Problem parsing pride OWL file

Hello Tobias,

I had now a more detailed look at the pride-cv.obo file. I made some little changes in order to make them loadable into OBO-Edit:

1) I put the

[Typedef] id: part_of name: part_of is_transitive: true

before the terms (as is recommended by the OBO file recommendations) and added the is_transitive: true

2) I made sure that all definitions in def: ... lines are enclosed in quotes and that they have all a cross-ref, i.e. [PRIDE:PRIDE]

3) I replaced all [Curator:JAV] cross-ref's by [PRIDE:PRIDE]

4) at the beginning I set the default-namespace to default-namespace: PRIDE

Afterwards the pride-cv.obo was loadable into OBO-Edit without any errors / warnings.

Then I converted it again with Protégé - the produced files are attached.

The .owl files are now bigger than the ones from yesterday. Maybe you can try the parsing with them again.

I'm not an expert in the different syntax versions, but I think the OWL/XML is the preferred syntax. Most parsers can read the OWL/XML and functional syntax, e.g. the OWLAPI (http://owlapi.sourceforge.net) but not all can read the Manchester syntax. There was also a warning from Protégé when converting to Manchester syntax, that this can lead to some data loss, so I would recommend to use the Manchester syntax.

I found one validator (http://mowl-power.cs.man.ac.uk:8080/validator/) out there, but it seems to have no support for the OWL/XML syntax (and offers an additional DL (description logic) syntax.

Best regards, Gerhard

Am 18.02.2016 um 10:30 schrieb Tobias Ternent:

We had used Protoege to export the OBO file as OWL/XML syntax. I tried looking at the schema documentation but I got a quite lost. Is OWL/XML the preferable syntax? Is there a recommended syntax validator tool to use to give some useful output for an OWL formatted file about what's exactly wrong and why?

We have now exported to Manchester OWL: https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.owl_Manchester.owl As well as OWL Functional: https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride_cv.owl_functional.owl

Apparently the OBO file has a history of being manually edited by different people over time, so it might not be in the best state.

— Reply to this email directly or view it on GitHub https://github.com/PRIDE-Utilities/pride-ontology/issues/1#issuecomment-185625460.

Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Meesmannstraße 40 D-58456 Witten - Herbede

Phone: +49(0)2302/171 51 52 Email: gerhard64mayer@gmx.de

format-version: 1.2 date: 06:03:2012 11:34 saved-by: jg auto-generated-by: OBO-Edit 2.3 default-namespace: PRIDE

[Typedef] id: part_of name: part_of is_transitive: true

[Term] id: PRIDE:0000000 name: Reference additional parameter comment: Root node for terms relating to Reference additional parameters, in the context of ExperimentCollection/Experiment/Reference/additional/CvParam

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

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

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

[Term] id: PRIDE:0000004 name: Identification additional parameter comment: Root node for terms relating to the description of an Identification in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/additional/cvParam

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

[Term] id: PRIDE:0000006 name: Experiment additional parameter comment: Root node for terms relating to the description of an Experiment in relation to the PRIDE.xml element ExperimentCollection/Experiment/additional/cvParam

[Term] id: PRIDE:0000007 name: SearchEngineVersion comment: Version number / identifier for search engine. is_obsolete: true

[Term] id: PRIDE:0000008 name: Protein search engine output parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000009 name: Ion mass tolerance is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000010 name: PrecursorIon mass tolerance is_a: PRIDE:0000009 ! Ion mass tolerance

[Term] id: PRIDE:0000011 name: MS2 ion mass tolerance is_a: PRIDE:0000009 ! Ion mass tolerance

[Term] id: PRIDE:0000012 name: Delta Cn def: "1.0 - normalized correlation score." [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000013 name: X correlation is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000014 name: X correlation (+1) is_a: PRIDE:0000013 ! X correlation

[Term] id: PRIDE:0000015 name: X correlation (+2) is_a: PRIDE:0000013 ! X correlation

[Term] id: PRIDE:0000016 name: X correlation (+3) is_a: PRIDE:0000013 ! X correlation

[Term] id: PRIDE:0000017 name: Sample description additional parameter comment: Root term for parameters in the context of ExperimentCollection/Experiment/mzData/description/admin/sampleDescription/cvParam

[Term] id: PRIDE:0000018 name: Disease free comment: Term to describe the fact that the sample derives from an organism which has been positively shown to be free of disease, e.g. as the consequence of a broad-spectrum screen. NOTE: A request has been made to have this concept added to MeSH. Once this has been achieved, this term will be dropped from the PRIDE CV and all uses of the this term will be updated to the appropriate MeSH concept. is_a: PRIDE:0000017 ! Sample description additional parameter

[Term] id: PRIDE:0000019 name: Solubilization def: "To make something soluble or more soluble, especially in water, by the action of a detergent or other agent." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000020 name: Depletion def: "The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000021 name: Fractionation def: "The removal of some components of a complex mixture of proteins or peptides on the basis of some general property of those components to yeild a less complex mixture." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000022 name: Separation def: "To divide a complex mixture of proteins or peptides into the component individual proteins or peptides." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000023 name: Band excision def: "The removal of a region of a gel which contains protein(s) of interest." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000024 name: Enzyme digestion def: "The fragmentation of proteins into peptides through the use of an enzyme such as trypsin." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000025 name: Reduction is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000026 name: Alkylation def: "The transfer of an alkyl group from one molecule to another." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000027 name: Mass spectrometry def: "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." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000028 name: Cv Label comment: Valid values for cvLabel entries referencing external database / CV / ontology.

[Term] id: PRIDE:0000029 name: PubMed comment: Valid value for the cvLabel entry referencing PubMed. is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000030 name: PRIDE comment: Valid value for the cvLabel entry referencing PRIDE is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000031 name: GO comment: Valid value for the cvLabel entry referencing GO. is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000032 name: MeSH comment: Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH) is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000033 name: NEWT comment: Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy. is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000034 name: PSI comment: Valid value for the cvLabel entry referencing the PSI ontology is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000035 name: UNIMOD comment: Valid value for the cvLabel entry referencing UNIMOD is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000036 name: RESID comment: Valid value for the cvLabel entry referencing RESID. is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000037 name: Staining is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000038 name: ISBN comment: Valid value for the cvLabel entry referencing ISBN is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000039 name: Organelle isolation def: "Any technique which separates differentiated structures from the cell." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000040 name: Experiment description comment: This CV term should be used in association with a value that is a free-text description of the experiment. is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000041 name: Search database protein sequence is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000042 name: DOI is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000043 name: FIX is_a: PRIDE:0000028 ! Cv Label

[Term] id: PRIDE:0000044 name: Search algorithm

[Term] id: PRIDE:0000045 name: Sequest is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000046 name: Mascot is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000047 name: X|Tandem comment: Really X is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000048 name: OutputParameter is_obsolete: true

[Term] id: PRIDE:0000049 name: Peptide search engine output parameter is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000050 name: Rank/Sp def: "Final correlation score rank and preliminary score rank." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000051 name: (M+H)+ def: "m/z of the singly-charged precursor (precursor mass + mass of hydrogen atom)." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000052 name: Cn def: "normalized correlation score." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000053 name: Sequest score def: "raw correlation score (Sequest)." [PRIDE:PRIDE] synonym: "C*10^4" RELATED [] is_a: PRIDE:0000008 ! Protein search engine output parameter is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000054 name: Sp def: "preliminary score." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000055 name: Ions def: "the number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000056 name: Bioworks is_a: PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000057 name: Molecular weight def: "Molecular weight of a protein." [PRIDE:PRIDE] is_a: PRIDE:0000008 ! Protein search engine output parameter relationship: part_of PRIDE:0000056 ! Bioworks

[Term] id: PRIDE:0000058 name: z is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000056 ! Bioworks

[Term] id: PRIDE:0000059 name: File is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000060 name: Scan is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000061 name: Coverage is_a: PRIDE:0000008 ! Protein search engine output parameter relationship: part_of PRIDE:0000056 ! Bioworks

[Term] id: PRIDE:0000062 name: rsp is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000056 ! Bioworks

[Term] id: PRIDE:0000063 name: Protein description line is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000064 name: Secondary accession is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000065 name: Upstream flanking sequence def: "Any sequence reported before the start of the peptide." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000066 name: Downstream flanking seqeuence def: "Any sequence reported after the end of the peptide seqeuence." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000067 name: Reference reporting this experiment is_a: PRIDE:0000000 ! Reference additional parameter

[Term] id: PRIDE:0000068 name: Reference describing sample preparation is_a: PRIDE:0000000 ! Reference additional parameter

[Term] id: PRIDE:0000069 name: Mascot score def: "Score as defined for the Mascot search algorithm." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000046 ! Mascot

[Term] id: PRIDE:0000070 name: Peptide cleavage def: "Cleavage of the peptide bond." [PRIDE:PRIDE] is_a: PRIDE:0000024 ! Enzyme digestion

[Term] id: PRIDE:0000071 name: Search engine setting is_a: PRIDE:0000001 ! Protocol step description additional parameter is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000072 name: Fixed modification setting is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000073 name: Variable modification setting is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000074 name: Maximum Missed Cleavages Setting is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000075 name: Mass value type setting is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000076 name: Mass value type setting monoisotopic is_a: PRIDE:0000075 ! Mass value type setting

[Term] id: PRIDE:0000077 name: Mass value type setting average is_a: PRIDE:0000075 ! Mass value type setting

[Term] id: PRIDE:0000078 name: Peptide mass tolerance setting is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000079 name: Accurate mass mode setting is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000080 name: Accurate mass mode setting true is_a: PRIDE:0000079 ! Accurate mass mode setting

[Term] id: PRIDE:0000081 name: Accurate mass mode setting false is_a: PRIDE:0000079 ! Accurate mass mode setting

[Term] id: PRIDE:0000082 name: Mass error type setting is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000083 name: mass error type setting ppm is_a: PRIDE:0000082 ! Mass error type setting

[Term] id: PRIDE:0000084 name: mass error type setting mmu is_a: PRIDE:0000082 ! Mass error type setting

[Term] id: PRIDE:0000085 name: mass error type setting percent is_a: PRIDE:0000082 ! Mass error type setting

[Term] id: PRIDE:0000086 name: mass error type setting Daltons is_a: PRIDE:0000082 ! Mass error type setting

[Term] id: PRIDE:0000087 name: Protonated setting is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000088 name: Protonated setting MH+ is_a: PRIDE:0000087 ! Protonated setting

[Term] id: PRIDE:0000089 name: Protonated setting Mr is_a: PRIDE:0000087 ! Protonated setting

[Term] id: PRIDE:0000090 name: Protonated setting M-H- is_a: PRIDE:0000087 ! Protonated setting

[Term] id: PRIDE:0000091 name: Rank is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000092 name: All peptides matched is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000093 name: All peptides matched true is_a: PRIDE:0000092 ! All peptides matched

[Term] id: PRIDE:0000094 name: All peptides matched false is_a: PRIDE:0000092 ! All peptides matched

[Term] id: PRIDE:0000095 name: Masses matched is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000096 name: Reported Chromosome is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000097 name: Project def: "Allows experiments to be grouped or organised under projects. Experiments may be grouped under more than one project." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000098 name: Indistinguishable alternative protein accession def: "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." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000099 name: PeptideProphet probability score def: "The probability score for this peptide assignment to be correct, as calculated by PeptideProphet." [PRIDE:PRIDE "PRIDE"] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000101 ! PeptideProphet

[Term] id: PRIDE:0000100 name: ProteinProphet probability score def: "The probability score for this protein identification to be correct, as calculated by ProteinProphet." [PRIDE:PRIDE "PRIDE"] is_a: PRIDE:0000008 ! Protein search engine output parameter relationship: part_of PRIDE:0000102 ! ProteinProphet

[Term] id: PRIDE:0000101 name: PeptideProphet def: "The PeptideProphet algorithm." [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000102 name: ProteinProphet def: "The ProteinProphet algorithm." [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000103 name: Gel run date def: "The date upon which the gel was run. A value is mandatory - must be formatted as xsd:dateTime." [PRIDE:PRIDE] is_a: PRIDE:0000005 ! Gel additional parameter

[Term] id: PRIDE:0000104 name: Sample volume loaded def: "The volume of sample loaded on to the gel measured in micro litres. Mandatory value must be formatted as xsd:Double." [PRIDE:PRIDE] xref: PRIDE:PRIDE is_a: PRIDE:0000005 ! Gel additional parameter

[Term] id: PRIDE:0000105 name: Width in pixels def: "The width of the referenced gel image in pixels. Mandatory value of type xsd:int." [PRIDE:PRIDE] is_a: PRIDE:0000005 ! Gel additional parameter

[Term] id: PRIDE:0000106 name: Height in pixels def: "The height of the referenced gel image in pixels. Mandatory value of type xsd:int." [PRIDE:PRIDE] is_a: PRIDE:0000005 ! Gel additional parameter

[Term] id: PRIDE:0000107 name: Gel spot parameter def: "Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000108 name: Gel spot intensity def: "The intensity of the spot on the gel. Mandatory value of type xsd:double." [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter

[Term] id: PRIDE:0000109 name: Gel spot area def: "The area of the spot on the gel measured in millimetres squared. Mandatory value of type xsd:double." [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter

[Term] id: PRIDE:0000110 name: Gel spot volume def: "The volume of the spot on the gel measured in millimetres cubed. Mandatory value of type xsd:double." [PRIDE:PRIDE] relationship: part_of PRIDE:0000131 ! Spot normalized volume

[Term] id: PRIDE:0000111 name: Reference describing data analysis def: "A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment." [PRIDE:PRIDE] is_a: PRIDE:0000000 ! Reference additional parameter

[Term] id: PRIDE:0000112 name: Identified by peptide mass fingerprint def: "The annotated protein identification arises from peptide mass fingerprinting. Peptide identifications may or may not be included." [PRIDE:PRIDE] synonym: "PMF" EXACT [] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000113 name: Identified by peptide fragmentation def: "The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching." [PRIDE:PRIDE] synonym: "PFF" EXACT [] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000114 name: iTRAQ reagent 114 comment: The name of the sample labelled with iTRAQ reagent 114. is_a: PRIDE:0000329 ! iTRAQ reagent

[Term] id: PRIDE:0000115 name: iTRAQ reagent 115 comment: The name of the sample labelled with iTRAQ reagent 115. is_a: PRIDE:0000329 ! iTRAQ reagent

[Term] id: PRIDE:0000116 name: iTRAQ reagent 116 comment: The name of the sample labelled with iTRAQ reagent 116. is_a: PRIDE:0000329 ! iTRAQ reagent

[Term] id: PRIDE:0000117 name: iTRAQ reagent 117 comment: The name of the sample labelled with iTRAQ reagent 117. is_a: PRIDE:0000329 ! iTRAQ reagent

[Term] id: PRIDE:0000118 name: iTRAQ intensity 114 comment: The intensity of the sample labelled with iTRAQ reagent 114. is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000119 name: iTRAQ intensity 115 comment: The intensity of the sample labelled with iTRAQ reagent 115. is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000120 name: iTRAQ intensity 116 comment: The intensity of the sample labelled with iTRAQ reagent 116. is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000121 name: iTRAQ intensity 117 comment: The intensity of the sample labelled with iTRAQ reagent 117. is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000122 name: Two Dimensional Polyacrylamide Gel Electrophoresis def: "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." [PRIDE:PRIDE] is_a: PRIDE:0000022 ! Separation

[Term] id: PRIDE:0000123 name: Immobilized pH Gradient Electrophoresis def: "Electrophoresis using an gel which has a pH gradient along its length. ." [PRIDE:PRIDE] relationship: part_of PRIDE:0000122 ! Two Dimensional Polyacrylamide Gel Electrophoresis

[Term] id: PRIDE:0000124 name: Sodium dodecyl sulfate polyacrylamide gel electrophoresis def: "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." [PRIDE:PRIDE] relationship: part_of PRIDE:0000122 ! Two Dimensional Polyacrylamide Gel Electrophoresis

[Term] id: PRIDE:0000125 name: pH low value def: "The lowest pH of an immobilised pH gradient gel." [PRIDE:PRIDE] relationship: part_of PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis

[Term] id: PRIDE:0000126 name: pH high value def: "The highest pH of an immobilised pH gradient gel." [PRIDE:PRIDE] relationship: part_of PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis

[Term] id: PRIDE:0000127 name: IPG strip length cm def: "The length in centimeters of an immobilised pH gradient gel." [PRIDE:PRIDE] comment: This value associated with this CV term should always be in centimeters. relationship: part_of PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis

[Term] id: PRIDE:0000128 name: First dimension details def: "Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters." [PRIDE:PRIDE] comment: This CV term should be used in association with a value that is a free-text description of the first dimension details relationship: part_of PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis

[Term] id: PRIDE:0000129 name: Second dimension details def: "Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis." [PRIDE:PRIDE] comment: This CV term should be used in association with a value that is a free-text description of the second dimension details relationship: part_of PRIDE:0000124 ! Sodium dodecyl sulfate polyacrylamide gel electrophoresis

[Term] id: PRIDE:0000130 name: Obsoleted parameters def: "Obsoleted terms." [Curator:Rc] is_obsolete: true

[Term] id: PRIDE:0000131 name: Spot normalized volume def: "A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values." [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter

[Term] id: PRIDE:0000132 name: Spot normalized volume method def: "The method by which the normalized value for spot volume is derived from the individual gel spot volume values." [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter

[Term] id: PRIDE:0000133 name: Isobaric residue K/Q def: "The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146)." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000134 name: Anticoagulant def: "A substance that prevents coagulation; that is, it stops blood from clotting." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000135 name: Mapping date def: "Date of last mapping of given identifier to current UniProt accession number." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000136 name: Mapping status def: "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' ." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000137 name: Mapping history def: "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' ." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000138 name: Discriminant score def: "PeptideProphet discriminant score fval." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000101 ! PeptideProphet

[Term] id: PRIDE:0000139 name: Not Mapped SOAP Error def: "Error message: SOAP protocol failed." [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status

[Term] id: PRIDE:0000140 name: Not Mapped Database Error def: "Error message: Error with queried database." [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status

[Term] id: PRIDE:0000141 name: Not Mapped No Mapping Found def: "Error message: Unable to match given identifier." [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status

[Term] id: PRIDE:0000142 name: Not Mapped Peptide Mismatch def: "Error message: One or more peptide sequences did not match query sequence." [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status

[Term] id: PRIDE:0000143 name: Mapped Taxon Not Found def: "Error message: No mapping to proteins from defined taxon." [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status

[Term] id: PRIDE:0000144 name: Mapped All Ok def: "Sucessful completion of operation message." [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status

[Term] id: PRIDE:0000145 name: PepSplice def: "The PepSplice algorithm." [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000146 name: PepSplice precision def: " ." [PRIDE:PRIDE] relationship: part_of PRIDE:0000145 ! PepSplice

[Term] id: PRIDE:0000147 name: PepSplice False Discovery Rate def: "The ." [PRIDE:PRIDE] relationship: part_of PRIDE:0000145 ! PepSplice

[Term] id: PRIDE:0000148 name: PepSplice P-value def: "A Score based on the hypergeometric model." [PRIDE:PRIDE] relationship: part_of PRIDE:0000145 ! PepSplice

[Term] id: PRIDE:0000149 name: PepSplice Deltascore def: "The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together." [PRIDE:PRIDE] relationship: part_of PRIDE:0000145 ! PepSplice

[Term] id: PRIDE:0000150 name: PepSplice Score Count def: "The score count." [PRIDE:PRIDE] relationship: part_of PRIDE:0000145 ! PepSplice

[Term] id: PRIDE:0000151 name: PepSplice Penalty def: "The Sum of all penalties for the peptide assignment." [PRIDE:PRIDE] relationship: part_of PRIDE:0000145 ! PepSplice

[Term] id: PRIDE:0000152 name: PepSplice Read Direction def: "The reading direction on the DNA." [PRIDE:PRIDE] relationship: part_of PRIDE:0000145 ! PepSplice

[Term] id: PRIDE:0000153 name: PepSplice Forward Read Direction def: "The reading direction on the DNA is 5' to 3'." [PRIDE:PRIDE] is_a: PRIDE:0000152 ! PepSplice Read Direction

[Term] id: PRIDE:0000154 name: PepSplice Reverse Read Direction def: "The reading direction on the DNA 3' to 5'." [PRIDE:PRIDE] is_a: PRIDE:0000152 ! PepSplice Read Direction

[Term] id: PRIDE:0000155 name: Unmappable def: "unsucessful mapping." [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status

[Term] id: PRIDE:0000156 name: Project identifier def: "unique identifier of project." [PRIDE:PRIDE] synonym: "Project ID" EXACT [] relationship: part_of PRIDE:0000097 ! Project

[Term] id: PRIDE:0000157 name: Search type def: "type of search." [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000158 name: MS search is_a: PRIDE:0000157 ! Search type

[Term] id: PRIDE:0000159 name: MS/MS search is_a: PRIDE:0000157 ! Search type

[Term] id: PRIDE:0000160 name: Enzyme def: "type of enzyme used to fragment the protein. The value will equal the name of the enxzyme used e.g. ." [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000161 name: Fragment mass tolerance setting def: "range of acceptable fragment masses accepted by instrument." [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000162 name: Allowed missed cleavages def: "number of missed cleavage sites taken into account." [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000163 name: Instrument type def: "name of instrument used in analysis." [PRIDE:PRIDE] is_a: PRIDE:0000071 ! Search engine setting

[Term] id: PRIDE:0000164 name: Mapped Without Supporting Peptides def: "Sucessful mapping without supporting evidence from peptides." [PRIDE:PRIDE] is_a: PRIDE:0000136 ! Mapping status

[Term] id: PRIDE:0000165 name: Automatic allocation def: "PICR tool has allocated the accession number." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000166 name: Ambiguous modification def: "Modification with a MonoDeltaMass, which can not unambiguously be assigned to only one modification and for which several possibilities exist." [PRIDE:PRIDE] is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term] id: PRIDE:0000167 name: Novel locus information def: "Detailed information about a genomic locus identified by whole genome searches." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000168 name: Nucleic acid sequence is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000169 name: Start position of the nucleic acid sequence on the chromosome is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000170 name: Stop position of the nucleic acid sequence on the chromosome is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000171 name: funding reference is_a: PRIDE:0000000 ! Reference additional parameter

[Term] id: PRIDE:0000172 name: Search database protein sequence length def: "Value of average of all individual peptide identifications for this protein." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000173 name: MeanOfPeptideScores def: "Value of average of all individual peptide scores." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000174 name: Isoelectric point def: "Isoelectric point of a protein." [PRIDE:PRIDE] synonym: "pI" EXACT [] is_a: PRIDE:0000008 ! Protein search engine output parameter relationship: part_of PRIDE:0000056 ! Bioworks

[Term] id: PRIDE:0000175 name: XML generation software def: "The software which was used to generate the PRIDE XML file." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000176 name: X!Tandem Hyperscore def: "The X!Tandem hyperscore for the peptide." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000177 name: Spectrum Mill peptide score def: "The Spectrum Mill score for the peptide." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000178 name: Peptide selection def: "A protocol step to select for a particular type of peptides." [PRIDE:PRIDE] is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term] id: PRIDE:0000179 name: dotproduct def: "X|Tandem dot product score." [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem

[Term] id: PRIDE:0000180 name: delta def: "X|Tandem delta score." [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem

[Term] id: PRIDE:0000181 name: deltastar def: "X|Tandem delta star score." [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem

[Term] id: PRIDE:0000182 name: zscore def: "X|Tandem Z score." [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem

[Term] id: PRIDE:0000183 name: expect def: "X|Tandem expectancy score." [PRIDE:PRIDE] is_a: PRIDE:0000047 ! X|Tandem

[Term] id: PRIDE:0000184 name: Query number def: "Search parameter that allows users to find query results from old data." [PRIDE:PRIDE] is_a: PRIDE:0000046 ! Mascot

[Term] id: PRIDE:0000185 name: OMSSA E-value def: "E-value parameter from OMSSA." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000186 name: OMSSA P-value def: "P-value parameter from OMSSA." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term] id: PRIDE:0000187 name: Fragment Ion Annotation def: "Fragment ion annotation of the peptide." [PRIDE:PRIDE] synonym: "product ion property" EXACT [] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000188 name: product ion m/z def: "Mass." [PRIDE:PRIDE] synonym: "fragment ion mass" EXACT [] is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term] id: PRIDE:0000189 name: product ion intensity def: "Intensity." [PRIDE:PRIDE] synonym: "fragment ion intensity" EXACT [] is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term] id: PRIDE:0000190 name: product ion mass error def: "Mass error." [PRIDE:PRIDE] synonym: "fragment ion mass error" EXACT [] is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term] id: PRIDE:0000191 name: product ion retention time error def: "Retention time error in minutes." [PRIDE:PRIDE] synonym: "fragment ion retention time error" EXACT [] is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term] id: PRIDE:0000192 name: product ion type def: "Product ion type." [PRIDE:PRIDE] synonym: "fragment ion type" EXACT [] is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term] id: PRIDE:0000193 name: y ion def: "Y ion type." [PRIDE:PRIDE] synonym: "y fragment ion" EXACT [] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000194 name: b ion def: "B ion type." [PRIDE:PRIDE] synonym: "b fragment ion" EXACT [] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000195 name: b ion -NH3 def: "B ion type with a neutral loss of an ammonia group." [PRIDE:PRIDE] synonym: "b fragment ion -NH3" EXACT [] is_a: PRIDE:0000194 ! b ion

[Term] id: PRIDE:0000196 name: b ion -H2O def: "B ion type with a neutral loss of a water molecule." [PRIDE:PRIDE] synonym: "b fragment ion -H2O" EXACT [] is_a: PRIDE:0000194 ! b ion

[Term] id: PRIDE:0000197 name: y ion -H2O def: "Y ion type with the neutral loss of a molecule water." [PRIDE:PRIDE] synonym: "y fragment ion -H2O" EXACT [] is_a: PRIDE:0000193 ! y ion

[Term] id: PRIDE:0000198 name: y ion -NH3 def: "Y ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE] synonym: "y fragment ion -NH3" EXACT [] is_a: PRIDE:0000193 ! y ion

[Term] id: PRIDE:0000199 name: in source ion def: "Ion resulting from in-source fragmentation." [PRIDE:PRIDE] synonym: "in source fragment ion" EXACT [] synonym: "in-source ion" EXACT [] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000200 name: non-identified ion def: "Fragment ion that could not be assigned to a predicted fragment ion mass." [PRIDE:PRIDE] synonym: "unidentified ion" EXACT [] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000201 name: co-eluting ion def: "Fragment ion that was matched to another, co-eluting peptide precursor." [PRIDE:PRIDE] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000202 name: Parent Ion Annotation def: "Parent ion annotation of the peptide." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000203 name: parent ion retention time def: "Retention time in minutes." [PRIDE:PRIDE] is_a: PRIDE:0000202 ! Parent Ion Annotation

[Term] id: PRIDE:0000204 name: product ion charge def: "Charge state." [PRIDE:PRIDE] synonym: "fragment ion charge" EXACT [] is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term] id: PRIDE:0000205 name: Heavy stable isotope label def: "A general term for any stable isotope method." [PRIDE:PRIDE] is_obsolete: true

[Term] id: PRIDE:0000206 name: Heavy stable isotope label residue def: "The precise amino acid that has been modified." [PRIDE:PRIDE] is_obsolete: true

[Term] id: PRIDE:0000207 name: Light stable isotope label def: "A general term for any stable isotope method." [PRIDE:PRIDE] is_obsolete: true

[Term] id: PRIDE:0000208 name: Light stable isotope label residue def: "The precise amino acid that has been modified." [PRIDE:PRIDE] is_obsolete: true

[Term] id: PRIDE:0000209 name: Peptide pair id def: "Facilitate mapping between peptide pairs (usually heavy/light) to which the stable isotope ratio below relates." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000210 name: Stable isotope ratio def: "Ratio of peptide pair the sequence/sample is the numerator in the ratio." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000211 name: Quantitative sample reference def: "This links back to the value given to the heavy/light stable isotope label to relate the peptide ratio back to the sample." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000212 name: Mascot expect value def: "Expect value as defined for the Mascot search algorithm." [PRIDE:PRIDE] is_a: PRIDE:0000046 ! Mascot

[Term] id: PRIDE:0000213 name: Inspect def: "The Inspect search algorithm." [PRIDE:PRIDE] is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000214 name: Inspect MQScore def: "Quality score of a match." [PRIDE:PRIDE] is_a: PRIDE:0000213 ! Inspect

[Term] id: PRIDE:0000215 name: Inspect p-value def: "Probability that the top match is correct." [PRIDE:PRIDE] is_a: PRIDE:0000213 ! Inspect

[Term] id: PRIDE:0000216 name: ProteomExchange project accession number def: "ProteomExchange accession number of the project where the PRIDE experiment is included." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000217 name: ProteomExchange project hash def: "Hash in Tranche of the whole ProteomExchange project where the PRIDE experiment is included." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000218 name: Original MS data file format def: "Original format of the file containing MS data." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000219 name: Date of search def: "Date when the search was performed." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000220 name: Calculated Mass To Charge Ratio def: "m/z value converted from the MH+ value, according to this formula: CalculatedMZ = (precursorMH+ - HYDROGEN_MASS + (precursorCharge * HYDROGEN_MASS))/ precursorCharge." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term] id: PRIDE:0000221 name: parent ion retention time error def: "Retention time error in minutes." [PRIDE:PRIDE] is_a: PRIDE:0000202 ! Parent Ion Annotation

[Term] id: PRIDE:0000222 name: spectrum iTRAQ ratio def: "average iTRAQ ratio sample over control." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_obsolete: true

[Term] id: PRIDE:0000223 name: peptide iTRAQ ratio average def: "Average spectrum iTRAQ ratio (=geometric mean) for the peptide." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter is_obsolete: true

[Term] id: PRIDE:0000224 name: protein iTRAQ ratio average def: "Average spectrum iTRAQ ratio (=geometric mean) for the protein." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter is_obsolete: true

[Term] id: PRIDE:0000225 name: protein iTRAQ ratio number of contributing spectra def: "Number of quantified spectra contributing to the protein iTRAQ ratio." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter is_obsolete: true

[Term] id: PRIDE:0000226 name: protein iTRAQ ratio standard deviation def: "Geometric sample standard deviation of the protein iTRAQ ratio." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter is_obsolete: true

[Term] id: PRIDE:0000227 name: x ion def: "X ion type." [PRIDE:PRIDE] synonym: "x fragment ion" EXACT [] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000228 name: x ion -H2O def: "X ion type with the neutral loss of a molecule water." [PRIDE:PRIDE] synonym: "x fragment ion -H2O" EXACT [] is_a: PRIDE:0000227 ! x ion

[Term] id: PRIDE:0000229 name: x ion -NH3 def: "X ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE] synonym: "x fragment ion -NH3" EXACT [] is_a: PRIDE:0000227 ! x ion

[Term] id: PRIDE:0000230 name: z ion def: "Z ion type." [PRIDE:PRIDE] synonym: "z fragment ion" EXACT [] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000231 name: z ion -H2O def: "Z ion type with the neutral loss of a molecule water." [PRIDE:PRIDE] synonym: "z fragment ion -H2O" EXACT [] is_a: PRIDE:0000230 ! z ion

[Term] id: PRIDE:0000232 name: z ion -NH3 def: "Z ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE] synonym: "z fragment ion -NH3" EXACT [] is_a: PRIDE:0000230 ! z ion

[Term] id: PRIDE:0000233 name: a ion def: "A ion type." [PRIDE:PRIDE] synonym: "a fragment ion" EXACT [] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000234 name: a ion -H2O def: "A ion type with the neutral loss of a molecule water." [PRIDE:PRIDE] synonym: "a fragment ion -H2O" EXACT [] is_a: PRIDE:0000233 ! a ion

[Term] id: PRIDE:0000235 name: a ion -NH3 def: "A ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE] synonym: "a fragment ion -NH3" EXACT [] is_a: PRIDE:0000233 ! a ion

[Term] id: PRIDE:0000236 name: c ion def: "C ion type." [PRIDE:PRIDE] synonym: "c fragment ion" EXACT [] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000237 name: c ion -H2O def: "C ion type with the neutral loss of a molecule water." [PRIDE:PRIDE] synonym: "c fragment ion -H2O" EXACT [] is_a: PRIDE:0000236 ! c ion

[Term] id: PRIDE:0000238 name: c ion -NH3 def: "C ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE] synonym: "c fragment ion -NH3" EXACT [] is_a: PRIDE:0000236 ! c ion

[Term] id: PRIDE:0000239 name: immonium ion def: "Immonium ion type." [PRIDE:PRIDE] is_a: PRIDE:0000192 ! product ion type

[Term] id: PRIDE:0000240 name: immonium A def: "Immonium ion type for alanine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000241 name: immonium C def: "Immonium ion type for cysteine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000242 name: immonium D def: "Immonium ion type for aspartic acid." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000243 name: immonium E def: "Immonium ion type for glutamic acid." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000244 name: immonium F def: "Immonium ion type for phenylalanine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000245 name: immonium G def: "Immonium ion type for glycine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000246 name: immonium H def: "Immonium ion type for histidine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000247 name: immonium I def: "Immonium ion type for isoleucine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000248 name: immonium K def: "Immonium ion type for lysine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000249 name: immonium L def: "Immonium ion type for leucine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000250 name: immonium M def: "Immonium ion type for methionine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000251 name: immonium N def: "Immonium ion type for asparagine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000252 name: immonium P def: "Immonium ion type for proline." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000253 name: immonium Q def: "Immonium ion type for glutamine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000254 name: immonium R def: "Immonium ion type for arginine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000255 name: immonium S def: "Immonium ion type for serine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000256 name: immonium T def: "Immonium ion type for threnine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000257 name: immonium V def: "Immonium ion type for valine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000258 name: immonium W def: "Immonium ion type for tryptophan." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000259 name: immonium Y def: "Immonium ion type for tyrosine." [PRIDE:PRIDE] is_a: PRIDE:0000239 ! immonium ion

[Term] id: PRIDE:0000260 name: precursor ion type def: "precursor ion type." [PRIDE:PRIDE] synonym: "parent ion type" EXACT [] is_a: PRIDE:0000202 ! Parent Ion Annotation

[Term] id: PRIDE:0000261 name: precursor ion -H2O def: "Precursor ion type with the neutral loss of a molecule water." [PRIDE:PRIDE] synonym: "parent ion -H2O" EXACT [] is_a: PRIDE:0000263 ! precursor ion

[Term] id: PRIDE:0000262 name: precursor ion -NH3 def: "Precursor ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE] synonym: "parent ion -NH3" EXACT [] is_a: PRIDE:0000263 ! precursor ion

[Term] id: PRIDE:0000263 name: precursor ion def: "Precursor ion." [PRIDE:PRIDE] synonym: "parent ion" EXACT [] is_a: PRIDE:0000260 ! precursor ion type

[Term] id: PRIDE:0000264 name: iTRAQ reagent 113 comment: The name of the sample labelled with iTRAQ reagent 113 [PRIDE:PRIDE]. is_a: PRIDE:0000329 ! iTRAQ reagent

[Term] id: PRIDE:0000265 name: iTRAQ reagent 118 comment: The name of the sample labelled with iTRAQ reagent 118 [PRIDE:PRIDE]. is_a: PRIDE:0000329 ! iTRAQ reagent

[Term] id: PRIDE:0000266 name: iTRAQ reagent 119 comment: The name of the sample labelled with iTRAQ reagent 119 [PRIDE:PRIDE]. is_a: PRIDE:0000329 ! iTRAQ reagent

[Term] id: PRIDE:0000267 name: iTRAQ reagent 121 comment: The name of the sample labelled with iTRAQ reagent 121 [PRIDE:PRIDE]. is_a: PRIDE:0000329 ! iTRAQ reagent

[Term] id: PRIDE:0000268 name: iTRAQ intensity 113 comment: The intensity of the sample labelled with iTRAQ reagent 113 [PRIDE:PRIDE]. is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000269 name: iTRAQ intensity 118 comment: The intensity of the sample labelled with iTRAQ reagent 118 [PRIDE:PRIDE]. is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000270 name: iTRAQ intensity 119 comment: The intensity of the sample labelled with iTRAQ reagent 119 [PRIDE:PRIDE]. is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000271 name: iTRAQ intensity 121 comment: The intensity of the sample labelled with iTRAQ reagent 121 [PRIDE:PRIDE]. is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000272 name: Project secondary name def: "Allows experiments inside the same project to be grouped or organised as subprojects. This will not be displayed in the PRIDE web page." [PRIDE:PRIDE] is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000273 name: SloMo score threshold for valid modification location is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000274 name: MaxQuant percentage threshold for valid modification location is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000275 name: SloMo score is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000276 name: MaxQuant percentage is_a: PRIDE:0000044 ! Search algorithm

[Term] id: PRIDE:0000277 name: Valid location is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term] id: PRIDE:0000278 name: Processing method additional parameter

[Term] id: PRIDE:0000279 name: In silico enzyme digestion def: "Enzyme that is selected as a parameter of the search engine." [PRIDE:PRIDE] is_a: PRIDE:0000278 ! Processing method additional parameter

[Term] id: PRIDE:0000280 name: zH ion def: "Z ion type with one extra proton" [Curator:RWANG] synonym: "zH fragment ion" EXACT [] is_a: PRIDE:0000230 ! z ion

[Term] id: PRIDE:0000281 name: zHH ion def: "Z ion type with two extra protons" [Curator:RWANG] synonym: "zHH fragment ion" EXACT [] is_a: PRIDE:0000230 ! z ion

[Term] id: PRIDE:0000282 name: Fixed modification def: "Fixed type of post-translational modification." [PRIDE:PRIDE] is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term] id: PRIDE:0000283 name: Variable modification def: "Variable type of post-translational modification." [PRIDE:PRIDE] is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term] id: PRIDE:0000284 name: Sf def: "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." [PRIDE:PRIDE] is_a: PRIDE:0000049 ! Peptide search engine output parameter relationship: part_of PRIDE:0000045 ! Sequest

[Term] id: PRIDE:0000285 name: TMT reagent 126 comment: The name of the sample labelled with TMT reagent 126 is_a: PRIDE:0000337 ! TMT reagent

[Term] id: PRIDE:0000286 name: TMT reagent 127 comment: The name of the sample labelled with TMT reagent 127 is_a: PRIDE:0000337 ! TMT reagent

[Term] id: PRIDE:0000287 name: TMT reagent 128 comment: The name of the sample labelled with TMT reagent 128 is_a: PRIDE:0000337 ! TMT reagent

[Term] id: PRIDE:0000288 name: TMT reagent 129 comment: The name of the sample labelled with TMT reagent 129 is_a: PRIDE:0000337 ! TMT reagent

[Term] id: PRIDE:0000289 name: TMT reagent 130 comment: The name of the sample labelled with TMT reagent 130 is_a: PRIDE:0000337 ! TMT reagent

[Term] id: PRIDE:0000290 name: TMT reagent 131 comment: The name of the sample labelled with TMT reagent 131 is_a: PRIDE:0000337 ! TMT reagent

[Term] id: PRIDE:0000291 name: TMT intensity 126 comment: The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000292 name: TMT intensity 127 comment: The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000293 name: TMT intensity 128 comment: The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000294 name: TMT intensity 129 comment: The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000295 name: TMT intensity 130 comment: The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000296 name: TMT intensity 131 comment: The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS] is_a: PRIDE:0000003 ! Peptide item additional parameter is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000297 name: Gene name comment: Name of the gene that has been identified (if a nucleotide database was used to perform the search) is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000298 name: Modification Position in Protein Sequence comment: Position of the modification in the protein sequence is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000299 name: Submitted Protein Accession comment: The original submitted protein accession for this identification. This might have been curated as part of the submission process. is_a: PRIDE:0000004 ! Identification additional parameter

[Term] id: PRIDE:0000300 name: Gel spot identifier def: "The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication." [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter created_by: jg creation_date: 2011-05-12T11:32:07Z

[Term] id: PRIDE:0000301 name: Non-significant protein identification def: "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)." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter created_by: jg creation_date: 2011-05-12T11:39:59Z

[Term] id: PRIDE:0000302 name: Non-significant peptide identification def: "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)." [PRIDE:PRIDE] is_a: PRIDE:0000003 ! Peptide item additional parameter created_by: jg creation_date: 2011-05-12T11:50:00Z

[Term] id: PRIDE:0000303 name: Decoy hit def: "Indicates that this protein identification comes from the used decoy database." [PRIDE:PRIDE] is_a: PRIDE:0000004 ! Identification additional parameter created_by: jg creation_date: 2011-05-12T11:58:52Z

[Term] id: PRIDE:0000304 name: Gel identifier def: "The gel's identifier. This identifier should resemble the one used in, for example, the associated publication." [PRIDE:PRIDE] is_a: PRIDE:0000107 ! Gel spot parameter created_by: jg creation_date: 2011-05-25T11:22:05Z

[Term] id: PRIDE:0000305 name: Gel-based experiment def: "Defines a gel-based proteomics experiment." [PRIDE:PRIDE] is_a: PRIDE:0000428 ! Bottom-up proteomics created_by: jg creation_date: 2011-05-25T05:44:24Z

[Term] id: PRIDE:0000306 name: Imported from NCBI Peptidome comment: Experiment.[Curator:ACSORDAS] is_a: PRIDE:0000006 ! Experiment additional parameter

[Term] id: PRIDE:0000307 name: Quantification method comment: Defines various quantification methods is_a: PRIDE:0000391 ! Quantification parameter created_by: jg creation_date: 2011-07-22T09:15:33Z

[Term] id: PRIDE:0000308 name: Gel-based quantification method comment: Describes gel-based quantification methods is_a: PRIDE:0000307 ! Quantification method created_by: jg creation_date: 2011-07-22T09:16:24Z

[Term] id: PRIDE:0000309 name: Gel-free quantification method comment: Describes gel-free quantification methods is_a: PRIDE:0000307 ! Quantification method created_by: jg creation_date: 2011-07-22T09:17:03Z

[Term] id: PRIDE:0000310 name: Isotope labeling comment: Describes quantification techniques using isotope labeling is_a: PRIDE:0000309 ! Gel-free quantification method created_by: jg creation_date: 2011-07-22T09:17:34Z

[Term] id: PRIDE:0000311 name: Selected Reaction Monitoring comment: Describes quantification techniques based on selected / multiple reaction monitoring is_a: PRIDE:0000309 ! Gel-free quantification method created_by: jg creation_date: 2011-07-22T09:18:39Z

[Term] id: PRIDE:0000312 name: Label free comment: Describes label free quantification techniques. is_a: PRIDE:0000309 ! Gel-free quantification method created_by: jg creation_date: 2011-07-22T09:19:54Z

[Term] id: PRIDE:0000313 name: iTRAQ comment: Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level is_a: PRIDE:0000317 ! MS2 based isotope labeling created_by: jg creation_date: 2011-07-22T09:20:23Z

[Term] id: PRIDE:0000314 name: TMT comment: Tandem Mass Tag is a MS2 based isotope labeling quantification technique synonym: "Tandem Mass Tag" EXACT [] is_a: PRIDE:0000317 ! MS2 based isotope labeling created_by: jg creation_date: 2011-07-22T09:23:12Z

[Term] id: PRIDE:0000315 name: SILAC comment: Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification synonym: "Stable isotope labeling with amino acids in cell culture" EXACT [] is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:25:50Z

[Term] id: PRIDE:0000316 name: MS1 based isotope labeling comment: Describes isotope labeling quantification techniques detectable at MS1 level. is_a: PRIDE:0000310 ! Isotope labeling created_by: jg creation_date: 2011-07-22T09:28:05Z

[Term] id: PRIDE:0000317 name: MS2 based isotope labeling comment: Describes isotope labeling quantification techniques detectable at MS1 level. is_a: PRIDE:0000310 ! Isotope labeling created_by: jg creation_date: 2011-07-22T09:29:15Z

[Term] id: PRIDE:0000318 name: 18O comment: The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen. is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:30:12Z

[Term] id: PRIDE:0000319 name: ICAT comment: Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements. synonym: "Isotope-Coded Affinity Tags" EXACT [] is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:31:24Z

[Term] id: PRIDE:0000320 name: AQUA comment: AQUA is an isotope labeling based quantification technique that uses known peptides. is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:32:46Z

[Term] id: PRIDE:0000321 name: ICPL comment: Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses. synonym: "Isotope-coded protein label" EXACT [] is_a: PRIDE:0000316 ! MS1 based isotope labeling created_by: jg creation_date: 2011-07-22T09:34:37Z

[Term] id: PRIDE:0000322 name: emPAI comment: The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantification of the proteins in a mixture based on protein coverage by the peptide matches in a database search result. synonym: "Exponentially Modified Protein Abundance Index" EXACT [] is_a: PRIDE:0000312 ! Label free created_by: jg creation_date: 2011-07-22T09:36:57Z

[Term] id: PRIDE:0000323 name: TIC comment: The Total Ion Current (TIC) can be measured or calculated in order to target specific ions. synonym: "Total Ion Current" EXACT [] is_a: PRIDE:0000312 ! Label free created_by: jg creation_date: 2011-07-22T09:38:17Z

[Term] id: PRIDE:0000324 name: Quantification reagent comment: A reagent used for quantification. is_a: PRIDE:0000017 ! Sample description additional parameter is_a: PRIDE:0000391 ! Quantification parameter created_by: jg creation_date: 2011-07-22T09:43:30Z

[Term] id: PRIDE:0000325 name: SILAC heavy comment: The heavy label used in SILAC experiments. is_a: PRIDE:0000328 ! SILAC reagent created_by: jg creation_date: 2011-07-22T09:44:18Z

[Term] id: PRIDE:0000326 name: SILAC light comment: The light reagent used in SILAC experiments. is_a: PRIDE:0000328 ! SILAC reagent created_by: jg creation_date: 2011-07-22T09:45:40Z

[Term] id: PRIDE:0000327 name: SILAC medium comment: The medium weight reagent used in SILAC experiments. is_a: PRIDE:0000328 ! SILAC reagent created_by: jg creation_date: 2011-07-22T09:47:09Z

[Term] id: PRIDE:0000328 name: SILAC reagent comment: Reagent used in SILAC labeling. is_a: PRIDE:0000433 ! Reagents used in Labeled Method created_by: jg creation_date: 2011-07-22T09:48:42Z

[Term] id: PRIDE:0000329 name: iTRAQ reagent comment: Reagent used in iTRAQ experiments. is_a: PRIDE:0000433 ! Reagents used in Labeled Method created_by: jg creation_date: 2011-07-22T09:49:46Z

[Term] id: PRIDE:0000330 name: Arbitrary quantification unit comment: A unit describing values that can only be interpreted within the same spectrum but cannot be compared to values found in other spectra and or experiments. is_a: PRIDE:0000392 ! Quantification unit created_by: jg creation_date: 2012-03-06T11:32:24Z

[Term] id: PRIDE:0000331 name: Counts comment: Quantification values reported as arbitrary counts (most often ion counts). is_a: PRIDE:0000330 ! Arbitrary quantification unit created_by: jg creation_date: 2012-03-06T11:33:13Z

[Term] id: PRIDE:0000337 name: TMT reagent comment: Reagent used in TMT experiments. is_a: PRIDE:0000433 ! Reagents used in Labeled Method created_by: jg creation_date: 2011-07-22T10:08:04Z

[Term] id: PRIDE:0000344 name: ICAT reagent comment: Reagent used in ICAT experiments. is_a: PRIDE:0000433 ! Reagents used in Labeled Method created_by: jg creation_date: 2011-07-22T10:19:04Z

[Term] id: PRIDE:0000345 name: ICAT light reagent is_a: PRIDE:0000344 ! ICAT reagent created_by: jg creation_date: 2011-07-22T10:19:38Z

[Term] id: PRIDE:0000346 name: ICAT heavy reagent is_a: PRIDE:0000344 ! ICAT reagent created_by: jg creation_date: 2011-07-22T10:19:38Z

[Term] id: PRIDE:0000347 name: ICPL reagent comment: Reagent used in ICPL experiments. is_a: PRIDE:0000433 ! Reagents used in Labeled Method created_by: jg creation_date: 2011-07-22T10:22:42Z

[Term] id: PRIDE:0000348 name: ICPL 0 reagent is_a: PRIDE:0000347 ! ICPL reagent created_by: jg creation_date: 2011-07-22T10:24:42Z

[Term] id: PRIDE:0000349 name: ICPL 4 reagent is_a: PRIDE:0000347 ! ICPL reagent created_by: jg creation_date: 2011-07-22T10:24:42Z

[Term] id: PRIDE:0000350 name: ICPL 6 reagent is_a: PRIDE:0000347 ! ICPL reagent created_by: jg creation_date: 2011-07-22T10:24:42Z

PRIDE-Archive / pride-ontology

Problem parsing pride OWL file #1