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Review CTD #48

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EvanDietzMorris opened this issue Apr 16, 2024 · 4 comments
Open

Review CTD #48

EvanDietzMorris opened this issue Apr 16, 2024 · 4 comments
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@EvanDietzMorris @eKathleenCarter
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improve an existing source We already have this source but it needs improving Tracking This data was added to DMOG's tracking list under review This dataset is being considered for incorporation

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@EvanDietzMorris
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We only get parts of CTD, do we want more? Additionally, the parser has a reference to 'RO:0001001' (derives_into) but the code prevents that predicate from ever occurring, the get_chemical_label_id function can only return 'CTD:ameliorates' 'CTD:contributes_to' or 'biolink:related_to' (and currently never returns related_to as far as I can tell). Did we lose derives_into edges that we should be getting?
@EvanDietzMorris
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We also need to consult with Jim, it would be nice if we could incorporate the pipeline for the custom file he builds into ORION.

@eKathleenCarter
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I think we should consider incorporating the pathway files from CTD. (gene-pathway/chemical-pathway/disease-pathway). Without importing Kegg, I think that we are lacking in this realm.

@eKathleenCarter eKathleenCarter transferred this issue from RobokopU24/Feedback Apr 16, 2024
@eKathleenCarter
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Moving to new source repo

@eKathleenCarter eKathleenCarter added improve an existing source We already have this source but it needs improving under review This dataset is being considered for incorporation labels Apr 16, 2024
@eKathleenCarter
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@eKathleenCarter to review parser and refactor. Discuss with Jim about curated file that was made.

@eKathleenCarter eKathleenCarter added the Tracking This data was added to DMOG's tracking list label Oct 7, 2024
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@EvanDietzMorris EvanDietzMorris

@eKathleenCarter eKathleenCarter

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improve an existing source We already have this source but it needs improving Tracking This data was added to DMOG's tracking list under review This dataset is being considered for incorporation
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@EvanDietzMorris @karafecho @eKathleenCarter