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biothings / mygene.info

MyGene.info: A BioThings API for gene annotations
http://mygene.info
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Data source: load ClinGen gene-disease validity data #69

Closed andrewsu closed 4 years ago

andrewsu commented 5 years ago

more info: https://github.com/SuLab/GeneWikiCentral/issues/116

newgene commented 4 years ago

Integrated to MyGene.info API now:

http://mygene.info/v3/query?q=_exists_:clingen&fields=clingen,name,symbol

An example data object:

{
    "_id": "23676",
    "_score": 1.55,
    "clingen": {
        "_license": "https://www.clinicalgenome.org/docs/terms-of-use/",
        "clinical_validity": {
            "classification": "definitive",
            "disease_label": "nonsyndromic genetic deafness",
            "mondo": "MONDO:0019497",
            "online_report": "https://search.clinicalgenome.org/kb/gene-validity/29773bee-1f13-43f6-bda0-c5a646efccd7--2017-09-12T16:00:00",
            "sop": "SOP6"
        }
    },
    "name": "small muscle protein X-linked",
    "symbol": "SMPX"
}

MyGene.info data source:

src/hub/dataload/sources/clingen

Based on the code from @chvbs2000:

https://github.com/chvbs2000/ClinGen