Jim Balhoff

Created general_subset, to replace CARO ontology

4

Related to #2349 I created a `general_subset` containing terms that must be applicable outside of Metazoa. I'm open to suggestions for an alternative name for the subset. For all these...

unsatisfiability from COB interaction

8

I'm trying to resolve unsatisfiable classes found in the [Ubergraph](https://github.com/INCATools/ubergraph) build. This issue overlaps OBI, SO, and COB. ## [genotyping assay](http://purl.obolibrary.org/obo/OBI_0000435) EquivalentTo [Nothing](http://www.w3.org/2002/07/owl#Nothing) ## - [genotyping assay](http://purl.obolibrary.org/obo/OBI_0000435) SubClassOf [has_specified_output](http://purl.obolibrary.org/obo/OBI_0000299) some...

more specific label for 'results in formation of'; add relation for ENVO use

3

ENVO is currently using [results in formation of](http://purl.obolibrary.org/obo/RO_0002297) in logical definitions like this: - [ecosystem fragmentation process](http://purl.obolibrary.org/obo/ENVO_01001168) EquivalentTo [ecosystem process](http://purl.obolibrary.org/obo/ENVO_01001795) and ([has input](http://purl.obolibrary.org/obo/RO_0002233) some [ecosystem](http://purl.obolibrary.org/obo/ENVO_01001110)) and ([results in formation of](http://purl.obolibrary.org/obo/RO_0002297)...

body limit exceeded error

3

I'm submitting a query to Qlever containing a large VALUES block. It responds with a server error, and this message is printed to the Qlever log: ``` ERROR: body limit...

'results in formation of' - incorrect relation usage; COB incompatibility

2

I'm looking into various incoherencies when merging OBO ontologies, as part of the Ubergraph build. Here is one unsatisfiable class: ## [exposure to mine drainage](http://purl.obolibrary.org/obo/ECTO_5000003) SubClassOf [Nothing](http://www.w3.org/2002/07/owl#Nothing) ## - [exposure...

It would be great if Oxigraph provides a built-in [quad pattern fragments](https://linkeddatafragments.org/specification/quad-pattern-fragments/) endpoint. The server could make this available alongside `/query` and `/update` at a path like `/qpf`. There is...

invalid xref check is too strict

2

The invalid xref [check](http://robot.obolibrary.org/report_queries/invalid_xref) uses this regex: `"^[a-z|A-Z|_|\\-|0-9]*:(?!$)\\S*$"` It should allow `.` in the prefix part: https://www.w3.org/TR/1999/REC-xml-names-19990114/#NT-NCName

This issue was noted by @cmungall. My guess is that it's due to the fact that the property assertion generator requests both object property assertions and data property assertions, and...

For example #27263 and #27268.

For terms like this: ``` id: GO:0003842 name: 1-pyrroline-5-carboxylate dehydrogenase activity namespace: molecular_function def: “H2O + L-glutamate 5-semialdehyde + NAD+ = 2 H+ + L-glutamate + NADH.” [RHEA:30235] synonym: “1-pyrroline...