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cv_sequence_ontology.txt
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format-version: 1.2
data-version: 1.0
date: 24:10:2011 14:42
saved-by: kareneilbeck
auto-generated-by: OBO-Edit 2.1-beta10
subsetdef: biosapiens "biosapiens protein feature ontology"
subsetdef: DBVAR "database of genomic structural variation"
subsetdef: SOFA "SO feature annotation"
synonymtypedef: aa1 "amino acid 1 letter code"
synonymtypedef: aa3 "amino acid 3 letter code"
synonymtypedef: AAMOD "amino acid modification"
synonymtypedef: BS "biosapiens"
synonymtypedef: dbsnp "dbsnp variant terms"
synonymtypedef: dbvar "DBVAR"
synonymtypedef: ebi_variants "ensembl variant terms"
synonymtypedef: RNAMOD "RNA modification" EXACT
default-namespace: sequence
remark: autogenerated-by\: DAG-Edit version 1.417\nsaved-by\: eilbeck\ndate\: Tue May 11 15\:18\:44 PDT 2004\nversion\: $Revision\: 1.45 $
[Term]
id: SO:0001778
name: germline_variant
synonym: "germline variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:31:46Z
[Term]
id: SO:0001777
name: somatic_variant
synonym: "somatic variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:31:12Z
[Term]
id: SO:0000159
name: deletion
alt_id: SO:1000033
def: "The point at which one or more contiguous nucleotides were excised." [SO:ke]
subset: SOFA
synonym: "deleted_sequence" EXACT []
synonym: "nucleotide deletion" EXACT []
synonym: "nucleotide_deletion" EXACT []
xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region
[Term]
id: SO:1000032
name: indel
def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http\://www.hgvs.org/mutnomen/recs-DNA.html#indel]
comment: Indels can have a different number of bases than the corresponding reference sequence.
xref: http://en.wikipedia.org/wiki/Indel "wiki"
is_a: SO:0001059 ! sequence_alteration
[Term]
id: SO:0000667
name: insertion
alt_id: SO:1000034
def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]
subset: DBVAR
subset: SOFA
synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "nucleotide insertion" EXACT []
synonym: "nucleotide_insertion" EXACT []
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region
[Term]
id: SO:1000002
name: substitution
def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]
subset: SOFA
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0001624
name: 3_prime_UTR_variant
def: "A UTR variant of the 3' UTR." [SO:ke]
comment: EBI term 3prime UTR variations - In 3prime UTR.
synonym: "3'UTR variant" EXACT []
synonym: "3PRIME_UTR" EXACT ebi_variants [http://uswest.ensembl.org/info/docs/variation/index.html]
synonym: "three prime UTR variant" EXACT []
synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
is_a: SO:0001622 ! UTR_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:23:54Z
[Term]
id: SO:0001577
name: complex_change_in_transcript
def: "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://uswest.ensembl.org/info/docs/variation/index.html]
comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
synonym: "complex_indel" EXACT ebi_variants [http://uswest.ensembl.org/info/docs/variation/index.html]
synonym: "complext change in transcript" EXACT []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:33:03Z
[Term]
id: SO:0001589
name: frameshift_variant
def: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]
comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
synonym: "frameshift variant" EXACT []
synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "frameshift_coding" EXACT ebi_variants [http://uswest.ensembl.org/info/docs/variation/index.html]
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:40:19Z
[Term]
id: SO:0001651
name: inframe_codon_gain
def: "A sequence variant which gains a codon, and does not cause a disruption of the translational reading frame." [SO:ke]
synonym: "inframe codon gain" RELATED []
is_a: SO:0001821 ! inframe_increase_in_CDS_length
created_by: kareneilbeck
creation_date: 2010-07-19T01:29:08Z
[Term]
id: SO:0001652
name: inframe_codon_loss
def: "A sequence variant which loses a codon, and does not cause a disruption of the translational reading frame." [SO:ke]
synonym: "inframe codon loss" RELATED []
is_a: SO:0001822 ! inframe_decrease_in_CDS_length
created_by: kareneilbeck
creation_date: 2010-07-19T01:29:35Z
[Term]
id: SO:0001583
name: non_synonymous_codon
alt_id: SO:0001584
def: "A sequence variant, where the change may be longer than 3 bases, and at least one base of a codon is changed resulting in a codon that encodes for a different amino acid or stop codon." [EBI:gr, SO:ke]
comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.
synonym: "non synonymous codon" EXACT []
synonym: "non_synonymous_coding" EXACT ebi_variants [http://uswest.ensembl.org/info/docs/variation/index.html]
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001581 ! codon_variant
is_a: SO:0001818 ! non_synonymous_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:35:49Z