tripal/legacy/tripal_feature/files/feature_property.obo

format-version: 1.2
date: 10:06:2005 15:07
saved-by: cjm
default-namespace: unknown
autogenerated-by: /Users/cjm/cvs/go-dev/go-perl/scripts/go2fmt.pl
default-namespace: feature_property
remark: Initially generated by Chris Mungall, sourced from FB and Rice chado. TODO: TIGR Chado; TODO: GFF3
subsetdef: fpo_sgd "SGD and related dbs subset"
subsetdef: fpo_gff "GFF3 specific tags"
subsetdef: fpo_apollo "properties with fixed semantics in apollo"

[Typedef]
id: SOFP:feature_property
name: feature_property
namespace: feature_property
def: "A general purpose relation between a biological feature and some value" [so:cjm]

[Typedef]
id: SOFP:aminoacid
name: aminoacid
namespace: feature_property
def: "amino acid coded for by a tRNA transcript feature" [so:cjm]
is_a: SOFP:feature_property
domain: SO:0000253
range: CHEBI:22477

[Typedef]
id: SOFP:anticodon
name: anticodon
namespace: feature_property
def: "anticodon coded for by a tRNA transcript feature" [so:cjm]
is_a: SOFP:feature_property
domain: SO:0000253
range: xsd:string
range_def: "A 3 character string representing the anticodon using the IUPAC DNA Sequence alphabet; for example ATG. RNA seqs MUST be converted to DNA seqs" []
comments: Note the difference between GENBANK_SOFP:anticodon and SOFP:anticodon; the former includes the base range

[Typedef]
id: SOFP:citation
name: citation
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110

[Typedef]
id: SOFP:comment
name: comment
namespace: feature_property
def: "Annotation comments, from a human curator" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:cyto_range
name: cyto_range
namespace: feature_property
def: "The cytological range covered by a feature. May be auto-generated from sequence coordinates, or determined by experimental methods" [so:cjm]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "Must conform to naming standard for that species; typically fly-style (eg 41A2-B3) or normal (eg 14p28.1-q32.2)" [so:cjm]
comments: If auto-derived, may be redundant with feature location

[Typedef]
id: SOFP:description
name: description
namespace: feature_property
def: "Free-text description of feature" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comments: Often sourced from fasta header, in which case it includes everything after the > symbol

[Typedef]
id: SOFP:dicistronic
name: dicistronic
namespace: feature_property
def: "true if transcript codes for >1 non-overlapping CDSs" []
is_a: SOFP:feature_property
domain: SO:0000115      ! transcript_feature
range: xsd:boolean
comments: redundant with secondary classification term SO:0000079

[Typedef]
id: SOFP:element
name: element
namespace: feature_property
def: "name of transposable element class" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: in chado or gff, this may also be indicated by a reference to a class in an ontology of TE classes

[Typedef]
id: SOFP:encoded_symbol
name: encoded_symbol
namespace: feature_property
def: "dicistronic CDS/proteins are attached to a single gene feature representing the whole cassette - in which case the symbol refers to the cassette. encoded_symbol refers to a gene in the sense of non-overlapping CDS set. cf Adh and Adhr in dmel" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:evidenceGB
name: evidenceGB
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "'experimental'"
comment: same as GENBANK_SOFP:experimental??

[Typedef]
id: SOFP:linked_to
name: linked_to
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: someone please define.. to do with restriction fragments?

[Typedef]
id: SOFP:missing_start_codon
name: missing_start_codon
namespace: feature_property
def: "true if start of CDS is unknown" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:boolean
comment: in chado, redundant with featureloc.is_{fmin,fmax}_partial

[Typedef]
id: SOFP:missing_stop_codon
name: missing_stop_codon
namespace: feature_property
def: "true if end of CDS is unknown" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:boolean
comment: in chado, redundant with featureloc.is_{fmin,fmax}_partial

[Typedef]
id: SOFP:na_change
name: na_change
namespace: feature_property
def: "A nucleic acid modification in some variant feature relative to the reference sequence" []
is_a: SOFP:feature_property
domain: SO:0000109         ! sequence_variant
range: xsd:string
range_def: "<na_seq-REFERENCE><position><na_seq-VARIANT>"
comment: in chado, this is redundant with featureloc.residue_info[rank=0,1]

[Typedef]
id: SOFP:non_canonical_start_codon
name: non_canonical_start_codon
namespace: feature_property
def: "The sequence of the biological start codon" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "3-character DNA sequence, must be different from ATG" []

[Typedef]
id: SOFP:owner
name: owner
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:pr_change
name: pr_change
namespace: feature_property
def: "An amino acid modification in some variant feature relative to the reference sequence" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "<aa_seq-ORIGINAL><position><aa_seq-NEW>. @ represents stop codon"
comment: see also: na_change; in chado, this is redundant with featureloc.residue_info[rank=0,1]

[Typedef]
id: SOFP:problem
name: problem
namespace: feature_property
def: "True if the annotation for this feature is problematic in some way; more details can be found in the comments property" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:boolean

[Typedef]
id: SOFP:readthrough_stop_codon
name: readthrough_stop_codon
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:boolean

[Typedef]
id: SOFP:reported_na_change
name: reported_na_change
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "As for na_change, suffixed with |<dbxref>" []

[Typedef]
id: SOFP:reported_pr_change
name: reported_pr_change
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "As for pr_change, suffixed with |<dbxref>" []

[Typedef]
id: SOFP:sp_comment
name: sp_comment
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: is this deprecated? originally sourced from gadfly pep validation pipeline - of little interest to others than flybase

[Typedef]
id: SOFP:sp_status
name: sp_status
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: is this deprecated? originally sourced from gadfly pep validation pipeline - of little interest to others than flybase

[Typedef]
id: SOFP:status
name: status
namespace: feature_property
def: "Annotation workflow status" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "'not done'"

[Typedef]
id: SOFP:source
name: source
namespace: feature_property
def: "Source from which feature originates - may be a computer program or analysis, or a group. Corresponds to GFF column 2" []
subset: fpo_gff
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:symbol
name: symbol
namespace: feature_property
def: "Community symbol" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:validation_flag
name: validation_flag
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "TODO: define the list of allowed values in an ontology" []

[Typedef]
id: SOFP:synonym
name: synonym
exact_synonym: "Alias" []
namespace: feature_property
def: "Historic community symbol, may have originally been symbol" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: In chado, this is redundant with the synonym table. GFF3 uses the tag "Alias"

[Typedef]
id: SOFP:date
name: date
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:date
comment: date of what?? Annotation??

[Typedef]
id: SOFP:internal_synonym
name: internal_synonym
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: FB specific?

[Typedef]
id: SOFP:qseq_type
name: qseq_type
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: deprecated?

[Typedef]
id: SOFP:unixdate
name: unixdate
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:integer
range_def: "No of seconds since unix time zero, 1 Jan 1970" []
comment: date of what?? Annotation??

[Typedef]
id: SOFP:gbunit
name: gbunit
namespace: feature_property
def: "Name of genbank scaffold sequence intersected by the feature" []
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "<dbxref> - taken from NCBI/EMBL/DDBJ" []

[Typedef]
id: SOFP:keywords
name: keywords
namespace: feature_property
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:orf_classification
name: orf_classification
namespace: feature_property
def: "gene call confidence flag"
subset: fpo_sgd
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "'Dubious'|'Uncharacterized'|'Verified'" []
comment: Currently only used by SGD

[Typedef]
id: SOFP:ontology_term
name: ontology_term
namespace: feature_property
def: "A term from some ontology classifying the feature" []
subset: fpo_gff
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
range_def: "<dbxref> of a term in some ontology" []
comment: In chado, this is redundant with the feature_cvterm table

[Typedef]
id: SOFP:protein_id
name: protein_id
namespace: feature_property
def: "A protein sequence identifier" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: Should really be a dbxref [so:sjc]

[Typedef]
id: SOFP:organism
name: organism
namespace: feature_property
def: "The name of the organism" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: In chado, this is redundant with the organism table [so:sjc]

[Typedef]
id: SOFP:mol_type
name: mol_type
namespace: feature_property
def: "The type of molecule" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: Presumably, this could be inferred from the SO type [so:sjc]

[Typedef]
id: SOFP:dev_stage
name: dev_stage
namespace: feature_property
def: "Stage of development" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:chromosome
name: chromosome
namespace: feature_property
def: "Name of chromosome the feature occurs on(?)" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string
comment: What is this for? [so:sjc]

[Typedef]
id: SOFP:map
name: map
namespace: feature_property
def: "A map location" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:finished
name: finished
namespace: feature_property
def: "If the annotation of the feature is complete" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:boolean

[Typedef]
id: SOFP:Note
name: Note
namespace: feature_property
def: "A GFF3 Note attribute" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:Gap
name: Gap
namespace: feature_property
def: "A GFF3 Gap cigar string" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string

[Typedef]
id: SOFP:score
name: score
namespace: feature_property
def: "A GFF3 score" [so:sjc]
is_a: SOFP:feature_property
domain: SO:0000110
range: xsd:string