Ontology meeting 2014-07-03

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Taxon constraints

Taxon constraints can now be edited in gene_ontology_write.obo/owl. But for the GOA pipeline/QuickGO to work, taxon_triggers.obo needs to be kept up to date - including axiom IDs. If this is to be phased out in favour relesaing these in go-plus.owl, GOA need a way to pull the same info from there.

AI: for Heiko - add jobs to Jenkins, stuff to go-plus

CHEBI roles

did you have a chance to speak to them Jane?

Yes - estrogen is genuinely a role there is no common structure for estrogens. Direct annotations could probably be moved to a subclass that is a particular structure. Same for androgen.

AI: for David OS: Need to edit structure by role file to accommodate this. Whoever owns the ticket for 'response to estrogen' needs to go back to Michael Rice and ask him for a more specific compound.

embryonic X development

Should these be restricted to structures only present in the embryo? e.g. notochord, heart tube, placenta.

Yes. We want to avoid adding any for just the embryonic stage of development. Perhaps move the stage to ae and use 'during'? We do need separate terms for larval development - these are completely different processes.

AI: David OS - policy is that embryo organ development is the development of embryo-specific structures such as placenta. Obsolete the terms under embryo organ development that do not conform. Work on whole branch eventually.

update on cell type logical definitions - chris

  • muscle cell issues

timeline for uberon logical defs



Can we do better for ontology work on the new website? http://geneontology.org/page/download-ontology

Post-translational modifications

Have we decided whether these are functions or processes?