4
annotated property: definition
annotated target: Y ion type with a neutral loss of a phosphate molecule.
database_cross_reference: PRIDE:PRIDE

y ion -2H3PO4
type: Class
subclass of: y ion
definition: Y ion type with a neutral loss of 2 phosphate molecules.
has_exact_synonym: y fragment ion -2H3PO4
has_obo_namespace: PRIDE
id: PRIDE:0000423

Axiom
annotated source: y ion -2H3PO4
annotated property: definition
annotated target: Y ion type with a neutral loss of 2 phosphate molecules.
database_cross_reference: PRIDE:PRIDE

y ion -3H3PO4
type: Class
subclass of: y ion
definition: Y ion type with a neutral loss of 3 phosphate molecules.
has_exact_synonym: y fragment ion -3H3PO4
has_obo_namespace: PRIDE
id: PRIDE:0000424

Axiom
annotated source: y ion -3H3PO4
annotated property: definition
annotated target: Y ion type with a neutral loss of 3 phosphate molecules.
database_cross_reference: PRIDE:PRIDE

MS1 intensity based label-free quantification method
type: Class
subclass of: Gel-free quantification method
created by: rw
has_obo_namespace: PRIDE
id: PRIDE:0000425

Mass spectrometry proteomics experimental strategy
type: Class
subclass of: Experiment additional parameter
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000426
comment: The basic mass spectrometry strategy used in the experiment.

Top-down proteomics
type: Class
subclass of: Mass spectrometry proteomics experimental strategy
subclass of: Experiment Type
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000427
comment: Proteins enter directly the mass spectrometer.

Bottom-up proteomics
type: Class
subclass of: Mass spectrometry proteomics experimental strategy
subclass of: Experiment Type
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000428
comment: Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer.

MS/MS shotgun proteomics
type: Class
subclass of: Bottom-up proteomics
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000429
comment: Bottom-up MS/MS shotgun experiment with data-dependent acquisition, using nomenclature in PMID 20622845, the method of choice for the a priori identification of the protein components of complex samples.

Chemical cross-linking coupled with mass spectrometry proteomics
type: Class
subclass of: Bottom-up proteomics
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000430
comment: Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) to provide information about protein folding and protein-protein interaction.

Affinity purification coupled with mass spectrometry proteomics
type: Class
subclass of: Bottom-up proteomics
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000431
comment: Affinity purification combined with mass spectrometry (AP-MS) has been used to understand protein-complex composition and protein-protein interaction.

Dataset with its publication pending
type: Class
subclass of: Experiment additional parameter
created by: rw
has_obo_namespace: PRIDE
id: PRIDE:0000432
comment: A dataset which has an associated manuscript pending for publication.

Reagents used in Labeled Methods
type: Class
subclass of: Quantification reagent
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000433
comment: Labeled reagents used for quantification.

Unlabeled sample
type: Class
subclass of: Quantification reagent
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000434
comment: An unlabeled sample used for quantification.

Peptide counting
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000435
comment: Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140.

Spectrum counting
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000436
comment: Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140

PAI
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000437
comment: Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140

Spectrum count/molecular weight
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000438
comment: Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140

SAF
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000439
comment: The spectrum count is normalized for protein length. Method reviewed in PMID 22772140

NSAF
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000440
comment: Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140

APEX - Absolute Protein Expression
type: Class
subclass of: Label free
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000441
comment: Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140

Tissue not applicable to dataset
type: Class
subclass of: Experiment additional parameter
definition: Tissue not applicable to dataset.
created by: rw
has_obo_namespace: PRIDE
id: PRIDE:0000442

Axiom
annotated source: Tissue not applicable to dataset
annotated property: definition
annotated target: Tissue not applicable to dataset.
database_cross_reference: PRIDE:PRIDE

Original NCBI Peptidome submission files
type: Class
subclass of: Experiment additional parameter
definition: The NCBI FTP location of the original Sample - Experiment level Peptidome submission data.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000443

Axiom
annotated source: Original NCBI Peptidome submission files
annotated property: definition
annotated target: The NCBI FTP location of the original Sample - Experiment level Peptidome submission data.
database_cross_reference: PRIDE:PRIDE

PRIDE experiment accession
type: Class
subclass of: Experiment additional parameter
definition: Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system).
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000444

Axiom
annotated source: PRIDE experiment accession
annotated property: definition
annotated target: Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system).
database_cross_reference: PRIDE:PRIDE

PRIDE Cluster score
type: Class
subclass of: Peptide item additional parameter
definition: It is an integer that gives an indication about the quality of a peptide spectrum match in PRIDE-Q. It uses the PRIDE-Cluster algorithm (described in PMID: 23361086) and different criteria to assign it (number of spectra in a cluster, ratio of the predominant peptide identification in the cluster, etc).
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000445

Axiom
annotated source: PRIDE Cluster score
annotated property: definition
annotated target: It is an integer that gives an indication about the quality of a peptide spectrum match in PRIDE-Q. It uses the PRIDE-Cluster algorithm (described in PMID: 23361086) and different criteria to assign it (number of spectra in a cluster, ratio of the predominant peptide identification in the cluster, etc).
database_cross_reference: PRIDE:PRIDE

PRIDE peptide score
type: Class
subclass of: Peptide item additional parameter
definition: Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243.
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000446

Axiom
annotated source: PRIDE peptide score
annotated property: definition
annotated target: Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243.
database_cross_reference: PRIDE:PRIDE

SWATH MS
type: Class
subclass of: Data-independent acquisition
definition: ABsciex Data Independent Acquisition method that consists of unfractionated samples acquisition by using duty cycles adapted to HPLC chromatography, acquiring sequential wide fragment ions spectra, typically covering the precursor mass space from 400 m/z to 1200 m/z on each duty cycle. Acquired data is interrogated by using libraries of peptide coordinates (normalised elution time, fragment ion masses and intensities). It is described in PMID:22261725.
created by: jav
has_obo_namespace: PRIDE
id: PRIDE:0000447

Axiom
annotated source: SWATH MS
annotated property: definition
annotated target: ABsciex Data Independent Acquisition method that consists of unfractionated samples acquisition by using duty cycles adapted to HPLC chromatography, acquiring sequential wide fragment ions spectra, typically covering the precursor mass space from 400 m/z to 1200 m/z on each duty cycle. Acquired data is interrogated by using libraries of peptide coordinates (normalised elution time, fragment ion masses and intensities). It is described in PMID:22261725.
database_cross_reference: PRIDE:PRIDE

Additional associated raw file URI
type: Class
subclass of: Associated file URI
subclass of: file uri
created by: jav
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000448
comment: Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE.

The allowed value-type for this CV term.
type: Axiom
annotated source: Additional associated raw file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Gel image file URI
type: Class
subclass of: Associated file URI
subclass of: file uri
created by: tt
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000449
comment: URI of one gel image file associated to one PX submission.

The allowed value-type for this CV term.
type: Axiom
annotated source: Gel image file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Data-independent acquisition
type: Class
subclass of: Bottom-up proteomics
definition: Predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. See review in PMID:24281846.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000450

Axiom
annotated source: Data-independent acquisition
annotated property: definition
annotated target: Predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. See review in PMID:24281846.
database_cross_reference: PRIDE:PRIDE

MSE
type: Class
subclass of: Data-independent acquisition
definition: Waters data independent acquisition method based on UPLC chromatography and MS acquisition of cycles of two spectra, in low and high energy respectively, in a QQ-TOF instrument. It is described in PMID: 16755610.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000451

Axiom
annotated source: MSE
annotated property: definition
annotated target: Waters data independent acquisition method based on UPLC chromatography and MS acquisition of cycles of two spectra, in low and high energy respectively, in a QQ-TOF instrument. It is described in PMID: 16755610.
database_cross_reference: PRIDE:PRIDE

HDMSE
type: Class
subclass of: Data-independent acquisition
definition: Waters data independent acquisition method, which consists of using an additional on-line separation dimension (Ion Mobility drift) and an MSE acquisition. It is described in PMID: 22811061.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000452

Axiom
annotated source: HDMSE
annotated property: definition
annotated target: Waters data independent acquisition method, which consists of using an additional on-line separation dimension (Ion Mobility drift) and an MSE acquisition. It is described in PMID: 22811061.
database_cross_reference: PRIDE:PRIDE

PAcIFIC
type: Class
subclass of: Data-independent acquisition
definition: Precursor Acquisition Independent From Ion Count. A Data Independent Acquisition method performed in ion traps that consists of the acquisition of 2.5 m/z width sequential windows over several injections of the same material, until a precursor m/z range of about 400 to 1200 m/z is covered. It is described in PMID: 21341720.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000453

Axiom
annotated source: PAcIFIC
annotated property: definition
annotated target: Precursor Acquisition Independent From Ion Count. A Data Independent Acquisition method performed in ion traps that consists of the acquisition of 2.5 m/z width sequential windows over several injections of the same material, until a precursor m/z range of about 400 to 1200 m/z is covered. It is described in PMID: 21341720.
database_cross_reference: PRIDE:PRIDE

All-ion fragmentation
type: Class
subclass of: Data-independent acquisition
definition: MS Data Independent Acquisition performed in Thermo Orbitrap instruments. It consists of the acquisition of cycles of two spectra, a precursor mass MS1 spectrum, and a fragment ions MS2 spectrum where a wide mass filter (typically over 800 m/z) is applied to the precursors. It is described in PMID: 20610777.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000454

Axiom
annotated source: All-ion fragmentation
annotated property: definition
annotated target: MS Data Independent Acquisition performed in Thermo Orbitrap instruments. It consists of the acquisition of cycles of two spectra, a precursor mass MS1 spectrum, and a fragment ions MS2 spectrum where a wide mass filter (typically over 800 m/z) is applied to the precursors. It is described in PMID: 20610777.
database_cross_reference: PRIDE:PRIDE

Protein-protein cross-linking experiment
type: Class
subclass of: Chemical cross-linking coupled with mass spectrometry proteomics
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000455
comment: Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction.

Protein-RNA cross-linking experiment
type: Class
subclass of: Chemical cross-linking coupled with mass spectrometry proteomics
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000456
comment: Protein-RNA cross-linking experiment to provide information about Protein-RNA interaction.

Experiment Type
type: Class
has_obo_namespace: PRIDE
id: PRIDE:0000457
comment: Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method.

Metaproteomics
type: Class
subclass of: Experiment Type
definition: Studying all protein samples of diverse host environments like the human body, soil or sea water.
created by: acsordas
has_exact_synonym: Community Proteomics
has_obo_namespace: PRIDE
has_related_synonym: Environmental Proteomics
id: PRIDE:0000458

Axiom
annotated source: Metaproteomics
annotated property: definition
annotated target: Studying all protein samples of diverse host environments like the human body, soil or sea water.
database_cross_reference: PRIDE:PRIDE

Human Metaproteomics
type: Class
subclass of: Metaproteomics
definition: Investigating both human host proteins and associated microbial proteins at the same time from human samples.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000459

Axiom
annotated source: Human Metaproteomics
annotated property: definition
annotated target: Investigating both human host proteins and associated microbial proteins at the same time from human samples.
database_cross_reference: PRIDE:PRIDE

Proteogenomics
type: Class
subclass of: Experiment Type
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000460
comment: "Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies."

Multi-omics study
type: Class
subclass of: Experiment Type
definition: Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000461

Axiom
annotated source: Multi-omics study
annotated property: definition
annotated target: Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples.
database_cross_reference: PRIDE:PRIDE

SONAR
type: Class
subclass of: Data-independent acquisition
definition: Waters data independent acquisition method.
created by: acsordas
has_obo_namespace: PRIDE
id: PRIDE:0000462

Axiom
annotated source: SONAR
annotated property: definition
annotated target: Waters data independent acquisition method.
database_cross_reference: PRIDE:PRIDE

PRM
type: Class
subclass of: Selected Reaction Monitoring
definition: Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis.
has_obo_namespace: PRIDE
id: PRIDE:0000463

Axiom
annotated source: PRM
annotated property: definition
annotated target: Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis.
database_cross_reference: PRIDE:PRIDE

Fasta file URI
type: Class
subclass of: Experiment additional parameter
created by: ypriverol
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000464
comment: URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission).

The allowed value-type for this CV term.
type: Axiom
annotated source: Fasta file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Spectral Library file URI
type: Class
subclass of: Experiment additional parameter
created by: ypriverol
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000465
comment: URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission).

The allowed value-type for this CV term.
type: Axiom
annotated source: Spectral Library file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Quantification result file URI
type: Class
subclass of: Experiment additional parameter
created by: ypriverol
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000466
comment: URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission).

The allowed value-type for this CV term.
type: Axiom
annotated source: Quantification result file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

MS Image file URI
type: Class
subclass of: Experiment additional parameter
created by: ypriverol
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000467
comment: URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission).

The allowed value-type for this CV term.
type: Axiom
annotated source: MS Image file URI
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Aspera Protocol
type: Class
subclass of: Experiment additional parameter
created by: ypriverol
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000468
comment: URI for an Aspera Download Protocol

The allowed value-type for this CV term.
type: Axiom
annotated source: Aspera Protocol
annotated property: database_cross_reference
annotated target: value-type:xsd:string

FTP Protocol
type: Class
subclass of: Experiment additional parameter
created by: ypriverol
creation date: 2018-08-29T14:26:28Z
has_obo_namespace: PRIDE
id: PRIDE:0000469

File Properties
type: Class
definition: PRIDE File Properties for all type of files.
created by: ypriverol
creation date: 2018-08-29T14:26:28Z
has_obo_namespace: PRIDE
id: PRIDE:0000470

Axiom
annotated source: File Properties
annotated property: definition
annotated target: PRIDE File Properties for all type of files.
database_cross_reference: PRIDE:PRIDE

MS File Properties
type: Class
subclass of: File Properties
definition: Properties for MS , Peaks files
created by: ypriverol
creation date: 2018-08-29T14:31:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000471

Axiom
annotated source: MS File Properties
annotated property: definition
annotated target: Properties for MS , Peaks files
database_cross_reference: PRIDE:PRIDE

MS min charge
type: Class
subclass of: MS File Properties
definition: Minimum charge for all precursor in the file.
created by: ypriverol
creation date: 2018-08-29T14:33:01Z
has_obo_namespace: PRIDE
id: PRIDE:0000472

Axiom
annotated source: MS min charge
annotated property: definition
annotated target: Minimum charge for all precursor in the file.
database_cross_reference: PRIDE:PRIDE

MS max charge
type: Class
subclass of: MS File Properties
definition: Maximum charge for all precursor in the file.
created by: ypriverol
creation date: 2018-08-29T14:35:57Z
has_obo_namespace: PRIDE
id: PRIDE:0000473

Axiom
annotated source: MS max charge
annotated property: definition
annotated target: Maximum charge for all precursor in the file.
database_cross_reference: PRIDE:PRIDE

MS min RT
type: Class
subclass of: MS File Properties
definition: Minimum retention time in the File.
created by: ypriverol
creation date: 2018-08-29T14:36:50Z
has_obo_namespace: PRIDE
id: PRIDE:0000474

Axiom
annotated source: MS min RT
annotated property: definition
annotated target: Minimum retention time in the File.
database_cross_reference: PRIDE:PRIDE

MS max RT
type: Class
subclass of: MS File Properties
definition: Maximum retention time in the file.
created by: ypriverol
creation date: 2018-08-29T14:37:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000475

Axiom
annotated source: MS max RT
annotated property: definition
annotated target: Maximum retention time in the file.
database_cross_reference: PRIDE:PRIDE

MS min MZ
type: Class
subclass of: MS File Properties
definition: Minimum precursor mass to charge in the file.
created by: ypriverol
creation date: 2018-08-29T14:38:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000476

Axiom
annotated source: MS min MZ
annotated property: definition
annotated target: Minimum precursor mass to charge in the file.
database_cross_reference: PRIDE:PRIDE

MS max MZ
type: Class
subclass of: MS File Properties
definition: Maximum precursor mass to charge in the file.
created by: ypriverol
creation date: 2018-08-29T14:39:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000477

Axiom
annotated source: MS max MZ
annotated property: definition
annotated target: Maximum precursor mass to charge in the file.
database_cross_reference: PRIDE:PRIDE

Number of scans
type: Class
subclass of: MS File Properties
definition: Total number of scans in the file.
created by: ypriverol
creation date: 2018-08-29T14:40:05Z
has_obo_namespace: PRIDE
id: PRIDE:0000478

Axiom
annotated source: Number of scans
annotated property: definition
annotated target: Total number of scans in the file.
database_cross_reference: PRIDE:PRIDE

MS scan range
type: Class
subclass of: MS File Properties
definition: Range of scan number in the ms file.
created by: ypriverol
creation date: 2018-08-29T14:41:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000479

Axiom
annotated source: MS scan range
annotated property: definition
annotated target: Range of scan number in the ms file.
database_cross_reference: PRIDE:PRIDE

Number of MS
type: Class
subclass of: MS File Properties
definition: Number of MS in the file.
created by: ypriverol
creation date: 2018-08-29T14:43:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000480

Axiom
annotated source: Number of MS
annotated property: definition
annotated target: Number of MS in the file.
database_cross_reference: PRIDE:PRIDE

Number of MS1 spectra
type: Class
subclass of: Number of MS
definition: Number of MS1 spectra.
created by: ypriverol
creation date: 2018-08-29T14:45:21Z
has_obo_namespace: PRIDE
id: PRIDE:0000481

Axiom
annotated source: Number of MS1 spectra
annotated property: definition
annotated target: Number of MS1 spectra.
database_cross_reference: PRIDE:PRIDE

Number of MS2 spectra
type: Class
subclass of: Number of MS
definition: Number of MS2 spectra in the file.
created by: ypriverol
creation date: 2018-08-29T14:46:01Z
has_obo_namespace: PRIDE
id: PRIDE:0000482

Axiom
annotated source: Number of MS2 spectra
annotated property: definition
annotated target: Number of MS2 spectra in the file.
database_cross_reference: PRIDE:PRIDE

Number of MS3 spectra
type: Class
subclass of: Number of MS
definition: Total number of MS3 spectra in the file.
created by: ypriverol
creation date: 2018-08-29T14:48:35Z
has_obo_namespace: PRIDE
id: PRIDE:0000483

Axiom
annotated source: Number of MS3 spectra
annotated property: definition
annotated target: Total number of MS3 spectra in the file.
database_cross_reference: PRIDE:PRIDE

Result analysis parameters
type: Class
definition: The result analysis parameters is a term to group all the parameters for proteomics data analysis.
created by: yperez
creation date: 2018-09-05T09:08:58Z
has_obo_namespace: PRIDE
id: PRIDE:0000484

Axiom
annotated source: Result analysis parameters
annotated property: definition
annotated target: The result analysis parameters is a term to group all the parameters for proteomics data analysis.
database_cross_reference: PRIDE:PRIDE

Global result parameters
type: Class
subclass of: Result analysis parameters
definition: Result analysis parameters share by multiple search engine and Quantiative tools.
created by: yperez
creation date: 2018-09-05T09:11:41Z
has_obo_namespace: PRIDE
id: PRIDE:0000485

Axiom
annotated source: Global result parameters
annotated property: definition
annotated target: Result analysis parameters share by multiple search engine and Quantiative tools.
database_cross_reference: PRIDE:PRIDE

Tool specific analysis parameters
type: Class
subclass of: Result analysis parameters
created by: yperez
creation date: 2018-09-05T09:14:02Z
has_obo_namespace: PRIDE
id: PRIDE:0000486

Min charge
type: Class
subclass of: Global result parameters
definition: Minimum charge of precursor to be search.
created by: yperez
creation date: 2018-09-05T09:26:36Z
has_obo_namespace: PRIDE
id: PRIDE:0000487

Axiom
annotated source: Min charge
annotated property: definition
annotated target: Minimum charge of precursor to be search.
database_cross_reference: PRIDE:PRIDE

Max charge
type: Class
subclass of: Global result parameters
definition: Maximum charge of precursor to be search.
created by: yperez
creation date: 2018-09-05T09:28:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000488

Axiom
annotated source: Max charge
annotated property: definition
annotated target: Maximum charge of precursor to be search.
database_cross_reference: PRIDE:PRIDE

Min RT
type: Class
subclass of: Global result parameters
definition: Min Retention time for precursor to be search.
created by: yperez
creation date: 2018-09-05T09:30:51Z
has_obo_namespace: PRIDE
id: PRIDE:0000489

Axiom
annotated source: Min RT
annotated property: definition
annotated target: Min Retention time for precursor to be search.
database_cross_reference: PRIDE:PRIDE

Max RT
type: Class
subclass of: Global result parameters
definition: Maximum precursor RT to be search.
created by: yperez
creation date: 2018-09-05T09:31:35Z
has_obo_namespace: PRIDE
id: PRIDE:0000490

Axiom
annotated source: Max RT
annotated property: definition
annotated target: Maximum precursor RT to be search.
database_cross_reference: PRIDE:PRIDE

Number of missed cleavages
type: Class
subclass of: Global result parameters
definition: Number of missed cleavages.
created by: yperez
creation date: 2018-09-05T09:37:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000491

Axiom
annotated source: Number of missed cleavages
annotated property: definition
annotated target: Number of missed cleavages.
database_cross_reference: PRIDE:PRIDE

Max peptide AA length
type: Class
subclass of: Global result parameters
definition: Max peptide amino acid length for search.
created by: yperez
creation date: 2018-09-05T09:43:03Z
has_obo_namespace: PRIDE
id: PRIDE:0000492

Axiom
annotated source: Max peptide AA length
annotated property: definition
annotated target: Max peptide amino acid length for search.
database_cross_reference: PRIDE:PRIDE

Min peptide AA length
type: Class
subclass of: Global result parameters
definition: Minimum peptide amino acid length for search.
created by: yperez
creation date: 2018-09-05T09:43:54Z
has_obo_namespace: PRIDE
id: PRIDE:0000493

Axiom
annotated source: Min peptide AA length
annotated property: definition
annotated target: Minimum peptide amino acid length for search.
database_cross_reference: PRIDE:PRIDE

Min precursor MZ
type: Class
subclass of: Global result parameters
definition: Min precursor MZ (mass) for precursor to search.
created by: yperez
creation date: 2018-09-05T09:47:03Z
has_obo_namespace: PRIDE
id: PRIDE:0000494

Axiom
annotated source: Min precursor MZ
annotated property: definition
annotated target: Min precursor MZ (mass) for precursor to search.
database_cross_reference: PRIDE:PRIDE

Max precursor MZ
type: Class
subclass of: Global result parameters
definition: Max precursor MZ (mass) for precursor to search.
created by: yperez
creation date: 2018-09-05T09:48:08Z
has_obo_namespace: PRIDE
id: PRIDE:0000495

Axiom
annotated source: Max precursor MZ
annotated property: definition
annotated target: Max precursor MZ (mass) for precursor to search.
database_cross_reference: PRIDE:PRIDE

Min peak length
type: Class
subclass of: Global result parameters
definition: Min number of peaks in the spectrum to be search.
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000496

Axiom
annotated source: Min peak length
annotated property: definition
annotated target: Min number of peaks in the spectrum to be search.
database_cross_reference: PRIDE:PRIDE

Use Multi Modification
type: Class
subclass of: Global result parameters
definition: Use Multi Modification
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000497

Axiom
annotated source: Use Multi Modification
annotated property: definition
annotated target: Use Multi Modification
database_cross_reference: PRIDE:PRIDE

Use Additional Variable Modifications
type: Class
subclass of: Global result parameters
definition: Use Additional Variable Modifications
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000498

Axiom
annotated source: Use Additional Variable Modifications
annotated property: definition
annotated target: Use Additional Variable Modifications
database_cross_reference: PRIDE:PRIDE

Do Mass Filtering
type: Class
subclass of: Global result parameters
definition: Do Mass Filtering
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000499

Axiom
annotated source: Do Mass Filtering
annotated property: definition
annotated target: Do Mass Filtering
database_cross_reference: PRIDE:PRIDE

Intensity Threshold
type: Class
subclass of: Global result parameters
definition: Intensity Threshold
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000500

Axiom
annotated source: Intensity Threshold
annotated property: definition
annotated target: Intensity Threshold
database_cross_reference: PRIDE:PRIDE

Max Labeled AA
type: Class
subclass of: Global result parameters
definition: Max Labeled AA
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000501

Axiom
annotated source: Max Labeled AA
annotated property: definition
annotated target: Max Labeled AA
database_cross_reference: PRIDE:PRIDE

Max Number of Modifications (PTMs)
type: Class
subclass of: Global result parameters
definition: Max Number of Modifications (PTMs)
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000502

Axiom
annotated source: Max Number of Modifications (PTMs)
annotated property: definition
annotated target: Max Number of Modifications (PTMs)
database_cross_reference: PRIDE:PRIDE

First Search Precursor Tolerance
type: Class
subclass of: Global result parameters
definition: First Search Precursor Tolerance
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000503

Axiom
annotated source: First Search Precursor Tolerance
annotated property: definition
annotated target: First Search Precursor Tolerance
database_cross_reference: PRIDE:PRIDE

Main Search Precursor Tolerance
type: Class
subclass of: Global result parameters
definition: Main Search Precursor Tolerance
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000504

Axiom
annotated source: Main Search Precursor Tolerance
annotated property: definition
annotated target: Main Search Precursor Tolerance
database_cross_reference: PRIDE:PRIDE

Individual Accession
type: Class
subclass of: Sample description additional parameter
definition: Accession or Code of the individual in the sample.
created by: yperez
creation date: 2018-09-05T10:38:29Z
has_obo_namespace: PRIDE
id: PRIDE:0000505

Axiom
annotated source: Individual Accession
annotated property: definition
annotated target: Accession or Code of the individual in the sample.
database_cross_reference: PRIDE:PRIDE

Number identified proteins
type: Class
subclass of: Global result parameters
definition: Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment.
created by: yperez
creation date: 2019-06-06T13:51:41Z
has_obo_namespace: PRIDE
id: PRIDE:0000506

Axiom
annotated source: Number identified proteins
annotated property: definition
annotated target: Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment.
database_cross_reference: PRIDE:PRIDE

Number of identified peptides
type: Class
subclass of: Global result parameters
definition: Total number of identified peptides in an experiment or assay.
created by: yperez
creation date: 2019-06-06T13:53:23Z
has_obo_namespace: PRIDE
id: PRIDE:0000507

Axiom
annotated source: Number of identified peptides
annotated property: definition
annotated target: Total number of identified peptides in an experiment or assay.
database_cross_reference: PRIDE:PRIDE

Number of modified peptides
type: Class
subclass of: Global result parameters
definition: The total number of peptides identified with post-translational modifications.
created by: yperez
creation date: 2019-06-06T13:54:46Z
has_obo_namespace: PRIDE
id: PRIDE:0000508

Axiom
annotated source: Number of modified peptides
annotated property: definition
annotated target: The total number of peptides identified with post-translational modifications.
database_cross_reference: PRIDE:PRIDE

Number of PSMs
type: Class
subclass of: Global result parameters
definition: Total number of reported identified Peptide Spectrum matches (PSMs)
created by: yperez
creation date: 2019-06-06T13:56:00Z
has_obo_namespace: PRIDE
id: PRIDE:0000509

Axiom
annotated source: Number of PSMs
annotated property: definition
annotated target: Total number of reported identified Peptide Spectrum matches (PSMs)
database_cross_reference: PRIDE:PRIDE

File size
type: Class
subclass of: File Properties
definition: The size of the file in MB.
created by: mwalzer
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000510

Axiom
annotated source: File size
annotated property: definition
annotated target: The size of the file in MB.
database_cross_reference: PRIDE:PRIDE

Pass submitter threshold
type: Class
subclass of: Peptide item additional parameter
definition: Pass submitter threshold
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000511

Axiom
annotated source: Pass submitter threshold
annotated property: definition
annotated target: Pass submitter threshold
database_cross_reference: PRIDE:PRIDE

RNA mass spectrometry
type: Class
subclass of: Bottom-up proteomics
definition: RNA mass spectrometry
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000512

Axiom
annotated source: RNA mass spectrometry
annotated property: definition
annotated target: RNA mass spectrometry
database_cross_reference: PRIDE:PRIDE

Dimethyl Labeling
type: Class
subclass of: Isotope labeling
definition: Dimethyl Labeling (DML)
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000513

Axiom
annotated source: Dimethyl Labeling
annotated property: definition
annotated target: Dimethyl Labeling (DML)
database_cross_reference: PRIDE:PRIDE

Label
type: Class
subclass of: Sample description additional parameter
definition: Quantification channel label
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000514

Axiom
annotated source: Label
annotated property: definition
annotated target: Quantification channel label
database_cross_reference: PRIDE:PRIDE

TMT
type: Class
subclass of: Label
definition: TMT
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000515

Axiom
annotated source: TMT
annotated property: definition
annotated target: TMT
database_cross_reference: PRIDE:PRIDE

TMT126
type: Class
subclass of: TMT
definition: TMT126
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000516

Axiom
annotated source: TMT126
annotated property: definition
annotated target: TMT126
database_cross_reference: PRIDE:PRIDE

TMT127
type: Class
subclass of: TMT
definition: TMT127
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000517

Axiom
annotated source: TMT127
annotated property: definition
annotated target: TMT127
database_cross_reference: PRIDE:PRIDE

TMT127C
type: Class
subclass of: TMT
definition: TMT127C
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000518

Axiom
annotated source: TMT127C
annotated property: definition
annotated target: TMT127C
database_cross_reference: PRIDE:PRIDE

TMT127N
type: Class
subclass of: TMT
definition: TMT127N
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000519

Axiom
annotated source: TMT127N
annotated property: definition
annotated target: TMT127N
database_cross_reference: PRIDE:PRIDE

TMT128
type: Class
subclass of: TMT
definition: TMT128
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000520

Axiom
annotated source: TMT128
annotated property: definition
annotated target: TMT128
database_cross_reference: PRIDE:PRIDE

TMT128C
type: Class
subclass of: TMT
definition: TMT128C
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000521

Axiom
annotated source: TMT128C
annotated property: definition
annotated target: TMT128C
database_cross_reference: PRIDE:PRIDE

TMT128N
type: Class
subclass of: TMT
definition: TMT128N
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000522

Axiom
annotated source: TMT128N
annotated property: definition
annotated target: TMT128N
database_cross_reference: PRIDE:PRIDE

TMT129
type: Class
subclass of: TMT
definition: TMT129
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000523

Axiom
annotated source: TMT129
annotated property: definition
annotated target: TMT129
database_cross_reference: PRIDE:PRIDE

TMT129C
type: Class
subclass of: TMT
definition: TMT129C
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000524

Axiom
annotated source: TMT129C
annotated property: definition
annotated target: TMT129C
database_cross_reference: PRIDE:PRIDE

TMT129N
type: Class
subclass of: TMT
definition: TMT129N
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000525

Axiom
annotated source: TMT129N
annotated property: definition
annotated target: TMT129N
database_cross_reference: PRIDE:PRIDE

TMT130
type: Class
subclass of: TMT
definition: TMT130
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000526

Axiom
annotated source: TMT130
annotated property: definition
annotated target: TMT130
database_cross_reference: PRIDE:PRIDE

TMT130C
type: Class
subclass of: TMT
definition: TMT130C
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000527

Axiom
annotated source: TMT130C
annotated property: definition
annotated target: TMT130C
database_cross_reference: PRIDE:PRIDE

TMT130N
type: Class
subclass of: TMT
definition: TMT130N
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000528

Axiom
annotated source: TMT130N
annotated property: definition
annotated target: TMT130N
database_cross_reference: PRIDE:PRIDE

TMT131
type: Class
subclass of: TMT
definition: TMT131
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000529

Axiom
annotated source: TMT131
annotated property: definition
annotated target: TMT131
database_cross_reference: PRIDE:PRIDE

ITRAQ
type: Class
subclass of: Label
definition: ITRAQ channel label
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000530

Axiom
annotated source: ITRAQ
annotated property: definition
annotated target: ITRAQ channel label
database_cross_reference: PRIDE:PRIDE

ITRAQ113
type: Class
subclass of: ITRAQ
created by: yperez
creation date: 2020-03-16T18:02:43Z
has_obo_namespace: PRIDE
id: PRIDE:0000531

ITRAQ114
type: Class
subclass of: ITRAQ
created by: yperez
creation date: 2020-03-16T18:03:15Z
has_obo_namespace: PRIDE
id: PRIDE:0000532

ITRAQ115
type: Class
subclass of: ITRAQ
created by: yperez
creation date: 2020-03-16T18:03:31Z
has_obo_namespace: PRIDE
id: PRIDE:0000533

ITRAQ116
type: Class
subclass of: ITRAQ
created by: yperez
creation date: 2020-03-16T18:03:49Z
has_obo_namespace: PRIDE
id: PRIDE:0000534

ITRAQ117
type: Class
subclass of: ITRAQ
created by: yperez
creation date: 2020-03-16T18:04:10Z
has_obo_namespace: PRIDE
id: PRIDE:0000535

ITRAQ118
type: Class
subclass of: ITRAQ
created by: yperez
creation date: 2020-03-16T18:04:30Z
has_obo_namespace: PRIDE
id: PRIDE:0000536

ITRAQ119
type: Class
subclass of: ITRAQ
created by: yperez
creation date: 2020-03-16T18:04:49Z
has_obo_namespace: PRIDE
id: PRIDE:0000537

ITRAQ121
type: Class
subclass of: ITRAQ
created by: yperez
creation date: 2020-03-16T18:05:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000538

SILAC
type: Class
subclass of: Label
definition: SILAC channel label
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000539

Axiom
annotated source: SILAC
annotated property: definition
annotated target: SILAC channel label
database_cross_reference: PRIDE:PRIDE

ICAT
type: Class
subclass of: Label
definition: ICAT channel label
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000540

Axiom
annotated source: ICAT
annotated property: definition
annotated target: ICAT channel label
database_cross_reference: PRIDE:PRIDE

ICAT heavy
type: Class
subclass of: ICAT
definition: ICAT heavy
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000541

Axiom
annotated source: ICAT heavy
annotated property: definition
annotated target: ICAT heavy
database_cross_reference: PRIDE:PRIDE

ICAT light
type: Class
subclass of: ICAT
definition: ICAT light
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000542

Axiom
annotated source: ICAT light
annotated property: definition
annotated target: ICAT light
database_cross_reference: PRIDE:PRIDE

Quality Control
type: Class
subclass of: Experiment Type
definition: MS experiments conducted to control the quality of measurements. Includes the acquisition of samples for SST and longitudinal monitoring.
has_obo_namespace: PRIDE
id: PRIDE:0000543
comment: Example description of such experiments in 10.1002/pmic.201000578

Axiom
annotated source: Quality Control
annotated property: definition
annotated target: MS experiments conducted to control the quality of measurements. Includes the acquisition of samples for SST and longitudinal monitoring.
database_cross_reference: PRIDE:PRIDE

Quality Control Sample
type: Class
subclass of: Sample description additional parameter
definition: Sample with known content and quantities designed to control the consistent quality of measurement for a particular method and settings.
has_obo_namespace: PRIDE
id: PRIDE:0000544
comment: Example description of such samples in 10.1002/pmic.201000578

Axiom
annotated source: Quality Control Sample
annotated property: definition
annotated target: Sample with known content and quantities designed to control the consistent quality of measurement for a particular method and settings.
database_cross_reference: PRIDE:PRIDE

QC1 sample
type: Class
subclass of: Quality Control Sample
definition: QC1 sample as described in 10.1371/journal.pone.0189209.
has_obo_namespace: PRIDE
id: PRIDE:0000545

Axiom
annotated source: QC1 sample
annotated property: definition
annotated target: QC1 sample as described in 10.1371/journal.pone.0189209.
database_cross_reference: PRIDE:PRIDE

QC2 sample
type: Class
subclass of: Quality Control Sample
definition: QC2 sample as described in 10.1371/journal.pone.0189209.
has_obo_namespace: PRIDE
id: PRIDE:0000546

Axiom
annotated source: QC2 sample
annotated property: definition
annotated target: QC2 sample as described in 10.1371/journal.pone.0189209.
database_cross_reference: PRIDE:PRIDE

Instrument properties
type: Class
definition: Instrument properties
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000547

Axiom
annotated source: Instrument properties
annotated property: definition
annotated target: Instrument properties
database_cross_reference: PRIDE:PRIDE

MS1 mass analyzer
type: Class
subclass of: mass analyzer
definition: MS1 mass analyzer
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000548

Axiom
annotated source: MS1 mass analyzer
annotated property: definition
annotated target: MS1 mass analyzer
database_cross_reference: PRIDE:PRIDE

MS2 mass analyzer
type: Class
subclass of: mass analyzer
definition: MS2 mass analyzer
created by: yperez
creation date: 2020-03-16T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000549

Axiom
annotated source: MS2 mass analyzer
annotated property: definition
annotated target: MS2 mass analyzer
database_cross_reference: PRIDE:PRIDE

Fractionation method
type: Class
subclass of: Fractionation
definition: Umbrella term for different types of fractionation methods.
has_obo_namespace: PRIDE
id: PRIDE:0000550

Axiom
annotated source: Fractionation method
annotated property: definition
annotated target: Umbrella term for different types of fractionation methods.
database_cross_reference: PRIDE:PRIDE

Separation method
type: Class
subclass of: Separation
definition: Umbrella term for different types of fractionation methods.
has_obo_namespace: PRIDE
id: PRIDE:0000551

Axiom
annotated source: Separation method
annotated property: definition
annotated target: Umbrella term for different types of fractionation methods.
database_cross_reference: PRIDE:PRIDE

Off-gel electrophoresis
type: Class
subclass of: Fractionation method
definition: Fractionate peptides into discrete liquid fractions based on isoelectric electrophoresis (10.1002/elps.200390030).
has_obo_namespace: PRIDE
id: PRIDE:0000552

Axiom
annotated source: Off-gel electrophoresis
annotated property: definition
annotated target: Fractionate peptides into discrete liquid fractions based on isoelectric electrophoresis (10.1002/elps.200390030).
database_cross_reference: PRIDE:PRIDE

Isoelectric focusing
type: Class
subclass of: Fractionation method
definition: An electrophoresis method for the separation of amphoteric analytes according to their isoelectric points by the application of an electric field along a pH gradient.
has_obo_namespace: PRIDE
id: PRIDE:0000553

Axiom
annotated source: Isoelectric focusing
annotated property: definition
annotated target: An electrophoresis method for the separation of amphoteric analytes according to their isoelectric points by the application of an electric field along a pH gradient.
database_cross_reference: PRIDE:PRIDE

Hydrophilic interaction chromatography (HILIC)
type: Class
subclass of: Normal-phase liquid chromatography (NP)
definition: Liquid chromatography where the stationary phase is hydrophilic, the mobile phase is organic and separation is achieved based on polarity.
has_obo_namespace: PRIDE
id: PRIDE:0000554

Axiom
annotated source: Hydrophilic interaction chromatography (HILIC)
annotated property: definition
annotated target: Liquid chromatography where the stationary phase is hydrophilic, the mobile phase is organic and separation is achieved based on polarity.
database_cross_reference: PRIDE:PRIDE

ERLIC
type: Class
subclass of: Normal-phase liquid chromatography (NP)
definition: Electrostatic repulsion hydrophilic interaction chromatography (ERLIC). Hydrophilic interaction chromatography where the chromatography column is an ion-exchange column and the mobile phase is predominantly organic.
has_obo_namespace: PRIDE
id: PRIDE:0000555

Axiom
annotated source: ERLIC
annotated property: definition
annotated target: Electrostatic repulsion hydrophilic interaction chromatography (ERLIC). Hydrophilic interaction chromatography where the chromatography column is an ion-exchange column and the mobile phase is predominantly organic.
database_cross_reference: PRIDE:PRIDE

Ion-exchange chromatography
type: Class
subclass of: High-performance liquid chromatography
definition: A chromatography method where the separation is caused by differences in ion-exchange affinity.
has_obo_namespace: PRIDE
id: PRIDE:0000556

Axiom
annotated source: Ion-exchange chromatography
annotated property: definition
annotated target: A chromatography method where the separation is caused by differences in ion-exchange affinity.
database_cross_reference: PRIDE:PRIDE

Size-exclusion chromatography (SEC)
type: Class
subclass of: High-performance liquid chromatography
definition: A chromatography method where the separation is caused by differences in molecular size.
has_obo_namespace: PRIDE
id: PRIDE:0000557

Axiom
annotated source: Size-exclusion chromatography (SEC)
annotated property: definition
annotated target: A chromatography method where the separation is caused by differences in molecular size.
database_cross_reference: PRIDE:PRIDE

Strong anion-exchange chromatography (SAX)
type: Class
subclass of: Ion-exchange chromatography
definition: A chromatography method with the stationary phase being a strong anion exchanger.
has_obo_namespace: PRIDE
id: PRIDE:0000558

Axiom
annotated source: Strong anion-exchange chromatography (SAX)
annotated property: definition
annotated target: A chromatography method with the stationary phase being a strong anion exchanger.
database_cross_reference: PRIDE:PRIDE

Weak anion-exchange chromatography (WAX)
type: Class
subclass of: Ion-exchange chromatography
definition: A chromatography method with the stationary phase being a weak anion exchanger.
has_obo_namespace: PRIDE
id: PRIDE:0000559

Axiom
annotated source: Weak anion-exchange chromatography (WAX)
annotated property: definition
annotated target: A chromatography method with the stationary phase being a weak anion exchanger.
database_cross_reference: PRIDE:PRIDE

Weak cation-exchange chromatography (WCX)
type: Class
subclass of: Ion-exchange chromatography
definition: A chromatography method with the stationary phase being a weak cation exchanger.
has_obo_namespace: PRIDE
id: PRIDE:0000560

Axiom
annotated source: Weak cation-exchange chromatography (WCX)
annotated property: definition
annotated target: A chromatography method with the stationary phase being a weak cation exchanger.
database_cross_reference: PRIDE:PRIDE

Strong cation-exchange chromatography (SCX)
type: Class
subclass of: Ion-exchange chromatography
definition: A chromatography method with the stationary phase being a strong cation exchanger.
has_obo_namespace: PRIDE
id: PRIDE:0000561

Axiom
annotated source: Strong cation-exchange chromatography (SCX)
annotated property: definition
annotated target: A chromatography method with the stationary phase being a strong cation exchanger.
database_cross_reference: PRIDE:PRIDE

Normal-phase liquid chromatography (NP)
type: Class
subclass of: High-performance liquid chromatography
definition: Liquid chromatography where the stationary phase is more polar than the mobile phase. This is the default for liquid chromatography.
has_obo_namespace: PRIDE
id: PRIDE:0000562

Axiom
annotated source: Normal-phase liquid chromatography (NP)
annotated property: definition
annotated target: Liquid chromatography where the stationary phase is more polar than the mobile phase. This is the default for liquid chromatography.
database_cross_reference: PRIDE:PRIDE

Reversed-phase chromatography (RP)
type: Class
subclass of: High-performance liquid chromatography
definition: Liquid chromatography where the mobile phase is significantly more polar than the stationary phase.
has_obo_namespace: PRIDE
id: PRIDE:0000563

Axiom
annotated source: Reversed-phase chromatography (RP)
annotated property: definition
annotated target: Liquid chromatography where the mobile phase is significantly more polar than the stationary phase.
database_cross_reference: PRIDE:PRIDE

High-pH reversed-phase chromatography (hpHRP)
type: Class
subclass of: Reversed-phase chromatography (RP)
definition: Liquid chromatography where the mobile phase is of high pH and significantly more polar than the stationary phase.
has_obo_namespace: PRIDE
id: PRIDE:0000564

Axiom
annotated source: High-pH reversed-phase chromatography (hpHRP)
annotated property: definition
annotated target: Liquid chromatography where the mobile phase is of high pH and significantly more polar than the stationary phase.
database_cross_reference: PRIDE:PRIDE

High-performance liquid chromatography
type: Class
subclass of: Fractionation method
subclass of: Separation method
definition: Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high.
database_cross_reference: http://purl.obolibrary.org/obo/CHMO_0001009
has_obo_namespace: PRIDE
id: PRIDE:0000565

Axiom
annotated source: High-performance liquid chromatography
annotated property: definition
annotated target: Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high.
database_cross_reference: PRIDE:PRIDE

High-resolution isoelectric focusing (HiRIEF)
type: Class
subclass of: Isoelectric focusing
definition: An electrophoresis method with significantly higher resolution than common isoelectric focusing methods.
has_obo_namespace: PRIDE
id: PRIDE:0000566

Axiom
annotated source: High-resolution isoelectric focusing (HiRIEF)
annotated property: definition
annotated target: An electrophoresis method with significantly higher resolution than common isoelectric focusing methods.
database_cross_reference: PRIDE:PRIDE

Gel electrophoresis
type: Class
subclass of: Fractionation method
subclass of: Separation method
definition: Gel electrophoresis
has_obo_namespace: PRIDE
id: PRIDE:0000567

Axiom
annotated source: Gel electrophoresis
annotated property: definition
annotated target: Gel electrophoresis
database_cross_reference: PRIDE:PRIDE

SDS PAGE
type: Class
subclass of: Gel electrophoresis
definition: SDS-PAGE is an electrophoresis method that allows protein separation by mass. The medium/matrix is a polyacrylamide-based discontinuous gel
has_obo_namespace: PRIDE
id: PRIDE:0000568

Axiom
annotated source: SDS PAGE
annotated property: definition
annotated target: SDS-PAGE is an electrophoresis method that allows protein separation by mass. The medium/matrix is a polyacrylamide-based discontinuous gel
database_cross_reference: PRIDE:PRIDE

2D PAGE
type: Class
subclass of: Gel electrophoresis
definition: 2D-PAGE is a form of gel electrophoresis in which separation and identification of proteins in a sample are done by displacement in 2 dimensions oriented at right angles to one another(orthogonal)
has_obo_namespace: PRIDE
id: PRIDE:0000569

Axiom
annotated source: 2D PAGE
annotated property: definition
annotated target: 2D-PAGE is a form of gel electrophoresis in which separation and identification of proteins in a sample are done by displacement in 2 dimensions oriented at right angles to one another(orthogonal)
database_cross_reference: PRIDE:PRIDE

Decoy protein
type: Class
subclass of: Identification additional parameter
definition: Indicates that this protein identification comes from the used decoy database.
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000570

Axiom
annotated source: Decoy protein
annotated property: definition
annotated target: Indicates that this protein identification comes from the used decoy database.
database_cross_reference: PRIDE:PRIDE

Quantification software
type: Class
definition: A software that perform protein quantification using mass spectrometry data.
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000571

Axiom
annotated source: Quantification software
annotated property: definition
annotated target: A software that perform protein quantification using mass spectrometry data.
database_cross_reference: PRIDE:PRIDE

OpenMS
type: Class
subclass of: Quantification software
subclass of: Identification software
definition: OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000572

Axiom
annotated source: OpenMS
annotated property: definition
annotated target: OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.
database_cross_reference: PRIDE:PRIDE

Identification software
type: Class
definition: A software that perform peptide/protein identification using mass spectrometry data.
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000573

Axiom
annotated source: Identification software
annotated property: definition
annotated target: A software that perform peptide/protein identification using mass spectrometry data.
database_cross_reference: PRIDE:PRIDE

MaxQuant
type: Class
subclass of: Quantification software
subclass of: Identification software
definition: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000574

Axiom
annotated source: MaxQuant
annotated property: definition
annotated target: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.
database_cross_reference: PRIDE:PRIDE

precursor mass tolerance
type: Class
subclass of: Peptide item additional parameter
definition: Threshold at precursor level to compare experimental mass with theoretical mass
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000575

Axiom
annotated source: precursor mass tolerance
annotated property: definition
annotated target: Threshold at precursor level to compare experimental mass with theoretical mass
database_cross_reference: PRIDE:PRIDE

fragment mass tolerance
type: Class
subclass of: Peptide item additional parameter
definition: Threshold at fragment level to compare experimental mass with theoretical mass
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000576

Axiom
annotated source: fragment mass tolerance
annotated property: definition
annotated target: Threshold at fragment level to compare experimental mass with theoretical mass
database_cross_reference: PRIDE:PRIDE

file uri
type: Class
subclass of: Experiment additional parameter
definition: URI of one external file associated to the PRIDE experiment (maybe through a PX submission)
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000577

Axiom
annotated source: file uri
annotated property: definition
annotated target: URI of one external file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: PRIDE:PRIDE

Bound fraction
type: Class
subclass of: Depletion
definition: The bound fraction after a depletion process
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000578

Axiom
annotated source: Bound fraction
annotated property: definition
annotated target: The bound fraction after a depletion process
database_cross_reference: PRIDE:PRIDE

Depleted fraction
type: Class
subclass of: Depletion
definition: The depleted fraction after a depletion process
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000579

Axiom
annotated source: Depleted fraction
annotated property: definition
annotated target: The depleted fraction after a depletion process
database_cross_reference: PRIDE:PRIDE

TMT131N
type: Class
subclass of: TMT
definition: TMT131N
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000580

Axiom
annotated source: TMT131N
annotated property: definition
annotated target: TMT131N
database_cross_reference: PRIDE:PRIDE

TMT131C
type: Class
subclass of: TMT
definition: TMT131C
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000581

Axiom
annotated source: TMT131C
annotated property: definition
annotated target: TMT131C
database_cross_reference: PRIDE:PRIDE

TMT132N
type: Class
subclass of: TMT
definition: TMT132N
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000582

Axiom
annotated source: TMT132N
annotated property: definition
annotated target: TMT132N
database_cross_reference: PRIDE:PRIDE

TMT132C
type: Class
subclass of: TMT
definition: TMT132C
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000583

Axiom
annotated source: TMT132C
annotated property: definition
annotated target: TMT132C
database_cross_reference: PRIDE:PRIDE

Experimental design file URI
type: Class
subclass of: Associated file URI
subclass of: file uri
definition: Experimental design file URI
created by: yperez
creation date: 2019-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000584

Axiom
annotated source: Experimental design file URI
annotated property: definition
annotated target: Experimental design file URI
database_cross_reference: PRIDE:PRIDE

Enrichment
type: Class
subclass of: Protocol step description additional parameter
definition: Enrichment of specific post-translational modifications
has_obo_namespace: PRIDE
id: PRIDE:0000585

Axiom
annotated source: Enrichment
annotated property: definition
annotated target: Enrichment of specific post-translational modifications
database_cross_reference: PRIDE:PRIDE

Enrichment method
type: Class
subclass of: Enrichment
definition: Enrichment method Enrichment of specific post-translational modifications
has_obo_namespace: PRIDE
id: PRIDE:0000586

Axiom
annotated source: Enrichment method
annotated property: definition
annotated target: Enrichment method Enrichment of specific post-translational modifications
database_cross_reference: PRIDE:PRIDE

IMAC
type: Class
subclass of: Enrichment method
definition: The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides
has_obo_namespace: PRIDE
id: PRIDE:0000587

Axiom
annotated source: IMAC
annotated property: definition
annotated target: The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides
database_cross_reference: PRIDE:PRIDE

TIO2
type: Class
subclass of: Enrichment method
definition: Titanium dioxide (TiO2) has very high affinity for phosphopeptides and in recent years it has become one of the most popular methods for phosphopeptide enrichment from complex biological samples
has_obo_namespace: PRIDE
id: PRIDE:0000588

Axiom
annotated source: TIO2
annotated property: definition
annotated target: Titanium dioxide (TiO2) has very high affinity for phosphopeptides and in recent years it has become one of the most popular methods for phosphopeptide enrichment from complex biological samples
database_cross_reference: PRIDE:PRIDE

EThcD
type: Class
subclass of: dissociation method
subclass of: MS2 dissociation method
subclass of: MS3 dissociation method
definition: A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy).
has_obo_namespace: PRIDE
id: PRIDE:0000589

Axiom
annotated source: EThcD
annotated property: definition
annotated target: A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy).
database_cross_reference: PRIDE:PRIDE

HCD
type: Class
subclass of: dissociation method
subclass of: MS2 dissociation method
subclass of: MS3 dissociation method
definition: beam-type collision-induced dissociation
has_obo_namespace: PRIDE
id: PRIDE:0000590

Axiom
annotated source: HCD
annotated property: definition
annotated target: beam-type collision-induced dissociation
database_cross_reference: PRIDE:PRIDE

CID
type: Class
subclass of: dissociation method
subclass of: MS2 dissociation method
subclass of: MS3 dissociation method
definition: collision-induced dissociation
has_obo_namespace: PRIDE
id: PRIDE:0000591

Axiom
annotated source: CID
annotated property: definition
annotated target: collision-induced dissociation
database_cross_reference: PRIDE:PRIDE

ETciD
type: Class
subclass of: dissociation method
subclass of: MS2 dissociation method
subclass of: MS3 dissociation method
definition: ETD with supplemental activation
has_exact_synonym: ETcaD
has_obo_namespace: PRIDE
id: PRIDE:0000592

Axiom
annotated source: ETciD
annotated property: definition
annotated target: ETD with supplemental activation
database_cross_reference: PRIDE:PRIDE

CID collision energy
type: Class
subclass of: collision energy
subclass of: Restriction
  on property: part_of
  some values from: CID
definition: CID collision energy
has_obo_namespace: PRIDE
id: PRIDE:0000593

Axiom
annotated source: CID collision energy
annotated property: definition
annotated target: CID collision energy
database_cross_reference: PRIDE:PRIDE

HCD collision energy
type: Class
subclass of: collision energy
subclass of: Restriction
  on property: part_of
  some values from: HCD
definition: HCD collision energy
has_obo_namespace: PRIDE
id: PRIDE:0000594

Axiom
annotated source: HCD collision energy
annotated property: definition
annotated target: HCD collision energy
database_cross_reference: PRIDE:PRIDE

EThcD collision energy
type: Class
subclass of: collision energy
subclass of: Restriction
  on property: part_of
  some values from: EThcD
definition: EThcD collision energy
has_obo_namespace: PRIDE
id: PRIDE:0000595

Axiom
annotated source: EThcD collision energy
annotated property: definition
annotated target: EThcD collision energy
database_cross_reference: PRIDE:PRIDE

ETciD collision energy
type: Class
subclass of: collision energy
subclass of: Restriction
  on property: part_of
  some values from: ETciD
definition: ETciD collision energy
has_obo_namespace: PRIDE
id: PRIDE:0000596

Axiom
annotated source: ETciD collision energy
annotated property: definition
annotated target: ETciD collision energy
database_cross_reference: PRIDE:PRIDE

metabolic label
type: Class
subclass of: Label
definition: metabolic label
created by: yperez
creation date: 2020-05-12T11:58:52Z
has_obo_namespace: PRIDE
id: PRIDE:0000597

Axiom
annotated source: metabolic label
annotated property: definition
annotated target: metabolic label
database_cross_reference: PRIDE:PRIDE

Alkylation reagent
type: Class
subclass of: Alkylation
definition: The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000598

Axiom
annotated source: Alkylation reagent
annotated property: definition
annotated target: The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds
database_cross_reference: PRIDE:PRIDE

Iodoacetamide (IAA)
type: Class
subclass of: Alkylation reagent
definition: The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000599

Axiom
annotated source: Iodoacetamide (IAA)
annotated property: definition
annotated target: The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da
database_cross_reference: PRIDE:PRIDE

Chloroacetamide (ClAA)
type: Class
subclass of: Alkylation reagent
definition: The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000600

Axiom
annotated source: Chloroacetamide (ClAA)
annotated property: definition
annotated target: The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da
database_cross_reference: PRIDE:PRIDE

Iodoacetic acid (IAC)
type: Class
subclass of: Alkylation reagent
definition: The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000601

Axiom
annotated source: Iodoacetic acid (IAC)
annotated property: definition
annotated target: The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da
database_cross_reference: PRIDE:PRIDE

Chloroacetic acid (ClAC)
type: Class
subclass of: Alkylation reagent
definition: The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000602

Axiom
annotated source: Chloroacetic acid (ClAC)
annotated property: definition
annotated target: The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da
database_cross_reference: PRIDE:PRIDE

Acrylamide (AA)
type: Class
subclass of: Alkylation reagent
definition: The alkylation reagent acrylamide (or acrylic amide) with the chemical formula - C3H5NO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 24) - 71.037 Da
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000603

Axiom
annotated source: Acrylamide (AA)
annotated property: definition
annotated target: The alkylation reagent acrylamide (or acrylic amide) with the chemical formula - C3H5NO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 24) - 71.037 Da
database_cross_reference: PRIDE:PRIDE

4-Vinylpyridine (4-VP)
type: Class
subclass of: Alkylation reagent
definition: The derivative of pyridine with a vinyl group in the 4-position with the chemical formula - C7H7N. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 31) - 105.058 Da
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000604

Axiom
annotated source: 4-Vinylpyridine (4-VP)
annotated property: definition
annotated target: The derivative of pyridine with a vinyl group in the 4-position with the chemical formula - C7H7N. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 31) - 105.058 Da
database_cross_reference: PRIDE:PRIDE

Methyl methanethiosulfonate (MMTS)
type: Class
subclass of: Alkylation reagent
definition: The alkylation reagent that can reversibly sulfenylate thiol-containing molecules, chemical formula - C2H6O2S2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 39) - 45.988 Da
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000605

Axiom
annotated source: Methyl methanethiosulfonate (MMTS)
annotated property: definition
annotated target: The alkylation reagent that can reversibly sulfenylate thiol-containing molecules, chemical formula - C2H6O2S2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 39) - 45.988 Da
database_cross_reference: PRIDE:PRIDE

N-ethylmaleimide (NEM)
type: Class
subclass of: Alkylation reagent
definition: The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000606

Axiom
annotated source: N-ethylmaleimide (NEM)
annotated property: definition
annotated target: The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da
database_cross_reference: PRIDE:PRIDE

Reduction reagent
type: Class
subclass of: Reduction
definition: The chemical reagent that is used to break disulfide bonds in proteins
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000607

Axiom
annotated source: Reduction reagent
annotated property: definition
annotated target: The chemical reagent that is used to break disulfide bonds in proteins
database_cross_reference: PRIDE:PRIDE

Dithiothreitol (DTT)
type: Class
subclass of: Reduction reagent
definition: The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000608

Axiom
annotated source: Dithiothreitol (DTT)
annotated property: definition
annotated target: The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2
database_cross_reference: PRIDE:PRIDE

Tris(2-carboxyethyl)phosphine (TCEP)
type: Class
subclass of: Reduction reagent
definition: The reduction agent with chemincal formuls C9H15O6P
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000609

Axiom
annotated source: Tris(2-carboxyethyl)phosphine (TCEP)
annotated property: definition
annotated target: The reduction agent with chemincal formuls C9H15O6P
database_cross_reference: PRIDE:PRIDE

Beta-mercaptoethanol (BME)
type: Class
subclass of: Reduction reagent
definition: The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS
created by: lisavetasol
has_obo_namespace: PRIDE
id: PRIDE:0000610

Axiom
annotated source: Beta-mercaptoethanol (BME)
annotated property: definition
annotated target: The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS
database_cross_reference: PRIDE:PRIDE

SILAC light R:12C(6)14N(4)
type: Class
subclass of: SILAC light
created by: yperez
creation date: 2011-07-22T09:45:40Z
has_obo_namespace: PRIDE
id: PRIDE:0000611
comment: The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4)

SILAC light L:12C(6)
type: Class
subclass of: SILAC light
created by: yperez
creation date: 2011-07-22T09:45:40Z
has_obo_namespace: PRIDE
id: PRIDE:0000612
comment: The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6)

SILAC light K:12C(6)14N(2)
type: Class
subclass of: SILAC light
created by: yperez
creation date: 2011-07-22T09:45:40Z
has_obo_namespace: PRIDE
id: PRIDE:0000613
comment: The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2)

SILAC light P:12C(5)
type: Class
subclass of: SILAC light
created by: yperez
creation date: 2011-07-22T09:45:40Z
has_obo_namespace: PRIDE
id: PRIDE:0000614
comment: The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5)

SILAC heavy R:13C(6)15N(4)
type: Class
subclass of: SILAC heavy
created by: yperez
creation date: 2011-07-22T09:45:40Z
has_obo_namespace: PRIDE
id: PRIDE:0000615
comment: The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4)

SILAC heavy L:13C(6)
type: Class
subclass of: SILAC heavy
created by: yperez
creation date: 2011-07-22T09:45:40Z
has_obo_namespace: PRIDE
id: PRIDE:0000616
comment: The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6)

SILAC heavy K:13C(6)15N(2)
type: Class
subclass of: SILAC heavy
created by: yperez
creation date: 2011-07-22T09:45:40Z
has_obo_namespace: PRIDE
id: PRIDE:0000617
comment: The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2)

SILAC medium R:13C(6)14N(4)
type: Class
subclass of: SILAC medium
created by: yperez
creation date: 2011-07-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000618
comment: The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4).

SILAC medium K:13C(6)14N(2)
type: Class
subclass of: SILAC medium
created by: yperez
creation date: 2011-07-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000619
comment: The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2).

15N
type: Class
subclass of: metabolic label
created by: yperez
creation date: 2011-07-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000620
comment: Metabolic label 15N

13C
type: Class
subclass of: metabolic label
created by: yperez
creation date: 2011-07-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000621
comment: Metabolic label 13C

18O
type: Class
subclass of: metabolic label
created by: yperez
creation date: 2011-07-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000622
comment: Metabolic label 18O

original source name
type: Class
subclass of: Experiment additional parameter
created by: yperez
creation date: 2020-23-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000623
comment: Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics

SpectraCluster MaxRatio
type: Class
subclass of: Peptide search engine output parameter
created by: yperez
creation date: 2020-23-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000624
comment: Spectra Cluster Maximum Ratio for the cluster

NIST ProbCorr
type: Class
subclass of: Peptide search engine output parameter
created by: yperez
creation date: 2020-23-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000625
comment: NIST Probability Correlation

NIST Dotbest
type: Class
subclass of: Peptide search engine output parameter
created by: yperez
creation date: 2020-23-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000626
comment: NIST best dot product

Data-dependent acquisition
type: Class
subclass of: Bottom-up proteomics
created by: yperez
creation date: 2020-23-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000627
comment: Data-dependent acquisition

Parallel reaction monitoring
type: Class
subclass of: Bottom-up proteomics
created by: yperez
creation date: 2020-23-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000629
comment: Parallel Reaction Monitoring (PRM)

Selected reaction monitoring
type: Class
subclass of: Bottom-up proteomics
created by: yperez
creation date: 2020-23-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000630
comment: Selected reaction monitoring (SRM)

Mass spectrometry imaging
type: Class
subclass of: Mass spectrometry proteomics experimental strategy
created by: yperez
creation date: 2020-23-22T09:47:09Z
has_obo_namespace: PRIDE
id: PRIDE:0000631
comment: Mass spectrometry imaging

TMT133N
type: Class
subclass of: TMT
definition: TMT133N
created by: yperez
creation date: 2022-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000632

Axiom
annotated source: TMT133N
annotated property: definition
annotated target: TMT133N
database_cross_reference: PRIDE:PRIDE

TMT133C
type: Class
subclass of: TMT
definition: TMT133C
created by: yperez
creation date: 2022-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000633

Axiom
annotated source: TMT133C
annotated property: definition
annotated target: TMT133C
database_cross_reference: PRIDE:PRIDE

TMT134N
type: Class
subclass of: TMT
definition: TMT134N
created by: yperez
creation date: 2022-08-07T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000634

Axiom
annotated source: TMT134N
annotated property: definition
annotated target: TMT134N
database_cross_reference: PRIDE:PRIDE

Affinity proteomics
type: Class
subclass of: Experiment Type
created by: yperez
creation date: 2023-08-05T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000635
comment: The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes.

SomaScan affinity proteomics
type: Class
subclass of: Affinity proteomics
created by: yperez
creation date: 2023-08-05T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000636
comment: Refer to technologies like SomaScan that employ aptamers as the binding agents for protein detection. SomaScan utilizes Slow Off-rate Modified Aptamers (SOMAmers) for protein targeting and measurement.

Olink affinity proteomics
type: Class
subclass of: Affinity proteomics
created by: yperez
creation date: 2023-08-05T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000637
comment: Refer to technologies like Olink that utilize antibodies as the primary binding agents for protein detection. Olink's Proximity Extension Assay (PEA) technology relies on using antibody pairs to generate protein-specific signals.

Instrument model
type: Class
definition: Instrument model
created by: yperez
creation date: 2023-08-05T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000638

Axiom
annotated source: Instrument model
annotated property: definition
annotated target: Instrument model
database_cross_reference: PRIDE:PRIDE

Somalogic instrument model
type: Class
subclass of: Instrument model
definition: Somalogic instrument model
created by: yperez
creation date: 2023-08-05T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000639

Axiom
annotated source: Somalogic instrument model
annotated property: definition
annotated target: Somalogic instrument model
database_cross_reference: PRIDE:PRIDE

SomaScan assay v4.0
type: Class
subclass of: Somalogic instrument model
definition: SomaScan assay v4.0
created by: yperez
creation date: 2023-08-05T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000640

Axiom
annotated source: SomaScan assay v4.0
annotated property: definition
annotated target: SomaScan assay v4.0
database_cross_reference: PRIDE:PRIDE

SomaScan assay v4.1
type: Class
subclass of: Somalogic instrument model
definition: SomaScan assay v4.1
created by: yperez
creation date: 2023-08-05T15:21:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000641

Axiom
annotated source: SomaScan assay v4.1
annotated property: definition
annotated target: SomaScan assay v4.1
database_cross_reference: PRIDE:PRIDE

TMT134C
type: Class
subclass of: TMT
definition: TMT134C
created by: Roman-Si
creation date: 2023-10-05T11:44:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000642

Axiom
annotated source: TMT134C
annotated property: definition
annotated target: TMT134C
database_cross_reference: PRIDE:PRIDE

TMT135N
type: Class
subclass of: TMT
definition: TMT135N
created by: Roman-Si
creation date: 2023-10-05T11:44:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000643

Axiom
annotated source: TMT135N
annotated property: definition
annotated target: TMT135N
database_cross_reference: PRIDE:PRIDE

MS2 dissociation method
type: Class
subclass of: dissociation method
definition: Fragmentation method used for dissociation or fragmentation for MS2
created by: yperez
creation date: 2023-10-12T11:44:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000644

Axiom
annotated source: MS2 dissociation method
annotated property: definition
annotated target: Fragmentation method used for dissociation or fragmentation for MS2
database_cross_reference: PRIDE:PRIDE

MS3 dissociation method
type: Class
subclass of: dissociation method
definition: Fragmentation method used for dissociation or fragmentation for MS3
created by: yperez
creation date: 2023-10-12T11:44:19Z
has_obo_namespace: PRIDE
id: PRIDE:0000645

Axiom
annotated source: MS3 dissociation method
annotated property: definition
annotated target: Fragmentation method used for dissociation or fragmentation for MS3
database_cross_reference: PRIDE:PRIDE

MS3 mass analyzer
type: Class
subclass of: mass analyzer
definition: MS3 mass analyzer
created by: yperez
creation date: 2023-10-12T18:01:06Z
has_obo_namespace: PRIDE
id: PRIDE:0000646

Axiom
annotated source: MS3 mass analyzer
annotated property: definition
annotated target: MS3 mass analyzer
database_cross_reference: PRIDE:PRIDE

Immunopeptidomics
type: Class
subclass of: Mass spectrometry proteomics experimental strategy
subclass of: Experiment Type
created by: yperez
has_obo_namespace: PRIDE
id: PRIDE:0000649
comment: Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome.

diaPASEF
type: Class
subclass of: Data-independent acquisition
definition: Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825
created by: yperez
has_obo_namespace: PRIDE
id: PRIDE:0000650

Axiom
annotated source: diaPASEF
annotated property: definition
annotated target: Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825
database_cross_reference: PRIDE:PRIDE

Absolute quantification
type: Class
subclass of: Quantification method
definition: Absolute quantification precisely measures the concentration of a specific analyte in a sample
created by: deepti
creation date: 2024-01-22T14:42:08Z
has_obo_namespace: PRIDE
id: PRIDE:0000651

Axiom
annotated source: Absolute quantification
annotated property: definition
annotated target: Absolute quantification precisely measures the concentration of a specific analyte in a sample
database_cross_reference: PRIDE:PRIDE

Relative quantification
type: Class
subclass of: Quantification method
definition: Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples
created by: deepti
creation date: 2024-01-23T16:25:25Z
has_obo_namespace: PRIDE
id: PRIDE:0000652

Axiom
annotated source: Relative quantification
annotated property: definition
annotated target: Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples
database_cross_reference: PRIDE:PRIDE

NPX
type: Class
subclass of: Relative quantification
definition: Normalized Protein eXpression
created by: deepti
creation date: 2024-01-23T16:25:25Z
has_obo_namespace: PRIDE
id: PRIDE:0000653

Axiom
annotated source: NPX
annotated property: definition
annotated target: Normalized Protein eXpression
database_cross_reference: PRIDE:PRIDE

Olink instrument model
type: Class
subclass of: Instrument model
definition: Olink instrument model
created by: deepti
creation date: 2024-01-30T15:45:45Z
has_obo_namespace: PRIDE
id: PRIDE:0000654

Axiom
annotated source: Olink instrument model
annotated property: definition
annotated target: Olink instrument model
database_cross_reference: PRIDE:PRIDE

Olink Target 96
type: Class
subclass of: Olink instrument model
definition: Olink Target 96
created by: deepti
creation date: 2024-01-30T15:55:50Z
has_obo_namespace: PRIDE
id: PRIDE:0000655

Axiom
annotated source: Olink Target 96
annotated property: definition
annotated target: Olink Target 96
database_cross_reference: PRIDE:PRIDE

Olink Explore 1536
type: Class
subclass of: Olink instrument model
definition: Olink Explore 1536
created by: deepti
creation date: 2024-01-30T15:55:50Z
has_obo_namespace: PRIDE
id: PRIDE:0000656

Axiom
annotated source: Olink Explore 1536
annotated property: definition
annotated target: Olink Explore 1536
database_cross_reference: PRIDE:PRIDE

Olink Explore 3072
type: Class
subclass of: Olink instrument model
definition: Olink Explore 3072
created by: deepti
creation date: 2024-01-30T15:55:50Z
has_obo_namespace: PRIDE
id: PRIDE:0000657

Axiom
annotated source: Olink Explore 3072
annotated property: definition
annotated target: Olink Explore 3072
database_cross_reference: PRIDE:PRIDE

Olink Explore 384
type: Class
subclass of: Olink instrument model
definition: Olink Explore 384
created by: deepti
creation date: 2024-01-30T15:55:50Z
has_obo_namespace: PRIDE
id: PRIDE:0000658

Axiom
annotated source: Olink Explore 384
annotated property: definition
annotated target: Olink Explore 384
database_cross_reference: PRIDE:PRIDE