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 geneontology/go-ontology
General comment: I think putting TCs on regulation terms should be a rare occurrence now we have propagation over regulation. In theory some species could have process P but never internally regula...
cmungall created a comment on an issue on ga4gh/pedigree_family_history_terminology
From @lindsmith: > I think one of the main reasons we didn’t use colloquial wording like “aunt” is because it doesn’t well accommodate our global audience Good point. > For that reason, ...
cmungall created a comment on an issue on INCATools/kgcl
https://w3id.org/kgcl/kgcl.owl.ttl still has non-DL axioms and hence ErrorNs show up in bioportal I think running `make all` on fresh main will fix, let's close when BP looks good
cmungall reopened an issue on INCATools/kgcl
Fix bioportal/OWL view of KGCL
https://bioportal.bioontology.org/ontologies/KGCL/?p=classes&conceptid=root <img width="397" alt="image" src="https://github.com/user-attachments/assets/1fc6c518-55c0-4f0a-92cc-64f7c173fb2c">
cmungall opened an issue on ebi-chebi/ChEBI
The label 'phosphate' is misleading in CHEBI
In CHEBI: - The string `phosphate ion` means an inorganic molecule like (P4O](https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A18367 )`[O-]P([O-])([O-])=O` - The string [phosphate](https...
cmungall opened an issue on cmungall/chemessence
phosphate is inappropriately collapsed
In CHEBI: - `phosphate ion`s are e.g. https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI%3A18367 `[O-]P([O-])([O-])=O` and clearly inorganic - `phosphate` is "Salts and esters of phosphoric ...
cmungall created a comment on a pull request on obophenotype/uberon
LGTM. I cannot promise to monitor and respond in a timely fashion to these review requests, but having me be assigned is still a useful signal, and if people do not mind prodding me e.g. on slack I...
cmungall closed a pull request on geneontology/go-ontology
created new term fixes #29172
Fixes #29172 Created a new term and imported a CL term "brush cell" @pgaudet I have added the new term ‘tuft’ with a more detailed definition to make the apical tuft's unique features more dis...
cmungall created a comment on an issue on linkml/linkml
Should be straightforward hopefully! http://docs.sqlalchemy.org/en/latest/core/metadata.html
cmungall created a review comment on a pull request on geneontology/go-ontology
Should be unique initials, no spaces
cmungall created a comment on an issue on monarch-initiative/mondo
Hi @paola-scibite Thanks for pointing this out. Quite appropriate that this loop happened for Möbius syndrome. ǝɯoɹpuʎs snᴉqöɯ ɹoɟ pǝuǝddɐɥ dool sᴉɥʇ ʇɐɥʇ ǝʇɐᴉɹdoɹddɐ ǝʇᴉnq. Quite appropriate...
cmungall created a comment on an issue on INCATools/ontology-access-kit
The option to emit markdown in `diff` is a bit quirky. What is it that is incomplete about the current YAML output of diff (which follows the KGCL schema)? As far as I can tell what you need ...
cmungall opened a pull request on INCATools/kgcl
Change config to use the standard one for OWL generation
Fixes #86 See https://github.com/linkml/linkml/issues/2353 for explanation
cmungall created a branch on INCATools/kgcl
issue-86-config - Datamodel for KGCL (Knowledge Graph Change Language)
cmungall opened a pull request on INCATools/kgcl
Fix use of undefined slots in slot usage (#88)
Fixes #88
cmungall created a branch on INCATools/kgcl
issue-88 - Datamodel for KGCL (Knowledge Graph Change Language)
cmungall opened an issue on INCATools/kgcl
Some slot_usage fields refer to undefined slots
This is a cause of the issues in #86
cmungall closed an issue on oborel/obo-relations
Increase the frequency of RO meetings?
Should we increase the frequency of the RO meetings? E..g.: Monthly
cmungall created a comment on an issue on information-artifact-ontology/ontology-metadata
A horrible workaround is to use sparql to inject oboInOwl:is_metadata_tag into APs before conversion to OWL But as you say there has never been an obo version so I think it's fine to officially ...
cmungall opened an issue on owlcollab/oboformat
Roundtrip to annotation properties does not work
This converts to OWL as expected ```yaml [Typedef] id: OMO:1 name: test is_metadata_tag: true ``` the `is_metadata_tag` is retained as an annotation, which is not strictly necessary. If ...
cmungall created a comment on an issue on linkml/linkml
I'll add something to the FAQ about this. There are nuances here...
cmungall created a comment on an issue on biopragmatics/bioregistry
@cthoyt @bgyori - I think we are agreed that levels 1-3 should use dashes?
cmungall created a comment on an issue on linkml/linkml
Continuing part of email discussion with @eilis This is what a target for conversion of the obographs schema might look like https://github.com/ielis/obographs/blob/master/src/model.rs happi...
cmungall created a comment on an issue on obophenotype/uberon
I agree that different terminology is not sufficient reason for a different class. But the challenge is that different relationships may hold for taxonomically restricted structures. But we could b...
cmungall created a comment on an issue on OBOFoundry/OBOFoundry.github.io
> Maybe also consider to have a different name then 'PRIDE' to differentiate the project from the Ontology? This is the current state of things in bioregistry: https://bioregistry.io/registry...