varfish-org / varfish-server

VarFish: comprehensive DNA variant analysis for diagnostics and research
MIT License
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Integrate phenix-like method from varfish-server-worker #936

Closed holtgrewe closed 9 months ago

holtgrewe commented 1 year ago

Is your feature request related to a problem? Please describe. The upcoming version of varfish-server-worker has a builtin method for prioritizing genes using a patient HPO term list.

Describe the solution you'd like Integrate querying the prioritizer as "VarFish Phenix-like".

Describe alternatives you've considered N/A

Additional context For example, a GET request to /hpo/sim/term-gene?terms=HP:0001166,HP:0000098&gene_symbols=FBN1,TGDS,TTN gives the following response:

{
  "hpo_version":"2023-04-05",
  "varfish_version":"0.5.1",
  "score_method":"phenomizer",
  "query":[
    {
      "term_id":"HP:0000098",
      "term_name":"Tall stature"
    },
    {
      "term_id":"HP:0001166",
      "term_name":"Arachnodactyly"
    }
  ],
  "result":[
    {
      "gene_symbol":"FBN1",
      "p_value":0.15187,
      "score":8.18528,
      "terms":[
        {
          "term_query":{
            "term_id":"HP:0001166",
            "term_name":"Arachnodactyly"
          },
          "term_gene":{
            "term_id":"HP:0001166",
            "term_name":"Arachnodactyly"
          },
          "score":3.664172
        },
        // ...
        {
          "term_query":null,
          "term_gene":{
            "term_id":"HP:0410280",
            "term_name":"Pediatric onset"
          },
          "score":0.0
        }
      ]
    },
    {
      "gene_symbol":"TTN",
      "p_value":0.27473,
      "score":5.610939,
      "terms":[
        {
          "term_query":{
            "term_id":"HP:0001166",
            "term_name":"Arachnodactyly"
          },
          "term_gene":{
            "term_id":"HP:0100807",
            "term_name":"Long fingers"
          },
          "score":2.8340273
        },
        // ...
     ]
    }
  ]
}
holtgrewe commented 9 months ago

Turned out to be inefficient for current overannotated HPO, we have cada-prio now in addition to Exomiser.