PHI-base / PHI5_web_display

PHI5_web_display will allow to display PHI-Canto data
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Display PHI-base 4 interaction IDs in annotations #106

Closed jseager7 closed 9 months ago

jseager7 commented 11 months ago

In the latest JSON export, each annotation object will have a phi4_id array of PHI IDs from PHI-base 4. For example:

"annotations": [
    {
        "checked": "yes",
        "conditions": [],
        "creation_date": "2014-11-01",
        "curator": {
            "community_curated": false
        },
        "evidence_code": "Unknown",
        "extension": [
            {
                "rangeDisplayName": "reduced virulence",
                "rangeType": "Ontology",
                "rangeValue": "PHIPO:0000015",
                "relation": "infective_ability"
            }
        ],
        "figure": "",
        "metagenotype": "00014f904fb22f27-metagenotype-1",
        "phi4_id": [
            "PHI:3258"  // PHI-base 4 interaction IDs
        ],
        "publication": "PMID:25340392",
        "status": "new",
        "submitter_comment": "The mutants showed severely reduced virulence in mice but were highly resistant to itraconazole and amphotericin B, two drugs targeting sterol synthesis.",
        "term": "PHIPO:0000001",
        "type": "pathogen_host_interaction_phenotype"
    },
]

These PHI IDs should be shown in the annotation details section of the gene page, in a new column called 'PHI-base 4 ID' to the right of the 'High level term' column.

The mockup below is for the C14DM gene of Leishmania major (UniProtKB:Q4QGX0).

image

Each PHI ID should link to the search results for that PHI ID on the PHI-base 4 website, using the following template:

http://www.phi-base.org/searchFacet.htm?queryTerm={{phi4_id}}

For example:

http://www.phi-base.org/searchFacet.htm?queryTerm=PHI:3258

If there is more than one PHI ID in the phi4_id array, then each PHI ID should be shown on a separate line. For example:

image

jseager7 commented 11 months ago

In the last meeting we agreed that 'PHI-base 4 ID' would be a better heading for the column than 'PHI ID'. I'll update the images in the original comment.

jseager7 commented 9 months ago

This is implemented on the new proof-of concept server.

image