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 ontology-tools/py-horned-owl
Aside: the link to the changelog in https://github.com/ontology-tools/py-horned-owl/releases/tag/v1.0.1 goes to the wrong version...
cmungall opened an issue on ontology-tools/py-horned-owl
add_prefix_mapping disappeared in the transition from 1.0.0 to 1.0.1
This example here: https://github.com/ontology-tools/py-horned-owl/blob/main/docs/source/quickstart.rst#L26 shows a method `add_prefix_mapping` This worked in 1.0.0, and I have been using ...
cmungall opened an issue on linkml/linkml
Define semantics for referential integrity
A non-inlined class range may be intended as: - a reference to an object in the *same* document, database, or graph - a reference to an object in the *external* document, database, or graph ...
cmungall opened an issue on linkml/linkml-model
Add example instances of example schemas
This repo uses the linkml-example-runner framework, including examples of the schema, and testing those examples https://github.com/linkml/linkml-model/tree/main/tests/input/examples but thi...
cmungall opened an issue on linkml/linkml
Add example instances of example schemas
This repo uses the linkml-example-runner framework, including examples of the schema, and testing those examples https://github.com/linkml/linkml-model/tree/main/tests/input/examples but thi...
cmungall created a comment on an issue on TranslatorSRI/NodeNormalization
May be related: https://github.com/TranslatorSRI/Babel/issues/369 apologies if I got the wrong tracker!
cmungall created a comment on an issue on TranslatorSRI/Babel
> Note that in some cases (e.g. MONDO) deprecated terms can point to a non-deprecated term that replaces them, while in other cases (e.g. UMLS) there does not appear to be a clear mapping to a non-...
cmungall opened an issue on monarch-initiative/mondo
Classification of familial hypercholesterolemia, by gene, and by zygosity (Orphanet)
Familial hypercholesterolemia (as represented in this PS) https://omim.org/phenotypicSeries/PS143890 has 4 main subtypes (ignoring susceptibility) - FHCL1 AD/AR LDLR - FHCL2 AD APOB - FHCL3 ...
cmungall opened an issue on INCATools/kgcl
Fix bioportal 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 a pull request on EnvironmentOntology/envo
Added logical definitions for multiple biomes.
These were all converted from existing subClassOf axioms, thus ensuring consistency. (note of course that these subClassOf axioms come back in the release version through reasoning). See also #1416
cmungall pushed 2 commits to 1538-scope-of-astronomical-body-part EnvironmentOntology/envo
cmungall created a comment on an issue on EnvironmentOntology/envo
The new term should be "rainforest biome", placed under "biome", with an exact synonym "rainforest". If in future we need a more general "rainforest ecosystem" we can add that (I do not understa...
cmungall closed an issue on EnvironmentOntology/envo
NTR: rainforest/rainforest biome and subtypes
I'm looking for terms: - "tropical rainforest" or "tropical rainforest biome" - "temperate rainforest" or "temperate rainforest biome" I would expect a general concept for "rainforest" a...
cmungall created a comment on an issue on EnvironmentOntology/envo
I agree the lack of a rainforest term is surprising possible duplicate of: - #1174 - #1204
cmungall created a comment on an issue on EnvironmentOntology/envo
Thanks for noticing the typo! Regarding marine vs saline, can you say more about the motivation? Is it because "marine" is more circular? - Many definitions of "marine" are something like "se...
cmungall created a comment on an issue on TranslatorSRI/NodeNormalization
`runoak -i sqlite:obo:hp info HP:0001250 -O obo` ```yaml id: HP:0001250 name: Seizure def: "A seizure is an intermittent abnormality of nervous system physiology characterized by a transient ...
cmungall opened an issue on TranslatorSRI/NodeNormalization
Use curated MONDO mappings where possible
MONDO has rich mappings using SSSOM dyskeratosis congenita, autosomal dominant 6 http://purl.obolibrary.org/obo/MONDO_0014690 Here we see mappings to DOID:0070023, OMIM:616553, and others <...
cmungall created a comment on an issue on berkeleybop/artificial-intelligence-ontology
This bridge file appears to be complete? Every AIO root is represented. So this issue can be closed? (perhaps after adding a link to the README)
cmungall created a comment on an issue on geneontology/go-ontology
Thanks @Caroline-99! Can you say more about how this differs from a brush border? My understanding is that they are analogous, with tufts playing more of a sensory role. However CL seems to treat ...
cmungall created a comment on an issue on geneontology/go-ontology
These look great! On Wed, Nov 6, 2024 at 11:56 AM Joel Weiser ***@***.***> wrote: > Hi @balhoff <https://github.com/balhoff> - Here is the Pathways2GoTerms > file for v90 of Reactome: > >...
cmungall created a comment on an issue on geneontology/go-ontology
hmm, @ialarmedalien made some good points on that issue (some time ago :-O) but I am in favor of splitting.
cmungall created a comment on an issue on berkeleybop/artificial-intelligence-ontology
Looks like this is done?
cmungall closed an issue on berkeleybop/artificial-intelligence-ontology
Layer hierarchy potentially overly flat
Consider the context of an AI ontology, which of these DNN Layers could be grouped into categories? GPT4o #### Normalization Layers Batch Normalization Layers: BatchNorm1D Layer BatchNo...
cmungall created a comment on an issue on berkeleybop/artificial-intelligence-ontology
What's the actual problem here? I'm assuming this is fixed whatever it was