From eee5f2808e25cd49542aeafd6000d990bf46d272 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Mon, 7 Nov 2022 14:44:52 -0800 Subject: [PATCH 1/2] add mappings to sequence variant and examples to the 'type' slot --- biolink-model.yaml | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index 06f48d70aa..e994fd219d 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -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 @@ -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 From dee7aad18e1a3a456d9cdb92ea954cc5271190d3 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Tue, 8 Jul 2025 17:28:50 -0700 Subject: [PATCH 2/2] fix test --- biolink-model.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/biolink-model.yaml b/biolink-model.yaml index 25f449a7cf..dd25e6aa06 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -9105,7 +9105,7 @@ classes: - 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:0001792 # non_coding_transcript_exon_variant - SO:0001825 # conservative_inframe_deletion - SO:0001823 # conservative_inframe_insertion - SO:0001826 # disruptive_inframe_deletion