Ecosyste.ms: Timeline
Browse the timeline of events for every public repo on GitHub. Data updated hourly from GH Archive.
cmungall closed an issue on INCATools/ontology-access-kit
Integrate notebooks into sphinx documentation (will break URLs)
Currently the notebooks in OAK are separate from the docs, and the user is invited to click on the ipynb file in github. This gives a decent rendering of the notebook, but it's not connected to the...
cmungall pushed 1 commit to main INCATools/ontology-access-kit
- Moved Jupter notebooks to be part of sphinx docs (#816) * Moved Jupter notebooks to be part of sphinx docs Fixes ... cec9d19
cmungall closed an issue on INCATools/ontology-access-kit
Integrate notebooks into sphinx documentation (will break URLs)
Currently the notebooks in OAK are separate from the docs, and the user is invited to click on the ipynb file in github. This gives a decent rendering of the notebook, but it's not connected to the...
cmungall closed a pull request on INCATools/ontology-access-kit
Moved Jupter notebooks to be part of sphinx docs
Fixes #758
cmungall created a comment on a pull request on oborel/obo-relations
We need to make sure this won't break existing ontologies or their downstream ontologies. All regulates axioms are likely in GO - if GO passes with this then we should be good to GO. If GO axiom...
cmungall created a comment on an issue on geneontology/go-ontology
Sarcollema TC will be inherited from CL next release: - #29075
cmungall created a comment on an issue on geneontology/go-ontology
Yes, ideally we would have a CC for the synapse and place the TC there
cmungall closed an issue on geneontology/go-ontology
Add part_of between sarcolemma and muscle cell
Hey ontobot! apply: * create edge GO:0042383 BFO:0000050 CL:0000187
cmungall pushed 3 commits to master geneontology/go-ontology
cmungall closed a pull request on geneontology/go-ontology
Applying changes for: Add part_of between sarcolemma and muscle cell
The following commands were executed: </br> * create edge GO:0042383 BFO:0000050 CL:0000187</br></br>Fixes #29074
cmungall pushed 1 commit to ochange_automation_29074-df3730e geneontology/go-ontology
- fix comment eb47c9c
cmungall created a comment on an issue on geneontology/go-ontology
Not sure I understand the request for immunological synapse formation - it's already inheriting a constraint to Vertebrata?
cmungall opened an issue on geneontology/go-ontology
Add part_of between sarcolemma and muscle cell
Hey ontobot! apply: * create edge GO:0042383 BFO:0000050 CL:0000187
cmungall opened an issue on geneontology/go-ontology
Add more information to synaptic vesicle transport
> GO:0048489 synaptic vesicle transport This should be Eumetazoa (animals minus sponge) Ideally we would not assert this, but it can't be inferred from the current axioms: ``...
cmungall created a comment on an issue on geneontology/go-ontology
> GO:0048489 synaptic vesicle transport This should be Eumetazoa (animals minus sponge) Ideally we would not assert this, but it can't be inferred from the current axioms: ```yaml id: GO:...
cmungall created a comment on an issue on geneontology/go-ontology
> GO:0048499 synaptic vesicle membrane organization @balhoff I think we need to add more taxon property chains, e.g. for RO:0002592 `results in organization of`
cmungall created a comment on a pull request on obophenotype/uberon
This is turning out to be harder than I expected
cmungall opened an issue on obophenotype/uberon
Align with COB
Epic ticket covering - [ ] #3382 - [ ] #3374
cmungall created a comment on an issue on OBOFoundry/COB
@dosumis makes a good argument for why spaces are more natural for gross anatomical structures, in contrast to subcellular structures in GO. I could quibble about a few edge cases, but largely agre...
cmungall opened an issue on obophenotype/uberon
Decide on strategy for shadowing material immaterial entities as material anatomical entities
See: - https://github.com/OBOFoundry/COB/issues/87 - https://github.com/OBOFoundry/COB/issues/99 Let's keep the discussion about the relative benefits of having a distinction and a grouping ...
cmungall created a comment on an issue on obophenotype/uberon
I don't think the issues were fully resolved, but the main issue is with the pronephric sinus, see #2274
cmungall closed an issue on obophenotype/uberon
material structures needed to replace anatomical space fillers in GO logical definitions
I'm trying to resolve all [reasoning violations in GO](https://github.com/geneontology/go-ontology/issues/16524) resulting from property range axioms. The remaining issues have to do with anatomica...
cmungall reopened an issue on obophenotype/uberon
Query UBERON_0006174 pronephric sinus
**Uberon term** UBERON_0006174 pronephric sinus **Bug description** UBERON_0006174 pronephric sinus is causing some reasoning problems in GO (https://github.com/geneontology/go-ontology/issu...
cmungall reopened an issue on obophenotype/uberon
material structures needed to replace anatomical space fillers in GO logical definitions
I'm trying to resolve all [reasoning violations in GO](https://github.com/geneontology/go-ontology/issues/16524) resulting from property range axioms. The remaining issues have to do with anatomica...
cmungall pushed 16 commits to issue-2921 obophenotype/uberon
- Do not "add OBO shorthands" to the RO mirror. RO is currently mirrored in Uberon using a custom rule that bypasses t... 61e7f2f
- Upgrade custom ROBOT plugin. Use latest version (0.3.1) of the Uberon-specific ROBOT plugin, which provides a new co... 74832fb
- Refactor the rules to create taxon-specific subsets. The custom Makefile contains two sets of rules to create taxon ... da833f9
- Rename the euarchontologlires and amniote subsets. There is no reason to have two different naming conventions for t... 62df0d4
- Merge branch 'master' into overhaul-taxon-subsets ce74cf5
- Merge branch 'master' into 3016-dont-add-obo-shorthands-to-ro-mirror 9ab80e4
- Merge pull request #3359 from obophenotype/3016-dont-add-obo-shorthands-to-ro-mirror Do not "add OBO shorthands" to ... ae3f2f8
- Merge some taxon subset tags in the main release products. In addition to producing taxon subset files, we also want... 4bb1e9f
- Minor cleanup. The rule that produces the `uberon.json.gz` file has nothing to do in the main "BUILDING UBERON ITSEL... 9e175d5
- Merge branch 'master' into overhaul-taxon-subsets 37b230b
- Do not inject uberon-full.owl into uberon.owl. The infortunate use of $^ in the rule that produces `uberon.owl` lead... 6b519cb
- Merge pull request #3363 from obophenotype/overhaul-taxon-subsets Overhaul taxon subsets 3a11216
- Filter out dangling gene IRIs. When compiling the merged import module, make sure to filter out IRIs from <http://ww... bab8c69
- Commit re-generated Makefile. 5694045
- Merge pull request #3379 from obophenotype/remove-gene-dangling-classes Filter out dangling gene IRIs in imports 359ac1e
- Merge branch 'master' into issue-2921 e50c29a
cmungall created a comment on a pull request on obophenotype/uberon
<img width="1394" alt="image" src="https://github.com/user-attachments/assets/c1b24b28-04cc-43bc-af1f-3edc5c9eeee7">
cmungall pushed 1 commit to issue-758 INCATools/ontology-access-kit
- updated test to sync with labels being included e2840c9