[Psidev-ms-dev] New version 4.1.17 of psi-ms.obo

[mayerg97 <ger...@ru...>]

Dear proteomics/metabolomics community,

the new version 4.1.17 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 major updates to the PEFF CV terms:

[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]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000009
name: Prefix
def: "PEFF keyword for the sequence database prefix." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000010
name: DbDescription
def: "PEFF keyword for the sequence database short description." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000011
name: Decoy
def: "PEFF keyword for the specifying whether the sequence database is a 
decoy database." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:boolean "The allowed value-type for this CV term."

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

[Term]
id: PEFF:0000013
name: DbVersion
def: "PEFF keyword for the database version (release date) according to 
database provider." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV 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]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:integer "The allowed value-type for this CV 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]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000017
name: SequenceType
def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV 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]
is_a: PEFF:0000002 ! PEFF 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 keyword for the specific values for a custom key." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000020
name: DatabaseDescription
def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF 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 keyword for a general comment." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0000022
name: ProteoformDb
def: "PEFF keyword that when set to 'true' indicates that the database 
contains complete proteoforms." [PSI:PEFF]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV 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]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV 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]
is_a: PEFF:0000002 ! PEFF file header section term
xref: value-type:xsd\:string "The allowed value-type for this CV 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.
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_obsolete: true

[Term]
id: PEFF:0001002
name: PName
def: "PEFF keyword for the protein full name." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001003
name: NcbiTaxId
def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:int "The allowed value-type for this CV term."

[Term]
id: PEFF:0001004
name: TaxName
def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001005
name: GName
def: "PEFF keyword for the gene name." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001006
name: Length
def: "PEFF keyword for the sequence length." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:int "The allowed value-type for this CV term."

[Term]
id: PEFF:0001007
name: SV
def: "PEFF keyword for the sequence version." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001008
name: EV
def: "PEFF keyword for the entry version." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001009
name: PE
def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:int "The allowed value-type for this CV 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]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[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.
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line
is_obsolete: true

[Term]
id: PEFF:0001012
name: ModResPsi
def: "PEFF keyword for the modified residue with PSI-MOD identifier." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001013
name: ModRes
def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod 
identifier." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001014
name: AltAC
def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001015
name: SeqStatus
def: "PEFF keyword for the sequence status. Complete or Fragment." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV 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]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001017
name: KW
def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001018
name: GO
def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001019
name: XRef
def: "PEFF keyword for the cross-reference to an external resource." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV 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]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[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]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[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]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001023
name: Conflict
def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

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

[Term]
id: PEFF:0001025
name: Domain
def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001026
name: ID
def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a 
UniProtKB term." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001027
name: ModResUnimod
def: "PEFF keyword for the modified residue with UniMod identifier." 
[PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[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]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[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]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:0001030
name: Proteoform
def: "PEFF keyword for the proteoforms of this protein, constructed as a 
set of annotation identifiers." [PSI:PEFF]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV 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]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV 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]
is_a: PEFF:0000003 ! PEFF file sequence entry term
xref: value-type:xsd\:string "The allowed value-type for this CV term."

[Term]
id: PEFF:0001034
name: maturation peptide
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]
is_a: PEFF:0001032 ! PEFF molecule processing keyword
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002001 ! regular expression for PEFF 
description line

[Term]
id: PEFF:1002001
name: regular expression for each VariantSimple item
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

Best Regards,
Gerhard

-- 

*--------------------------------------------------------------------*

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

*PhD student*

*Medizinisches Proteom-Center*

*DEPARTMENT Medical Bioinformatics*

*Building *ZKF E.055 | Universitätsstraße 150 | D-44801 Bochum

*Fon *+49 (0)234 32-29272 | *Fax *+49 (0)234 32-14554

*E-mail***ger...@ru... <mailto:ger...@ru...>

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