format-version: 1.2 data-version: 4.1.25 date: 06:04:2019 14:50 saved-by: Gerhard Mayer auto-generated-by: OBO-Edit 2.3.1 default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ remark: coverage: Mass spectrometer output files and spectra interpretation remark: creator: Andreas Bertsch informatik.uni-tuebingen.de> remark: creator: Eric Deutsch systemsbiology.org> remark: creator: Fredrik Levander immun.lth.se> remark: creator: Gerhard Mayer rub.de> remark: creator: Marius Kallhardt bdal.de> remark: creator: Matt Chambers vanderbilt.edu> remark: creator: Pierre-Alain Binz chuv.ch> remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net remark: namespace: MS remark: namespace: PEFF remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. remark: URL: https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page import: http://ontologies.berkeleybop.org/pato.obo import: http://ontologies.berkeleybop.org/uo.obo ontology: ms owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion(Annotation( \"PSI:MS\"^^xsd:string) \"The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material.\"^^xsd:string)\nAnnotationAssertion( \"MS\"^^xsd:string)\nAnnotationAssertion( \"MS:1000393\"^^xsd:string)\nAnnotationAssertion(rdfs:label \"laser desorption ionization\"^^xsd:string)\n) [Term] id: MS:0000000 name: Proteomics Standards Initiative Mass Spectrometry Vocabularies def: "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [PSI:MS] [Term] id: MS:1000001 name: sample number def: "A reference number relevant to the sample under study." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute [Term] id: MS:1000002 name: sample name def: "A reference string relevant to the sample under study." [PSI:MS] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute [Term] id: MS:1000003 name: sample state def: "The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS] is_a: MS:1000548 ! sample attribute [Term] id: MS:1000004 name: sample mass def: "Total mass of sample used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000021 [Term] id: MS:1000005 name: sample volume def: "Total volume of solution used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000098 [Term] id: MS:1000006 name: sample concentration def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000175 [Term] id: MS:1000007 name: inlet type def: "The nature of the sample inlet." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1000008 name: ionization type def: "The method by which gas phase ions are generated from the sample." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1000009 name: ionization mode def: "OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer." [PSI:MS] comment: This term was made obsolete because it was replaced by scan polarity (MS:1000465). is_obsolete: true [Term] id: MS:1000010 name: analyzer type def: "OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: PEFF:0000001 name: PEFF CV term def: "PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: PEFF:0000002 name: PEFF file header section term def: "CV term that may appear in a PEFF file header section." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000003 name: PEFF file sequence entry term def: "CV term that may appear in a description line of a PEFF file individual sequence entry." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000008 name: DbName def: "PEFF keyword for the sequence database name." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000009 name: Prefix def: "PEFF keyword for the sequence database prefix." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000010 name: DbDescription def: "PEFF keyword for the sequence database short description." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000011 name: Decoy def: "PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF] xref: value-type:xsd\:boolean "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000012 name: DbSource def: "PEFF keyword for the source of the database file." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000013 name: DbVersion def: "PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000014 name: DbDate def: "OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider." [PSI:PEFF] comment: This term was obsoleted. is_a: PEFF:0000002 ! PEFF file header section term is_obsolete: true [Term] id: PEFF:0000015 name: NumberOfEntries def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF] xref: value-type:xsd\:integer "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000016 name: Conversion def: "PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000017 name: SequenceType def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term relationship: has_regexp PEFF:1002002 ! regular expression for PEFF molecular sequence type [Term] id: PEFF:0000018 name: SpecificKey def: "PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000019 name: SpecificValue def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000020 name: DatabaseDescription def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000021 name: GeneralComment def: "PEFF keyword for a general comment." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000022 name: ProteoformDb def: "PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000023 name: OptionalTagDef def: "PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0000024 name: HasAnnotationIdentifiers def: "PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000002 ! PEFF file header section term [Term] id: PEFF:0001001 name: DbUniqueId def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF] comment: This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant. xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term is_obsolete: true [Term] id: PEFF:0001002 name: PName def: "PEFF keyword for the protein full name." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001003 name: NcbiTaxId def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001004 name: TaxName def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001005 name: GName def: "PEFF keyword for the gene name." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001006 name: Length def: "PEFF keyword for the sequence length." [PSI:PEFF] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001007 name: SV def: "PEFF keyword for the sequence version." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001008 name: EV def: "PEFF keyword for the entry version." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001009 name: PE def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF] xref: value-type:xsd\:int "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001010 name: Processed def: "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001011 name: Variant def: "OBSOLETE Sequence variation (substitution, insertion, deletion)." [PSI:PEFF] comment: This term was made obsolete in favor of VariantSimple and VariantComplex. xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment is_obsolete: true [Term] id: PEFF:0001012 name: ModResPsi def: "PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001013 name: ModRes def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001014 name: AltAC def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001015 name: SeqStatus def: "PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002003 ! regular expression for PEFF sequence status [Term] id: PEFF:0001016 name: CC def: "PEFF keyword for the entry associated comment." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001017 name: KW def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001018 name: GO def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001019 name: XRef def: "PEFF keyword for the cross-reference to an external resource." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001020 name: mature protein def: "Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001021 name: signal peptide def: "Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001022 name: transit peptide def: "Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001023 name: Conflict def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001024 name: Crc64 def: "PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001025 name: Domain def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001026 name: ID def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001027 name: ModResUnimod def: "PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001028 name: VariantSimple def: "PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001029 name: VariantComplex def: "PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001030 name: Proteoform def: "PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001031 name: DisulfideBond def: "PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001032 name: PEFF molecule processing keyword def: "PEFF keyword describing the type of processing event being described." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001033 name: Comment def: "PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001034 name: propeptide def: "Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:0001035 name: initiator methionine def: "N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment [Term] id: PEFF:1002001 name: regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment def: "([0-9]+|[A-Z*](|.+)?)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002002 name: regular expression for PEFF molecular sequence type def: "(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002003 name: regular expression for PEFF sequence status def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Typedef] id: has_domain name: has_domain [Typedef] id: has_order name: has_order [Typedef] id: has_regexp name: has regexp [Typedef] id: has_units name: has_units [Typedef] id: part_of name: part_of is_transitive: true