Where to get anatomical ontology term hierarchy?

Data Access
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I’m looking at the association_overall_direct’table’ and I’m finding the disease ontology information in the disease table super useful for mapping associations up to disease groups. I’d like to do the same for (baseline_)expression data using similar ‘descendents’ data for the UBERON ontology, but I can’t find the location of this data… sorry if I’m just being blind!

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Hi Danzo,

Glad you’re finding the platform and disease ontology information useful! At present we don’t have equivalent ontology mappings (or their ancestors/descendents) for the expression data but we are aware of this oversight and plan to address it in upcoming releases.

All the best,

Tobi

1 Like
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Thanks Tobi, what’s the timeline? I guess I could grab UBERON from somewhere and do it myself?

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The plan is to deprecate the baseline widget and data entirely then replace it with updated data where every ID has a corresponding UBERON (or Cell Ontology) ID. This is likely to be public early next year but I can make no guarantees.

If all you want is the ontology structure you can use our biosample index which has UBERON and Cell Ontology contained within, but unfortunately no direct links to the baseline expression labels currently in the platform.

All the best,
Tobi

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Thanks Tobi!

The biosample dataset looks like exactly what I was after!

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I should note that I realised for UBERON our biosample index has a bug in it where the relationships aren’t perfectly captured. You can read about the exact issue here if you’d like: Add part of to biosample index relationships by Tobi1kenobi · Pull Request #1164 · opentargets/gentropy · GitHub

This has been fixed now however and will be updated next week when we do our December release.

Kind regards,

Tobi