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/cell-ontology
I think practicality and simplicity dictates that we strip the GCIs from obo format, so I approve the PR. Non-normative comments follow: I do think this is different from the case of strippin...
cmungall created a review comment on a pull request on EnvironmentOntology/envo
I wouldn't use an xref here..
cmungall created a review comment on a pull request on EnvironmentOntology/envo
I prefer exponential notation, but is it even true that this is an accepted cutoff? Sources would be good
cmungall created a comment on an issue on EnvironmentOntology/envo
I think like a lot of concepts (e.g. energy), convincing philosophical arguments can be made for material entities, qualities, disposition, processes. In fact I see that RBO uses "energy" as the...
cmungall opened an issue on EnvironmentOntology/envo
Separate classification of areas under environmental zone causes confusion: merge these or make these a truly distinct hierarchy
ENVO frequently has shadow classifications between zones and other branches such as landform. And example is "desert", which is in both zone and landform branches: <img width="705" alt="image...
cmungall created a comment on an issue on geneontology/go-ontology
I agree with both points from @pgaudet
cmungall created a comment on an issue on geneontology/go-ontology
This is an interesting one in that the CHEBI grouping is basically recapitulating what we should be representing with pathways: id: CHEBI:22658 name: aspartate family amino acid def: "An L-alp...
cmungall created a comment on an issue on monarch-initiative/mondo
oh I didn't read the request properly, sorry about that! agree with yr analysis!
cmungall pushed 1 commit to main microbiomedata/nmdc-schema
- Update CODE_OF_CONDUCT.md Adding bullet formatting ecdcdad
cmungall created a comment on an issue on monarch-initiative/mondo
I think this is the same as id: MONDO:0007294 name: central core myopathy I think we should relabel this so it's clearer it's a gene-specific form of a series, consistent with https://omim.o...
cmungall created a comment on an issue on EnvironmentOntology/envo
> I think this is the core issue - are we trying to describe ecosystems, or to describe the classification schemes that people use to classify the ecosystems? You have hit the nail on the head....
cmungall created a comment on an issue on DominikMartinat/membrane_ontology
Note that most obo groups are achieving bfo compatibility via cob On Fri, Dec 13, 2024 at 12:58 AM Egon Willighagen ***@***.***> wrote: > Thank you. I will try to solve it as soon as I can. ...
cmungall created a comment on an issue on OBOFoundry/OBOFoundry.github.io
Discussed on bioportal call 2024-12-09, my group will work on this
cmungall created a comment on an issue on OBOFoundry/OBOFoundry.github.io
I put some comments here: https://github.com/DominikMartinat/membrane_ontology/issues
cmungall opened an issue on DominikMartinat/membrane_ontology
should the root class for physical and in-silico models be "independent continuant"
currently everything is rooted in BFO:0000004. It's not clear that simulations are ICs, I think you want to treat physical models and simulations differently, shared by something like membrane_o...
cmungall opened an issue on OBOFoundry/COB
Where do simulations and computational models live in COB
Examples: - climate model - reaction-diffusion model - metabolic model - simulated membrane (https://github.com/DominikMartinat/membrane_ontology) I think this should go under IAO:0000030 ...
cmungall opened an issue on DominikMartinat/membrane_ontology
Switch dce to dcterms
dcterms is favored by OBO, and in fact by the the Dublin Core group themselves, see https://github.com/OBOFoundry/OBOFoundry.github.io/issues/540
cmungall opened an issue on INCATools/ontology-access-kit
Update docs on pystow/sqlite cache management
We have a FAQ entry "My cached SQLite ontology is out of date" https://incatools.github.io/ontology-access-kit/faq/troubleshooting.html#my-cached-sqlite-ontology-is-out-of-date This recommends ...
cmungall created a review on a pull request on EnvironmentOntology/envo
The qualities seem to fit a pattern - any reason not to use equivalence axioms?
cmungall created a review comment on a pull request on microbiomedata/nmdc-runtime
use centralized vocabulary constants