remove covid_phenotypes from MyDisease

colleenXu commented 2 years ago

The data is obsolete, and an updated version should be accessible to BTE through the Automat CORD19 API (smartapi registration here). @andrewsu and I discussed how it didn't need to be included in MyDisease anymore...

Details: The covid_phenotypes info is a old, cached version of what Automat covidphenotypes API provided - which was a hand-curated list of phenotypes that were associated with the disease COVID-19.

zcqian commented 2 years ago

The plan is to remove the data from builds, and then later remove the plugin entirely.

Does this plan sound fine, @newgene ?

newgene commented 2 years ago

@zcqian Yes, remove the data first, and we will probably still keep the code. You can label at top of this plugin code as "predicated" and pointing it to this issue.

colleenXu commented 5 months ago

@everaldorodrigo @andrewsu @newgene

This would be a useful issue to address, but I don't know if it's in-scope for Everaldo to work on

colleenXu commented 4 months ago

Update: discussed with Dylan last Friday (2/16). Note to @DylanWelzel that we'll want to remove the mapping (covid_phenotypes showing up in v1/metadata and v1/metadata/fields endpoints)

DylanWelzel commented 2 months ago

The newest release has removed covid_phenotypes from the v1/metadata and v1/metadata/fields endpoints. The recent PR #62 removes the code as well, @newgene is this plugin still something we want to save knowing the parser just contains hardcoded metadata? If so I can undo this change before merging the PR

def load_data(data_folder):
    yield {
        "_id": "MONDO:0100096",
        "covid_phenotypes": [
            {"hp": "HP:0011899", "label": "Hyperfibrinogenemia"},
            {"hp": "HP:0025143", "label": "Chills"},
            {"hp": "HP:0025439", "label": "Pharyngitis"},
            {"hp": "HP:0002027", "label": "Abdominal pain"},
            {"hp": "HP:0032141", "label": "Precordial pain"},
            {"hp": "HP:0005403", "label": "Decrease in T cell count"},
            {"hp": "HP:0002017", "label": "Nausea and vomiting"},
            {
                "hp": "HP:0005407",
                "label": "Decreased proportion of CD4-positive T cells",
            },
            {"hp": "HP:0012649", "label": "Increased inflammatory response"},
            {"hp": "HP:0003326", "label": "Myalgia"},
            {"hp": "HP:0012735", "label": "Cough"},
            {"hp": "HP:0030783", "label": "Increased serum interleukin-6"},
            {"hp": "HP:0002098", "label": "Respiratory distress"},
            {"hp": "HP:0000224", "label": "Decreased taste sensation"},
        ],
    }

newgene commented 2 months ago

@DylanWelzel it's ok to remove it. It was used as a temp solution, which is no longer needed.

colleenXu commented 2 months ago

@DylanWelzel asked me to review and close this issue.

Based on a quick look, it looks like covid_phenotypes have been removed from the docs and both metadata endpoints.

So I think this is good and I'm closing the issue.

biothings / mydisease.info

remove covid_phenotypes from MyDisease #45