Proteomics Identification Database Ontology
type: Ontology
version IRI: pride.owl
imports: chmo.owl
imports: efo.owl
IAO_0000700: human gut
IAO_0000700: soil
IAO_0000700: water
creator: Deepti Jaiswal Kundu
creator: Nithu Sara John
creator: Yasset Perez-Riverol
description: Proteomics Identification Database Ontology, terms describing proteomics data and experimental metadata
homepage: https://github.com/PRIDE-Archive/pride-ontology
license: https://creativecommons.org/licenses/by/4.0/
namespace-id-rule: * PRIDE:$sequence(7,0,9999999)$
date: 14:01:2026 10:00
default-namespace: PRIDE
has_obo_format_version: 1.4
saved-by: Yasset Perez-Riverol
comment: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
comment: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/
comment: URL: http://purl.obolibrary.org/obo/pride/pride_cv.obo

definition
type: AnnotationProperty

namespace-id-rule
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

id
type: AnnotationProperty

diet
type: Class
definition: The regular course of eating and drinking adopted by a person or animal.
has_obo_namespace: PRIDE
id: EFO:0002755

Axiom
annotated source: diet
annotated property: definition
annotated target: The regular course of eating and drinking adopted by a person or animal.
database_cross_reference: EFO:EFO

body weights and measures
type: Class
definition: Measurements of the height, weight, length, area, etc., of the human and animal body or its parts.
has_obo_namespace: PRIDE
id: EFO:0004324

Axiom
annotated source: body weights and measures
annotated property: definition
annotated target: Measurements of the height, weight, length, area, etc., of the human and animal body or its parts.
database_cross_reference: EFO:EFO

genomic measurement
type: Class
definition: A quantification of some aspect of the genome, e.g. copy number variation at some locus.
has_obo_namespace: PRIDE
id: EFO:0004554

Axiom
annotated source: genomic measurement
annotated property: definition
annotated target: A quantification of some aspect of the genome, e.g. copy number variation at some locus.
database_cross_reference: EFO:EFO

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
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
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

Anatomic Structure, System, or Substance
type: Class
definition: A human biological structure, fluid or other substance; excludes single molecular entities.
has_obo_namespace: PRIDE
id: NCIT:C12219

Axiom
annotated source: Anatomic Structure, System, or Substance
annotated property: definition
annotated target: A human biological structure, fluid or other substance; excludes single molecular entities.
NCIT P378: NCI

Healthcare Activity
type: Class
definition: The actions of prevention, treatment, and management of illness and the preservation of mental and physical well-being through the services offered by the medical and allied health professions.
has_obo_namespace: PRIDE
id: NCIT:C16205

Axiom
annotated source: Healthcare Activity
annotated property: definition
annotated target: The actions of prevention, treatment, and management of illness and the preservation of mental and physical well-being through the services offered by the medical and allied health professions.
NCIT P378: NCI

Occupation or Discipline
type: Class
definition: A grouping of occupations and fields of study.
has_obo_namespace: PRIDE
id: NCIT:C19160

Axiom
annotated source: Occupation or Discipline
annotated property: definition
annotated target: A grouping of occupations and fields of study.
NCIT P378: NCI

Property or Attribute
type: Class
definition: A distinguishing quality or prominent aspect of a person, object, action, process, or substance.
has_obo_namespace: PRIDE
id: NCIT:C20189

Axiom
annotated source: Property or Attribute
annotated property: definition
annotated target: A distinguishing quality or prominent aspect of a person, object, action, process, or substance.
NCIT P378: NCI

Code
type: Class
definition: A symbol or combination of symbols which is assigned to the members of a collection.
has_obo_namespace: PRIDE
id: NCIT:C25162

Axiom
annotated source: Code
annotated property: definition
annotated target: A symbol or combination of symbols which is assigned to the members of a collection.
NCIT P378: NCI

Temperature
type: Class
definition: A measure of the average kinetic energy of a system of particles.
has_obo_namespace: PRIDE
id: NCIT:C25206

Axiom
annotated source: Temperature
annotated property: definition
annotated target: A measure of the average kinetic energy of a system of particles.
NCIT P378: NCI

Height
type: Class
definition: The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension.
has_obo_namespace: PRIDE
id: NCIT:C25347

Axiom
annotated source: Height
annotated property: definition
annotated target: The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension.
NCIT P378: NCI

Characteristic
type: Class
subclass of: Property or Attribute
definition: The distinguishing qualities or prominent aspect of a person, object, action, process, or substance.
has_obo_namespace: PRIDE
id: NCIT:C25447

Axiom
annotated source: Characteristic
annotated property: definition
annotated target: The distinguishing qualities or prominent aspect of a person, object, action, process, or substance.
NCIT P378: NCI

Data Field
type: Class
definition: An area of database record, or graphical user interface form, into which a particular item of data is entered.
has_obo_namespace: PRIDE
id: NCIT:C25507

Axiom
annotated source: Data Field
annotated property: definition
annotated target: An area of database record, or graphical user interface form, into which a particular item of data is entered.
NCIT P378: NCI

Log
type: Class
definition: A written record of events.
has_obo_namespace: PRIDE
id: NCIT:C45279

Axiom
annotated source: Log
annotated property: definition
annotated target: A written record of events.
NCIT P378: NCI

Content Creation date
type: Class
subclass of: File Properties
definition: The date on which data creation began [NCI]
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

Meal
type: Class
definition: Any of the occasions for eating food that occur by custom or habit at more or less fixed times.
has_obo_namespace: PRIDE
id: NCIT:C80248

Axiom
annotated source: Meal
annotated property: definition
annotated target: Any of the occasions for eating food that occur by custom or habit at more or less fixed times.
NCIT P378: NCI

Reference additional parameter
type: Class
subclass of: BFO_0000001
definition: Root node for terms relating to Reference additional parameters
has_obo_namespace: PRIDE
id: PRIDE:0000000

Axiom
annotated source: Reference additional parameter
annotated property: definition
annotated target: Root node for terms relating to Reference additional parameters
database_cross_reference: PRIDE:PRIDE

Protocol step description additional parameter
type: Class
subclass of: BFO_0000001
definition: Root node for terms relating to the description of a protocol as ordered steps
has_obo_namespace: PRIDE
id: PRIDE:0000001

Axiom
annotated source: Protocol step description additional parameter
annotated property: definition
annotated target: Root node for terms relating to the description of a protocol as ordered steps
database_cross_reference: PRIDE:PRIDE

ModificationItem additional parameter
type: Class
subclass of: BFO_0000001
definition: Root node for terms relating to the description of a ModificationItem
has_obo_namespace: PRIDE
id: PRIDE:0000002

Axiom
annotated source: ModificationItem additional parameter
annotated property: definition
annotated target: Root node for terms relating to the description of a ModificationItem
database_cross_reference: PRIDE:PRIDE

Peptide item additional parameter
type: Class
subclass of: BFO_0000001
definition: Root node for terms relating to the description of a PeptideItem
has_obo_namespace: PRIDE
id: PRIDE:0000003

Axiom
annotated source: Peptide item additional parameter
annotated property: definition
annotated target: Root node for terms relating to the description of a PeptideItem
database_cross_reference: PRIDE:PRIDE

Identification additional parameter
type: Class
subclass of: BFO_0000001
definition: Root node for terms relating to the description of an Identification
has_obo_namespace: PRIDE
id: PRIDE:0000004

Axiom
annotated source: Identification additional parameter
annotated property: definition
annotated target: Root node for terms relating to the description of an Identification
database_cross_reference: PRIDE:PRIDE

Gel additional parameter
type: Class
subclass of: BFO_0000001
definition: Root node for terms relating to the description of a Gel parameter
has_obo_namespace: PRIDE
id: PRIDE:0000005

Axiom
annotated source: Gel additional parameter
annotated property: definition
annotated target: Root node for terms relating to the description of a Gel parameter
database_cross_reference: PRIDE:PRIDE

Experiment additional parameter
type: Class
subclass of: BFO_0000001
definition: Root node for terms relating to the description of an Experiment
has_obo_namespace: PRIDE
id: PRIDE:0000006

Axiom
annotated source: Experiment additional parameter
annotated property: definition
annotated target: Root node for terms relating to the description of an Experiment
database_cross_reference: PRIDE:PRIDE

SearchEngineVersion
type: Class
subclass of: BFO_0000001
definition: Version number or identifier for search engine
has_obo_namespace: PRIDE
id: PRIDE:0000007

Axiom
annotated source: SearchEngineVersion
annotated property: definition
annotated target: Version number or identifier for search engine
database_cross_reference: PRIDE:PRIDE

Protein search engine output parameter
type: Class
subclass of: Identification additional parameter
definition: Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification
has_obo_namespace: PRIDE
id: PRIDE:0000008

Axiom
annotated source: Protein search engine output parameter
annotated property: definition
annotated target: Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification
database_cross_reference: PRIDE:PRIDE

Ion mass tolerance
type: Class
subclass of: Protein search engine output parameter
subclass of: Peptide search engine output parameter
definition: Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass
has_obo_namespace: PRIDE
id: PRIDE:0000009

Axiom
annotated source: Ion mass tolerance
annotated property: definition
annotated target: Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass
database_cross_reference: PRIDE:PRIDE

Precursor ion mass tolerance
type: Class
subclass of: Ion mass tolerance
definition: Precursor ion mass tolerance defines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches
has_obo_namespace: PRIDE
id: PRIDE:0000010

Axiom
annotated source: Precursor ion mass tolerance
annotated property: definition
annotated target: Precursor ion mass tolerance defines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches
database_cross_reference: PRIDE:PRIDE

MS2 ion mass tolerance
type: Class
subclass of: Ion mass tolerance
definition: MS2 ion mass tolerance refers to the acceptable deviation range between the experimentally measured fragment ion masses and their theoretical values during the identification of peptides and proteins in tandem mass spectrometry (MS/MS)
has_obo_namespace: PRIDE
id: PRIDE:0000011

Axiom
annotated source: MS2 ion mass tolerance
annotated property: definition
annotated target: MS2 ion mass tolerance refers to the acceptable deviation range between the experimentally measured fragment ion masses and their theoretical values during the identification of peptides and proteins in tandem mass spectrometry (MS/MS)
database_cross_reference: PRIDE:PRIDE

Delta Cn
type: Class
subclass of: Protein search engine output parameter
subclass of: Sequest
subclass of: Peptide search engine output parameter
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
definition: A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data
has_obo_namespace: PRIDE
id: PRIDE:0000013

Axiom
annotated source: X correlation
annotated property: definition
annotated target: A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data
database_cross_reference: PRIDE:PRIDE

X correlation (+1)
type: Class
subclass of: X correlation
definition: XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST
has_obo_namespace: PRIDE
id: PRIDE:0000014

Axiom
annotated source: X correlation (+1)
annotated property: definition
annotated target: XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST
database_cross_reference: PRIDE:PRIDE

X correlation (+2)
type: Class
subclass of: X correlation
definition: XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics
has_obo_namespace: PRIDE
id: PRIDE:0000015

Axiom
annotated source: X correlation (+2)
annotated property: definition
annotated target: XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics
database_cross_reference: PRIDE:PRIDE

X correlation (+3)
type: Class
subclass of: X correlation
definition: XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis
has_obo_namespace: PRIDE
id: PRIDE:0000016

Axiom
annotated source: X correlation (+3)
annotated property: definition
annotated target: XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis
database_cross_reference: PRIDE:PRIDE

Sample description additional parameter
type: Class
subclass of: BFO_0000001
definition: Root term for parameters in the context of ExperimentCollection
has_obo_namespace: PRIDE
id: PRIDE:0000017

Axiom
annotated source: Sample description additional parameter
annotated property: definition
annotated target: Root term for parameters in the context of ExperimentCollection
database_cross_reference: PRIDE:PRIDE

Disease free
type: Class
subclass of: Sample description additional parameter
definition: 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
has_obo_namespace: PRIDE
id: PRIDE:0000018

Axiom
annotated source: Disease free
annotated property: definition
annotated target: 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
database_cross_reference: PRIDE:PRIDE

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
definition: Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins
has_obo_namespace: PRIDE
id: PRIDE:0000025

Axiom
annotated source: Reduction
annotated property: definition
annotated target: Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins
database_cross_reference: PRIDE:PRIDE

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
subclass of: Protocol step description additional parameter
definition: Valid values for cvLabel entries referencing external database or ontology
has_obo_namespace: PRIDE
id: PRIDE:0000028

Axiom
annotated source: Cv Label
annotated property: definition
annotated target: Valid values for cvLabel entries referencing external database or ontology
database_cross_reference: PRIDE:PRIDE

PubMed
type: Class
subclass of: Cv Label
definition: PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)
has_obo_namespace: PRIDE
id: PRIDE:0000029

Axiom
annotated source: PubMed
annotated property: definition
annotated target: PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: PRIDE
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing PRIDE
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: GO
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing GO
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: MeSH
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH)
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: NEWT
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: PSI
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing the PSI ontology
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: UNIMOD
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing UNIMOD
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: RESID
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing RESID
database_cross_reference: PRIDE:PRIDE

Staining
type: Class
subclass of: Protocol step description additional parameter
definition: A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope
has_obo_namespace: PRIDE
id: PRIDE:0000037

Axiom
annotated source: Staining
annotated property: definition
annotated target: A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: ISBN
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing ISBN
database_cross_reference: PRIDE:PRIDE

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
definition: This CV term should be used in association with a value that is a free-text description of the experiment
has_obo_namespace: PRIDE
id: PRIDE:0000040

Axiom
annotated source: Experiment description
annotated property: definition
annotated target: This CV term should be used in association with a value that is a free-text description of the experiment
database_cross_reference: PRIDE:PRIDE

Search database protein sequence
type: Class
subclass of: Identification additional parameter
definition: Database used to search the protein sequence
has_obo_namespace: PRIDE
id: PRIDE:0000041

Axiom
annotated source: Search database protein sequence
annotated property: definition
annotated target: Database used to search the protein sequence
database_cross_reference: PRIDE:PRIDE

DOI
type: Class
subclass of: Cv Label
definition: The DOI system provides a persistent link to the journal's location on the internet, even if the URL changes
has_obo_namespace: PRIDE
id: PRIDE:0000042

Axiom
annotated source: DOI
annotated property: definition
annotated target: The DOI system provides a persistent link to the journal's location on the internet, even if the URL changes
database_cross_reference: PRIDE:PRIDE

FIX
type: Class
subclass of: Cv Label
definition: Valid value for the cvLabel entry referencing FIX
has_obo_namespace: PRIDE
id: PRIDE:0000043

Axiom
annotated source: FIX
annotated property: definition
annotated target: Valid value for the cvLabel entry referencing FIX
database_cross_reference: PRIDE:PRIDE

Search algorithm
type: Class
subclass of: Identification additional parameter
definition: A method used to retrieve specific data from a collection of data, based on a given criterion
has_obo_namespace: PRIDE
id: PRIDE:0000044

Axiom
annotated source: Search algorithm
annotated property: definition
annotated target: A method used to retrieve specific data from a collection of data, based on a given criterion
database_cross_reference: PRIDE:PRIDE

Sequest
type: Class
subclass of: Search algorithm
subclass of: Identification software
definition: Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics
has_obo_namespace: PRIDE
id: PRIDE:0000045

Axiom
annotated source: Sequest
annotated property: definition
annotated target: Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics
database_cross_reference: PRIDE:PRIDE

Mascot
type: Class
subclass of: Search algorithm
subclass of: Quantification software
subclass of: Identification software
definition: Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics
has_obo_namespace: PRIDE
id: PRIDE:0000046

Axiom
annotated source: Mascot
annotated property: definition
annotated target: Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics
database_cross_reference: PRIDE:PRIDE

X
type: Class
subclass of: Search algorithm
subclass of: Identification software
definition: X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics
has_obo_namespace: PRIDE
id: PRIDE:0000047

Axiom
annotated source: X
annotated property: definition
annotated target: X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics
database_cross_reference: PRIDE:PRIDE

Output parameter
type: Class
subclass of: Identification additional parameter
definition: Output parameters in mass spectrometry search engines refer to the results and metrics provided after analyzing the experimental MS/MS spectra and comparing them to theoretical spectra from a protein database
has_obo_namespace: PRIDE
id: PRIDE:0000048

Axiom
annotated source: Output parameter
annotated property: definition
annotated target: Output parameters in mass spectrometry search engines refer to the results and metrics provided after analyzing the experimental MS/MS spectra and comparing them to theoretical spectra from a protein database
database_cross_reference: PRIDE:PRIDE

Peptide search engine output parameter
type: Class
subclass of: Peptide item additional parameter
definition: The output parameters of a peptide search engine refer to the key metrics, scores, and information that describe the results of matching experimental mass spectra (MS/MS) to theoretical spectra from a protein sequence database
has_obo_namespace: PRIDE
id: PRIDE:0000049

Axiom
annotated source: Peptide search engine output parameter
annotated property: definition
annotated target: The output parameters of a peptide search engine refer to the key metrics, scores, and information that describe the results of matching experimental mass spectra (MS/MS) to theoretical spectra from a protein sequence database
database_cross_reference: PRIDE:PRIDE

Rank/Sp
type: Class
subclass of: Sequest
subclass of: Peptide search engine output parameter
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: Sequest
subclass of: Peptide search engine output parameter
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: Sequest
subclass of: Peptide search engine output parameter
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: Sequest
subclass of: Peptide search engine output parameter
definition: Raw correlation score (Sequest)
has_obo_namespace: PRIDE
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: Sequest
subclass of: Peptide search engine output parameter
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: Sequest
subclass of: Peptide search engine output parameter
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
definition: A companion tool often used for processing and analyzing mass spectrometry data
has_obo_namespace: PRIDE
id: PRIDE:0000056

Axiom
annotated source: Bioworks
annotated property: definition
annotated target: A companion tool often used for processing and analyzing mass spectrometry data
database_cross_reference: PRIDE:PRIDE

Molecular weight
type: Class
subclass of: Protein search engine output parameter
subclass of: 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 score
type: Class
subclass of: Peptide search engine output parameter
subclass of: Bioworks
definition: Bioworks z score
has_obo_namespace: PRIDE
id: PRIDE:0000058

Axiom
annotated source: z score
annotated property: definition
annotated target: Bioworks z score
database_cross_reference: PRIDE:PRIDE

File
type: Class
subclass of: Peptide search engine output parameter
definition: File is a digital container used to store information on a computer or other electronic device
has_obo_namespace: PRIDE
id: PRIDE:0000059

Axiom
annotated source: File
annotated property: definition
annotated target: File is a digital container used to store information on a computer or other electronic device
database_cross_reference: PRIDE:PRIDE

Scan
type: Class
subclass of: Peptide search engine output parameter
definition: The scan refers to a unique identifier for a specific mass spectrum acquired during the experiment. Each scan corresponds to a particular fragmentation event in the mass spectrometer
has_obo_namespace: PRIDE
id: PRIDE:0000060

Axiom
annotated source: Scan
annotated property: definition
annotated target: The scan refers to a unique identifier for a specific mass spectrum acquired during the experiment. Each scan corresponds to a particular fragmentation event in the mass spectrometer
database_cross_reference: PRIDE:PRIDE

Coverage
type: Class
subclass of: Protein search engine output parameter
subclass of: Bioworks
definition: Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment
has_obo_namespace: PRIDE
id: PRIDE:0000061

Axiom
annotated source: Coverage
annotated property: definition
annotated target: Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment
database_cross_reference: PRIDE:PRIDE

rsp
type: Class
subclass of: Peptide search engine output parameter
subclass of: Bioworks
definition: It is used as a measure to assess the confidence of peptide identifications based on the output of peptide search engines such as Mascot, SEQUEST, X! Tandem, and others
has_obo_namespace: PRIDE
id: PRIDE:0000062

Axiom
annotated source: rsp
annotated property: definition
annotated target: It is used as a measure to assess the confidence of peptide identifications based on the output of peptide search engines such as Mascot, SEQUEST, X! Tandem, and others
database_cross_reference: PRIDE:PRIDE

Protein description line
type: Class
subclass of: Identification additional parameter
definition: A protein description line typically refers to a concise textual entry or annotation that provides information about a specific protein, such as its function, molecular characteristics, or role in biological processes
has_obo_namespace: PRIDE
id: PRIDE:0000063

Axiom
annotated source: Protein description line
annotated property: definition
annotated target: A protein description line typically refers to a concise textual entry or annotation that provides information about a specific protein, such as its function, molecular characteristics, or role in biological processes
database_cross_reference: PRIDE:PRIDE

Secondary accession
type: Class
subclass of: Identification additional parameter
definition: A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt
has_obo_namespace: PRIDE
id: PRIDE:0000064

Axiom
annotated source: Secondary accession
annotated property: definition
annotated target: A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt
database_cross_reference: PRIDE:PRIDE

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
definition: Referencing an experiment in scientific contexts, it's important to cite the original publication that reports the methods, results, or analysis involved in the experiment. Typically, this will involve citing the DOI (Digital Object Identifier), journal title, and other relevant details
has_obo_namespace: PRIDE
id: PRIDE:0000067

Axiom
annotated source: Reference reporting this experiment
annotated property: definition
annotated target: Referencing an experiment in scientific contexts, it's important to cite the original publication that reports the methods, results, or analysis involved in the experiment. Typically, this will involve citing the DOI (Digital Object Identifier), journal title, and other relevant details
database_cross_reference: PRIDE:PRIDE

Reference describing sample preparation
type: Class
subclass of: Reference additional parameter
definition: Referencing sample preparation for mass spectrometry or proteomics, the specific protocols and methods can vary depending on the type of analysis being conducted (e.g., quantitative proteomics, post-translational modification analysis, etc.)
has_obo_namespace: PRIDE
id: PRIDE:0000068

Axiom
annotated source: Reference describing sample preparation
annotated property: definition
annotated target: Referencing sample preparation for mass spectrometry or proteomics, the specific protocols and methods can vary depending on the type of analysis being conducted (e.g., quantitative proteomics, post-translational modification analysis, etc.)
database_cross_reference: PRIDE:PRIDE

Mascot score
type: Class
subclass of: Mascot
subclass of: Peptide search engine output parameter
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
definition: Search engine settings refer to the specific parameters and configurations that are used to optimize how a peptide or protein search engine identifies and matches experimental data (e.g., MS/MS spectra) to theoretical peptide sequences in a database
has_obo_namespace: PRIDE
id: PRIDE:0000071

Axiom
annotated source: Search engine setting
annotated property: definition
annotated target: Search engine settings refer to the specific parameters and configurations that are used to optimize how a peptide or protein search engine identifies and matches experimental data (e.g., MS/MS spectra) to theoretical peptide sequences in a database
database_cross_reference: PRIDE:PRIDE

Fixed modification setting
type: Class
subclass of: Search engine setting
definition: Fixed modifications refer to chemical modifications that are consistently present in all peptides of a given experiment, typically due to a sample preparation step or reagent used
has_obo_namespace: PRIDE
id: PRIDE:0000072

Axiom
annotated source: Fixed modification setting
annotated property: definition
annotated target: Fixed modifications refer to chemical modifications that are consistently present in all peptides of a given experiment, typically due to a sample preparation step or reagent used
database_cross_reference: PRIDE:PRIDE

Variable modification setting
type: Class
subclass of: Search engine setting
definition: Variable modifications refer to post-translational modifications (PTMs) or other chemical changes that can occur at specific amino acid residues but do not necessarily occur in every peptide or protein
has_obo_namespace: PRIDE
id: PRIDE:0000073

Axiom
annotated source: Variable modification setting
annotated property: definition
annotated target: Variable modifications refer to post-translational modifications (PTMs) or other chemical changes that can occur at specific amino acid residues but do not necessarily occur in every peptide or protein
database_cross_reference: PRIDE:PRIDE

Maximum Missed Cleavages Setting
type: Class
subclass of: Search engine setting
definition: The maximum missed cleavages setting refers to the number of missed enzyme cleavages allowed during peptide digestion
has_obo_namespace: PRIDE
id: PRIDE:0000074

Axiom
annotated source: Maximum Missed Cleavages Setting
annotated property: definition
annotated target: The maximum missed cleavages setting refers to the number of missed enzyme cleavages allowed during peptide digestion
database_cross_reference: PRIDE:PRIDE

Mass value type setting
type: Class
subclass of: Search engine setting
definition: It refers to how the mass of peptides, ions, or proteins is represented during a search or analysis
has_obo_namespace: PRIDE
id: PRIDE:0000075

Axiom
annotated source: Mass value type setting
annotated property: definition
annotated target: It refers to how the mass of peptides, ions, or proteins is represented during a search or analysis
database_cross_reference: PRIDE:PRIDE

Mass value type setting monoisotopic
type: Class
subclass of: Mass value type setting
definition: The monoisotopic mass setting refers to the mass of a molecule based on the lightest isotope of each element, typically the most abundant isotope, like carbon-12 (12C) for carbon, hydrogen-1 (1H) for hydrogen, and oxygen-16 (16O) for oxygen
has_obo_namespace: PRIDE
id: PRIDE:0000076

Axiom
annotated source: Mass value type setting monoisotopic
annotated property: definition
annotated target: The monoisotopic mass setting refers to the mass of a molecule based on the lightest isotope of each element, typically the most abundant isotope, like carbon-12 (12C) for carbon, hydrogen-1 (1H) for hydrogen, and oxygen-16 (16O) for oxygen
database_cross_reference: PRIDE:PRIDE

Mass value type setting average
type: Class
subclass of: Mass value type setting
definition: The average mass setting refers to the weighted average mass of all isotopes of each element present in a molecule
has_obo_namespace: PRIDE
id: PRIDE:0000077

Axiom
annotated source: Mass value type setting average
annotated property: definition
annotated target: The average mass setting refers to the weighted average mass of all isotopes of each element present in a molecule
database_cross_reference: PRIDE:PRIDE

Peptide mass tolerance setting
type: Class
subclass of: Search engine setting
definition: The peptide mass tolerance setting is a critical parameter used to define how much variation is acceptable between the observed mass of a peptide in the mass spectrum and the theoretical mass calculated from a database search
has_obo_namespace: PRIDE
id: PRIDE:0000078

Axiom
annotated source: Peptide mass tolerance setting
annotated property: definition
annotated target: The peptide mass tolerance setting is a critical parameter used to define how much variation is acceptable between the observed mass of a peptide in the mass spectrum and the theoretical mass calculated from a database search
database_cross_reference: PRIDE:PRIDE

Accurate mass mode setting
type: Class
subclass of: Search engine setting
definition: The Accurate Mass Mode setting refers to a mode of operation where the mass spectrometer is configured to measure the mass of ions with a higher degree of precision than in standard scanning modes
has_obo_namespace: PRIDE
id: PRIDE:0000079

Axiom
annotated source: Accurate mass mode setting
annotated property: definition
annotated target: The Accurate Mass Mode setting refers to a mode of operation where the mass spectrometer is configured to measure the mass of ions with a higher degree of precision than in standard scanning modes
database_cross_reference: PRIDE:PRIDE

Accurate mass mode setting true
type: Class
subclass of: Accurate mass mode setting
definition: Accurate mass mode setting typically refers to configuring the instrument to measure ion masses with high precision
has_obo_namespace: PRIDE
id: PRIDE:0000080

Axiom
annotated source: Accurate mass mode setting true
annotated property: definition
annotated target: Accurate mass mode setting typically refers to configuring the instrument to measure ion masses with high precision
database_cross_reference: PRIDE:PRIDE

Accurate mass mode setting false
type: Class
subclass of: Accurate mass mode setting
definition: Accurate mass mode setting is set to false in mass spectrometry, it means that the instrument will not prioritize high-resolution mass measurements
has_obo_namespace: PRIDE
id: PRIDE:0000081

Axiom
annotated source: Accurate mass mode setting false
annotated property: definition
annotated target: Accurate mass mode setting is set to false in mass spectrometry, it means that the instrument will not prioritize high-resolution mass measurements
database_cross_reference: PRIDE:PRIDE

Mass error type setting
type: Class
subclass of: Search engine setting
definition: The mass error type setting refers to how mass errors are reported and interpreted during data acquisition and analysis
has_obo_namespace: PRIDE
id: PRIDE:0000082

Axiom
annotated source: Mass error type setting
annotated property: definition
annotated target: The mass error type setting refers to how mass errors are reported and interpreted during data acquisition and analysis
database_cross_reference: PRIDE:PRIDE

mass error type setting ppm
type: Class
subclass of: Mass error type setting
definition: The mass error type is set to ppm (parts per million), it specifies that the acceptable mass error is calculated relative to the theoretical mass of the ion, and it is expressed as parts per million (ppm)
has_obo_namespace: PRIDE
id: PRIDE:0000083

Axiom
annotated source: mass error type setting ppm
annotated property: definition
annotated target: The mass error type is set to ppm (parts per million), it specifies that the acceptable mass error is calculated relative to the theoretical mass of the ion, and it is expressed as parts per million (ppm)
database_cross_reference: PRIDE:PRIDE

mass error type setting mmu
type: Class
subclass of: Mass error type setting
definition: Mass errors refer to discrepancies in the measured mass of ions compared to their theoretical or expected mass values
has_obo_namespace: PRIDE
id: PRIDE:0000084

Axiom
annotated source: mass error type setting mmu
annotated property: definition
annotated target: Mass errors refer to discrepancies in the measured mass of ions compared to their theoretical or expected mass values
database_cross_reference: PRIDE:PRIDE

mass error type setting percent
type: Class
subclass of: Mass error type setting
definition: Mass error type setting percent refers to the percentage of mass error in the measured mass-to-charge ratio (m/z) compared to the expected or theoretical value
has_obo_namespace: PRIDE
id: PRIDE:0000085

Axiom
annotated source: mass error type setting percent
annotated property: definition
annotated target: Mass error type setting percent refers to the percentage of mass error in the measured mass-to-charge ratio (m/z) compared to the expected or theoretical value
database_cross_reference: PRIDE:PRIDE

mass error type setting Daltons
type: Class
subclass of: Mass error type setting
definition: Mass error type daltons, how the discrepancy between the measured and expected mass is expressed in absolute units of mass (daltons), rather than as a percentage
has_obo_namespace: PRIDE
id: PRIDE:0000086

Axiom
annotated source: mass error type setting Daltons
annotated property: definition
annotated target: Mass error type daltons, how the discrepancy between the measured and expected mass is expressed in absolute units of mass (daltons), rather than as a percentage
database_cross_reference: PRIDE:PRIDE

Protonated setting
type: Class
subclass of: Search engine setting
definition: Protonated setting refers to the protonation of a molecule or ion during the ionization process, particularly in positive ion mode
has_obo_namespace: PRIDE
id: PRIDE:0000087

Axiom
annotated source: Protonated setting
annotated property: definition
annotated target: Protonated setting refers to the protonation of a molecule or ion during the ionization process, particularly in positive ion mode
database_cross_reference: PRIDE:PRIDE

Protonated setting MH+
type: Class
subclass of: Protonated setting
definition: Protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton
has_obo_namespace: PRIDE
id: PRIDE:0000088

Axiom
annotated source: Protonated setting MH+
annotated property: definition
annotated target: Protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton
database_cross_reference: PRIDE;PRIDE

Protonated setting M-H-
type: Class
subclass of: Protonated setting
definition: Protonated setting M-H⁻ refers to the deprotonated molecular ion (also known as the negative ion form), where M represents the neutral molecule, and H⁻ signifies the loss of a proton (H⁺), resulting in a negatively charged ion
has_obo_namespace: PRIDE
id: PRIDE:0000090

Axiom
annotated source: Protonated setting M-H-
annotated property: definition
annotated target: Protonated setting M-H⁻ refers to the deprotonated molecular ion (also known as the negative ion form), where M represents the neutral molecule, and H⁻ signifies the loss of a proton (H⁺), resulting in a negatively charged ion
database_cross_reference: PRIDE:PRIDE

Rank
type: Class
subclass of: Peptide search engine output parameter
definition: Rank represents the quality or confidence of the peptide-spectrum match (PSM), with the rank value showing the best match and progressively lower-ranked results indicating less confident identifications
has_obo_namespace: PRIDE
id: PRIDE:0000091

Axiom
annotated source: Rank
annotated property: definition
annotated target: Rank represents the quality or confidence of the peptide-spectrum match (PSM), with the rank value showing the best match and progressively lower-ranked results indicating less confident identifications
database_cross_reference: PRIDE:PRIDE

All peptides matched
type: Class
subclass of: Peptide search engine output parameter
definition: The output of a peptide search engine where every peptide in a sample has been identified and matched against a database
has_obo_namespace: PRIDE
id: PRIDE:0000092

Axiom
annotated source: All peptides matched
annotated property: definition
annotated target: The output of a peptide search engine where every peptide in a sample has been identified and matched against a database
database_cross_reference: PRIDE:PRIDE

All peptides matched true
type: Class
subclass of: All peptides matched
definition: All peptides matched true is in a peptide search engine output (like Mascot, SEQUEST, X! Tandem, or Andromeda), it generally means that all detected peptide spectra were successfully matched to corresponding peptides in the protein database
has_obo_namespace: PRIDE
id: PRIDE:0000093

Axiom
annotated source: All peptides matched true
annotated property: definition
annotated target: All peptides matched true is in a peptide search engine output (like Mascot, SEQUEST, X! Tandem, or Andromeda), it generally means that all detected peptide spectra were successfully matched to corresponding peptides in the protein database
database_cross_reference: PRIDE:PRIDE

All peptides matched false
type: Class
subclass of: All peptides matched
definition: Some mass spectra from the experiment could not be linked to a known peptide sequence from the protein database
has_obo_namespace: PRIDE
id: PRIDE:0000094

Axiom
annotated source: All peptides matched false
annotated property: definition
annotated target: Some mass spectra from the experiment could not be linked to a known peptide sequence from the protein database
database_cross_reference: PRIDE:PRIDE

Masses matched
type: Class
subclass of: Peptide search engine output parameter
definition: Masses matched refers to the number (or percentage) of experimental mass-to-charge ratios (m/z) from a mass spectrum that were successfully matched to theoretical peptide masses in a protein database
has_obo_namespace: PRIDE
id: PRIDE:0000095

Axiom
annotated source: Masses matched
annotated property: definition
annotated target: Masses matched refers to the number (or percentage) of experimental mass-to-charge ratios (m/z) from a mass spectrum that were successfully matched to theoretical peptide masses in a protein database
database_cross_reference: PRIDE:PRIDE

Reported Chromosome
type: Class
subclass of: Identification additional parameter
definition: Reported chromosome is the chromosomal location of the protein or peptide that has been identified
has_obo_namespace: PRIDE
id: PRIDE:0000096

Axiom
annotated source: Reported Chromosome
annotated property: definition
annotated target: Reported chromosome is the chromosomal location of the protein or peptide that has been identified
database_cross_reference: PRIDE:PRIDE

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: 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: 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
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: 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

Axiom
annotated source: Identified by peptide mass fingerprint
annotated property: has_exact_synonym
annotated target: PMF
database_cross_reference: 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

Axiom
annotated source: Identified by peptide fragmentation
annotated property: has_exact_synonym
annotated target: PFF
database_cross_reference: PRIDE

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

Axiom
annotated source: iTRAQ reagent 114
annotated property: definition
annotated target: The name of the sample labelled with iTRAQ reagent 114
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ reagent 115
annotated property: definition
annotated target: The name of the sample labelled with iTRAQ reagent 115
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ reagent 116
annotated property: definition
annotated target: The name of the sample labelled with iTRAQ reagent 116
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ reagent 117
annotated property: definition
annotated target: The name of the sample labelled with iTRAQ reagent 117
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ intensity 114
annotated property: definition
annotated target: The intensity of the sample labelled with iTRAQ reagent 114
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ intensity 115
annotated property: definition
annotated target: The intensity of the sample labelled with iTRAQ reagent 115
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ intensity 116
annotated property: definition
annotated target: The intensity of the sample labelled with iTRAQ reagent 116
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ intensity 117
annotated property: definition
annotated target: The intensity of the sample labelled with iTRAQ reagent 117
database_cross_reference: PRIDE:PRIDE

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: Two Dimensional Polyacrylamide Gel Electrophoresis
subclass of: SDS PAGE
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: Two Dimensional Polyacrylamide Gel Electrophoresis
subclass of: SDS PAGE
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

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: 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

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

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

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: 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
definition: PepSplice precision refers to the accuracy of peptide-spectrum matches (PSMs) produced by the PepSplice search engine, a specialized tool used for the identification of peptides, particularly for novel or unexpected peptide sequences. Precision is a key metric used to assess the quality and reliability of search results in proteomics
has_obo_namespace: PRIDE
id: PRIDE:0000146

Axiom
annotated source: PepSplice precision
annotated property: definition
annotated target: PepSplice precision refers to the accuracy of peptide-spectrum matches (PSMs) produced by the PepSplice search engine, a specialized tool used for the identification of peptides, particularly for novel or unexpected peptide sequences. Precision is a key metric used to assess the quality and reliability of search results in proteomics
database_cross_reference: PRIDE:PRIDE

PepSplice false discovery rate
type: Class
subclass of: PepSplice
definition: PepSlice false discovery rate is a critical metric used to control the number of false positives (incorrect peptide-spectrum matches or PSMs) in the search results
has_obo_namespace: PRIDE
id: PRIDE:0000147

Axiom
annotated source: PepSplice false discovery rate
annotated property: definition
annotated target: PepSlice false discovery rate is a critical metric used to control the number of false positives (incorrect peptide-spectrum matches or PSMs) in the search results
database_cross_reference: PRIDE:PRIDE

PepSplice P-value
type: Class
subclass of: 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
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
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
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
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: Project
definition: Unique identifier of project
has_exact_synonym: Project Identifier
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

Axiom
annotated source: Project identifier
annotated property: has_exact_synonym
annotated target: Project Identifier
database_cross_reference: NCIT

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
definition: It refers to the process of identifying and characterizing molecules, especially proteins, peptides, metabolites, and small molecules, using mass spectrometry (MS) data
has_obo_namespace: PRIDE
id: PRIDE:0000158

Axiom
annotated source: MS search
annotated property: definition
annotated target: It refers to the process of identifying and characterizing molecules, especially proteins, peptides, metabolites, and small molecules, using mass spectrometry (MS) data
database_cross_reference: PRIDE:PRIDE

MS/MS search
type: Class
subclass of: Search type
definition: MS/MS Search refers to the process of identifying molecules (typically proteins, peptides, metabolites, or small molecules) using tandem mass spectrometry (MS/MS) data. Unlike simple mass spectrometry (MS1), MS/MS involves fragmenting precursor ions into smaller product ions, generating a detailed fragmentation pattern or spectra that can be used to identify the structure or sequence of the molecule
has_obo_namespace: PRIDE
id: PRIDE:0000159

Axiom
annotated source: MS/MS search
annotated property: definition
annotated target: MS/MS Search refers to the process of identifying molecules (typically proteins, peptides, metabolites, or small molecules) using tandem mass spectrometry (MS/MS) data. Unlike simple mass spectrometry (MS1), MS/MS involves fragmenting precursor ions into smaller product ions, generating a detailed fragmentation pattern or spectra that can be used to identify the structure or sequence of the molecule
database_cross_reference: PRIDE:PRIDE

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
definition: A nucleic acid sequence refers to the linear arrangement of nucleotides (the basic building blocks of DNA and RNA) in a specific order
has_obo_namespace: PRIDE
id: PRIDE:0000168

Axiom
annotated source: Nucleic acid sequence
annotated property: definition
annotated target: A nucleic acid sequence refers to the linear arrangement of nucleotides (the basic building blocks of DNA and RNA) in a specific order
database_cross_reference: PRIDE:PRIDE

Start position of the nucleic acid sequence on the chromosome
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
definition: The start position of a nucleic acid sequence on a chromosome refers to the location or coordinate where the sequence begins within the linear structure of a chromosome
has_obo_namespace: PRIDE
id: PRIDE:0000169

Axiom
annotated source: Start position of the nucleic acid sequence on the chromosome
annotated property: definition
annotated target: The start position of a nucleic acid sequence on a chromosome refers to the location or coordinate where the sequence begins within the linear structure of a chromosome
database_cross_reference: PRIDE:PRIDE

Stop position of the nucleic acid sequence on the chromosome
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
definition: The stop position of a nucleic acid sequence on a chromosome refers to the ending coordinate where the sequence finishes on the chromosome
has_obo_namespace: PRIDE
id: PRIDE:0000170

Axiom
annotated source: Stop position of the nucleic acid sequence on the chromosome
annotated property: definition
annotated target: The stop position of a nucleic acid sequence on a chromosome refers to the ending coordinate where the sequence finishes on the chromosome
database_cross_reference: PRIDE:PRIDE

funding reference
type: Class
subclass of: Reference additional parameter
definition: A funding reference is a formal acknowledgment of financial support provided by an organization, institution, or agency for a research project, study, or publication
has_obo_namespace: PRIDE
id: PRIDE:0000171

Axiom
annotated source: funding reference
annotated property: definition
annotated target: A funding reference is a formal acknowledgment of financial support provided by an organization, institution, or agency for a research project, study, or publication
database_cross_reference: PRIDE:PRIDE

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: 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

Axiom
annotated source: Isoelectric point
annotated property: has_exact_synonym
annotated target: pI
database_cross_reference: 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: X
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: X
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: X
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: X
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: X
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

Axiom
annotated source: Fragment Ion Annotation
annotated property: has_exact_synonym
annotated target: Product ion property
database_cross_reference: 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

Axiom
annotated source: product ion m/z
annotated property: has_exact_synonym
annotated target: Fragment ion mass
database_cross_reference: 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

Axiom
annotated source: product ion intensity
annotated property: has_exact_synonym
annotated target: Fragment ion intensity
database_cross_reference: 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

Axiom
annotated source: product ion mass error
annotated property: has_exact_synonym
annotated target: Fragment ion mass error
database_cross_reference: PRIDE

product ion retention time error
type: Class
subclass of: Fragment Ion Annotation
definition: Product ion 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: Product ion retention time error in minutes
database_cross_reference: PRIDE:PRIDE

Axiom
annotated source: product ion retention time error
annotated property: has_exact_synonym
annotated target: Fragment ion retention time error
database_cross_reference: 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

Axiom
annotated source: product ion type
annotated property: has_exact_synonym
annotated target: Fragment ion type
database_cross_reference: 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

Axiom
annotated source: y ion
annotated property: has_exact_synonym
annotated target: y fragment ion
database_cross_reference: 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

Axiom
annotated source: b ion
annotated property: has_exact_synonym
annotated target: b fragment ion
database_cross_reference: 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

Axiom
annotated source: b ion -NH3
annotated property: has_exact_synonym
annotated target: b fragment ion -NH3
database_cross_reference: 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

Axiom
annotated source: b ion -H2O
annotated property: has_exact_synonym
annotated target: b fragment ion -H2O
database_cross_reference: 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

Axiom
annotated source: y ion -H2O
annotated property: has_exact_synonym
annotated target: y fragment ion -H2O
database_cross_reference: 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

Axiom
annotated source: y ion -NH3
annotated property: has_exact_synonym
annotated target: y fragment ion -NH3
database_cross_reference: 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

Axiom
annotated source: in source ion
annotated property: has_exact_synonym
annotated target: In source fragment ion
database_cross_reference: PRIDE

Axiom
annotated source: in source ion
annotated property: has_exact_synonym
annotated target: In-source ion
database_cross_reference: 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

Axiom
annotated source: non-identified ion
annotated property: has_exact_synonym
annotated target: unidentified ion
database_cross_reference: 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

Axiom
annotated source: product ion charge
annotated property: has_exact_synonym
annotated target: Fragment ion charge
database_cross_reference: PRIDE

Heavy stable isotope label
type: Class
subclass of: Peptide item additional parameter
definition: A general term for any stable isotope method
has_obo_namespace: PRIDE
id: PRIDE:0000205

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
subclass of: Heavy stable isotope label
definition: Heavy stable isotope label residue
has_obo_namespace: PRIDE
id: PRIDE:0000206

Axiom
annotated source: Heavy stable isotope label residue
annotated property: definition
annotated target: Heavy stable isotope label residue
database_cross_reference: PRIDE:PRIDE

Light stable isotope label
type: Class
subclass of: Peptide item additional parameter
definition: Light stable isotope label
has_obo_namespace: PRIDE
id: PRIDE:0000207

Axiom
annotated source: Light stable isotope label
annotated property: definition
annotated target: Light stable isotope label
database_cross_reference: PRIDE:PRIDE

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

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: Parent 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: Parent retention time error in minutes
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

Axiom
annotated source: x ion
annotated property: has_exact_synonym
annotated target: x fragment ion
database_cross_reference: 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

Axiom
annotated source: x ion -H2O
annotated property: has_exact_synonym
annotated target: x fragment ion -H2O
database_cross_reference: 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

Axiom
annotated source: x ion -NH3
annotated property: has_exact_synonym
annotated target: x fragment ion -NH3
database_cross_reference: 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

Axiom
annotated source: z ion
annotated property: has_exact_synonym
annotated target: z fragment ion
database_cross_reference: 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

Axiom
annotated source: z ion -H2O
annotated property: has_exact_synonym
annotated target: z fragment ion -H2O
database_cross_reference: 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

Axiom
annotated source: z ion -NH3
annotated property: has_exact_synonym
annotated target: z fragment ion -NH3
database_cross_reference: 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

Axiom
annotated source: a ion
annotated property: has_exact_synonym
annotated target: a fragment ion
database_cross_reference: 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

Axiom
annotated source: a ion -H2O
annotated property: has_exact_synonym
annotated target: a fragment ion -H2O
database_cross_reference: 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

Axiom
annotated source: a ion -NH3
annotated property: has_exact_synonym
annotated target: A fragment ion -NH3
database_cross_reference: 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

Axiom
annotated source: c ion
annotated property: has_exact_synonym
annotated target: c fragment ion
database_cross_reference: 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

Axiom
annotated source: c ion -H2O
annotated property: has_exact_synonym
annotated target: c fragment ion -H2O
database_cross_reference: 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

Axiom
annotated source: c ion -NH3
annotated property: has_exact_synonym
annotated target: c fragment ion -NH3
database_cross_reference: 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

Axiom
annotated source: precursor ion type
annotated property: has_exact_synonym
annotated target: Parent ion type
database_cross_reference: 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

Axiom
annotated source: precursor ion -H2O
annotated property: has_exact_synonym
annotated target: Parent ion -H2O
database_cross_reference: 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

Axiom
annotated source: precursor ion -NH3
annotated property: has_exact_synonym
annotated target: Parent ion -NH3
database_cross_reference: 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

Axiom
annotated source: precursor ion
annotated property: has_exact_synonym
annotated target: Parent ion
database_cross_reference: PRIDE

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

Axiom
annotated source: iTRAQ reagent 113
annotated property: definition
annotated target: The name of the sample labelled with iTRAQ reagent 113
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ reagent 118
annotated property: definition
annotated target: The name of the sample labelled with iTRAQ reagent 118
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ reagent 119
annotated property: definition
annotated target: The name of the sample labelled with iTRAQ reagent 119
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ reagent 121
annotated property: definition
annotated target: The name of the sample labelled with iTRAQ reagent 121
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ intensity 113
annotated property: definition
annotated target: The intensity of the sample labelled with iTRAQ reagent 113
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ intensity 118
annotated property: definition
annotated target: The intensity of the sample labelled with iTRAQ reagent 118
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ intensity 119
annotated property: definition
annotated target: The intensity of the sample labelled with iTRAQ reagent 119
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: iTRAQ intensity 121
annotated property: definition
annotated target: The intensity of the sample labelled with iTRAQ reagent 121
database_cross_reference: PRIDE:PRIDE

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
definition: The SloMo score threshold for a valid modification location is a statistical cutoff used in mass spectrometry (MS/MS) to determine the confidence that a specific position within a peptide or protein is modified
has_obo_namespace: PRIDE
id: PRIDE:0000273

Axiom
annotated source: SloMo score threshold for valid modification location
annotated property: definition
annotated target: The SloMo score threshold for a valid modification location is a statistical cutoff used in mass spectrometry (MS/MS) to determine the confidence that a specific position within a peptide or protein is modified
database_cross_reference: PRIDE:PRIDE

MaxQuant percentage threshold for valid modification location
type: Class
subclass of: Search algorithm
definition: In MaxQuant, the percentage threshold for a valid modification location is typically based on the site probability for post-translational modification (PTM) localization. This probability indicates the confidence that a particular amino acid (residue) within a peptide is modified
has_obo_namespace: PRIDE
id: PRIDE:0000274

Axiom
annotated source: MaxQuant percentage threshold for valid modification location
annotated property: definition
annotated target: In MaxQuant, the percentage threshold for a valid modification location is typically based on the site probability for post-translational modification (PTM) localization. This probability indicates the confidence that a particular amino acid (residue) within a peptide is modified
database_cross_reference: PRIDE:PRIDE

SloMo score
type: Class
subclass of: Search algorithm
definition: The SloMo score is a quantitative measure used in mass spectrometry (MS/MS) for the localization of modification sites within a peptide or protein sequence
has_obo_namespace: PRIDE
id: PRIDE:0000275

Axiom
annotated source: SloMo score
annotated property: definition
annotated target: The SloMo score is a quantitative measure used in mass spectrometry (MS/MS) for the localization of modification sites within a peptide or protein sequence
database_cross_reference: PRIDE:PRIDE

MaxQuant percentage
type: Class
subclass of: Search algorithm
definition: It refers to typically relates to the localization probability of a post-translational modification (PTM) on a peptide
has_obo_namespace: PRIDE
id: PRIDE:0000276

Axiom
annotated source: MaxQuant percentage
annotated property: definition
annotated target: It refers to typically relates to the localization probability of a post-translational modification (PTM) on a peptide
database_cross_reference: PRIDE:PRIDE

Valid location
type: Class
subclass of: ModificationItem additional parameter
definition: A valid location refers to a site on a peptide or protein sequence that has been confidently identified as being modified
has_obo_namespace: PRIDE
id: PRIDE:0000277

Axiom
annotated source: Valid location
annotated property: definition
annotated target: A valid location refers to a site on a peptide or protein sequence that has been confidently identified as being modified
database_cross_reference: PRIDE:PRIDE

Processing method additional parameter
type: Class
subclass of: BFO_0000001
definition: A processing method refers to the specific steps or algorithms used to analyze raw MS data, identify peptides, and assign modifications. These processing methods often come with additional parameters that allow users to customize the analysis based on their experimental needs
has_obo_namespace: PRIDE
id: PRIDE:0000278

Axiom
annotated source: Processing method additional parameter
annotated property: definition
annotated target: A processing method refers to the specific steps or algorithms used to analyze raw MS data, identify peptides, and assign modifications. These processing methods often come with additional parameters that allow users to customize the analysis based on their experimental needs
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: zH ion
annotated property: has_exact_synonym
annotated target: zH fragment ion
database_cross_reference: 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

Axiom
annotated source: zHH ion
annotated property: has_exact_synonym
annotated target: zHH fragment ion
database_cross_reference: 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: Sequest
subclass of: Peptide search engine output parameter
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
definition: The name of the sample labelled with TMT reagent 126
has_obo_namespace: PRIDE
id: PRIDE:0000285

Axiom
annotated source: TMT reagent 126
annotated property: definition
annotated target: The name of the sample labelled with TMT reagent 126
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT reagent 127
annotated property: definition
annotated target: The name of the sample labelled with TMT reagent 127
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT reagent 128
annotated property: definition
annotated target: The name of the sample labelled with TMT reagent 128
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT reagent 129
annotated property: definition
annotated target: The name of the sample labelled with TMT reagent 129
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT reagent 130
annotated property: definition
annotated target: The name of the sample labelled with TMT reagent 130
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT reagent 131
annotated property: definition
annotated target: The name of the sample labelled with TMT reagent 131
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT intensity 126
annotated property: definition
annotated target: The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS]
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT intensity 127
annotated property: definition
annotated target: The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS]
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT intensity 128
annotated property: definition
annotated target: The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS]
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT intensity 129
annotated property: definition
annotated target: The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS]
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT intensity 130
annotated property: definition
annotated target: The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS]
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: TMT intensity 131
annotated property: definition
annotated target: The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS]
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Gene name
annotated property: definition
annotated target: Name of the gene that has been identified (if a nucleotide database was used to perform the search)
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Modification Position in Protein Sequence
annotated property: definition
annotated target: Position of the modification in the protein sequence
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Submitted Protein Accession
annotated property: definition
annotated target: The original submitted protein accession for this identification. This might have been curated as part of the submission process
database_cross_reference: PRIDE:PRIDE

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
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)
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)
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
has_obo_namespace: PRIDE
id: PRIDE:0000303

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
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
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
definition: It refers to the process of retrieving peptide data from the NCBI Peptidome database for use in various proteomics analyses
has_obo_namespace: PRIDE
id: PRIDE:0000306

Axiom
annotated source: Imported from NCBI Peptidome
annotated property: definition
annotated target: It refers to the process of retrieving peptide data from the NCBI Peptidome database for use in various proteomics analyses
database_cross_reference: PRIDE:PRIDE

Quantification method
type: Class
subclass of: Quantification parameter
definition: Defines various quantification methods
has_obo_namespace: PRIDE
id: PRIDE:0000307

Axiom
annotated source: Quantification method
annotated property: definition
annotated target: Defines various quantification methods
database_cross_reference: PRIDE:PRIDE

Gel-based quantification method
type: Class
subclass of: Quantification method
definition: Describes gel-based quantification methods
has_obo_namespace: PRIDE
id: PRIDE:0000308

Axiom
annotated source: Gel-based quantification method
annotated property: definition
annotated target: Describes gel-based quantification methods
database_cross_reference: PRIDE:PRIDE

Gel-free quantification method
type: Class
subclass of: Quantification method
definition: Describes gel-free quantification methods
has_obo_namespace: PRIDE
id: PRIDE:0000309

Axiom
annotated source: Gel-free quantification method
annotated property: definition
annotated target: Describes gel-free quantification methods
database_cross_reference: PRIDE:PRIDE

Isotope labeling
type: Class
subclass of: Gel-free quantification method
definition: Describes quantification techniques using isotope labeling
has_obo_namespace: PRIDE
id: PRIDE:0000310

Axiom
annotated source: Isotope labeling
annotated property: definition
annotated target: Describes quantification techniques using isotope labeling
database_cross_reference: PRIDE:PRIDE

Selected Reaction Monitoring
type: Class
subclass of: Gel-free quantification method
definition: Describes quantification techniques based on selected / multiple reaction monitoring
has_obo_namespace: PRIDE
id: PRIDE:0000311

Axiom
annotated source: Selected Reaction Monitoring
annotated property: definition
annotated target: Describes quantification techniques based on selected / multiple reaction monitoring
database_cross_reference: PRIDE:PRIDE

Label free
type: Class
subclass of: Gel-free quantification method
definition: Describes label free quantification techniques
has_obo_namespace: PRIDE
id: PRIDE:0000312

Axiom
annotated source: Label free
annotated property: definition
annotated target: Describes label free quantification techniques
database_cross_reference: PRIDE:PRIDE

iTRAQ
type: Class
subclass of: MS2 based isotope labeling
definition: Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level
has_obo_namespace: PRIDE
id: PRIDE:0000313

Axiom
annotated source: iTRAQ
annotated property: definition
annotated target: Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level
database_cross_reference: PRIDE:PRIDE

TMT
type: Class
subclass of: MS2 based isotope labeling
subclass of: Label
definition: Tandem Mass Tag is a MS2 based isotope labeling quantification technique
has_exact_synonym: Tandem Mass Tag
has_obo_namespace: PRIDE
id: PRIDE:0000314

Axiom
annotated source: TMT
annotated property: definition
annotated target: Tandem Mass Tag is a MS2 based isotope labeling quantification technique
database_cross_reference: PRIDE:PRIDE

Axiom
annotated source: TMT
annotated property: has_exact_synonym
annotated target: Tandem Mass Tag
database_cross_reference: PRIDE

SILAC
type: Class
subclass of: MS1 based isotope labeling
subclass of: Label
definition: Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification
has_exact_synonym: Stable isotope labeling with amino acids in cell culture
has_obo_namespace: PRIDE
id: PRIDE:0000315

Axiom
annotated source: SILAC
annotated property: definition
annotated target: Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification
database_cross_reference: PRIDE:PRIDE

Axiom
annotated source: SILAC
annotated property: has_exact_synonym
annotated target: Stable isotope labeling with amino acids in cell culture
database_cross_reference: PRIDE

MS1 based isotope labeling
type: Class
subclass of: Isotope labeling
definition: Describes isotope labeling quantification techniques detectable at MS1 level
has_obo_namespace: PRIDE
id: PRIDE:0000316

Axiom
annotated source: MS1 based isotope labeling
annotated property: definition
annotated target: Describes isotope labeling quantification techniques detectable at MS1 level
database_cross_reference: PRIDE:PRIDE

MS2 based isotope labeling
type: Class
subclass of: Isotope labeling
definition: Describes isotope labeling quantification techniques detectable at MS2 level
has_obo_namespace: PRIDE
id: PRIDE:0000317

Axiom
annotated source: MS2 based isotope labeling
annotated property: definition
annotated target: Describes isotope labeling quantification techniques detectable at MS2 level
database_cross_reference: PRIDE:PRIDE

18O
type: Class
subclass of: MS1 based isotope labeling
subclass of: metabolic label
definition: The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen
has_obo_namespace: PRIDE
id: PRIDE:0000318

Axiom
annotated source: 18O
annotated property: definition
annotated target: The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen
database_cross_reference: PRIDE:PRIDE

ICAT
type: Class
subclass of: MS1 based isotope labeling
subclass of: Label
definition: Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements
has_exact_synonym: Isotope-Coded Affinity Tags
has_obo_namespace: PRIDE
id: PRIDE:0000319

Axiom
annotated source: ICAT
annotated property: definition
annotated target: Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements
database_cross_reference: PRIDE:PRIDE

Axiom
annotated source: ICAT
annotated property: has_exact_synonym
annotated target: Isotope-Coded Affinity Tags
database_cross_reference: PRIDE

AQUA
type: Class
subclass of: MS1 based isotope labeling
definition: AQUA is an isotope labeling based quantification technique that uses known peptides
has_obo_namespace: PRIDE
id: PRIDE:0000320

Axiom
annotated source: AQUA
annotated property: definition
annotated target: AQUA is an isotope labeling based quantification technique that uses known peptides
database_cross_reference: PRIDE:PRIDE

ICPL
type: Class
subclass of: MS1 based isotope labeling
definition: Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses
has_exact_synonym: Isotope-coded protein label
has_obo_namespace: PRIDE
id: PRIDE:0000321

Axiom
annotated source: ICPL
annotated property: definition
annotated target: Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses
database_cross_reference: PRIDE:PRIDE

Axiom
annotated source: ICPL
annotated property: has_exact_synonym
annotated target: Isotope-coded protein label
database_cross_reference: PRIDE

emPAI
type: Class
subclass of: Label free
definition: 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
has_exact_synonym: Exponentially Modified Protein Abundance Index
has_obo_namespace: PRIDE
id: PRIDE:0000322

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

Axiom
annotated source: emPAI
annotated property: has_exact_synonym
annotated target: Exponentially Modified Protein Abundance Index
database_cross_reference: PRIDE

TIC
type: Class
subclass of: Label free
definition: The Total Ion Current (TIC) can be measured or calculated in order to target specific ions
has_exact_synonym: Total Ion Current
has_obo_namespace: PRIDE
id: PRIDE:0000323

Axiom
annotated source: TIC
annotated property: definition
annotated target: The Total Ion Current (TIC) can be measured or calculated in order to target specific ions
database_cross_reference: PRIDE:PRIDE

Axiom
annotated source: TIC
annotated property: has_exact_synonym
annotated target: Total Ion Current
database_cross_reference: PRIDE

Quantification reagent
type: Class
subclass of: Sample description additional parameter
subclass of: Quantification parameter
definition: A reagent used for quantification
has_obo_namespace: PRIDE
id: PRIDE:0000324

Axiom
annotated source: Quantification reagent
annotated property: definition
annotated target: A reagent used for quantification
database_cross_reference: PRIDE:PRIDE

SILAC heavy
type: Class
subclass of: SILAC
subclass of: SILAC reagent
definition: The heavy label used in SILAC experiments
has_obo_namespace: PRIDE
id: PRIDE:0000325

Axiom
annotated source: SILAC heavy
annotated property: definition
annotated target: The heavy label used in SILAC experiments
database_cross_reference: PRIDE:PRIDE

SILAC light
type: Class
subclass of: SILAC
subclass of: SILAC reagent
definition: The light reagent used in SILAC experiments
has_obo_namespace: PRIDE
id: PRIDE:0000326

Axiom
annotated source: SILAC light
annotated property: definition
annotated target: The light reagent used in SILAC experiments
database_cross_reference: PRIDE:PRIDE

SILAC medium
type: Class
subclass of: SILAC
subclass of: SILAC reagent
definition: The medium weight reagent used in SILAC experiments
has_obo_namespace: PRIDE
id: PRIDE:0000327

Axiom
annotated source: SILAC medium
annotated property: definition
annotated target: The medium weight reagent used in SILAC experiments
database_cross_reference: PRIDE:PRIDE

SILAC reagent
type: Class
subclass of: Reagents used in Labeled Methods
definition: Reagent used in SILAC labeling
has_obo_namespace: PRIDE
id: PRIDE:0000328

Axiom
annotated source: SILAC reagent
annotated property: definition
annotated target: Reagent used in SILAC labeling
database_cross_reference: PRIDE:PRIDE

iTRAQ reagent
type: Class
subclass of: Reagents used in Labeled Methods
definition: Reagent used in iTRAQ experiments
has_obo_namespace: PRIDE
id: PRIDE:0000329

Axiom
annotated source: iTRAQ reagent
annotated property: definition
annotated target: Reagent used in iTRAQ experiments
database_cross_reference: PRIDE:PRIDE

Arbitrary quantification unit
type: Class
subclass of: Quantification unit
definition: 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
has_obo_namespace: PRIDE
id: PRIDE:0000330

Axiom
annotated source: Arbitrary quantification unit
annotated property: definition
annotated target: 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
database_cross_reference: PRIDE:PRIDE

Counts
type: Class
subclass of: Arbitrary quantification unit
definition: Quantification values reported as arbitrary counts (most often ion counts)
has_obo_namespace: PRIDE
id: PRIDE:0000331

Axiom
annotated source: Counts
annotated property: definition
annotated target: Quantification values reported as arbitrary counts (most often ion counts)
database_cross_reference: PRIDE:PRIDE

TMT reagent
type: Class
subclass of: Reagents used in Labeled Methods
definition: Reagent used in TMT experiments
has_obo_namespace: PRIDE
id: PRIDE:0000337

Axiom
annotated source: TMT reagent
annotated property: definition
annotated target: Reagent used in TMT experiments
database_cross_reference: PRIDE:PRIDE

ICAT reagent
type: Class
subclass of: Reagents used in Labeled Methods
definition: Reagent used in ICAT experiments
has_obo_namespace: PRIDE
id: PRIDE:0000344

Axiom
annotated source: ICAT reagent
annotated property: definition
annotated target: Reagent used in ICAT experiments
database_cross_reference: PRIDE:PRIDE

ICAT light reagent
type: Class
subclass of: ICAT reagent
definition: The ICAT light reagent is a chemical reagent that labels proteins for comparison with heavy reagents
has_obo_namespace: PRIDE
id: PRIDE:0000345

Axiom
annotated source: ICAT light reagent
annotated property: definition
annotated target: The ICAT light reagent is a chemical reagent that labels proteins for comparison with heavy reagents
database_cross_reference: PRIDE:PRIDE

ICAT heavy reagent
type: Class
subclass of: ICAT reagent
definition: The ICAT heavy reagent is a chemical reagent used to label proteins for protein profiling
has_obo_namespace: PRIDE
id: PRIDE:0000346

Axiom
annotated source: ICAT heavy reagent
annotated property: definition
annotated target: The ICAT heavy reagent is a chemical reagent used to label proteins for protein profiling
database_cross_reference: PRIDE:PRIDE

ICPL reagent
type: Class
subclass of: Reagents used in Labeled Methods
definition: Reagent used in ICPL experiments
has_obo_namespace: PRIDE
id: PRIDE:0000347

Axiom
annotated source: ICPL reagent
annotated property: definition
annotated target: Reagent used in ICPL experiments
database_cross_reference: PRIDE:PRIDE

ICPL 0 reagent
type: Class
subclass of: ICPL reagent
definition: ICPL_0 reagent is a crucial component in the ICPL methodology, serving as the light isotopic label that provides a reference point for quantitative proteomic analyses
has_obo_namespace: PRIDE
id: PRIDE:0000348

Axiom
annotated source: ICPL 0 reagent
annotated property: definition
annotated target: ICPL_0 reagent is a crucial component in the ICPL methodology, serving as the light isotopic label that provides a reference point for quantitative proteomic analyses
database_cross_reference: PRIDE:PRIDE

ICPL 4 reagent
type: Class
subclass of: ICPL reagent
definition: ICPLn4 reagent is a specific labeling compound that incorporates four deuterium (^2H) atoms, resulting in a mass shift of approximately 4.0251 Da per labeled amino acid compared to the light ICPL_0 reagent
has_obo_namespace: PRIDE
id: PRIDE:0000349

Axiom
annotated source: ICPL 4 reagent
annotated property: definition
annotated target: ICPLn4 reagent is a specific labeling compound that incorporates four deuterium (^2H) atoms, resulting in a mass shift of approximately 4.0251 Da per labeled amino acid compared to the light ICPL_0 reagent
database_cross_reference: PRIDE:PRIDE

ICPL 6 reagent
type: Class
subclass of: ICPL reagent
definition: The ICPL 6 reagent is a labeling compounds, designed to introduce a mass shift of approximately 6.0204 Da per labeled amino group
has_obo_namespace: PRIDE
id: PRIDE:0000350

Axiom
annotated source: ICPL 6 reagent
annotated property: definition
annotated target: The ICPL 6 reagent is a labeling compounds, designed to introduce a mass shift of approximately 6.0204 Da per labeled amino group
database_cross_reference: PRIDE:PRIDE

ICPL 10 reagent
type: Class
subclass of: ICPL reagent
definition: The ICPL 10 reagent is a labeling compounds, designed to introduce a mass shift of approximately 10 Da per labeled amino group
has_obo_namespace: PRIDE
id: PRIDE:0000351

Axiom
annotated source: ICPL 10 reagent
annotated property: definition
annotated target: The ICPL 10 reagent is a labeling compounds, designed to introduce a mass shift of approximately 10 Da per labeled amino group
database_cross_reference: PRIDE:PRIDE

Quantification value
type: Class
subclass of: Quantification parameter
definition: Parameters to report quantification values
has_obo_namespace: PRIDE
id: PRIDE:0000352

Axiom
annotated source: Quantification value
annotated property: definition
annotated target: Parameters to report quantification values
database_cross_reference: PRIDE:PRIDE

Multiplexed quantification value
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
subclass of: Quantification value
definition: Parameters describing quantification values for multiplexed samples
has_obo_namespace: PRIDE
id: PRIDE:0000353

Axiom
annotated source: Multiplexed quantification value
annotated property: definition
annotated target: Parameters describing quantification values for multiplexed samples
database_cross_reference: PRIDE:PRIDE

Intensity subsample 1
type: Class
subclass of: Multiplexed quantification value
definition: Intensity subsampling 1 typically refers to selecting first subset of intensity values from a spectrum to analyze specific peaks or regions of interest
has_obo_namespace: PRIDE
id: PRIDE:0000354

Axiom
annotated source: Intensity subsample 1
annotated property: definition
annotated target: Intensity subsampling 1 typically refers to selecting first subset of intensity values from a spectrum to analyze specific peaks or regions of interest
database_cross_reference: PRIDE:PRIDE

Intensity subsample 2
type: Class
subclass of: Multiplexed quantification value
definition: Intensity subsampling 2 typically refers to selecting second subset of intensity values from a spectrum to analyze specific peaks or regions of interest
has_obo_namespace: PRIDE
id: PRIDE:0000355

Axiom
annotated source: Intensity subsample 2
annotated property: definition
annotated target: Intensity subsampling 2 typically refers to selecting second subset of intensity values from a spectrum to analyze specific peaks or regions of interest
database_cross_reference: PRIDE:PRIDE

Intensity subsample 3
type: Class
subclass of: Multiplexed quantification value
definition: Intensity subsampling 3 typically refers to selecting third subset of intensity values from a spectrum to analyze specific peaks or regions of interest
has_obo_namespace: PRIDE
id: PRIDE:0000356

Axiom
annotated source: Intensity subsample 3
annotated property: definition
annotated target: Intensity subsampling 3 typically refers to selecting third subset of intensity values from a spectrum to analyze specific peaks or regions of interest
database_cross_reference: PRIDE:PRIDE

Intensity subsample 4
type: Class
subclass of: Multiplexed quantification value
definition: Intensity subsampling 4 typically refers to selecting fourth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
has_obo_namespace: PRIDE
id: PRIDE:0000357

Axiom
annotated source: Intensity subsample 4
annotated property: definition
annotated target: Intensity subsampling 4 typically refers to selecting fourth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
database_cross_reference: PRIDE:PRIDE

Intensity subsample 5
type: Class
subclass of: Multiplexed quantification value
definition: Intensity subsampling 5 typically refers to selecting fifth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
has_obo_namespace: PRIDE
id: PRIDE:0000358

Axiom
annotated source: Intensity subsample 5
annotated property: definition
annotated target: Intensity subsampling 5 typically refers to selecting fifth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
database_cross_reference: PRIDE:PRIDE

Intensity subsample 6
type: Class
subclass of: Multiplexed quantification value
definition: Intensity subsampling 6 typically refers to selecting sixth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
has_obo_namespace: PRIDE
id: PRIDE:0000359

Axiom
annotated source: Intensity subsample 6
annotated property: definition
annotated target: Intensity subsampling 6 typically refers to selecting sixth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
database_cross_reference: PRIDE:PRIDE

Intensity subsample 7
type: Class
subclass of: Multiplexed quantification value
definition: Intensity subsampling 7 typically refers to selecting seventh subset of intensity values from a spectrum to analyze specific peaks or regions of interest
has_obo_namespace: PRIDE
id: PRIDE:0000360

Axiom
annotated source: Intensity subsample 7
annotated property: definition
annotated target: Intensity subsampling 7 typically refers to selecting seventh subset of intensity values from a spectrum to analyze specific peaks or regions of interest
database_cross_reference: PRIDE:PRIDE

Intensity subsample 8
type: Class
subclass of: Multiplexed quantification value
definition: Intensity subsampling 8 typically refers to selecting eighth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
has_obo_namespace: PRIDE
id: PRIDE:0000361

Axiom
annotated source: Intensity subsample 8
annotated property: definition
annotated target: Intensity subsampling 8 typically refers to selecting eighth subset of intensity values from a spectrum to analyze specific peaks or regions of interest
database_cross_reference: PRIDE:PRIDE

Other quantification value
type: Class
subclass of: Quantification value
definition: Values from other quantification techniques
has_obo_namespace: PRIDE
id: PRIDE:0000362

Axiom
annotated source: Other quantification value
annotated property: definition
annotated target: Values from other quantification techniques
database_cross_reference: PRIDE:PRIDE

emPAI value
type: Class
subclass of: Identification additional parameter
subclass of: Other quantification value
definition: The emPAI for the protein
has_obo_namespace: PRIDE
id: PRIDE:0000363

Axiom
annotated source: emPAI value
annotated property: definition
annotated target: The emPAI for the protein
database_cross_reference: PRIDE:PRIDE

TIC value
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
subclass of: Other quantification value
definition: The Total Ion Count for the given entity
has_obo_namespace: PRIDE
id: PRIDE:0000364

Axiom
annotated source: TIC value
annotated property: definition
annotated target: The Total Ion Count for the given entity
database_cross_reference: PRIDE:PRIDE

Multiplexed sample description
type: Class
subclass of: Sample description additional parameter
definition: Describes multiples subsamples
has_obo_namespace: PRIDE
id: PRIDE:0000365

Axiom
annotated source: Multiplexed sample description
annotated property: definition
annotated target: Describes multiples subsamples
database_cross_reference: PRIDE:PRIDE

Contains multiple subsamples
type: Class
subclass of: Multiplexed sample description
definition: Identifies samples that are made up of multiplexed subsamples
has_obo_namespace: PRIDE
id: PRIDE:0000366

Axiom
annotated source: Contains multiple subsamples
annotated property: definition
annotated target: Identifies samples that are made up of multiplexed subsamples
database_cross_reference: PRIDE:PRIDE

Quantification parameter
type: Class
subclass of: BFO_0000001
definition: Quantification related parameter
has_obo_namespace: PRIDE
id: PRIDE:0000391

Axiom
annotated source: Quantification parameter
annotated property: definition
annotated target: Quantification related parameter
database_cross_reference: PRIDE:PRIDE

Quantification unit
type: Class
subclass of: Peptide item additional parameter
subclass of: Identification additional parameter
subclass of: Quantification parameter
definition: Unit used to report quantification results
has_obo_namespace: PRIDE
id: PRIDE:0000392

Axiom
annotated source: Quantification unit
annotated property: definition
annotated target: Unit used to report quantification results
database_cross_reference: PRIDE:PRIDE

Relative quantification unit
type: Class
subclass of: Quantification unit
definition: Unit to report relative quantification results
has_obo_namespace: PRIDE
id: PRIDE:0000393

Axiom
annotated source: Relative quantification unit
annotated property: definition
annotated target: Unit to report relative quantification results
database_cross_reference: PRIDE:PRIDE

Absolute quantification unit
type: Class
subclass of: Quantification unit
definition: Unit used to describe absolute quantification results
has_obo_namespace: PRIDE
id: PRIDE:0000394

Axiom
annotated source: Absolute quantification unit
annotated property: definition
annotated target: Unit used to describe absolute quantification results
database_cross_reference: PRIDE:PRIDE

Ratio
type: Class
subclass of: Relative quantification unit
definition: Quantification results represent ratios
has_obo_namespace: PRIDE
id: PRIDE:0000395

Axiom
annotated source: Ratio
annotated property: definition
annotated target: Quantification results represent ratios
database_cross_reference: PRIDE:PRIDE

Copies per cell
type: Class
subclass of: Absolute quantification unit
definition: Quantification results are reported as copies per cell
has_obo_namespace: PRIDE
id: PRIDE:0000396

Axiom
annotated source: Copies per cell
annotated property: definition
annotated target: Quantification results are reported as copies per cell
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Data derived from previous dataset
annotated property: definition
annotated target: One dataset is a reanalysis of previously published data
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: No PTMs are included in the dataset
annotated property: definition
annotated target: No post-translational-modifications are been included in the identified peptides of one dataset
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Accepted manuscript
annotated property: definition
annotated target: A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet
database_cross_reference: PRIDE:PRIDE

Reference
type: Class
subclass of: Experiment additional parameter
definition: 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
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000400

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

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
definition: This means that the experimental information available has been improved, for instance precursor charges were added
has_obo_namespace: PRIDE
id: PRIDE:0000401

Axiom
annotated source: Experimental information has been refined since this experiment was originally made publicly available
annotated property: definition
annotated target: This means that the experimental information available has been improved, for instance precursor charges were added
database_cross_reference: PRIDE:PRIDE

Original data
type: Class
subclass of: Experiment additional parameter
definition: A dataset is not a reanalysis of previously published data
has_obo_namespace: PRIDE
id: PRIDE:0000402

Axiom
annotated source: Original data
annotated property: definition
annotated target: A dataset is not a reanalysis of previously published data
database_cross_reference: PRIDE:PRIDE

Associated 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)
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000403

Axiom
annotated source: Associated 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

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
definition: URI of a raw data file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000404

Axiom
annotated source: Associated raw file URI
annotated property: definition
annotated target: URI of a raw data file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: PRIDE:PRIDE

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
definition: Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (maybe through a PX submission)
has_obo_namespace: PRIDE
id: PRIDE:0000405

Axiom
annotated source: Submit PRIDE Experiment to IntAct
annotated property: definition
annotated target: Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (maybe through a PX submission)
database_cross_reference: PRIDE:PRIDE

ProteomeCentral dataset URI
type: Class
subclass of: Experiment additional parameter
definition: URI associated to one PX submission in ProteomeCentral
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
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
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
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
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
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
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
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
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
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
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
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
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

Axiom
annotated source: b ion -H3PO4
annotated property: has_exact_synonym
annotated target: B fragment ion -H3PO4
database_cross_reference: 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

Axiom
annotated source: b ion -2H3PO4
annotated property: has_exact_synonym
annotated target: B fragment ion -2H3PO4
database_cross_reference: 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

Axiom
annotated source: b ion -3H3PO4
annotated property: has_exact_synonym
annotated target: B fragment ion -3H3PO4
database_cross_reference: 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

Axiom
annotated source: y ion -H3PO4
annotated property: has_exact_synonym
annotated target: y fragment ion -H3PO4
database_cross_reference: 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

Axiom
annotated source: y ion -2H3PO4
annotated property: has_exact_synonym
annotated target: y fragment ion -2H3PO4
database_cross_reference: 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

Axiom
annotated source: y ion -3H3PO4
annotated property: has_exact_synonym
annotated target: y fragment ion -3H3PO4
database_cross_reference: PRIDE

MS1 intensity based label-free quantification method
type: Class
subclass of: Gel-free quantification method
definition: A a widely used approach in mass spectrometry-based proteomics for quantifying protein abundances across different samples
has_obo_namespace: PRIDE
id: PRIDE:0000425

Axiom
annotated source: MS1 intensity based label-free quantification method
annotated property: definition
annotated target: A a widely used approach in mass spectrometry-based proteomics for quantifying protein abundances across different samples
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Mass spectrometry proteomics experimental strategy
annotated property: definition
annotated target: The basic mass spectrometry strategy used in the experiment
database_cross_reference: PRIDE:PRIDE

Top-down proteomics
type: Class
subclass of: Mass spectrometry proteomics experimental strategy
subclass of: Experiment Type
definition: A mass spectrometry-based approach that analyzes intact proteins rather than digesting them into peptides (as in bottom-up proteomics)
has_obo_namespace: PRIDE
id: PRIDE:0000427

Axiom
annotated source: Top-down proteomics
annotated property: definition
annotated target: A mass spectrometry-based approach that analyzes intact proteins rather than digesting them into peptides (as in bottom-up proteomics)
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Bottom-up proteomics
annotated property: definition
annotated target: Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer
database_cross_reference: PRIDE:PRIDE

MS/MS shotgun proteomics
type: Class
subclass of: Bottom-up proteomics
definition: 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
has_obo_namespace: PRIDE
id: PRIDE:0000429

Axiom
annotated source: MS/MS shotgun proteomics
annotated property: definition
annotated target: 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
database_cross_reference: PRIDE:PRIDE

Chemical cross-linking coupled with mass spectrometry proteomics
type: Class
subclass of: Bottom-up proteomics
definition: Chemical cross-linking of proteins coupled with mass spectrometry analysis to provide information about protein folding and protein-protein interaction
has_obo_namespace: PRIDE
id: PRIDE:0000430

Axiom
annotated source: Chemical cross-linking coupled with mass spectrometry proteomics
annotated property: definition
annotated target: Chemical cross-linking of proteins coupled with mass spectrometry analysis to provide information about protein folding and protein-protein interaction
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Affinity purification coupled with mass spectrometry proteomics
annotated property: definition
annotated target: Affinity purification combined with mass spectrometry (AP-MS) has been used to understand protein-complex composition and protein-protein interaction
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Dataset with its publication pending
annotated property: definition
annotated target: A dataset which has an associated manuscript pending for publication
database_cross_reference: PRIDE:PRIDE

Reagents used in Labeled Methods
type: Class
subclass of: Quantification reagent
definition: Labeled reagents used for quantification
has_obo_namespace: PRIDE
id: PRIDE:0000433

Axiom
annotated source: Reagents used in Labeled Methods
annotated property: definition
annotated target: Labeled reagents used for quantification
database_cross_reference: PRIDE:PRIDE

Unlabeled sample
type: Class
subclass of: Quantification reagent
definition: An unlabeled sample used for quantification
has_obo_namespace: PRIDE
id: PRIDE:0000434

Axiom
annotated source: Unlabeled sample
annotated property: definition
annotated target: An unlabeled sample used for quantification
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Peptide counting
annotated property: definition
annotated target: Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Spectrum counting
annotated property: definition
annotated target: Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: PAI
annotated property: definition
annotated target: Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Spectrum count/molecular weight
annotated property: definition
annotated target: Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: SAF
annotated property: definition
annotated target: The spectrum count is normalized for protein length. Method reviewed in PMID 22772140
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: NSAF
annotated property: definition
annotated target: Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: APEX - Absolute Protein Expression
annotated property: definition
annotated target: Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140
database_cross_reference: PRIDE:PRIDE

Tissue not applicable to dataset
type: Class
subclass of: Experiment additional parameter
definition: Tissue not applicable to dataset
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
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)
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)
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
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
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
definition: 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
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000448

Axiom
annotated source: Additional associated raw file URI
annotated property: definition
annotated target: 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
database_cross_reference: PRIDE: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
definition: URI of one gel image file associated to one PX submission
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000449

Axiom
annotated source: Gel image file URI
annotated property: definition
annotated target: URI of one gel image file associated to one PX submission
database_cross_reference: PRIDE:PRIDE

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
subclass of: Proteomics data acquisition method
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
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
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
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
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
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
definition: Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction
has_obo_namespace: PRIDE
id: PRIDE:0000455

Axiom
annotated source: Protein-protein cross-linking experiment
annotated property: definition
annotated target: Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction
database_cross_reference: PRIDE:PRIDE

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

Axiom
annotated source: Protein-RNA cross-linking experiment
annotated property: definition
annotated target: Protein-RNA cross-linking experiment to provide information about Protein-RNA interaction
database_cross_reference: PRIDE:PRIDE

Experiment Type
type: Class
subclass of: BFO_0000001
definition: Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method
has_obo_namespace: PRIDE
id: PRIDE:0000457

Axiom
annotated source: Experiment Type
annotated property: definition
annotated target: Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method
database_cross_reference: PRIDE:PRIDE

Metaproteomics
type: Class
subclass of: Experiment Type
definition: Studying all protein samples of diverse host environments like the human body, soil or sea water
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

Axiom
annotated source: Metaproteomics
annotated property: has_exact_synonym
annotated target: Community Proteomics
database_cross_reference: PRIDE

Axiom
annotated source: Metaproteomics
annotated property: has_related_synonym
annotated target: Environmental Proteomics
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
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
definition: Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies
has_obo_namespace: PRIDE
id: PRIDE:0000460

Axiom
annotated source: Proteogenomics
annotated property: definition
annotated target: Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies
database_cross_reference: PRIDE:PRIDE

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
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
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
definition: URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000464

Axiom
annotated source: Fasta file URI
annotated property: definition
annotated target: URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: PRIDE:PRIDE

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
definition: URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000465

Axiom
annotated source: Spectral Library file URI
annotated property: definition
annotated target: URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: PRIDE:PRIDE

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
definition: URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000466

Axiom
annotated source: Quantification result file URI
annotated property: definition
annotated target: URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: PRIDE:PRIDE

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
definition: URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000467

Axiom
annotated source: MS Image file URI
annotated property: definition
annotated target: URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission)
database_cross_reference: PRIDE:PRIDE

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
definition: URI for an Aspera Download Protocol
database_cross_reference: value-type:xsd:string
has_obo_namespace: PRIDE
id: PRIDE:0000468

Axiom
annotated source: Aspera Protocol
annotated property: definition
annotated target: URI for an Aspera Download Protocol
database_cross_reference: PRIDE:PRIDE

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
definition: URI for an FTP Download Protocol
has_obo_namespace: PRIDE
id: PRIDE:0000469

Axiom
annotated source: FTP Protocol
annotated property: definition
annotated target: URI for an FTP Download Protocol
database_cross_reference: PRIDE:PRIDE

File Properties
type: Class
subclass of: BFO_0000001
definition: PRIDE File Properties for all type of files
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
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
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
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
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
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
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
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
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
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
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
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
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
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
subclass of: BFO_0000001
definition: The result analysis parameters is a term to group all the parameters for proteomics data analysis
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
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
definition: Result analysis parameters specific to a search engine or quantitative tool
has_obo_namespace: PRIDE
id: PRIDE:0000486

Axiom
annotated source: Tool specific analysis parameters
annotated property: definition
annotated target: Result analysis parameters specific to a search engine or quantitative tool
database_cross_reference: PRIDE:PRIDE

Min charge
type: Class
subclass of: Global result parameters
definition: Minimum charge of precursor to be search
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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)
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
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
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
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
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
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
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)
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
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
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
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)
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
has_obo_namespace: PRIDE
id: PRIDE:0000514

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

TMT126
type: Class
subclass of: TMT6PLEX
subclass of: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT126
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: TMT6PLEX
definition: TMT127
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: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT127C
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: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT127N
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: TMT6PLEX
definition: TMT128
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: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT128C
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: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT128N
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: TMT6PLEX
definition: TMT129
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: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT129C
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: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT129N
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: TMT6PLEX
definition: TMT130
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: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT130C
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: TMT10PLEX
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT130N
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: TMT6PLEX
subclass of: TMT10PLEX
definition: TMT131
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
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
definition: ITRAQ113 channel
has_obo_namespace: PRIDE
id: PRIDE:0000531

Axiom
annotated source: ITRAQ113
annotated property: definition
annotated target: ITRAQ113 channel
database_cross_reference: PRIDE:PRIDE

ITRAQ114
type: Class
subclass of: ITRAQ
definition: ITRAQ114 channel
has_obo_namespace: PRIDE
id: PRIDE:0000532

Axiom
annotated source: ITRAQ114
annotated property: definition
annotated target: ITRAQ114 channel
database_cross_reference: PRIDE:PRIDE

ITRAQ115
type: Class
subclass of: ITRAQ
definition: ITRAQ115 channel
has_obo_namespace: PRIDE
id: PRIDE:0000533

Axiom
annotated source: ITRAQ115
annotated property: definition
annotated target: ITRAQ115 channel
database_cross_reference: PRIDE:PRIDE

ITRAQ116
type: Class
subclass of: ITRAQ
definition: ITRAQ116 channel
has_obo_namespace: PRIDE
id: PRIDE:0000534

Axiom
annotated source: ITRAQ116
annotated property: definition
annotated target: ITRAQ116 channel
database_cross_reference: PRIDE:PRIDE

ITRAQ117
type: Class
subclass of: ITRAQ
definition: ITRAQ117 channel
has_obo_namespace: PRIDE
id: PRIDE:0000535

Axiom
annotated source: ITRAQ117
annotated property: definition
annotated target: ITRAQ117 channel
database_cross_reference: PRIDE:PRIDE

ITRAQ118
type: Class
subclass of: ITRAQ
definition: ITRAQ118 channel
has_obo_namespace: PRIDE
id: PRIDE:0000536

Axiom
annotated source: ITRAQ118
annotated property: definition
annotated target: ITRAQ118 channel
database_cross_reference: PRIDE:PRIDE

ITRAQ119
type: Class
subclass of: ITRAQ
definition: ITRAQ119 channel
has_obo_namespace: PRIDE
id: PRIDE:0000537

Axiom
annotated source: ITRAQ119
annotated property: definition
annotated target: ITRAQ119 channel
database_cross_reference: PRIDE:PRIDE

ITRAQ121
type: Class
subclass of: ITRAQ
definition: ITRAQ121 channel
has_obo_namespace: PRIDE
id: PRIDE:0000538

Axiom
annotated source: ITRAQ121
annotated property: definition
annotated target: ITRAQ121 channel
database_cross_reference: PRIDE:PRIDE

ICAT heavy
type: Class
subclass of: ICAT
definition: ICAT heavy
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
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
has_obo_namespace: PRIDE
id: PRIDE:0000543

Axiom
annotated source: Quality Control
annotated property: definition
annotated target: MS experiments conducted to control the quality of measurements
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

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
subclass of: BFO_0000001
definition: Instrument properties
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
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
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 separation methods
has_obo_namespace: PRIDE
id: PRIDE:0000551

Axiom
annotated source: Separation method
annotated property: definition
annotated target: Umbrella term for different types of separation 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

Quantification software
type: Class
subclass of: BFO_0000001
definition: A software that perform protein quantification using mass spectrometry data
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
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
subclass of: BFO_0000001
definition: A software that perform peptide/protein identification using mass spectrometry data
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
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
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
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 on SDRF files definitions
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 on SDRF files definitions
database_cross_reference: PRIDE:PRIDE

Bound fraction
type: Class
subclass of: Depletion
definition: The bound fraction after a depletion process
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
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: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT131N
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: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT131C
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: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT132N
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: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT132C
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
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

Axiom
annotated source: ETciD
annotated property: has_exact_synonym
annotated target: ETcaD
database_cross_reference: PRIDE

CID collision energy
type: Class
subclass of: collision energy
subclass of: 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: 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: 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: 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
definition: The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4)
has_obo_namespace: PRIDE
id: PRIDE:0000611

Axiom
annotated source: SILAC light R:12C(6)14N(4)
annotated property: definition
annotated target: The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4)
database_cross_reference: PRIDE:PRIDE

SILAC light L:12C(6)
type: Class
subclass of: SILAC light
definition: The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6)
has_obo_namespace: PRIDE
id: PRIDE:0000612

Axiom
annotated source: SILAC light L:12C(6)
annotated property: definition
annotated target: The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6)
database_cross_reference: PRIDE:PRIDE

SILAC light K:12C(6)14N(2)
type: Class
subclass of: SILAC light
definition: The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2)
has_obo_namespace: PRIDE
id: PRIDE:0000613

Axiom
annotated source: SILAC light K:12C(6)14N(2)
annotated property: definition
annotated target: The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2)
database_cross_reference: PRIDE:PRIDE

SILAC light P:12C(5)
type: Class
subclass of: SILAC light
definition: The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5)
has_obo_namespace: PRIDE
id: PRIDE:0000614

Axiom
annotated source: SILAC light P:12C(5)
annotated property: definition
annotated target: The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5)
database_cross_reference: PRIDE:PRIDE

SILAC heavy R:13C(6)15N(4)
type: Class
subclass of: SILAC heavy
definition: The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4)
has_obo_namespace: PRIDE
id: PRIDE:0000615

Axiom
annotated source: SILAC heavy R:13C(6)15N(4)
annotated property: definition
annotated target: The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4)
database_cross_reference: PRIDE:PRIDE

SILAC heavy L:13C(6)
type: Class
subclass of: SILAC heavy
definition: The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6)
has_obo_namespace: PRIDE
id: PRIDE:0000616

Axiom
annotated source: SILAC heavy L:13C(6)
annotated property: definition
annotated target: The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6)
database_cross_reference: PRIDE:PRIDE

SILAC heavy K:13C(6)15N(2)
type: Class
subclass of: SILAC heavy
definition: The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2)
has_obo_namespace: PRIDE
id: PRIDE:0000617

Axiom
annotated source: SILAC heavy K:13C(6)15N(2)
annotated property: definition
annotated target: The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2)
database_cross_reference: PRIDE:PRIDE

SILAC medium R:13C(6)14N(4)
type: Class
subclass of: SILAC medium
definition: The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4)
has_obo_namespace: PRIDE
id: PRIDE:0000618

Axiom
annotated source: SILAC medium R:13C(6)14N(4)
annotated property: definition
annotated target: The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4)
database_cross_reference: PRIDE:PRIDE

SILAC medium K:13C(6)14N(2)
type: Class
subclass of: SILAC medium
definition: The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2)
has_obo_namespace: PRIDE
id: PRIDE:0000619

Axiom
annotated source: SILAC medium K:13C(6)14N(2)
annotated property: definition
annotated target: The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2)
database_cross_reference: PRIDE:PRIDE

15N
type: Class
subclass of: metabolic label
definition: Metabolic label 15N
has_obo_namespace: PRIDE
id: PRIDE:0000620

Axiom
annotated source: 15N
annotated property: definition
annotated target: Metabolic label 15N
database_cross_reference: PRIDE:PRIDE

13C
type: Class
subclass of: metabolic label
definition: Metabolic label 13C
has_obo_namespace: PRIDE
id: PRIDE:0000621

Axiom
annotated source: 13C
annotated property: definition
annotated target: Metabolic label 13C
database_cross_reference: PRIDE:PRIDE

source name
type: Class
subclass of: Experiment additional parameter
definition: Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics
has_obo_namespace: PRIDE
id: PRIDE:0000623

Axiom
annotated source: source name
annotated property: definition
annotated target: Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics
database_cross_reference: PRIDE:PRIDE

SpectraCluster MaxRatio
type: Class
subclass of: Peptide search engine output parameter
definition: Spectra Cluster Maximum Ratio for the cluster
has_obo_namespace: PRIDE
id: PRIDE:0000624

Axiom
annotated source: SpectraCluster MaxRatio
annotated property: definition
annotated target: Spectra Cluster Maximum Ratio for the cluster
database_cross_reference: PRIDE:PRIDE

NIST ProbCorr
type: Class
subclass of: Peptide search engine output parameter
definition: NIST Probability Correlation
has_obo_namespace: PRIDE
id: PRIDE:0000625

Axiom
annotated source: NIST ProbCorr
annotated property: definition
annotated target: NIST Probability Correlation
database_cross_reference: PRIDE:PRIDE

NIST Dotbest
type: Class
subclass of: Peptide search engine output parameter
definition: NIST best dot product
has_obo_namespace: PRIDE
id: PRIDE:0000626

Axiom
annotated source: NIST Dotbest
annotated property: definition
annotated target: NIST best dot product
database_cross_reference: PRIDE:PRIDE

Data-dependent acquisition
type: Class
subclass of: Bottom-up proteomics
subclass of: Proteomics data acquisition method
definition: Data-dependent acquisition
has_obo_namespace: PRIDE
id: PRIDE:0000627

Axiom
annotated source: Data-dependent acquisition
annotated property: definition
annotated target: Data-dependent acquisition
database_cross_reference: PRIDE:PRIDE

Parallel reaction monitoring
type: Class
subclass of: Bottom-up proteomics
subclass of: Proteomics data acquisition method
definition: Parallel Reaction Monitoring (PRM)
has_obo_namespace: PRIDE
id: PRIDE:0000629

Axiom
annotated source: Parallel reaction monitoring
annotated property: definition
annotated target: Parallel Reaction Monitoring (PRM)
database_cross_reference: PRIDE:PRIDE

Selected reaction monitoring
type: Class
subclass of: Bottom-up proteomics
subclass of: Proteomics data acquisition method
definition: Selected reaction monitoring (SRM)
has_obo_namespace: PRIDE
id: PRIDE:0000630

Axiom
annotated source: Selected reaction monitoring
annotated property: definition
annotated target: Selected reaction monitoring (SRM)
database_cross_reference: PRIDE:PRIDE

Mass spectrometry imaging
type: Class
subclass of: Mass spectrometry proteomics experimental strategy
definition: Mass spectrometry imaging
has_obo_namespace: PRIDE
id: PRIDE:0000631

Axiom
annotated source: Mass spectrometry imaging
annotated property: definition
annotated target: Mass spectrometry imaging
database_cross_reference: PRIDE:PRIDE

TMT133N
type: Class
subclass of: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT133N
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: TMT16PLEX
subclass of: TMT18PLEX
definition: TMT133C
has_obo_namespace: PRIDE
id: PRIDE:0000633

Axiom
annotated source: TMT133C
annotated property: definition
annotated target: TMT133C
database_cross_reference: PRIDE:PRIDE

TMT134
type: Class
subclass of: TMT16PLEX
definition: TMT134
has_obo_namespace: PRIDE
id: PRIDE:0000634

Axiom
annotated source: TMT134
annotated property: definition
annotated target: TMT134
database_cross_reference: PRIDE:PRIDE

Affinity proteomics
type: Class
subclass of: Experiment Type
definition: The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes
has_obo_namespace: PRIDE
id: PRIDE:0000635

Axiom
annotated source: Affinity proteomics
annotated property: definition
annotated target: The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes
database_cross_reference: PRIDE:PRIDE

SomaScan affinity proteomics
type: Class
subclass of: Affinity proteomics
definition: 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
has_obo_namespace: PRIDE
id: PRIDE:0000636

Axiom
annotated source: SomaScan affinity proteomics
annotated property: definition
annotated target: 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
database_cross_reference: PRIDE:PRIDE

Olink affinity proteomics
type: Class
subclass of: Affinity proteomics
definition: 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
has_obo_namespace: PRIDE
id: PRIDE:0000637

Axiom
annotated source: Olink affinity proteomics
annotated property: definition
annotated target: 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
database_cross_reference: PRIDE:PRIDE

Instrument model
type: Class
subclass of: Instrument properties
definition: Instrument model
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
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
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
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: TMT18PLEX
definition: TMT134C
has_obo_namespace: PRIDE
id: PRIDE:0000642

Axiom
annotated source: TMT134C
annotated property: definition
annotated target: TMT134C
database_cross_reference: PRIDE:PRIDE

TMT134N
type: Class
subclass of: TMT18PLEX
definition: TMT134N
has_obo_namespace: PRIDE
id: PRIDE:0000643

Axiom
annotated source: TMT134N
annotated property: definition
annotated target: TMT134N
database_cross_reference: PRIDE:PRIDE

MS2 dissociation method
type: Class
subclass of: dissociation method
definition: Fragmentation method used for dissociation or fragmentation for MS2
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
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
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
definition: Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome
has_obo_namespace: PRIDE
id: PRIDE:0000649

Axiom
annotated source: Immunopeptidomics
annotated property: definition
annotated target: Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome
database_cross_reference: PRIDE:PRIDE

diaPASEF
type: Class
subclass of: Data-independent acquisition
definition: Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825
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
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
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
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
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 Target
definition: Olink Target 96 is a proteomics platform offering targeted analysis of 92 specific protein biomarkers per panel using proximity extension assay (PEA) technology
has_obo_namespace: PRIDE
id: PRIDE:0000655

Axiom
annotated source: Olink Target 96
annotated property: definition
annotated target: Olink Target 96 is a proteomics platform offering targeted analysis of 92 specific protein biomarkers per panel using proximity extension assay (PEA) technology
database_cross_reference: PRIDE:PRIDE

Olink Explore 1536
type: Class
subclass of: Olink Explore
definition: Olink Explore 1536
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 3072/384
type: Class
subclass of: Olink Explore
definition: Olink Explore 3072 includes eight 384-plex panels for efficient, large-scale, disease- and process-focused studies
has_obo_namespace: PRIDE
id: PRIDE:0000657

Axiom
annotated source: Olink Explore 3072/384
annotated property: definition
annotated target: Olink Explore 3072 includes eight 384-plex panels for efficient, large-scale, disease- and process-focused studies
database_cross_reference: PRIDE:PRIDE

Olink Explore 384
type: Class
subclass of: Olink Explore
definition: Olink Explore 384
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

Proteomics data acquisition method
type: Class
subclass of: Bottom-up proteomics
definition: Proteomics data acquisition method
has_obo_namespace: PRIDE
id: PRIDE:0000659

Axiom
annotated source: Proteomics data acquisition method
annotated property: definition
annotated target: Proteomics data acquisition method
database_cross_reference: PRIDE:PRIDE

Ion Mobility Separation
type: Class
subclass of: Separation method
definition: Ion Mobility Separation
has_obo_namespace: PRIDE
id: PRIDE:0000660

Axiom
annotated source: Ion Mobility Separation
annotated property: definition
annotated target: Ion Mobility Separation
database_cross_reference: PRIDE:PRIDE

Differential mobility Separation
type: Class
subclass of: Separation method
definition: Differential mobility Separation
has_obo_namespace: PRIDE
id: PRIDE:0000661

Axiom
annotated source: Differential mobility Separation
annotated property: definition
annotated target: Differential mobility Separation
database_cross_reference: PRIDE:PRIDE

SelexION Separation Method
type: Class
subclass of: Ion Mobility Separation
subclass of: Differential mobility Separation
definition: SelexION differential mobility separation device
has_obo_namespace: PRIDE
id: PRIDE:0000662

Axiom
annotated source: SelexION Separation Method
annotated property: definition
annotated target: SelexION differential mobility separation device
database_cross_reference: PRIDE:PRIDE

technology type
type: Class
subclass of: Experiment additional parameter
definition: The technology type or platform used to perform the study
has_obo_namespace: PRIDE
id: PRIDE:0000663

Axiom
annotated source: technology type
annotated property: definition
annotated target: The technology type or platform used to perform the study
database_cross_reference: EFO:EFO_0005521

proteomic profiling by mass spectrometry
type: Class
subclass of: technology type
definition: An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry
has_obo_namespace: PRIDE
id: PRIDE:0000664

Axiom
annotated source: proteomic profiling by mass spectrometry
annotated property: definition
annotated target: An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry
database_cross_reference: EFO:EFO_0002766

Glycoproteomics
type: Class
subclass of: Experiment Type
definition: Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications
has_obo_namespace: PRIDE
id: PRIDE:0000665

Axiom
annotated source: Glycoproteomics
annotated property: definition
annotated target: Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications
database_cross_reference: PRIDE:PRIDE

TMT6PLEX
type: Class
subclass of: TMT
definition: TMT 6-plex labeling kit has 6 channels
has_obo_namespace: PRIDE
id: PRIDE:0000666

Axiom
annotated source: TMT6PLEX
annotated property: definition
annotated target: TMT 6-plex labeling kit has 6 channels
database_cross_reference: PRIDE:PRIDE

TMT10PLEX
type: Class
subclass of: TMT
definition: TMT 10-plex labeling kit has 10 channels
has_obo_namespace: PRIDE
id: PRIDE:0000667

Axiom
annotated source: TMT10PLEX
annotated property: definition
annotated target: TMT 10-plex labeling kit has 10 channels
database_cross_reference: PRIDE:PRIDE

TMT16PLEX
type: Class
subclass of: TMT
definition: TMT 16-plex labeling kit has 16 channels
has_obo_namespace: PRIDE
id: PRIDE:0000668

Axiom
annotated source: TMT16PLEX
annotated property: definition
annotated target: TMT 16-plex labeling kit has 16 channels
database_cross_reference: PRIDE:PRIDE

TMT18PLEX
type: Class
subclass of: TMT
definition: TMT 18-plex labeling kit has 18 channels
has_obo_namespace: PRIDE
id: PRIDE:0000669

Axiom
annotated source: TMT18PLEX
annotated property: definition
annotated target: TMT 18-plex labeling kit has 18 channels
database_cross_reference: PRIDE:PRIDE

TMT135
type: Class
subclass of: TMT18PLEX
definition: TMT135
has_obo_namespace: PRIDE
id: PRIDE:0000670

Axiom
annotated source: TMT135
annotated property: definition
annotated target: TMT135
database_cross_reference: PRIDE:PRIDE

Olink Explore
type: Class
subclass of: Olink instrument model
definition: Olink Explore is a high-throughput proteomics platform that quantifies protein biomarkers across multiple samples using proximity extension assay (PEA) technology
has_obo_namespace: PRIDE
id: PRIDE:0000671

Axiom
annotated source: Olink Explore
annotated property: definition
annotated target: Olink Explore is a high-throughput proteomics platform that quantifies protein biomarkers across multiple samples using proximity extension assay (PEA) technology
database_cross_reference: PRIDE:PRIDE

Olink Target
type: Class
subclass of: Olink instrument model
definition: Olink Target is a proteomics platform designed for focused, customizable analysis of specific protein biomarker panels using proximity extension assay (PEA) technology
has_obo_namespace: PRIDE
id: PRIDE:0000672

Axiom
annotated source: Olink Target
annotated property: definition
annotated target: Olink Target is a proteomics platform designed for focused, customizable analysis of specific protein biomarker panels using proximity extension assay (PEA) technology
database_cross_reference: PRIDE:PRIDE

Olink Explore HT
type: Class
subclass of: Olink Explore
definition: The Olink Explore HT is a high-throughput proteomics platform for large-scale biomarker discovery, enabling simultaneous measurement of thousands of proteins from minimal sample volumes
has_obo_namespace: PRIDE
id: PRIDE:0000673

Axiom
annotated source: Olink Explore HT
annotated property: definition
annotated target: The Olink Explore HT is a high-throughput proteomics platform for large-scale biomarker discovery, enabling simultaneous measurement of thousands of proteins from minimal sample volumes
database_cross_reference: PRIDE:PRIDE

human gut
type: Class
subclass of: UBERON_0005409
definition: A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome.
has_obo_namespace: PRIDE
id: PRIDE:0000674

Axiom
annotated source: human gut
annotated property: definition
annotated target: A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome.
database_cross_reference: PRIDE:PRIDE

sample name
type: Class
subclass of: Data Field
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. MIXS:0001107
has_exact_synonym: sample name
has_obo_namespace: PRIDE
id: PRIDE:0000675

Axiom
annotated source: sample name
annotated property: definition
annotated target: A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. MIXS:0001107
database_cross_reference: PRIDE:PRIDE

project name
type: Class
subclass of: Data Field
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Name of the project within which the sequencing was organized. MIXS:0000092
has_exact_synonym: project name
has_obo_namespace: PRIDE
id: PRIDE:0000676

Axiom
annotated source: project name
annotated property: definition
annotated target: Name of the project within which the sequencing was organized. MIXS:0000092
database_cross_reference: PRIDE:PRIDE

gastrointestinal tract disorder
type: Class
subclass of: MONDO_0000001
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280
has_obo_namespace: PRIDE
id: PRIDE:0000677

Axiom
annotated source: gastrointestinal tract disorder
annotated property: definition
annotated target: History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280
database_cross_reference: PRIDE:PRIDE

liver disorder
type: Class
subclass of: MONDO_0000001
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: History of liver disorders; can include multiple disorders. MIXS:0000282
has_obo_namespace: PRIDE
id: PRIDE:0000678

Axiom
annotated source: liver disorder
annotated property: definition
annotated target: History of liver disorders; can include multiple disorders. MIXS:0000282
database_cross_reference: PRIDE:PRIDE

special diet
type: Class
subclass of: diet
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Specification of special diet; can include multiple special diets. MIXS:0000905
has_obo_namespace: PRIDE
id: PRIDE:0000679

Axiom
annotated source: special diet
annotated property: definition
annotated target: Specification of special diet; can include multiple special diets. MIXS:0000905
database_cross_reference: PRIDE:PRIDE

host subject id
type: Class
subclass of: Data Field
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: A unique identifier by which each subject can be referred to, de-identified. MIXS:0000861
has_obo_namespace: PRIDE
id: PRIDE:0000680

Axiom
annotated source: host subject id
annotated property: definition
annotated target: A unique identifier by which each subject can be referred to, de-identified. MIXS:0000861
database_cross_reference: PRIDE:PRIDE

host age
type: Class
subclass of: Data Field
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees. MIXS:0000255
has_exact_synonym: host age slot
has_obo_namespace: PRIDE
id: PRIDE:0000681

Axiom
annotated source: host age
annotated property: definition
annotated target: Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees. MIXS:0000255
database_cross_reference: PRIDE:PRIDE

host disease status
type: Class
subclass of: Data Field
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: List of diseases with which the host has been diagnosed; can include multiple diagnoses. MIXS:0000031
has_exact_synonym: host disease slot
has_obo_namespace: PRIDE
id: PRIDE:0000682

Axiom
annotated source: host disease status
annotated property: definition
annotated target: List of diseases with which the host has been diagnosed; can include multiple diagnoses. MIXS:0000031
database_cross_reference: PRIDE:PRIDE

IHMC medication code
type: Class
subclass of: Code
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Can include multiple medication codes. MIXS:0000884
has_obo_namespace: PRIDE
id: PRIDE:0000683

Axiom
annotated source: IHMC medication code
annotated property: definition
annotated target: Can include multiple medication codes. MIXS:0000884
database_cross_reference: PRIDE:PRIDE

chemical administration
type: Class
subclass of: PECO_0007086
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. MIXS:0000751
has_obo_namespace: PRIDE
id: PRIDE:0000684

Axiom
annotated source: chemical administration
annotated property: definition
annotated target: List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. MIXS:0000751
database_cross_reference: PRIDE:PRIDE

host body site
type: Class
subclass of: Anatomic Structure, System, or Substance
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc.). MIXS:0000867
has_obo_namespace: PRIDE
id: PRIDE:0000685

Axiom
annotated source: host body site
annotated property: definition
annotated target: Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc.). MIXS:0000867
database_cross_reference: PRIDE:PRIDE

host body product
type: Class
subclass of: Anatomic Structure, System, or Substance
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. MIXS:0000888
has_obo_namespace: PRIDE
id: PRIDE:0000686

Axiom
annotated source: host body product
annotated property: definition
annotated target: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. MIXS:0000888
database_cross_reference: PRIDE:PRIDE

host total mass
type: Class
subclass of: OBA_2045413
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Total mass of the host at collection, the unit depends on host. MIXS:0000263
has_obo_namespace: PRIDE
id: PRIDE:0000687

Axiom
annotated source: host total mass
annotated property: definition
annotated target: Total mass of the host at collection, the unit depends on host. MIXS:0000263
database_cross_reference: PRIDE:PRIDE

host height
type: Class
subclass of: Height
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: The height of subject. MIXS:0000264
has_exact_synonym: body height
has_obo_namespace: PRIDE
id: PRIDE:0000688

Axiom
annotated source: host height
annotated property: definition
annotated target: The height of subject. MIXS:0000264
database_cross_reference: PRIDE:PRIDE

host diet
type: Class
subclass of: diet
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types. MIXS:0000869
has_obo_namespace: PRIDE
id: PRIDE:0000689

Axiom
annotated source: host diet
annotated property: definition
annotated target: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types. MIXS:0000869
database_cross_reference: PRIDE:PRIDE

host last meal
type: Class
subclass of: Meal
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Content of last meal and time since feeding; can include multiple values. MIXS:0000870
has_obo_namespace: PRIDE
id: PRIDE:0000690

Axiom
annotated source: host last meal
annotated property: definition
annotated target: Content of last meal and time since feeding; can include multiple values. MIXS:0000870
database_cross_reference: PRIDE:PRIDE

host family relationship
type: Class
subclass of: BFO_0000016
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872
has_exact_synonym: family relationship
has_obo_namespace: PRIDE
id: PRIDE:0000691

Axiom
annotated source: host family relationship
annotated property: definition
annotated target: Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872
database_cross_reference: PRIDE:PRIDE

host genotype
type: Class
subclass of: genomic measurement
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Observed genotype MIXS:0000365
has_obo_namespace: PRIDE
id: PRIDE:0000692

Axiom
annotated source: host genotype
annotated property: definition
annotated target: Observed genotype MIXS:0000365
database_cross_reference: PRIDE:PRIDE

host phenotype
type: Class
subclass of: BFO_0000019
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274
has_obo_namespace: PRIDE
id: PRIDE:0000693

Axiom
annotated source: host phenotype
annotated property: definition
annotated target: Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274
database_cross_reference: PRIDE:PRIDE

host body temperature
type: Class
subclass of: Temperature
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Core body temperature of the host when sample was collected. MIXS:0000874
has_obo_namespace: PRIDE
id: PRIDE:0000694

Axiom
annotated source: host body temperature
annotated property: definition
annotated target: Core body temperature of the host when sample was collected. MIXS:0000874
database_cross_reference: PRIDE:PRIDE

host body-mass index
type: Class
subclass of: body weights and measures
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Body mass index, calculated as weight/(height)squared. MIXS:0000317
has_obo_namespace: PRIDE
id: PRIDE:0000695

Axiom
annotated source: host body-mass index
annotated property: definition
annotated target: Body mass index, calculated as weight/(height)squared. MIXS:0000317
database_cross_reference: PRIDE:PRIDE

ethnicity
type: Class
subclass of: BFO_0000019
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. MIXS:0000895
has_obo_namespace: PRIDE
id: PRIDE:0000696

Axiom
annotated source: ethnicity
annotated property: definition
annotated target: A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. MIXS:0000895
database_cross_reference: PRIDE:PRIDE

host occupation
type: Class
subclass of: Occupation or Discipline
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Most frequent job performed by subject. MIXS:0000896
has_obo_namespace: PRIDE
id: PRIDE:0000697

Axiom
annotated source: host occupation
annotated property: definition
annotated target: Most frequent job performed by subject. MIXS:0000896
database_cross_reference: PRIDE:PRIDE

medical history performed
type: Class
subclass of: Healthcare Activity
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Whether full medical history was collected. MIXS:0000897
has_obo_namespace: PRIDE
id: PRIDE:0000698

Axiom
annotated source: medical history performed
annotated property: definition
annotated target: Whether full medical history was collected. MIXS:0000897
database_cross_reference: PRIDE:PRIDE

host pulse
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Resting pulse, measured as beats per minutes. MIXS:0000333
has_obo_namespace: PRIDE
id: PRIDE:0000699

Axiom
annotated source: host pulse
annotated property: definition
annotated target: Resting pulse, measured as beats per minutes. MIXS:0000333
database_cross_reference: PRIDE:PRIDE

perturbation
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types. MIXS:0000754
has_obo_namespace: PRIDE
id: PRIDE:0000700

Axiom
annotated source: perturbation
annotated property: definition
annotated target: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types. MIXS:0000754
database_cross_reference: PRIDE:PRIDE

salinity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater. MIXS:0000183
has_obo_namespace: PRIDE
id: PRIDE:0000701

Axiom
annotated source: salinity
annotated property: definition
annotated target: The total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater. MIXS:0000183
database_cross_reference: PRIDE:PRIDE

oxygenation status of sample
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Oxygenation status of the sample. MIXS:0000753
has_obo_namespace: PRIDE
id: PRIDE:0000702

Axiom
annotated source: oxygenation status of sample
annotated property: definition
annotated target: Oxygenation status of the sample. MIXS:0000753
database_cross_reference: PRIDE:PRIDE

temperature
type: Class
subclass of: Characteristic
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Temperature of the sample at the time of sampling. MIXS:0000113
has_obo_namespace: PRIDE
id: PRIDE:0000703

Axiom
annotated source: temperature
annotated property: definition
annotated target: Temperature of the sample at the time of sampling. MIXS:0000113
database_cross_reference: PRIDE:PRIDE

organism count
type: Class
subclass of: MMO_0000222
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr). MIXS:0000103
has_obo_namespace: PRIDE
id: PRIDE:0000704

Axiom
annotated source: organism count
annotated property: definition
annotated target: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr). MIXS:0000103
database_cross_reference: PRIDE:PRIDE

sample storage temperature
type: Class
subclass of: Log
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Temperature at which sample was stored, e.g. -80 degree Celsius. MIXS:0000110
has_obo_namespace: PRIDE
id: PRIDE:0000705

Axiom
annotated source: sample storage temperature
annotated property: definition
annotated target: Temperature at which sample was stored, e.g. -80 degree Celsius. MIXS:0000110
database_cross_reference: PRIDE:PRIDE

sample volume or weight for DNA extraction
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001). MIXS:0000111
has_obo_namespace: PRIDE
id: PRIDE:0000706

Axiom
annotated source: sample volume or weight for DNA extraction
annotated property: definition
annotated target: Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001). MIXS:0000111
database_cross_reference: PRIDE:PRIDE

sample storage duration
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. MIXS:0000116
has_obo_namespace: PRIDE
id: PRIDE:0000707

Axiom
annotated source: sample storage duration
annotated property: definition
annotated target: Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. MIXS:0000116
database_cross_reference: PRIDE:PRIDE

observed host symbionts
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite). MIXS:0001298
has_obo_namespace: PRIDE
id: PRIDE:0000708

Axiom
annotated source: observed host symbionts
annotated property: definition
annotated target: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite). MIXS:0001298
database_cross_reference: PRIDE:PRIDE

sample storage location
type: Class
subclass of: GENEPIO_0100586
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
definition: Location at which sample was stored, usually name of a specific freezer/room. MIXS:0000755
has_obo_namespace: PRIDE
id: PRIDE:0000709

Axiom
annotated source: sample storage location
annotated property: definition
annotated target: Location at which sample was stored, usually name of a specific freezer/room. MIXS:0000755
database_cross_reference: PRIDE:PRIDE

miscellaneous parameter
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: human gut
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Any other measurement performed or parameter collected, that is not listed here. MIXS:0000752
has_obo_namespace: PRIDE
id: PRIDE:0000710

Axiom
annotated source: miscellaneous parameter
annotated property: definition
annotated target: Any other measurement performed or parameter collected, that is not listed here. MIXS:0000752
database_cross_reference: PRIDE:PRIDE

depth
type: Class
subclass of: Characteristic
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples MIXS:0000018
has_obo_namespace: PRIDE
id: PRIDE:0000711

Axiom
annotated source: depth
annotated property: definition
annotated target: The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples MIXS:0000018
database_cross_reference: PRIDE:PRIDE

elevation
type: Class
subclass of: PATO_0000140
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit MIXS:0000093
has_obo_namespace: PRIDE
id: PRIDE:0000712

Axiom
annotated source: elevation
annotated property: definition
annotated target: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit MIXS:0000093
database_cross_reference: PRIDE:PRIDE

current land use
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Present state of sample site MIXS:0001080
has_obo_namespace: PRIDE
id: PRIDE:0000713

Axiom
annotated source: current land use
annotated property: definition
annotated target: Present state of sample site MIXS:0001080
database_cross_reference: PRIDE:PRIDE

current vegetation
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Vegetation classification from one or more standard classification systems, or agricultural crop MIXS:0000312
has_obo_namespace: PRIDE
id: PRIDE:0000714

Axiom
annotated source: current vegetation
annotated property: definition
annotated target: Vegetation classification from one or more standard classification systems, or agricultural crop MIXS:0000312
database_cross_reference: PRIDE:PRIDE

current vegetation method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in vegetation classification MIXS:0000314
has_obo_namespace: PRIDE
id: PRIDE:0000715

Axiom
annotated source: current vegetation method
annotated property: definition
annotated target: Reference or method used in vegetation classification MIXS:0000314
database_cross_reference: PRIDE:PRIDE

history of previous land use
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Previous land use and dates MIXS:0000315
has_obo_namespace: PRIDE
id: PRIDE:0000716

Axiom
annotated source: history of previous land use
annotated property: definition
annotated target: Previous land use and dates MIXS:0000315
database_cross_reference: PRIDE:PRIDE

history of previous land use method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining previous land use and dates MIXS:0000316
has_obo_namespace: PRIDE
id: PRIDE:0000717

Axiom
annotated source: history of previous land use method
annotated property: definition
annotated target: Reference or method used in determining previous land use and dates MIXS:0000316
database_cross_reference: PRIDE:PRIDE

history of crop rotation
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Whether or not crop is rotated, and if yes, rotation schedule MIXS:0000318
has_obo_namespace: PRIDE
id: PRIDE:0000718

Axiom
annotated source: history of crop rotation
annotated property: definition
annotated target: Whether or not crop is rotated, and if yes, rotation schedule MIXS:0000318
database_cross_reference: PRIDE:PRIDE

history of agrochemical additions
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Addition of fertilizers, pesticides, etc. - amount and time of applications MIXS:0000639
has_obo_namespace: PRIDE
id: PRIDE:0000719

Axiom
annotated source: history of agrochemical additions
annotated property: definition
annotated target: Addition of fertilizers, pesticides, etc. - amount and time of applications MIXS:0000639
database_cross_reference: PRIDE:PRIDE

history of tillage
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Note method(s) used for tilling MIXS:0001081
has_obo_namespace: PRIDE
id: PRIDE:0000720

Axiom
annotated source: history of tillage
annotated property: definition
annotated target: Note method(s) used for tilling MIXS:0001081
database_cross_reference: PRIDE:PRIDE

history of fire
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Historical and/or physical evidence of fire MIXS:0001086
has_obo_namespace: PRIDE
id: PRIDE:0000721

Axiom
annotated source: history of fire
annotated property: definition
annotated target: Historical and/or physical evidence of fire MIXS:0001086
database_cross_reference: PRIDE:PRIDE

history of flooding
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Historical and/or physical evidence of flooding MIXS:0000319
has_obo_namespace: PRIDE
id: PRIDE:0000722

Axiom
annotated source: history of flooding
annotated property: definition
annotated target: Historical and/or physical evidence of flooding MIXS:0000319
database_cross_reference: PRIDE:PRIDE

history of extreme event
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Unusual physical events that may have affected microbial populations MIXS:0000320
has_obo_namespace: PRIDE
id: PRIDE:0000723

Axiom
annotated source: history of extreme event
annotated property: definition
annotated target: Unusual physical events that may have affected microbial populations MIXS:0000320
database_cross_reference: PRIDE:PRIDE

soil horizon
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath MIXS:0001082
has_obo_namespace: PRIDE
id: PRIDE:0000724

Axiom
annotated source: soil horizon
annotated property: definition
annotated target: Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath MIXS:0001082
database_cross_reference: PRIDE:PRIDE

horizon method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining the horizon MIXS:0000321
has_obo_namespace: PRIDE
id: PRIDE:0000725

Axiom
annotated source: horizon method
annotated property: definition
annotated target: Reference or method used in determining the horizon MIXS:0000321
database_cross_reference: PRIDE:PRIDE

sieving
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Collection design of pooled samples and/or sieve size and amount of sample sieved MIXS:0000322
has_obo_namespace: PRIDE
id: PRIDE:0000726

Axiom
annotated source: sieving
annotated property: definition
annotated target: Collection design of pooled samples and/or sieve size and amount of sample sieved MIXS:0000322
database_cross_reference: PRIDE:PRIDE

water content
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Water content measurement MIXS:0000185
has_obo_namespace: PRIDE
id: PRIDE:0000727

Axiom
annotated source: water content
annotated property: definition
annotated target: Water content measurement MIXS:0000185
database_cross_reference: PRIDE:PRIDE

water content method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining the water content of soil MIXS:0000323
has_obo_namespace: PRIDE
id: PRIDE:0000728

Axiom
annotated source: water content method
annotated property: definition
annotated target: Reference or method used in determining the water content of soil MIXS:0000323
database_cross_reference: PRIDE:PRIDE

pooling of DNA extracts
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given MIXS:0000325
has_obo_namespace: PRIDE
id: PRIDE:0000729

Axiom
annotated source: pooling of DNA extracts
annotated property: definition
annotated target: Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given MIXS:0000325
database_cross_reference: PRIDE:PRIDE

storage conditions
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) MIXS:0000327
has_obo_namespace: PRIDE
id: PRIDE:0000730

Axiom
annotated source: storage conditions
annotated property: definition
annotated target: Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) MIXS:0000327
database_cross_reference: PRIDE:PRIDE

link to climate information
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Link to climate resource MIXS:0000328
has_obo_namespace: PRIDE
id: PRIDE:0000731

Axiom
annotated source: link to climate information
annotated property: definition
annotated target: Link to climate resource MIXS:0000328
database_cross_reference: PRIDE:PRIDE

mean annual temperature
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Mean annual temperature MIXS:0000642
has_obo_namespace: PRIDE
id: PRIDE:0000732

Axiom
annotated source: mean annual temperature
annotated property: definition
annotated target: Mean annual temperature MIXS:0000642
database_cross_reference: PRIDE:PRIDE

mean seasonal temperature
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Mean seasonal temperature MIXS:0000643
has_obo_namespace: PRIDE
id: PRIDE:0000733

Axiom
annotated source: mean seasonal temperature
annotated property: definition
annotated target: Mean seasonal temperature MIXS:0000643
database_cross_reference: PRIDE:PRIDE

mean annual precipitation
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000644
has_obo_namespace: PRIDE
id: PRIDE:0000734

Axiom
annotated source: mean annual precipitation
annotated property: definition
annotated target: The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000644
database_cross_reference: PRIDE:PRIDE

mean seasonal precipitation
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000645
has_obo_namespace: PRIDE
id: PRIDE:0000735

Axiom
annotated source: mean seasonal precipitation
annotated property: definition
annotated target: The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000645
database_cross_reference: PRIDE:PRIDE

link to classification information
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Link to digitized soil maps or other soil classification information MIXS:0000329
has_obo_namespace: PRIDE
id: PRIDE:0000736

Axiom
annotated source: link to classification information
annotated property: definition
annotated target: Link to digitized soil maps or other soil classification information MIXS:0000329
database_cross_reference: PRIDE:PRIDE

soil taxonomic of FAO classification
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Soil classification from the FAO World soil distribution from International Soil Reference and Information Centre (ISRIC). The list of available soil classifications can be found at https://www.isric.org/explore/world-soil-distribution MIXS:0001083
has_obo_namespace: PRIDE
id: PRIDE:0000737

Axiom
annotated source: soil taxonomic of FAO classification
annotated property: definition
annotated target: Soil classification from the FAO World soil distribution from International Soil Reference and Information Centre (ISRIC). The list of available soil classifications can be found at https://www.isric.org/explore/world-soil-distribution MIXS:0001083
database_cross_reference: PRIDE:PRIDE

soil taxonomic of local classification
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Soil classification based on local soil classification system MIXS:0000330
has_obo_namespace: PRIDE
id: PRIDE:0000738

Axiom
annotated source: soil taxonomic of local classification
annotated property: definition
annotated target: Soil classification based on local soil classification system MIXS:0000330
database_cross_reference: PRIDE:PRIDE

soil taxonomic of local classification method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining the local soil classification MIXS:0000331
has_obo_namespace: PRIDE
id: PRIDE:0000739

Axiom
annotated source: soil taxonomic of local classification method
annotated property: definition
annotated target: Reference or method used in determining the local soil classification MIXS:0000331
database_cross_reference: PRIDE:PRIDE

slope gradient
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer MIXS:0000646
has_obo_namespace: PRIDE
id: PRIDE:0000740

Axiom
annotated source: slope gradient
annotated property: definition
annotated target: Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer MIXS:0000646
database_cross_reference: PRIDE:PRIDE

slope aspect
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration MIXS:0000647
has_obo_namespace: PRIDE
id: PRIDE:0000741

Axiom
annotated source: slope aspect
annotated property: definition
annotated target: The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration MIXS:0000647
database_cross_reference: PRIDE:PRIDE

profile position
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas MIXS:0001084
has_obo_namespace: PRIDE
id: PRIDE:0000742

Axiom
annotated source: profile position
annotated property: definition
annotated target: Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas MIXS:0001084
database_cross_reference: PRIDE:PRIDE

drainage classification
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Drainage classification from a standard system such as the USDA system MIXS:0001085
has_obo_namespace: PRIDE
id: PRIDE:0000743

Axiom
annotated source: drainage classification
annotated property: definition
annotated target: Drainage classification from a standard system such as the USDA system MIXS:0001085
database_cross_reference: PRIDE:PRIDE

soil texture
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional MIXS:0000335
has_obo_namespace: PRIDE
id: PRIDE:0000744

Axiom
annotated source: soil texture
annotated property: definition
annotated target: The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional MIXS:0000335
database_cross_reference: PRIDE:PRIDE

soil texture method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining soil texture MIXS:0000336
has_obo_namespace: PRIDE
id: PRIDE:0000745

Axiom
annotated source: soil texture method
annotated property: definition
annotated target: Reference or method used in determining soil texture MIXS:0000336
database_cross_reference: PRIDE:PRIDE

pH
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid MIXS:0001001
has_obo_namespace: PRIDE
id: PRIDE:0000746

Axiom
annotated source: pH
annotated property: definition
annotated target: Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid MIXS:0001001
database_cross_reference: PRIDE:PRIDE

pH method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining pH MIXS:0001106
has_obo_namespace: PRIDE
id: PRIDE:0000747

Axiom
annotated source: pH method
annotated property: definition
annotated target: Reference or method used in determining pH MIXS:0001106
database_cross_reference: PRIDE:PRIDE

organic matter
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Concentration of organic matter MIXS:0000204
has_obo_namespace: PRIDE
id: PRIDE:0000748

Axiom
annotated source: organic matter
annotated property: definition
annotated target: Concentration of organic matter MIXS:0000204
database_cross_reference: PRIDE:PRIDE

total organic carbon
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Total organic carbon content MIXS:0000533
has_obo_namespace: PRIDE
id: PRIDE:0000749

Axiom
annotated source: total organic carbon
annotated property: definition
annotated target: Total organic carbon content MIXS:0000533
database_cross_reference: PRIDE:PRIDE

total organic carbon method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining total organic carbon MIXS:0000337
has_obo_namespace: PRIDE
id: PRIDE:0000750

Axiom
annotated source: total organic carbon method
annotated property: definition
annotated target: Reference or method used in determining total organic carbon MIXS:0000337
database_cross_reference: PRIDE:PRIDE

total nitrogen content
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Total nitrogen content of the sample MIXS:0000530
has_obo_namespace: PRIDE
id: PRIDE:0000751

Axiom
annotated source: total nitrogen content
annotated property: definition
annotated target: Total nitrogen content of the sample MIXS:0000530
database_cross_reference: PRIDE:PRIDE

total nitrogen content method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining the total nitrogen MIXS:0000338
has_obo_namespace: PRIDE
id: PRIDE:0000752

Axiom
annotated source: total nitrogen content method
annotated property: definition
annotated target: Reference or method used in determining the total nitrogen MIXS:0000338
database_cross_reference: PRIDE:PRIDE

microbial biomass
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units MIXS:0000650
has_obo_namespace: PRIDE
id: PRIDE:0000753

Axiom
annotated source: microbial biomass
annotated property: definition
annotated target: The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units MIXS:0000650
database_cross_reference: PRIDE:PRIDE

microbial biomass method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining microbial biomass MIXS:0000339
has_obo_namespace: PRIDE
id: PRIDE:0000754

Axiom
annotated source: microbial biomass method
annotated property: definition
annotated target: Reference or method used in determining microbial biomass MIXS:0000339
database_cross_reference: PRIDE:PRIDE

links to additional analysis
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Link to additional analysis results performed on the sample MIXS:0000340
has_obo_namespace: PRIDE
id: PRIDE:0000755

Axiom
annotated source: links to additional analysis
annotated property: definition
annotated target: Link to additional analysis results performed on the sample MIXS:0000340
database_cross_reference: PRIDE:PRIDE

extreme unusual properties of heavy metals
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field MIXS:0000652
has_obo_namespace: PRIDE
id: PRIDE:0000756

Axiom
annotated source: extreme unusual properties of heavy metals
annotated property: definition
annotated target: Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field MIXS:0000652
database_cross_reference: PRIDE:PRIDE

extreme unusual properties of heavy metals method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining heavy metals MIXS:0000343
has_obo_namespace: PRIDE
id: PRIDE:0000757

Axiom
annotated source: extreme unusual properties of heavy metals method
annotated property: definition
annotated target: Reference or method used in determining heavy metals MIXS:0000343
database_cross_reference: PRIDE:PRIDE

extreme unusual properties of AI saturation
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Aluminum saturation (esp. For tropical soils) MIXS:0000607
has_obo_namespace: PRIDE
id: PRIDE:0000758

Axiom
annotated source: extreme unusual properties of AI saturation
annotated property: definition
annotated target: Aluminum saturation (esp. For tropical soils) MIXS:0000607
database_cross_reference: PRIDE:PRIDE

extreme unusual properties of AI saturation method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Reference or method used in determining Al saturation MIXS:0000324
has_obo_namespace: PRIDE
id: PRIDE:0000759

Axiom
annotated source: extreme unusual properties of AI saturation method
annotated property: definition
annotated target: Reference or method used in determining Al saturation MIXS:0000324
database_cross_reference: PRIDE:PRIDE

alkalinity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate MIXS:0000421
has_obo_namespace: PRIDE
id: PRIDE:0000760

Axiom
annotated source: alkalinity
annotated property: definition
annotated target: Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate MIXS:0000421
database_cross_reference: PRIDE:PRIDE

alkalinity method
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Method used for alkalinity measurement MIXS:0000298
has_obo_namespace: PRIDE
id: PRIDE:0000761

Axiom
annotated source: alkalinity method
annotated property: definition
annotated target: Method used for alkalinity measurement MIXS:0000298
database_cross_reference: PRIDE:PRIDE

alkyl diethers
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of alkyl diethers MIXS:0000490
has_obo_namespace: PRIDE
id: PRIDE:0000762

Axiom
annotated source: alkyl diethers
annotated property: definition
annotated target: Concentration of alkyl diethers MIXS:0000490
database_cross_reference: PRIDE:PRIDE

aminopeptidase activity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of aminopeptidase activity MIXS:0000172
has_obo_namespace: PRIDE
id: PRIDE:0000763

Axiom
annotated source: aminopeptidase activity
annotated property: definition
annotated target: Measurement of aminopeptidase activity MIXS:0000172
database_cross_reference: PRIDE:PRIDE

ammonium
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of ammonium in the sample MIXS:0000427
has_obo_namespace: PRIDE
id: PRIDE:0000764

Axiom
annotated source: ammonium
annotated property: definition
annotated target: Concentration of ammonium in the sample MIXS:0000427
database_cross_reference: PRIDE:PRIDE

atmospheric data
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of atmospheric data; can include multiple data MIXS:0001097
has_obo_namespace: PRIDE
id: PRIDE:0000765

Axiom
annotated source: atmospheric data
annotated property: definition
annotated target: Measurement of atmospheric data; can include multiple data MIXS:0001097
database_cross_reference: PRIDE:PRIDE

bacterial carbon production
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of bacterial carbon production MIXS:0000173
has_obo_namespace: PRIDE
id: PRIDE:0000766

Axiom
annotated source: bacterial carbon production
annotated property: definition
annotated target: Measurement of bacterial carbon production MIXS:0000173
database_cross_reference: PRIDE:PRIDE

bacterial production
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Bacterial production in the water column measured by isotope uptake MIXS:0000683
has_obo_namespace: PRIDE
id: PRIDE:0000767

Axiom
annotated source: bacterial production
annotated property: definition
annotated target: Bacterial production in the water column measured by isotope uptake MIXS:0000683
database_cross_reference: PRIDE:PRIDE

bacterial respiration
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of bacterial respiration in the water column MIXS:0000684
has_obo_namespace: PRIDE
id: PRIDE:0000768

Axiom
annotated source: bacterial respiration
annotated property: definition
annotated target: Measurement of bacterial respiration in the water column MIXS:0000684
database_cross_reference: PRIDE:PRIDE

biomass
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements MIXS:0000174
has_obo_namespace: PRIDE
id: PRIDE:0000769

Axiom
annotated source: biomass
annotated property: definition
annotated target: Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements MIXS:0000174
database_cross_reference: PRIDE:PRIDE

bishomohopanol
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of bishomohopanol MIXS:0000175
has_obo_namespace: PRIDE
id: PRIDE:0000770

Axiom
annotated source: bishomohopanol
annotated property: definition
annotated target: Concentration of bishomohopanol MIXS:0000175
database_cross_reference: PRIDE:PRIDE

bromide
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of bromide MIXS:0000176
has_obo_namespace: PRIDE
id: PRIDE:0000771

Axiom
annotated source: bromide
annotated property: definition
annotated target: Concentration of bromide MIXS:0000176
database_cross_reference: PRIDE:PRIDE

calcium
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of calcium in the sample MIXS:0000432
has_obo_namespace: PRIDE
id: PRIDE:0000772

Axiom
annotated source: calcium
annotated property: definition
annotated target: Concentration of calcium in the sample MIXS:0000432
database_cross_reference: PRIDE:PRIDE

carbon nitrogen ratio
type: Class
definition: Ratio of amount or concentrations of carbon to nitrogen MIXS:0000310
has_obo_namespace: PRIDE
id: PRIDE:0000773

Axiom
annotated source: carbon nitrogen ratio
annotated property: definition
annotated target: Ratio of amount or concentrations of carbon to nitrogen MIXS:0000310
database_cross_reference: PRIDE:PRIDE

chloride
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of chloride in the sample MIXS:0000429
has_obo_namespace: PRIDE
id: PRIDE:0000774

Axiom
annotated source: chloride
annotated property: definition
annotated target: Concentration of chloride in the sample MIXS:0000429
database_cross_reference: PRIDE:PRIDE

chlorophyll
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of chlorophyll MIXS:0000177
has_obo_namespace: PRIDE
id: PRIDE:0000775

Axiom
annotated source: chlorophyll
annotated property: definition
annotated target: Concentration of chlorophyll MIXS:0000177
database_cross_reference: PRIDE:PRIDE

conductivity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Electrical conductivity of water MIXS:0000692
has_obo_namespace: PRIDE
id: PRIDE:0000776

Axiom
annotated source: conductivity
annotated property: definition
annotated target: Electrical conductivity of water MIXS:0000692
database_cross_reference: PRIDE:PRIDE

density
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Density of the sample, which is its mass per unit volume (aka volumetric mass density) MIXS:0000435
has_obo_namespace: PRIDE
id: PRIDE:0000777

Axiom
annotated source: density
annotated property: definition
annotated target: Density of the sample, which is its mass per unit volume (aka volumetric mass density) MIXS:0000435
database_cross_reference: PRIDE:PRIDE

diether lipids
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of diether lipids; can include multiple types of diether lipids MIXS:0000178
has_obo_namespace: PRIDE
id: PRIDE:0000778

Axiom
annotated source: diether lipids
annotated property: definition
annotated target: Concentration of diether lipids; can include multiple types of diether lipids MIXS:0000178
database_cross_reference: PRIDE:PRIDE

dissolved carbon dioxide
type: Class
definition: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample MIXS:0000436
has_obo_namespace: PRIDE
id: PRIDE:0000779

Axiom
annotated source: dissolved carbon dioxide
annotated property: definition
annotated target: Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample MIXS:0000436
database_cross_reference: PRIDE:PRIDE

dissolved hydrogen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of dissolved hydrogen MIXS:0000179
has_obo_namespace: PRIDE
id: PRIDE:0000780

Axiom
annotated source: dissolved hydrogen
annotated property: definition
annotated target: Concentration of dissolved hydrogen MIXS:0000179
database_cross_reference: PRIDE:PRIDE

dissolved inorganic carbon
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter MIXS:0000434
has_obo_namespace: PRIDE
id: PRIDE:0000781

Axiom
annotated source: dissolved inorganic carbon
annotated property: definition
annotated target: Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter MIXS:0000434
database_cross_reference: PRIDE:PRIDE

dissolved inorganic nitrogen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of dissolved inorganic nitrogen MIXS:0000698
has_obo_namespace: PRIDE
id: PRIDE:0000784

Axiom
annotated source: dissolved inorganic nitrogen
annotated property: definition
annotated target: Concentration of dissolved inorganic nitrogen MIXS:0000698
database_cross_reference: PRIDE:PRIDE

dissolved inorganic phosphorus
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of dissolved inorganic phosphorus in the sample MIXS:0000106
has_obo_namespace: PRIDE
id: PRIDE:0000785

Axiom
annotated source: dissolved inorganic phosphorus
annotated property: definition
annotated target: Concentration of dissolved inorganic phosphorus in the sample MIXS:0000106
database_cross_reference: PRIDE:PRIDE

dissolved organic carbon
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid MIXS:0000433
has_obo_namespace: PRIDE
id: PRIDE:0000786

Axiom
annotated source: dissolved organic carbon
annotated property: definition
annotated target: Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid MIXS:0000433
database_cross_reference: PRIDE:PRIDE

dissolved organic nitrogen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 MIXS:0000162
has_obo_namespace: PRIDE
id: PRIDE:0000787

Axiom
annotated source: dissolved organic nitrogen
annotated property: definition
annotated target: Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 MIXS:0000162
database_cross_reference: PRIDE:PRIDE

dissolved oxygen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of dissolved oxygen MIXS:0000119
has_obo_namespace: PRIDE
id: PRIDE:0000788

Axiom
annotated source: dissolved oxygen
annotated property: definition
annotated target: Concentration of dissolved oxygen MIXS:0000119
database_cross_reference: PRIDE:PRIDE

downward PAR
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Visible waveband radiance and irradiance measurements in the water column MIXS:0000703
has_obo_namespace: PRIDE
id: PRIDE:0000789

Axiom
annotated source: downward PAR
annotated property: definition
annotated target: Visible waveband radiance and irradiance measurements in the water column MIXS:0000703
database_cross_reference: PRIDE:PRIDE

fluorescence
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Raw or converted fluorescence of water MIXS:0000704
has_obo_namespace: PRIDE
id: PRIDE:0000790

Axiom
annotated source: fluorescence
annotated property: definition
annotated target: Raw or converted fluorescence of water MIXS:0000704
database_cross_reference: PRIDE:PRIDE

glucosidase activity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of glucosidase activity MIXS:0000137
has_obo_namespace: PRIDE
id: PRIDE:0000791

Axiom
annotated source: glucosidase activity
annotated property: definition
annotated target: Measurement of glucosidase activity MIXS:0000137
database_cross_reference: PRIDE:PRIDE

light intensity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of light intensity MIXS:0000706
has_obo_namespace: PRIDE
id: PRIDE:0000792

Axiom
annotated source: light intensity
annotated property: definition
annotated target: Measurement of light intensity MIXS:0000706
database_cross_reference: PRIDE:PRIDE

magnesium
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of magnesium in the sample MIXS:0000431
has_obo_namespace: PRIDE
id: PRIDE:0000793

Axiom
annotated source: magnesium
annotated property: definition
annotated target: Concentration of magnesium in the sample MIXS:0000431
database_cross_reference: PRIDE:PRIDE

mean friction velocity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of mean friction velocity MIXS:0000498
has_obo_namespace: PRIDE
id: PRIDE:0000794

Axiom
annotated source: mean friction velocity
annotated property: definition
annotated target: Measurement of mean friction velocity MIXS:0000498
database_cross_reference: PRIDE:PRIDE

mean peak friction velocity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of mean peak friction velocity MIXS:0000502
has_obo_namespace: PRIDE
id: PRIDE:0000795

Axiom
annotated source: mean peak friction velocity
annotated property: definition
annotated target: Measurement of mean peak friction velocity MIXS:0000502
database_cross_reference: PRIDE:PRIDE

nitrate
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of nitrate in the sample MIXS:0000425
has_obo_namespace: PRIDE
id: PRIDE:0000796

Axiom
annotated source: nitrate
annotated property: definition
annotated target: Concentration of nitrate in the sample MIXS:0000425
database_cross_reference: PRIDE:PRIDE

nitrite
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of nitrite in the sample MIXS:0000426
has_obo_namespace: PRIDE
id: PRIDE:0000797

Axiom
annotated source: nitrite
annotated property: definition
annotated target: Concentration of nitrite in the sample MIXS:0000426
database_cross_reference: PRIDE:PRIDE

nitrogen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of nitrogen (total) MIXS:0000504
has_obo_namespace: PRIDE
id: PRIDE:0000798

Axiom
annotated source: nitrogen
annotated property: definition
annotated target: Concentration of nitrogen (total) MIXS:0000504
database_cross_reference: PRIDE:PRIDE

organic carbon
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of organic carbon MIXS:0000508
has_obo_namespace: PRIDE
id: PRIDE:0000799

Axiom
annotated source: organic carbon
annotated property: definition
annotated target: Concentration of organic carbon MIXS:0000508
database_cross_reference: PRIDE:PRIDE

organic nitrogen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
subclass of: Restriction
  on property: BFO_0000050
  some values from: water
definition: Concentration of organic nitrogen MIXS:0000205
has_obo_namespace: PRIDE
id: PRIDE:0000800

Axiom
annotated source: organic nitrogen
annotated property: definition
annotated target: Concentration of organic nitrogen MIXS:0000205
database_cross_reference: PRIDE:PRIDE

particulate organic carbon
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of particulate organic carbon MIXS:0000515
has_obo_namespace: PRIDE
id: PRIDE:0000801

Axiom
annotated source: particulate organic carbon
annotated property: definition
annotated target: Concentration of particulate organic carbon MIXS:0000515
database_cross_reference: PRIDE:PRIDE

particulate organic nitrogen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of particulate organic nitrogen MIXS:0000719
has_obo_namespace: PRIDE
id: PRIDE:0000802

Axiom
annotated source: particulate organic nitrogen
annotated property: definition
annotated target: Concentration of particulate organic nitrogen MIXS:0000719
database_cross_reference: PRIDE:PRIDE

petroleum hydrocarbon
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of petroleum hydrocarbon MIXS:0000516
has_obo_namespace: PRIDE
id: PRIDE:0000803

Axiom
annotated source: petroleum hydrocarbon
annotated property: definition
annotated target: Concentration of petroleum hydrocarbon MIXS:0000516
database_cross_reference: PRIDE:PRIDE

phaeopigments
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of phaeopigments; can include multiple phaeopigments MIXS:0000180
has_obo_namespace: PRIDE
id: PRIDE:0000804

Axiom
annotated source: phaeopigments
annotated property: definition
annotated target: Concentration of phaeopigments; can include multiple phaeopigments MIXS:0000180
database_cross_reference: PRIDE:PRIDE

phosphate
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of phosphate MIXS:0000505
has_obo_namespace: PRIDE
id: PRIDE:0000805

Axiom
annotated source: phosphate
annotated property: definition
annotated target: Concentration of phosphate MIXS:0000505
database_cross_reference: PRIDE:PRIDE

phospholipid fatty acid
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of phospholipid fatty acids; can include multiple values MIXS:0000181
has_obo_namespace: PRIDE
id: PRIDE:0000806

Axiom
annotated source: phospholipid fatty acid
annotated property: definition
annotated target: Concentration of phospholipid fatty acids; can include multiple values MIXS:0000181
database_cross_reference: PRIDE:PRIDE

photon flux
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of photon flux MIXS:0000725
has_obo_namespace: PRIDE
id: PRIDE:0000807

Axiom
annotated source: photon flux
annotated property: definition
annotated target: Measurement of photon flux MIXS:0000725
database_cross_reference: PRIDE:PRIDE

potassium
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of potassium in the sample MIXS:0000430
has_obo_namespace: PRIDE
id: PRIDE:0000808

Axiom
annotated source: potassium
annotated property: definition
annotated target: Concentration of potassium in the sample MIXS:0000430
database_cross_reference: PRIDE:PRIDE

pressure
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Pressure to which the sample is subject to, in atmospheres MIXS:0000412
has_obo_namespace: PRIDE
id: PRIDE:0000809

Axiom
annotated source: pressure
annotated property: definition
annotated target: Pressure to which the sample is subject to, in atmospheres MIXS:0000412
database_cross_reference: PRIDE:PRIDE

primary production
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of primary production, generally measured as isotope uptake MIXS:0000728
has_obo_namespace: PRIDE
id: PRIDE:0000810

Axiom
annotated source: primary production
annotated property: definition
annotated target: Measurement of primary production, generally measured as isotope uptake MIXS:0000728
database_cross_reference: PRIDE:PRIDE

redox potential
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential MIXS:0000182
has_obo_namespace: PRIDE
id: PRIDE:0000811

Axiom
annotated source: redox potential
annotated property: definition
annotated target: Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential MIXS:0000182
database_cross_reference: PRIDE:PRIDE

silicate
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of silicate MIXS:0000184
has_obo_namespace: PRIDE
id: PRIDE:0000812

Axiom
annotated source: silicate
annotated property: definition
annotated target: Concentration of silicate MIXS:0000184
database_cross_reference: PRIDE:PRIDE

size-fraction lower threshold
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials smaller than the size threshold are excluded from the sample MIXS:0000735
has_obo_namespace: PRIDE
id: PRIDE:0000813

Axiom
annotated source: size-fraction lower threshold
annotated property: definition
annotated target: Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials smaller than the size threshold are excluded from the sample MIXS:0000735
database_cross_reference: PRIDE:PRIDE

size-fraction upper threshold
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Mesh or pore size of the device used to retain the sample. Materials larger than the size threshold are excluded from the sample MIXS:0000736
has_obo_namespace: PRIDE
id: PRIDE:0000814

Axiom
annotated source: size-fraction upper threshold
annotated property: definition
annotated target: Mesh or pore size of the device used to retain the sample. Materials larger than the size threshold are excluded from the sample MIXS:0000736
database_cross_reference: PRIDE:PRIDE

sodium
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Sodium concentration in the sample MIXS:0000428
has_obo_namespace: PRIDE
id: PRIDE:0000815

Axiom
annotated source: sodium
annotated property: definition
annotated target: Sodium concentration in the sample MIXS:0000428
database_cross_reference: PRIDE:PRIDE

soluble reactive phosphorus
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of soluble reactive phosphorus MIXS:0000738
has_obo_namespace: PRIDE
id: PRIDE:0000816

Axiom
annotated source: soluble reactive phosphorus
annotated property: definition
annotated target: Concentration of soluble reactive phosphorus MIXS:0000738
database_cross_reference: PRIDE:PRIDE

sulfate
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of sulfate in the sample MIXS:0000423
has_obo_namespace: PRIDE
id: PRIDE:0000817

Axiom
annotated source: sulfate
annotated property: definition
annotated target: Concentration of sulfate in the sample MIXS:0000423
database_cross_reference: PRIDE:PRIDE

sulfide
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of sulfide in the sample MIXS:0000424
has_obo_namespace: PRIDE
id: PRIDE:0000818

Axiom
annotated source: sulfide
annotated property: definition
annotated target: Concentration of sulfide in the sample MIXS:0000424
database_cross_reference: PRIDE:PRIDE

suspended particulate matter
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Concentration of suspended particulate matter MIXS:0000741
has_obo_namespace: PRIDE
id: PRIDE:0000819

Axiom
annotated source: suspended particulate matter
annotated property: definition
annotated target: Concentration of suspended particulate matter MIXS:0000741
database_cross_reference: PRIDE:PRIDE

tidal stage
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Stage of tide MIXS:0000750
has_obo_namespace: PRIDE
id: PRIDE:0000820

Axiom
annotated source: tidal stage
annotated property: definition
annotated target: Stage of tide MIXS:0000750
database_cross_reference: PRIDE:PRIDE

total depth of water column
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measurement of total depth of water column MIXS:0000634
has_obo_namespace: PRIDE
id: PRIDE:0000821

Axiom
annotated source: total depth of water column
annotated property: definition
annotated target: Measurement of total depth of water column MIXS:0000634
database_cross_reference: PRIDE:PRIDE

total dissolved nitrogen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen MIXS:0000744
has_obo_namespace: PRIDE
id: PRIDE:0000822

Axiom
annotated source: total dissolved nitrogen
annotated property: definition
annotated target: Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen MIXS:0000744
database_cross_reference: PRIDE:PRIDE

total inorganic nitrogen
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Total inorganic nitrogen content MIXS:0000745
has_obo_namespace: PRIDE
id: PRIDE:0000823

Axiom
annotated source: total inorganic nitrogen
annotated property: definition
annotated target: Total inorganic nitrogen content MIXS:0000745
database_cross_reference: PRIDE:PRIDE

total nitrogen concentration
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen MIXS:0000102
has_obo_namespace: PRIDE
id: PRIDE:0000824

Axiom
annotated source: total nitrogen concentration
annotated property: definition
annotated target: Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen MIXS:0000102
database_cross_reference: PRIDE:PRIDE

total particulate carbon
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Total particulate carbon content MIXS:0000747
has_obo_namespace: PRIDE
id: PRIDE:0000825

Axiom
annotated source: total particulate carbon
annotated property: definition
annotated target: Total particulate carbon content MIXS:0000747
database_cross_reference: PRIDE:PRIDE

total phosphorus
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus MIXS:0000117
has_obo_namespace: PRIDE
id: PRIDE:0000826

Axiom
annotated source: total phosphorus
annotated property: definition
annotated target: Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus MIXS:0000117
database_cross_reference: PRIDE:PRIDE

turbidity
type: Class
subclass of: Restriction
  on property: BFO_0000050
  some values from: soil
definition: Measure of the amount of cloudiness or haziness in water caused by individual particles MIXS:0000191
has_obo_namespace: PRIDE
id: PRIDE:0000827

Axiom
annotated source: turbidity
annotated property: definition
annotated target: Measure of the amount of cloudiness or haziness in water caused by individual particles MIXS:0000191
database_cross_reference: PRIDE:PRIDE

soil
type: Class
subclass of: ENVO_00010483
definition: A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust, contributed by the Terragenome Consortium
has_obo_namespace: PRIDE
id: PRIDE:0000828

Axiom
annotated source: soil
annotated property: definition
annotated target: A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust, contributed by the Terragenome Consortium
database_cross_reference: PRIDE:PRIDE

water
type: Class
subclass of: ENVO_00002006
definition: A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment
has_obo_namespace: PRIDE
id: PRIDE:0000829

Axiom
annotated source: water
annotated property: definition
annotated target: A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment
database_cross_reference: PRIDE:PRIDE

Olink Reveal
type: Class
subclass of: Olink instrument model
definition: Olink Reveal is an NGS-based proteomics platform that measures approximately 1,000 proteins with high sensitivity from just 4 µL of sample, using standard lab equipment, with a focus on immune and inflammation markers
has_obo_namespace: PRIDE
id: PRIDE:0000830

Axiom
annotated source: Olink Reveal
annotated property: definition
annotated target: Olink Reveal is an NGS-based proteomics platform that measures approximately 1,000 proteins with high sensitivity from just 4 µL of sample, using standard lab equipment, with a focus on immune and inflammation markers
database_cross_reference: PRIDE:PRIDE

file_format
type: Class
subclass of: File Properties
definition: A defined organization or layout representing and structuring data in a file. The file format specifies how information is encoded, stored, and interpreted within the file.
database_cross_reference: NCIT:C171252
has_obo_namespace: PRIDE
id: PRIDE:0000831

Axiom
annotated source: file_format
annotated property: definition
annotated target: A defined organization or layout representing and structuring data in a file. The file format specifies how information is encoded, stored, and interpreted within the file.
database_cross_reference: PRIDE:PRIDE

template
type: Class
subclass of: File Properties
definition: A checklist of columns and properties that will be applied during a validation process to an SDRF or other PSI standard
has_obo_namespace: PRIDE
id: PRIDE:0000832

Axiom
annotated source: template
annotated property: definition
annotated target: A checklist of columns and properties that will be applied during a validation process to an SDRF or other PSI standard
database_cross_reference: PRIDE:PRIDE

template_version
type: Class
subclass of: File Properties
definition: The specific version of a template
has_obo_namespace: PRIDE
id: PRIDE:0000833

Axiom
annotated source: template_version
annotated property: definition
annotated target: The specific version of a template
database_cross_reference: PRIDE:PRIDE

validation_hash
type: Class
subclass of: File Properties
definition: A hash generated after validating an SDRF dataset; this is helpful to understand if one file has been validated or not
has_obo_namespace: PRIDE
id: PRIDE:0000834

Axiom
annotated source: validation_hash
annotated property: definition
annotated target: A hash generated after validating an SDRF dataset; this is helpful to understand if one file has been validated or not
database_cross_reference: PRIDE:PRIDE

cellosaurus accession
type: Class
subclass of: Sample description additional parameter
definition: An accession to a cellosaurus cell line that could be use to annotate SDRF samples
has_obo_namespace: PRIDE
id: PRIDE:0000835

Axiom
annotated source: cellosaurus accession
annotated property: definition
annotated target: An accession to a cellosaurus cell line that could be use to annotate SDRF samples
database_cross_reference: PRIDE:PRIDE

cellosaurus name
type: Class
subclass of: Sample description additional parameter
definition: A name to a cellosaurus cell line that could be use to annotate SDRF samples
has_obo_namespace: PRIDE
id: PRIDE:0000836

Axiom
annotated source: cellosaurus name
annotated property: definition
annotated target: A name to a cellosaurus cell line that could be use to annotate SDRF samples
database_cross_reference: PRIDE:PRIDE