Kim Rutherford
Kim Rutherford
Hi. We last updated Canto from http://purl.obolibrary.org/obo/go/snapshot/extensions/go-plus.owl last night at 2:55am GMT.
It looks like the term is going missing when we process go-plus.owl with OWLTools to apply the taxon constraints. We only do that for loading GO into Canto. So it's...
> @kimrutherford - does this work It works for me now.
> Perhaps even more straightforward would be a removal of all deprecated classes prior > to subsetting, but that may be too extreme for you? If I'm following, that would...
Sorry, I got my file names swapped. I've edited the issue.
Hi. In case it helps, we've found another example of this problem. The output of `owltools --save-closure-for-chado` is inconsistent for: - meiosis I spindle assembly checkpoint (GO:1905318) regulates: - sister...
There's another example in this issue: https://github.com/geneontology/go-ontology/issues/17171
GO:0060274 is now gone from PomBase.
The PomBase Chado DB uses option 2 but the ontologies we use only borrow terms in straightforward ways. We haven't had any problems with this plan. > @kimrutherford has experience/pain...
Hi Jared. Thanks very much for the speedy reply. I've made that change. I needed to change SAReader too to make it compile: https://github.com/kimrutherford/sga/commit/2572d3528e626c6d8f7ff487ada37eed9d1d8567 I hope that's an appropriate fix....