Ontology meeting 2022-02-28
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
Following up on previous discussion points
Ontology Curator Pathway book
Added a link in the GO doc: Ontology_Development#Documentation
InterPro file out of date
The file generated by InterPro is more recent: https://ftp.ebi.ac.uk/pub/databases/interpro/interpro2go
Actions from last week (but these were possibly incorrect)
- Change the Makefile (in go-ontology/src/ontology/Makefile )
- Check with InterPro for mappings of the databases they represent - are these maintained ? See also: https://github.com/geneontology/go-ontology/issues/16989
Transport or maintains localization relation
Here’s a link to a spreadsheet showing current associations between KEGG metabolic pathways and GO BP terms (as shown on the KEGG webpages). https://docs.google.com/spreadsheets/d/1K7Pzmo5wpFmbCA9NdxLlBC2NNA7VNviSSG-1pr2t9T8/edit#gid=0
I recently reviewed all the associations relevant to flies and suggested some corrections/additions to KEGG (which they mostly implemented) but there may be some other cases where a GO term could be added or changed etc.
As mentioned, might be useful to add all these KEGG pathway IDs as xrefs to BP terms within the GO. Looking at go-basic.obo, I only see 3 current xrefs of type “KEGG_PATHWAY:” (and one of them (map00440) looks slightly wrong)
FYI: I contacted them using firstname.lastname@example.org and my contact was Atsuko Yano.
Taxon constraints changed at each PR??
Recently there is always a big difference in changed files (specifically reasoned-pr.owl/reasoned.owl), that seem to related to taxon constraints: See for eg https://github.com/geneontology/go-ontology/pull/22879
I have been ignoring because I dont modify this file; but it would be interesting to know why this happens.
Hormone metabolic process
https://github.com/geneontology/go-ontology/issues/22899 https://github.com/geneontology/go-ontology/issues/19624 Obsolete, to only keep the chemical hierarchy for metabolic process?
Focus on specific topics?
- taxon constraints
- boomer tickets
- any other suggestion
- relations - review work that needs to be done for 'transports or maintains localization of' as outlined in ticket
Points from previous meetings not yet addressed
Next Priorities for Ontology group
- Finish Boomer tickets
- strategy to create new GO terms
- New taxon constraints
- Review single step BPs + BP refactoring
- Jamboree to close tickets?
- Design patterns: implement new design patterns and enforce usage in the ontology
- Content meetings?
Following up on previous items
- ChEBI: Chris, Paul: Make a list of requests for ChEBI - including requesting 'developer' versions of ChEBI so we can test it ahead of releases
- Design patterns
Changing the relation for transport and transporter activity from 'transports or maintains localization of' to 'has input'
- ACTIONS Decision is to use 'has primary input' -> https://github.com/geneontology/go-ontology/issues/22721
- See ticket for outline of steps needed to implement.
- Looks like an issue in GO, where 'cavity development' may be redundant with the equivalent 'tube' terms, or the 'tube terms are missing'?
ACTIONS: Review 'cavity terms
- subarachnoid space development | subarachnoid space
- tube lumen cavitation | tube lumen: https://github.com/geneontology/go-ontology/issues/22784
- neural rod cavitation | neural tube lumen: https://github.com/geneontology/go-ontology/issues/22784
- pronephric sinus development | pronephric sinus: see https://github.com/obophenotype/uberon/issues/2274
- 'neural rod cavitation' <http://purl.obolibrary.org/obo/GO_0014024>
- 'tube lumen cavitation' <http://purl.obolibrary.org/obo/GO_0060605>
- 'salivary gland cavitation' <http://purl.obolibrary.org/obo/GO_0060662> (no LD, so not causing problems in Jim's PR, but still needs reviewing)
- 'mammary gland duct cavitation' <http://purl.obolibrary.org/obo/GO_0060604> (no LD, so not causing problems in Jim's PR, but still needs reviewing)
- 'regulation of tube lumen cavitation' <http://purl.obolibrary.org/obo/GO_1903132>
- 'secondary neural tube rod cavitation' <http://purl.obolibrary.org/obo/GO_0014027>
- 'negative regulation of tube lumen cavitation' <http://purl.obolibrary.org/obo/GO_1903133>
- 'apoptotic process involved in tube lumen cavitation' <http://purl.obolibrary.org/obo/GO_0060609>
- 'apoptotic process involved in salivary gland cavitation' <http://purl.obolibrary.org/obo/GO_0060663>
Sinus terms: Not sure why only 'pronephric sinus development' is causing problems others do have LDs: Chris: only 'pronephric sinus development' describes a sinus; other describe valves, venosus
- 'sinus venosus development' <http://purl.obolibrary.org/obo/GO_0003235>
- 'sinus venosus formation' <http://purl.obolibrary.org/obo/GO_0003237>
- 'sinus venosus morphogenesis' <http://purl.obolibrary.org/obo/GO_0003236>
- 'coronary sinus valve development' <http://purl.obolibrary.org/obo/GO_0003178>
- 'coronary sinus valve formation' <http://purl.obolibrary.org/obo/GO_0003191>
- 'coronary sinus valve morphogenesis' <http://purl.obolibrary.org/obo/GO_0003182>
- 'pronephric sinus development' <http://purl.obolibrary.org/obo/GO_0039012>
- 'left horn of sinus venosus development' <http://purl.obolibrary.org/obo/GO_0061079>
- 'right horn of sinus venosus development' <http://purl.obolibrary.org/obo/GO_0061080>
Problem with relations used in logical definition https://github.com/geneontology/go-ontology/issues/22488
RO has been changed, so that the logical issue is fixed; however do we want to use 'results in assembly of' or 'has output' for protein-containing complex assembly? This decision impacts the relations used in GO-CAM and extensions, since we aim to align them.