[Psidev-ms-dev] New version 4.0.19 of psi-ms.obo

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Dear proteomics community,

the new version 4.0.19 of the psi-ms.obo file can be downloaded from
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

It contains the new terms for the upcoming PEFF standard.

New CV terms in version 4.0.19 of psi-ms.obo:
=============================================
[Term]
id: PEFF:0000001
name: PEFF CV term
def: "PSI Extended FASTA Format Controlled Vocabulary term." [PSI:PEFF]

[Term]
id: PEFF:0000002
name: 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: Individual Sequence Entries Section term
def: "CV term that may appear in a PEFF Individual Entry Section." 
[PSI:PEFF]
is_a: PEFF:0000001 ! PEFF CV term

[Term]
id: PEFF:0000008
name: DbName
def: "Sequence Database Name." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000009
name: Prefix
def: "Sequence Database Prefix." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000010
name: DbDescription
def: "Sequence Database Short description." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000011
name: Decoy
def: "Specifies whether the Sequence Database is a Decoy." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

[Term]
id: PEFF:0000012
name: DbSource
def: "Source of the database file." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000013
name: DbVersion
def: "Database version (release date) according to database provider." 
[PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000014
name: DbDate
def: "Database date (release or file date of the source) according to 
database provider." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
is_obsolete: true

[Term]
id: PEFF:0000015
name: NumberOfEntries
def: "Number of sequence entries in the database." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:integer "The allowed value-type for this CV term."

[Term]
id: PEFF:0000016
name: Conversion
def: "Description of the conversion from original format to this current 
one." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000018
name: SpecificKey
def: "Db specific information (not included in the current list of 
allowed keys)." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000019
name: SpecificValue
def: "PEFF specific values for a defined key." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000020
name: DatabaseDescription
def: "Short Description of the PEFF." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000021
name: GeneralComment
def: "PEFF file general comment." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000022
name: ProteoformDb
def: "Proteoform database flag." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000023
name: CustomTag
def: "A tag (short string) used to categorize a sequence annotation 
(variant or modification)." [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001001
name: DbUniqueId
def: "Sequence Database unique identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001002
name: PName
def: "Protein Name, description." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001003
name: NcbiTaxId
def: "NCBI taxonomy identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:int "The allowed value-type for this CV term."

[Term]
id: PEFF:0001004
name: TaxName
def: "Taxonomy name (latin or common name)." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001005
name: GName
def: "Gene name." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001006
name: Length
def: "Sequence length." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:int "The allowed value-type for this CV term."

[Term]
id: PEFF:0001007
name: SV
def: "Sequence version." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001008
name: EV
def: "Entry version." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001009
name: PE
def: "Protein Evidence; A UniprotKB code." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:int "The allowed value-type for this CV term."

[Term]
id: PEFF:0001010
name: Processed
def: "Processed Molecule." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001011
name: Variant
def: "DEPRECATED in favor of VariantSimple and VariantComplex. Former 
definition: Sequence variation (substitution, insertion, deletion)." 
[PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001012
name: ModResPsi
def: "Modified residue with PSI-MOD identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001013
name: ModRes
def: "Modified residue without PSI-MOD identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001014
name: AltAC
def: "Alternative Accession Code." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001015
name: SeqStatus
def: "Sequence Status. Complete or Fragment." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002003 ! \(Complete|Fragment|[a-z0-9A-Z]+)

[Term]
id: PEFF:0001016
name: CC
def: "Entry associated comment." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001017
name: KW
def: "Entry associated keyword(s)." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001018
name: GO
def: "Gene Ontology code." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001019
name: XRef
def: "Cross-reference to an external resource." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001020
name: Chain
def: "Sequence range of active processed polypeptide." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001021
name: Signal
def: "Sequence range of signal peptide." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001022
name: Transit
def: "Sequence range of transit peptide." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001023
name: Conflict
def: "Sequence conflict; a UniProtKB term." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001024
name: Crc64
def: "Sequence checksum in crc64." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001025
name: Domain
def: "Sequence range of a domain." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001026
name: ID
def: "UniProtKB specific Protein identifier ID; a UniProtKB term." 
[PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001027
name: ModResUnimod
def: "Modified residue with Unimod identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001028
name: VariantSimple
def: "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]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:0001029
name: VariantComplex
def: "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]
is_a: PEFF:0000003 ! Individual Sequence Entries Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)

[Term]
id: PEFF:1002001
name: \([0-9]+\|[0-9]+\|[a-zA-Z0-9]*\)
def: "Regular expression for PEFF description line value with three 
components." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

[Term]
id: PEFF:1002003
name: \(Complete|Fragment|[a-z0-9A-Z]+)
def: "Regular expression for the Sequence Status." [PSI:PEFF]
is_a: MS:1002479 ! regular expression

Best Regards, Merry Christmas and a happy New Year
Gerhard

-- 

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*Dipl. Inform. med., Dipl. Wirtsch. **Inf. GERHARD MAYER*

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

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