Add OBA to dynamic imports to EFO

[dosumis]

First set of terms:

• disease onset and progression traits Add age of onset (of disease) terms obophenotype/bio-attribute-ontology#49
• response to chemical traits add / update response to trait terms - needed for EFO/GWAS obophenotype/bio-attribute-ontology#50

(As discussed on GWAS measurement/trait calls)

Note - these are all cases where we don't currently have a measurement term.

Also - it will be important to update the response_to terms as GO plans to obsolete the response to xenobiotic branch, which includes many response to drug terms. These can be replaced buy OBA terms defined using CHEBI & compound entity pattern from GO.

@zoependlington - Anita - could potentially help.

[zoependlington]

Note to self: Dynamic import protocol here (under Step-by-step guide to create a dynamic import) : https://github.com/EBISPOT/efo/blob/master/src/ontology/README-editors.md

[zoependlington]

@dosumis Is there a list of terms from OBA that need to be in this import and the parent term they should sit under in EFO in existence? If so, I can try to get this in for the January or February release.

[dosumis]

Hi @zoependlington - @rays22 will provide a list in the next day or two once the new templates are activated. @rays22 - please also let Zoe know when there's a new release (you might need to run this yourself).

[zoependlington]

@rays22 Is there an update/estimate on the list of terms? I can't do the dynamic import until I have a list.

[rays22]

Sorry @zoependlington , the template has not been activated due to some issues.

[dosumis]

@rays22 - I believe both templates are now activated. Can you provide a list of OBA terms for import?

[dosumis]

• @rays22 to make OBA release ASAP
• Provide 'age of onset' terms in first batch (these don't need mapping to anything as they are new terms). This should be provided as a list in this ticket. Once dynamic import is in place new OBA terms should be added as PR to oba_terms.txt which will live here https://github.com/EBISPOT/efo/tree/master/src/ontology/iri_dependencies

We will wait to add the response to chemical OBA terms until we have a better mapping to EFO/GO terms that need replacing - see #1436

[dosumis]

Here's the current list of 'age of onset' terms from master. I believe more are coming but only these will be in the next OBA release, which @matentzn is doing right now.

OBA:2001000
OBA:2001001
OBA:2001002
OBA:2001004
OBA:2001007
OBA:2001008
OBA:2001009
OBA:2001010
OBA:2001011
OBA:2001012
OBA:2001013
OBA:2001015
OBA:2001016
OBA:2001017
OBA:2001018
OBA:2001019
OBA:2001020
OBA:2001022
OBA:2001024
OBA:2001026
OBA:2001027
OBA:2001028
OBA:2001029
OBA:2001030
OBA:2001031
OBA:2001032
OBA:2001033

[zoependlington]

@dosumis I see the latest release from 2 days ago, however none of the above term IDs seem to be in that release (at least from the mirror downloaded using the PURL) therefore I'm unable to continue to add the import. Please let me know if there is another release.

[matentzn]

Still waiting for some clarification from @dosumis re OBA release.. I didn't update OBA in this branch yet.

[zoependlington]

Ah, thanks @matentzn! 😁

[zoependlington]

Age at onset terms have been added to import (needs review).