terms and taxon triggers

[gocentral]

Consider the following terms: 'Glycoprotein networks' are part of a plant cell wall and 'ovarian follicle cell development' describes the development of an ovarian follicle cell as it exists in flies. Both of these terms trigger taxon checks in the GO qc process. It would be helpful to include some species specific designation in the term definition. 'Glycoprotein networks' mentions no species/kingdom restriction in the definition, and there are a couple of instances of this term in the ontology that don't have "cell wall" parents. 'ovarian follicle cell development' only mentions species in the definition like this: "An example of this is found in Drosophila melanogaster." It would be helpful if the species restriction was an integral part of the definition like "The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary in flies". In general for terms that are associated with taxon trigger checks, it would be helpful to curators and users if the term definitions included species-specific information.

Reported by: slaulederkind

Original Ticket: geneontology/ontology-requests/8057

[gocentral]

For glycoprotein network the term name may need to be more specific, as I don't think that as defined it can be restricted to plants, Val

Original comment by: ValWood

[gocentral]

The "an example of this" definition wording is used so that the definitions don't end up needlessly restrictive -- for example, although the definition of ovarian follicle cell development mentions the Drosophila example, the taxon restriction is to Arthropoda. We could, with much effort, update the example phrases to use the same taxa as in the restrictions file, and perhaps we should. But it would be a major manual undertaking, so if done at all it'll probably be done a bit at a time (unless a lot of demand for it arises).

p.s. glycoprotein network (GO:0048222) doesn't have an entry in the current taxon restrictions file -- has the QC check been run with an earlier version that did have a restriction?

m

Original comment by: mah11

[gocentral]

Hi Midori, All I know is that Emily sent me word that GOA was checking on annotations that came up from the taxon triggers and "glycoprotein network" for rat came up as an error based on taxon id.

Original comment by: slaulederkind

[gocentral]

Hi Stan,

Without knowing more about what checks were run with which versions of which files, all I can say is that I don't understand where the "glycoprotein network" error came from, because it hasn't been in the taxon triggers file (go/quality_control/annotation_checks/taxon_checks/taxon_go_triggers.obo) as far back as I can check in CVS.

m

Original comment by: mah11

[gocentral]

• labels: 397373 --> Taxon restriction

Original comment by: rebeccafoulger

[gocentral]

Hi Stan,

"glycoprotein network" inherits its taxon restriction from "plant-type cell wall".

We'd rather not include species-specific information in term names and definitions as that is what the taxon constraint really is for, but we'd be happy to add a comment to the definition if a particular term is confusing. Let us know if you'd like us to do that for "glycoprotein network". In the meantime, we're closing this request.

Thanks, Jane, Becky, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-works-for-me

Original comment by: paolaroncaglia