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Adding new ECO code for Genetics platform #873

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DSuveges opened this issue Mar 9, 2020 · 1 comment
Closed

Adding new ECO code for Genetics platform #873

DSuveges opened this issue Mar 9, 2020 · 1 comment
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Data Relates to Open Targets data team

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@DSuveges
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DSuveges commented Mar 9, 2020

This ticket is related to #856

The evidence_codes_info field was missing from the genetics portal evidences as the new source was not introduced into the ECO json file. The variant to gene mapping pipeline represents a new evidence class.

Affected repository: ECO ontology generation

A relatively straightforward resolution is to add the following line to the open_targets_terms dictionary:
'http://identifiers.org/eco/locus_to_gene_pipeline':'Open Targets Genetics portal locus to gene annotation pipeline,

This will lead to the addition of the following evidence class:

{
    "code": "http://identifiers.org/eco/locus_to_gene_pipeline",
    "label": "Open Targets Genetics portal locus to gene annotation pipeline",
    "path": [
        {
            "label": "evidence",
            "uri": "http://purl.obolibrary.org/obo/ECO_0000000"
        },
        {
            "label": "Open Targets Genetics portal locus to gene annotation pipeline",
            "uri": "http://identifiers.org/eco/locus_to_gene_pipeline"
        }
    ],
    "path_codes": [
        "ECO_0000000",
        "locus_to_gene_pipeline"
    ],
    "path_labels": [
        "evidence",
        "Open Targets Genetics portal locus to gene annotation pipeline"
    ]
}
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