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Metaproteomics term added #145

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Metaproteomics term added #145

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nithujohn
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@nithujohn nithujohn commented Feb 20, 2025 •
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User description

Added soil and water MIXs package

PR Type

Enhancement

Description

  • Updated references from BF_0000001 to BFO_0000001 across multiple ontology terms.

  • Removed unused ontology class BF_0000001 from the file.

  • Improved consistency in ontology hierarchy definitions.

Changes walkthrough 📝

Relevant files
Enhancement
pride_cv.owl
Updated ontology references and removed unused class         

pride_cv.owl

  • Replaced BF_0000001 with BFO_0000001 in subclass references.
  • Removed the unused ontology class BF_0000001.
  • Ensured consistent ontology hierarchy definitions.
    		• +6/-12   
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    Ontology Consistency

    Verify that all references to BFO_0000001 are appropriate for the ontology hierarchy and that no other BF_ prefixed terms remain in the ontology

        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
    <obo:IAO_0000115>Root node for terms relating to the description of a protocol as ordered steps</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000001</oboInOwl:id>
    <rdfs:label>Protocol step description additional parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Root node for terms relating to the description of a protocol as ordered steps</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000002 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000002">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
    <obo:IAO_0000115>Root node for terms relating to the description of a ModificationItem</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000002</oboInOwl:id>
    <rdfs:label>ModificationItem additional parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000002"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Root node for terms relating to the description of a ModificationItem</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000003 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000003">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
    <obo:IAO_0000115>Root node for terms relating to the description of a PeptideItem</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000003</oboInOwl:id>
    <rdfs:label>Peptide item additional parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000003"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Root node for terms relating to the description of a PeptideItem</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000004 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000004">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
    <obo:IAO_0000115>Root node for terms relating to the description of an Identification</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000004</oboInOwl:id>
    <rdfs:label>Identification additional parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000004"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Root node for terms relating to the description of an Identification</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000005 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000005">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
    <obo:IAO_0000115>Root node for terms relating to the description of a Gel parameter</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000005</oboInOwl:id>
    <rdfs:label>Gel additional parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000005"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Root node for terms relating to the description of a Gel parameter</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000006 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000006">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
    <obo:IAO_0000115>Root node for terms relating to the description of an Experiment</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000006</oboInOwl:id>
    <rdfs:label>Experiment additional parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000006"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Root node for terms relating to the description of an Experiment</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000007 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000007">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
    <obo:IAO_0000115>Version number or identifier for search engine</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000007</oboInOwl:id>
    <rdfs:label>SearchEngineVersion</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000007"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Version number or identifier for search engine</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000008 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000008">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000004"/>
    <obo:IAO_0000115>Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000008</oboInOwl:id>
    <rdfs:label>Protein search engine output parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000008"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000009 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000009">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000008"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000009</oboInOwl:id>
    <rdfs:label>Ion mass tolerance</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000009"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000010 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000010">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000009"/>
    <obo:IAO_0000115>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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000010</oboInOwl:id>
    <rdfs:label>Precursor ion mass tolerance</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000010"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000011 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000011">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000009"/>
    <obo:IAO_0000115>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)</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000011</oboInOwl:id>
    <rdfs:label>MS2 ion mass tolerance</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000011"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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)</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000012 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000012">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000008"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>1.0 - normalized correlation score</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000012</oboInOwl:id>
    <rdfs:label>Delta Cn</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000012"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>1.0 - normalized correlation score</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000013 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000013">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000008"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000013</oboInOwl:id>
    <rdfs:label>X correlation</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000013"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000014 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000014">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000013"/>
    <obo:IAO_0000115>XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000014</oboInOwl:id>
    <rdfs:label>X correlation (+1)</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000014"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000015 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000015">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000013"/>
    <obo:IAO_0000115>XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000015</oboInOwl:id>
    <rdfs:label>X correlation (+2)</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000015"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000016 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000016">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000013"/>
    <obo:IAO_0000115>XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000016</oboInOwl:id>
    <rdfs:label>X correlation (+3)</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000016"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000017 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000017">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
    <obo:IAO_0000115>Root term for parameters in the context of ExperimentCollection</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000017</oboInOwl:id>
    <rdfs:label>Sample description additional parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000017"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Root term for parameters in the context of ExperimentCollection</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000018 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000018">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000017"/>
    <obo:IAO_0000115>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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000018</oboInOwl:id>
    <rdfs:label>Disease free</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000018"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000019 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000019">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>To make something soluble or more soluble, especially in water, by the action of a detergent or other agent</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000019</oboInOwl:id>
    <rdfs:label>Solubilization</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000019"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>To make something soluble or more soluble, especially in water, by the action of a detergent or other agent</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000020 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000020">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000020</oboInOwl:id>
    <rdfs:label>Depletion</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000020"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000021 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000021">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>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)</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000021</oboInOwl:id>
    <rdfs:label>Fractionation</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000021"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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)</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000022 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000022">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000022</oboInOwl:id>
    <rdfs:label>Separation</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000022"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000023 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000023">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>The removal of a region of a gel which contains protein(s) of interest</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000023</oboInOwl:id>
    <rdfs:label>Band excision</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000023"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>The removal of a region of a gel which contains protein(s) of interest</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000024 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000024">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>The fragmentation of proteins into peptides through the use of an enzyme such as Trypsin</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000024</oboInOwl:id>
    <rdfs:label>Enzyme digestion</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000024"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>The fragmentation of proteins into peptides through the use of an enzyme such as Trypsin</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000025 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000025">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000025</oboInOwl:id>
    <rdfs:label>Reduction</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000025"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000026 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000026">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>The transfer of an alkyl group from one molecule to another</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000026</oboInOwl:id>
    <rdfs:label>Alkylation</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000026"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>The transfer of an alkyl group from one molecule to another</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000027 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000027">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000027</oboInOwl:id>
    <rdfs:label>Mass spectrometry</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000027"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000028 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000028">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>Valid values for cvLabel entries referencing external database or ontology</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000028</oboInOwl:id>
    <rdfs:label>Cv Label</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid values for cvLabel entries referencing external database or ontology</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000029 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000029">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000029</oboInOwl:id>
    <rdfs:label>PubMed</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000029"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000030 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000030">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing PRIDE</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000030</oboInOwl:id>
    <rdfs:label>PRIDE</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000030"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing PRIDE</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000031 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000031">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing GO</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000031</oboInOwl:id>
    <rdfs:label>GO</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000031"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing GO</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000032 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000032">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH)</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000032</oboInOwl:id>
    <rdfs:label>MeSH</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000032"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH)</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000033 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000033">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000033</oboInOwl:id>
    <rdfs:label>NEWT</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000033"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000034 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000034">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing the PSI ontology</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000034</oboInOwl:id>
    <rdfs:label>PSI</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000034"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing the PSI ontology</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000035 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000035">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing UNIMOD</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000035</oboInOwl:id>
    <rdfs:label>UNIMOD</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000035"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing UNIMOD</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000036 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000036">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing RESID</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000036</oboInOwl:id>
    <rdfs:label>RESID</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000036"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing RESID</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000037 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000037">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000037</oboInOwl:id>
    <rdfs:label>Staining</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000037"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000038 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000038">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing ISBN</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000038</oboInOwl:id>
    <rdfs:label>ISBN</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000038"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing ISBN</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000039 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000039">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000001"/>
    <obo:IAO_0000115>Any technique which separates differentiated structures from the cell</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000039</oboInOwl:id>
    <rdfs:label>Organelle isolation</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000039"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Any technique which separates differentiated structures from the cell</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000040 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000040">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000006"/>
    <obo:IAO_0000115>This CV term should be used in association with a value that is a free-text description of the experiment</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000040</oboInOwl:id>
    <rdfs:label>Experiment description</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000040"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>This CV term should be used in association with a value that is a free-text description of the experiment</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000041 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000041">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000004"/>
    <obo:IAO_0000115>Database used to search the protein sequence</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000041</oboInOwl:id>
    <rdfs:label>Search database protein sequence</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000041"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Database used to search the protein sequence</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000042 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000042">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>The DOI system provides a persistent link to the journal&apos;s location on the internet, even if the URL changes</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000042</oboInOwl:id>
    <rdfs:label>DOI</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000042"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>The DOI system provides a persistent link to the journal&apos;s location on the internet, even if the URL changes</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000043 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000043">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000028"/>
    <obo:IAO_0000115>Valid value for the cvLabel entry referencing FIX</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000043</oboInOwl:id>
    <rdfs:label>FIX</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000043"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Valid value for the cvLabel entry referencing FIX</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000044 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000044">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000004"/>
    <obo:IAO_0000115>A method used to retrieve specific data from a collection of data, based on a given criterion</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000044</oboInOwl:id>
    <rdfs:label>Search algorithm</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000044"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>A method used to retrieve specific data from a collection of data, based on a given criterion</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000045 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000045">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000044"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000573"/>
    <obo:IAO_0000115>Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000045</oboInOwl:id>
    <rdfs:label>Sequest</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000046 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000046">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000044"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000571"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000573"/>
    <obo:IAO_0000115>Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000046</oboInOwl:id>
    <rdfs:label>Mascot</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000046"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000047 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000047">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000044"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000573"/>
    <obo:IAO_0000115>X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000047</oboInOwl:id>
    <rdfs:label>X</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000047"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000048 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000048">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000004"/>
    <obo:IAO_0000115>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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000048</oboInOwl:id>
    <rdfs:label>Output parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000048"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000049 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000049">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000003"/>
    <obo:IAO_0000115>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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000049</oboInOwl:id>
    <rdfs:label>Peptide search engine output parameter</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000050 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000050">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>Final correlation score rank and preliminary score rank</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000050</oboInOwl:id>
    <rdfs:label>Rank/Sp</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000050"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Final correlation score rank and preliminary score rank</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000051 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000051">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>M/z of the singly-charged precursor (precursor mass + mass of hydrogen atom)</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000051</oboInOwl:id>
    <rdfs:label>(M+H)+</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000051"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>M/z of the singly-charged precursor (precursor mass + mass of hydrogen atom)</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000052 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000052">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>Normalized correlation score</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000052</oboInOwl:id>
    <rdfs:label>Cn</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000052"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Normalized correlation score</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000053 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000053">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000008"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>Raw correlation score (Sequest)</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000053</oboInOwl:id>
    <rdfs:label>Sequest score</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000053"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Raw correlation score (Sequest)</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000054 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000054">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>Preliminary score</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000054</oboInOwl:id>
    <rdfs:label>Sp</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000054"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Preliminary score</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000055 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000055">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>The number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000055</oboInOwl:id>
    <rdfs:label>Ions</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000055"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>The number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000056 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000056">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000045"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000573"/>
    <obo:IAO_0000115>A companion tool often used for processing and analyzing mass spectrometry data</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000056</oboInOwl:id>
    <rdfs:label>Bioworks</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000056"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>A companion tool often used for processing and analyzing mass spectrometry data</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000057 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000057">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000008"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000056"/>
    <obo:IAO_0000115>Molecular weight of a protein</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000057</oboInOwl:id>
    <rdfs:label>Molecular weight</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000057"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Molecular weight of a protein</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000058 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000058">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000056"/>
    <obo:IAO_0000115>Bioworks z score</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000058</oboInOwl:id>
    <rdfs:label>z score</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000058"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Bioworks z score</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000059 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000059">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>File is a digital container used to store information on a computer or other electronic device</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000059</oboInOwl:id>
    <rdfs:label>File</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000059"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>File is a digital container used to store information on a computer or other electronic device</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000060 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000060">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <obo:IAO_0000115>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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000060</oboInOwl:id>
    <rdfs:label>Scan</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000060"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000061 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000061">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000008"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000056"/>
    <obo:IAO_0000115>Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000061</oboInOwl:id>
    <rdfs:label>Coverage</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000061"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000062 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000062">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000049"/>
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000056"/>
    <obo:IAO_0000115>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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000062</oboInOwl:id>
    <rdfs:label>rsp</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000062"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000063 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000063">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000004"/>
    <obo:IAO_0000115>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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000063</oboInOwl:id>
    <rdfs:label>Protein description line</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000063"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000064 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000064">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000004"/>
    <obo:IAO_0000115>A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000064</oboInOwl:id>
    <rdfs:label>Secondary accession</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000064"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000065 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000065">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000003"/>
    <obo:IAO_0000115>Any sequence reported before the start of the peptide</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000065</oboInOwl:id>
    <rdfs:label>Upstream flanking sequence</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000065"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Any sequence reported before the start of the peptide</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000066 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000066">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000003"/>
    <obo:IAO_0000115>Any sequence reported after the end of the peptide sequence</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000066</oboInOwl:id>
    <rdfs:label>Downstream flanking seqeuence</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000066"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Any sequence reported after the end of the peptide sequence</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/PRIDE_0000067 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000067">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000000"/>
    <obo:IAO_0000115>Referencing an experiment in scientific contexts, it&apos;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</obo:IAO_0000115>
    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
    <oboInOwl:id>PRIDE:0000067</oboInOwl:id>
    <rdfs:label>Reference reporting this experiment</rdfs:label>
</owl:Class>
<owl:Axiom>
    <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/PRIDE_0000067"/>
    <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
    <owl:annotatedTarget>Referencing an experiment in scientific contexts, it&apos;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</owl:annotatedTarget>
    <oboInOwl:hasDbXref>PRIDE:PRIDE</oboInOwl:hasDbXref>
</owl:Axiom>



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    Possible issue
    Verify complete ontology class migration

    Verify that all classes that previously inherited from BF_0000001 have been
    properly updated to inherit from BFO_0000001. Some classes might have been
    missed in the migration.

    pride_cv.owl [287-292]

    +<owl:Class rdf:about="http://purl.obolibrary.org/obo/PRIDE_0000001">
+    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
+    <obo:IAO_0000115>Root node for terms relating to the description of a protocol as ordered steps</obo:IAO_0000115>
+    <oboInOwl:hasOBONamespace>PRIDE</oboInOwl:hasOBONamespace>
+    <oboInOwl:id>PRIDE:0000001</oboInOwl:id>
+    <rdfs:label>Protocol step description additional parameter</rdfs:label>
 
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    • Apply this suggestion
    Suggestion importance[1-10]: 7

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    Why: The suggestion correctly identifies the need to verify the systematic replacement of BF_0000001 with BFO_0000001 across all class definitions, which is crucial for maintaining ontology consistency. The PR shows multiple such replacements, making this validation important.

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    @ypriverol ypriverol closed this Feb 20, 2025
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