khanspers
commented
2 years ago Update: I used CASE 5 to test a bunch of queries, and came up with some results. I ran the queries in ARAX using "Post to Other" and specifying https://api.bte.ncats.io/v1 as the external API. The same queries in https://biothings.io/explorer/advanced did not always work give the same results and I have some questions in general about that interface (will ask seperately).
CASE 5 results:
- The variant is only linked to one NamedEntity, the SLC2A1 gene
- There are several links between SLC2A1 and Migraine/Epilepsy
- Many SmallMolecules are known to treat Migraine and Epilepsy
- From a query looking at small molecules that treat epilepsy and migraine, and have an effect on SLC2A1, there were several hits. Valproic Acid was one of the top-scoring ones, which is a known treatment for epilepsy
Query:
{
"message": {
"query_graph": {
"nodes": {
"n1": {
"ids":
["HP:0002076", "HP:0001250"], "is_set": true,
"categories": [
"biolink:PhenotypicFeature"
]
},
"n2": {
"categories": [
"biolink:SmallMolecule"
]
},
"n3": {
"ids": [
"NCBIGene:6513"
],
"categories": [
"biolink:Gene"
]
}
},
"edges": {
"e1": {
"subject": "n2",
"object": "n1",
"predicates": [
"biolink:treats"
]
},
"e2": {
"subject": "n2",
"object": "n3"
}
}
}
}
}https://docs.google.com/document/d/1f6R3x4DiYrCQkIhjDBavoHlLnswSY7gwT-9XqKWxUgo/edit?usp=sharing
andrewsu
colleenXu
From our colleagues at RCIGM, we have several example use cases related to genetic diseases. The goal is to take info about the variants and the phenotypes, and to propose candidate therapies. For these five cases, there are known therapies that we should be able to get. The goal is to assess the ability of skilled analyst to identify those therapies. Good set of starter cases for @khanspers to work on... (cc @AlexanderPico)
CASE 1 VARIANTS TH NM_199292.2. c.541C>T; p.Gln181Ter. chr11:2189760 TH NM_199292.2 c.785C>G; p.Thr262Ser. chr11:2188668 HPO: delayed speech and language development
CASE 2 - 6011 NPC1 (NM_000271.3) chr 18: 21119857G>A c.2713C>T; pGLN905* - Homozygous
CLINICAL PRESENTATION: Cholestasis, hyperbilirubinemia, hepatosplenomegaly (this was before HPO terms used)
CASE 3 - 6094 ASL c.706C>T, p.Arg236Trp (homozygous CLINICAL PRESENTATION: 7 day old female presented with lethargy and altered mental status found to have hyperammonemia. Concern for underlying diagnosis urea cycle disorder – likely citrullinemia. Parents are first cousins. (this was before HPO terms used)
CASE 4 - 243 ALDH7A1 c.328C>T, p.Arg110Ter HPO TERMS: Jaundice;Poor appetite;Ventriculomegaly;Seizure
CASE 5 - 3081 SLC2A1 c.1202C>T p.Pro401Leu HPO TERMS: Migraine, Seizure