Retrofit all molecular function regulators to follow latest pattern

[dosumis]

• DOSDP - activator activity
• tsv of existing terms + python code used to generate
• Use dosdp-scala

Needs to support keeping references. This should work, given pattern spec.

To be determined:

• How do we flush and replace old terms?
• Should we move this whole branch to autogeneration?

TODO:

• [x] Edit script so that tsv conforms to spec for dosdp-scala
• [ ] Generate terms
• [ ] ...

(Ticket split off from #12995) CC @cmungall @balhoff - This is a good branch for implementing generation with dosdp-scala. It'd be great if we could have this working before the Corvalis meeting.

[dosumis]

TSVs here: https://github.com/geneontology/go-ontology/tree/master/src/pattern_implementation_tsv

[cmungall]

Ignore the hash-mention above, wrong ticket

[dosumis]

This partly works

dosdp-scala generate --obo-prefixes=true --template=design_patterns/validated_patterns/activator_activity.yaml --infile=pattern_implementation_tsv/activator_activity.tsv --outfile=activator_activity.ofn --ontology=../go-simple.obo

But only after changing IDs in pattern to OBO style to fit with --obo-prefixes (should be discussed).

BUG: def_dbxrefs end up like this:

GOC:BHF,GOC:dph,GOC:tb

Looks like string gets cast to a uniq'd list of characters.

But report here: https://github.com/balhoff/dosdp-scala/issues/14

[balhoff]

New release: https://github.com/balhoff/dosdp-tools/releases/tag/v0.3.2

[dosumis]

Progress:

• Latest design pattern docs: https://github.com/geneontology/go-ontology/tree/master/src/design_patterns/validated_patterns
• Latest TSVs: https://github.com/geneontology/go-ontology/tree/master/src/pattern_implementation_tsv

Also see #13692

[pgaudet]

@balhoff Do you know what's the status on this one ?

Thanks, Pascale

[dosumis]

It should be possible to run dosdp-tools with tsv + pattern doc to generate a set of terms following the patterns.

TSV is here: https://gist.github.com/dosumis/4d899727896367c9b432e733e120b675. Will need to be split into regulator, activator, inhibitor. Separate patterns for these are:

https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/activator_activity.yaml https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/inhibitor_activity.yaml https://github.com/geneontology/go-ontology/blob/master/src/design_patterns/regulator_activity.yaml

[pgaudet]

Hi @dosumis Thanks for your response ! This is a little cryptic to me - who might be able to do this ?

Thanks, Pascale

[dosumis]

Just realised I already split out activator, inhibitor and regulator terms to separate TSVs already. I have moved the files into the design_patterns folder

dosdp_tools is here: https://github.com/INCATools/dosdp-tools

It's easy to install.

This command from the design_patterns folder generates an OWL file of regulator activity terms following the pattern:

dosdp-tools --obo-prefixes --ontology=../ontology/go-edit.obo --outfile=regulator_activity.owl --template=regulator_activity.yaml generate --infile=regulator_activity.tsv

This was all meant to have been hooked up to the INCA tools table editor as a replacement for TermGenie. I guess that still hasn't happened?

[dosumis]

Looks like the TermGenie replacement plan was tantalisingly close: https://github.com/geneontology/go-ontology/issues/13692

[balhoff]

I'll need to have a conversation with @cmungall and maybe @dosumis to see how I can help here.