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fixes #1034 : add mappings to sequence variant and examples to the 'type' slot #1147

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fixes #1034 : add mappings to sequence variant and examples to the 'type' slot #1147

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28 changes: 26 additions & 2 deletions biolink-model.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7713,9 +7713,22 @@ classes:
A single DBSNP rs ID could correspond to more than one sequence variants
(e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)
exact_mappings:
# slightly broader semantics than SO:0001059 - 'sequence alteration'
# describes a sequence feature that may have 1..* sequence alterations
- WIKIDATA:Q15304597
narrow_mappings:
- SO:0001632 # (downstream_gene_variant)
- SO:0001631 # (upstream_gene_variant)
- SO:0001627 # (intron_variant)
- SO:0001619 # (non_coding_transcript_variant)
- SO:0001970 # (non_coding_transcript_intron_variant)
- (SO:0001792) # non_coding_transcript_exon_variant
- SO:0001825 # conservative_inframe_deletion
- SO:0001823 # conservative_inframe_insertion
- SO:0001826 # disruptive_inframe_deletion
- SO:0001824 # disruptive_inframe_insertion
- SO:0001624 # 3_prime_UTR_variant
- SO:0001623 # 5_prime_UTR_variant
- SO:0001632 # downstream_gene_variant
- SO:0001619 # non_coding_transcript_variant
close_mappings:
- dcid:Allele
- SO:0001060
Expand Down Expand Up @@ -7758,6 +7771,17 @@ classes:
description: ti282a allele from ZFIN
- value: CLINVAR:17681
description: NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)
type:
description: >-
The type field of a Sequence Variant is used to indicate the nature of the variation. The value of this
field should be a Sequence Ontology compact URI (or CURIE).
examples:
- value: SO:0001632 # downstream gene variant
- value: SO:0001059 # sequence alteration
- value: SO:0002007 # multiple nucleotide variant (substitution)
- value: SO:0001825 # conservative inframe deletion


in_subset:
- model_organism_database

Expand Down