Encephalitis a subtype of testicular neoplasm????

cmungall commented 10 years ago

http://tartini.crbs.ucsd.edu/phenotype/HP_0010788

wrong:

screen shot 2014-02-06 at 4 32 46 pm

and wrong:

screen shot 2014-02-06 at 4 33 12 pm

cmungall commented 10 years ago

Confirmation that the issue does not reside in the ontology:

screen shot 2014-02-06 at 4 23 15 pm

No Encephalitis or CNS inflammation to be found

cmungall commented 10 years ago

Ontoquest is also returning sane descendants:

http://nif-services-stage.neuinfo.org//ontoquest-lamhdi/rel/parents/HP_0010788?level=5

cmungall commented 10 years ago

This issue is upstream of the monarch API - the federation query below is wrong:

http://beta.neuinfo.org/services/v1/federation/data/nlx_151835-1.json?includePrimaryData=true&count=1000&q=HP:0010788&includeSubclasses=true&

HP:0010788 = testicular neoplasm

"result": [

    {
        "Disorder": "<a class=\"external\" target=\"_blank\" href=\"http://www.omim.org/entry/109650\">Behcet Syndrome</a>",
        "Qualifier": "",
        "Phenotype": "<a class=\"external\" target=\"_blank\" href=\"http://www.human-phenotype-ontology.org/hpoweb/showterm?id=HP:0002383\">Encephalitis</a>",
        "Aspect": "organ abnormality",
        "Publication": "ORPHANET:117",
        "Evidence Code": "TAS Traceable Author Statement",
        "Onset": "",
        "Frequency": "occasional",
        "disorder_id": "OMIM:109650",
        "e_uid": "653c174e6762af6517a759c60e4ec0051ef5f3b151b9771d6b7949283cd61554",
        "disorder_database_prefix": "OMIM",
        "disorder_id_num": "109650",
        "disorder_name": "Behcet Syndrome",
        "disorder_qualifier": "",
        "phenotype_id": "HP:0002383",
        "phenotype_label": "Encephalitis",
        "publication_id": "ORPHANET:117",
        "evidence_code": "TAS",
        "onset": "",
        "frequency": "occasional",
        "aspect": "O",
        "synonyms": "BEHÇET DISEASE|http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=117",
        "aspect_text": "organ abnormality"
    },

cmungall commented 10 years ago

Issue with closure, filed under closure ticket:

https://support.crbs.ucsd.edu/browse/LAMHDI-140

This is a showstopper methinks

nlwashington commented 10 years ago

Can't test until data issues are resolved with identifier queries: https://support.crbs.ucsd.edu/browse/NIF-10234

harryhoch commented 10 years ago

This looks fixed - is it?

monarch-initiative / monarch-legacy

Encephalitis a subtype of testicular neoplasm???? #110