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 a pull request on obophenotype/mouse-anatomy-ontology
It would be great to have this merged. I can guarantee it won't break anything on the MGI side. This will vastly improve how EMAPA looks in browsers that follow standards like OLS (right now EMAPA ...
cmungall created a comment on an issue on monarch-initiative/mondo
Followed up on email re PD specifically. Apologies, I seem to have forked this discussion, I reopened #6593 because I think the immediate non-controversial action is change the documentation in ...
cmungall created a comment on an issue on monarch-initiative/mondo
My my main point here is that we should not equate being a leaf node with being a disease entity, the documentation just happened to have PD!
cmungall created a comment on an issue on monarch-initiative/mondo
@pnrobinson I don't necessarily disagree with any of that, but this issue is about the documentation for disease entities in general, not PD in particular. However, it's a good point that we should...
cmungall published a release on cmungall/chemessence
v2024-11-18
**Full Changelog**: https://github.com/cmungall/chemessence/compare/v2024-11-15...v2024-11-18
cmungall created a tag on cmungall/chemessence
v2024-11-18 - EXPERIMENTAL extraction of essence from CHEBI
cmungall created a comment on an issue on Knowledge-Graph-Hub/kg-registry
@jamesamcl suggests just cloning the obofoundry repo, scooping out the content, and replacing with kgs We can also use the OLS-like interfaces James set up to demo
cmungall opened an issue on Knowledge-Graph-Hub/kg-registry
resurrect this site - use this to store simple YAML modular KG entries
@jamesamcl @justaddcoffee @caufieldjh @matentzn @kevinschaper @DnlRKorn on our last call we discussed using this repo for bootstrapping our minimal KG registry Context slide44+ https://doc...
cmungall created a comment on an issue on monarch-initiative/mondo
I'm afraid the documentation is incorrect and misleading. "For instance, Parkinson’s Disease is NOT a disease entity; it is a grouping term because it has multiple children in Mondo" Leaf nod...
cmungall reopened an issue on monarch-initiative/mondo
redefine disease entity in Mondo FAQ
please edit the text below as needed, this will go on the [FAQ](https://mondo.monarchinitiative.org/pages/faq/) per our discussion on the Mondo medical expert call on 2023-08-24 --- ### What i...
cmungall created a comment on an issue on monarch-initiative/mondo
@twhetzel is correct in that we currently take OMIM as an authority. But I think this is a good example of where we could draw from other sources, particularly mitochondrial diseases; e.g the Cl...
cmungall published a release on cmungall/chemessence
v2024-11-15
**Full Changelog**: https://github.com/cmungall/chemessence/compare/v2024-08-23...v2024-11-15
cmungall created a tag on cmungall/chemessence
v2024-11-15 - EXPERIMENTAL extraction of essence from CHEBI
cmungall created a comment on an issue on biopragmatics/pyobo
Regarding appropriate ontologization, there is my slide deck, and I also filed an issue in the obo-db-ingest repo: https://github.com/biopragmatics/obo-db-ingest/issues/11
cmungall created a comment on an issue on monarch-initiative/phenio
need it to show up here https://monarchinitiative.org/HP:0030376
cmungall opened an issue on monarch-initiative/phenio
phenio drops xrefs
``` ✗ sqlite3 $db/hp.db SQLite version 3.37.0 2021-12-09 01:34:53 Enter ".help" for usage hints. sqlite> select * from statements where subject='HP:0030376' and predicate='oio:hasDbXref'; HP:0...
cmungall created a comment on an issue on monarch-initiative/phenio
phenio: ``` sqlite> select count(*) from statements where object='GO:0006915' and predicate='rdfs:subClassOf'; 66 ``` go: ``` sqlite> select count(*) from statements where object='GO:0...
cmungall opened an issue on monarch-initiative/phenio
phenio has redundant is-a links:
https://monarchinitiative.org/GO:0006915#hierarchy This is flattening everything here * Thing * [i] BFO:0000015 ! process * [i] GO:0008150 ! biological_process * [...
cmungall created a comment on an issue on ontodev/robot
Unfortunately strict mode is too strict, it flags many things that are common that are properly repaired by the OWLAPI (perhaps this could be considered over-postelian of the owlapi and these rdf f...
cmungall created a comment on a pull request on INCATools/kgcl
`robot convert -I https://raw.githubusercontent.com/INCATools/kgcl/f49dd3e56280eef8a40eafc629e1080819501dc2/project/owl/kgcl.owl.ttl -o /tmp/foo.owl && grep Error foo.owl` empty. Hurrah! yes ...
cmungall created a comment on an issue on geneontology/go-ontology
that paper is for biosynthesis - I imagine we want to be more conservative for metabolism as presumably many fungi have developed catabolism for host sterols...