Ecosyste.ms: Timeline
Browse the timeline of events for every public repo on GitHub. Data updated hourly from GH Archive.
cmungall created a comment on an issue on obi-ontology/obi
I urge caution when using universal restrictions. In my experience most people don't understand them and use them incorrectly. In addition you will fundamentally limit the scalability of OBI, all l...
cmungall created a comment on an issue on INCATools/ontology-development-kit
I regret to inform you that there hasn't been much progress on: - https://github.com/INCATools/semantic-sql/issues/41 Which would make this easier
cmungall created a comment on an issue on INCATools/ontology-access-kit
ideally all ontologies would start building sqlite/duckdbs for every release alongside obo, owl, json, everything would be versioned together, and the need for the semsql repo would go away
cmungall opened an issue on MolGenie/ontology
fix syntax
the obo format doesn't conform to the standard and will not parse with any obo parser. I think you want to be making use of `property_value` and `relationship` more I also recommend using pre...
cmungall opened an issue on MolGenie/ontology
Clarify license
the LICENSE file is Artistic (which is intended for code) the README claims dual license with code under Artistic and data/content under CC-BY. However, there is no code in the repo, only an obo...
cmungall opened an issue on monarch-initiative/curategpt
KeyError: '_venomx'
``` ✗ curategpt search -c ont_hp liver Traceback (most recent call last): File "/Users/cjm/Library/Caches/pypoetry/virtualenvs/curategpt-GcBFdKqh-py3.10/bin/curategpt", line 6, in <module> ...
cmungall opened an issue on geneontology/wc-gocam-viz
Pathway view is missing edges for cases with dual positive and negative regulation
consider this model http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A66b5638000001589 <img width="348" alt="image" src="https://github.com/user-attachme...
cmungall created a comment on an issue on ga4gh/pedigree_family_history_terminology
perfect, thanks! On Tue, Nov 26, 2024 at 9:51 AM Benjamin Berk ***@***.***> wrote: > @monicacecilia <https://github.com/monicacecilia> , @cmungall > <https://github.com/cmungall> - I'm happ...
cmungall created a comment on an issue on geneontology/go-ontology
there was a release today https://github.com/obophenotype/ncbitaxon/releases/tag/v2024-11-25 unless we are using 100% base we will get superpositions cc @balhoff
cmungall created a comment on an issue on monarch-initiative/mondo
oh my that hasn't been touched for a while mondo.owl | Main OWL edition | Complete ontology. Uses MONDO IDs. Imports merged. The original mondo.owl without merged imports and with equivalence ...
cmungall created a comment on an issue on monarch-initiative/mondo
can be closed when the metadata here is updated https://obofoundry.org/ontology/mondo !
cmungall created a comment on an issue on microbiomedata/issues
Looking at the JSON @sujaypatil96 has produced: - I think the `samp_collection_site` values are wrong ("unplanted soil" is not a site, nor is "arabidopsis") - it would be good to better represe...
cmungall opened an issue on EnvironmentOntology/envo
obsolete "solid layer" and rewire some of the terms under it
We received a submission in NMDC where env_local was "solid layer". This is quite an abstract term that encompasses 83 varied terms like: |id|label|definition| |---|---|---| |ENVO:00000098|isl...
cmungall created a comment on an issue on geneontology/go-ontology
I think choosing where the replacement lives is a great and interesting topic for a COB ticket! I'd be happy to comment over there. There are some things we can do to improve the overall process...
cmungall created a comment on an issue on geneontology/go-ontology
The definition of replicative senescence is still: "cell aging process associated with the dismantling of a cell as a response to telomere shortening and/or cellular aging." Which doesn't make an...
cmungall created a comment on an issue on OBOFoundry/OBOFoundry.github.io
Let's keep it here. The OBO metadata is inaccurate, until one of the 4 courses of action I outlined above are taken. On Sun, Nov 24, 2024 at 9:43 PM Nomi Harris ***@***.***> wrote: > Should...
cmungall created a comment on an issue on OBOFoundry/OBOFoundry.github.io
The situation is still exactly the same as in 2015. I made a proposal on Dec 15 2021, and this is still the course of action I think we should take On Sun, Nov 24, 2024 at 9:38 PM Nomi Harris *...
cmungall created a comment on an issue on OBOFoundry/OBOFoundry.github.io
I don't see bioportal listed at the top of pages like https://obofoundry.org/ontology/go - every other portal is represented though. OK to close this and make a new issue through as this one h...
cmungall opened an issue on geneontology/go-ontology
Add pyrenoid parts (matrix, sheath, tubule lumen and membrane)
Currently the representation of the pyrenoid (a structure found in eukaryotic algae and moss for boosting efficiency of rubisco) is incomplete and there is no strategy for population with gene pr...
cmungall created a comment on an issue on geneontology/go-ontology
What about adding a PATO axiom to specific INMBOs and other components?
cmungall created a review on a pull request on obophenotype/uberon
How is this different from the existing term "dorsal plus ventral thalamus"? Perhaps this could be renamed (the name is awkward, this was intentional due to terminological ambiguity of "thalamus")
cmungall created a comment on an issue on ontology-tools/py-horned-owl
I think from email discussions we have agreed to switch the order
cmungall created a comment on an issue on biopragmatics/bioregistry
@ialarmedalien - in fact GO is using SSSOM/skos predicates to capture whether the relation is exact/broad/narrow, so no need for a convention with the IDs!
cmungall created a review on a pull request on biolink/kgx
Of course we should use the pydantic from the linkml
cmungall created a review on a pull request on biolink/kgx
Of course we should use the pydantic from the linkml
cmungall created a comment on an issue on biopragmatics/bioregistry
Regexes: C elegans: I mess with your system D melanogaster: hold my beer D miranda: errm… On Wed, Nov 20, 2024 at 8:23 PM Nico Matentzoglu ***@***.***> wrote: > My two $: > > 1. ...