format-version: 1.0
data-version: 0.9
date: 26:04:2017 15:30
saved-by: pab
auto-generated-by: OBO-Edit 1.101
default-namespace: PEFF
namespace-id-rule: * PEFF:$sequence(7,0,9999999)$
remark: namespace: PEFF
remark: publisher: HUPO Proteomics Standards Initiative
remark: creator: Pierre-Alain Binz <pierre-alain.binz <-at-> chuv.ch>
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.
	
[Typedef]
id: has_regexp
name: has regexp

[Typedef]
id: has_units
name: has_units

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

[Typedef]
id: has_order
name: has_order

[Term]
id: PEFF:0000001
name: PEFF CV
def: "PSI Extended Fasta Format Controlled Vocabulary term." [PSI:PEFF]

[Term]
id: PEFF:0000002
name: File Header Section
def: "PEFF File Header Section."  [PSI:PEFF]
is_a: PEFF:0000001 ! PEFF CV term

[Term]
id: PEFF:0000003
name: Individual Sequence Entries Section
def: "PEFF Individual Entry Section."  [PSI:PEFF]
is_a: PEFF:0000001 ! PEFF CV term

[Term]
id: PEFF:0000004
name: File Description Block
def: "PEFF File Description Block."  [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:0000005
name: Database Description Block
def: "PEFF Database Description Block."  [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:0000006
name: Sequence Entry
def: "PEFF Sequence Entry."  [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term

[Term]
id: PEFF:0000007
name: Sequence Entry description
def: "PEFF Sequence Entry 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: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:0000017
name: SequenceType
def: "Molecular type of the sequences."  [PSI:PEFF]
is_a: PEFF:0000002 ! File Header Section term
xref: value-type:xsd\:string "The allowed value-type for this CV term."
relationship: has_regexp PEFF:1002002 !(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)

[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: "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."


[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: MS: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:1002480 ! regular expression

[Term]
id: MS:1002002
name: (AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)
def: "Regular expression for the molecular type of the sequences." [PSI:PEFF]
is_a: MS:1002480 ! regular expression