rjawesome
commented
1 year ago Looks like the SmartAPI annotation for myvariant.info clinvar uses the omim id to identify the disease. If you look at the myvariant info link you sent, the diseases lack an omim id but do have other id types (ie. mondo) which are not utilized by the smartapi annotation. Looking at the melanoma result from the myvariant query you sent above:
{
"accession":"RCV000442563",
"clinical_significance":"Likely pathogenic",
"conditions":{
"identifiers":{
"human_phenotype_ontology":"HP:0007474",
"medgen":"C0025202",
"mesh":"D008545",
"mondo":"MONDO:0005105"
},
"name":"Melanoma"
},
...
}Meanwhile, if you test other clinvar relations they seem to work on bte (ie. the example DBSNP:rs1193171808 -> OMIM:615592 given on the smartapi annotation)
andrewsu
colleenXu
Clinvar contains relationships between genetic variants and diseases (e.g., BRAF V600E -> melanoma), and that relationship appears to be captured in myvariant.info (e.g., http://myvariant.info/v1/variant/rs121913377). But I can't get this relationship via BTE when querying using any of these identifiers:
Note the DBSNP query gets results based on CIViC and Disgenet, but not clinvar. It appears that the clinvar fields are captured in the myvariant.info smartAPI annotation, but I can't quite figure out why those results aren't being captured.
TRAPI Query template
``` { "message": { "query_graph": { "nodes": { "n0": { "ids": ["CLINVAR:362948"], "categories": ["biolink:SequenceVariant"] }, "n1": { "categories": ["biolink:DiseaseOrPhenotypicFeature"] } }, "edges": { "t_edge": { "object": "n1", "subject": "n0" } } } } } ```