Provide mapping between EFO response to terms and new OBA replacements

[dosumis]

Generate list of all GO classes in the response to branch - this can be done easily with a query of UberGraph.

SPARQL query for xrefs to these terms => EFO terms.

Draft query here - needs some work.

TODO assign to @rays22 (needs to be added to EFO)

[rays22]

Here is an UberGraph query to get the EFO terms that are subclasses of

• GO:0042221 ; # "response to chemical"
• GO:0050896 ; # "response to stimulus" Feel free to modify it.

[dosumis]

1. We need a mapping between OBA terms and EFO/GO terms in use so that we can obsolete and replace.  For this, we can use Kalia’s mapping spreadsheet - but note, the OBA IDs in this or NOT correct.  Instead we can use CHEBI IDs. e.g. 

defined_class	defined_class_name	chemical	chemical_name
OBA:2040000		CHEBI:10033	warfarin

As a first step, we should create a 3 column spreadsheet:  OBA to EFO to GO mapping.

We need a mapping between OBA terms and EFO/GO terms in use so that we can obsolete and replace. For this, we can use [Kalia’s mapping spreadsheet](https://docs.google.com/spreadsheets/d/13qh7dLE38vMyz91oRqj6GzKjFohNazNKAJxKG6Plw1o/edit#gid=0) - but note, the OBA IDs in this are NOT correct. Instead we can use CHEBI IDs. e.g.

defined_class	defined_class_name	chemical	chemical_name
OBA:2040000		CHEBI:10033	warfarin

Kallia’s spreadsheet has the mapping:

EFO:0009167 response to warfarin GO:0042221 CHEBI:10033

From this we can map OBA:2040000 to EFO:0009167 and GO:0042221

As a first step, we should create a 3 column spreadsheet: OBA to EFO to GO mapping.

[rays22]

First draft of EFO/GO --> OBA mapping: https://docs.google.com/spreadsheets/d/13qh7dLE38vMyz91oRqj6GzKjFohNazNKAJxKG6Plw1o/edit#gid=1861483396

[dosumis]

DEPENDENCY: OBA release needed.

• [x] Ray to add an additional column showing obsoletion status to EFO/GO--> OBA mapping for response to chemical terms.

@zoependlington everything with SKOS:exactMatch in this sheet is good, but I think more discussion of transition is needed to ensure that labels match up and the imported terms sit in the right place in the hierarchy.

[rays22]

• [x] Ray to add an additional column showing obsoletion status to EFO/GO--> OBA mapping for response to chemical terms.

I have replaced the obsolete EFO classes with the replacement GO classes in the gsheet tab. Now there should be no obsolete EFO/GO classes in the table.

[rays22]

@dosumis , @zoependlington , Is there anything else to do to for this ticket or can I close it?

[dosumis]

The aims here has to be to get OBA response_to terms seamlessly integrated into EFO. For this I think we need a mapping sheet for role-based grouping classes as well as the ones here gsheet tab.

I think what's needed it:

• import all OBA response_to terms to EFO
• Using this mapping gsheet tab. + one for role-based grouping classes:
  • where we have an exact match between an OBA term and an EFO term, the EFO term should be obsoleted in favour of the OBA term. @zoependlington - I think we've agreed this but please let me know if problematic
  • where the EFO term is more specific (broad_match in the table)? it should be retained as subclass
  • where the EFO term is broader (narrow_match in the table?) it should be retained as a superclass.

This would be rather painful to do by hand. @matentzn - I'm wondering if there's a clever way to do this. It would probably take a few attempts to the tables right and review the results.

[matentzn]

Too complicated to answer in a ticket, needs meeting

[rays22]

2022-08-08:

• [x] raise this issue at the next OBA call.

[dosumis]

I think it will take a call to fix it - with some prep so that we can see plenty of examples of what. We have the mapping table - but this is a bit confusing to look at on its own. It would be good to have some examples where we can see the representation in OBA and EFO side by side.

Also before the call - @rays22 - can we get a status-update on the role-based terms? Are they now in OBA? Is there more work to do on them?

I propose that we discuss this on the next OBA call and invite Zoe along.

[rays22]

Also before the call - @rays22 - can we get a status-update on the role-based terms? Are they now in OBA? Is there more work to do on them?

Some role-based terms related toresponse_to_chemical_with_role_stimulus have been incorporated into OBA.

[dosumis]

I can't fix this simply with a response on the ticket. We need a call to discuss a general strategy for incorporating OBA terms into EFO where there are existing EFO terms to integrate with that are not in OBA.