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
Hi @DaiqingChen You can find some of the original discussion that led to the creation of this term here: - #17502 Interestingly, the original request from @hattrill was for a Drosophila-sp...
cmungall created a comment on an issue on OBOFoundry/OBOFoundry.github.io
I don't think use of non-OBO PURLs is a deal-breaker, but with my non-OBO hat I would strongly recommend that groups do not use their own domain name in PURLs or bespoke URLs. Use an existing sys...
cmungall created a comment on an issue on OBOFoundry/OBOFoundry.github.io
Agree. I suggest a variant of B. Have explicit opt in per group to retain an entry for twitter, mentioning that OBO itself no longer uses it and focuses presence on LinkedIn or fedi or Bsky (or h...
cmungall opened an issue on Radiobiology-Informatics-Consortium/RBO
Ensure that all IDs have fixed zero padding, or avoid clashes at numeric level
Most OBO ontologies have IDs that are zero-padded to 7 digits. Some employ mixed zero padding and no padding (e.g DOID). Some have mixed lengths (ENVO is 7 and 8 due to a historic misconfiguration ...
cmungall created a comment on an issue on Radiobiology-Informatics-Consortium/RBO
Relevant: https://github.com/EnvironmentOntology/envo/issues/1490
cmungall pushed 4 commits to main linkml/linkml-map
- Fix dependency specifications * Ensure all used dependencies are declared * Remove unused dependencies * Properly cl... bbf26ba
- Fix failing doctest after pint upgrade e3a1a73
- Install all dependency extras where required 93d15a6
- Merge pull request #46 from linkml/issue-43-dependencies-cleanup Clean up dependency specifications b3be278
cmungall closed an issue on linkml/linkml-map
Clean up dependencies in `pyproject.toml`
There are a few bad smells going on with the dependencies in `pyproject.toml`. 1. **Overlapping use of `tool.poetry.dev-dependencies` and `tool.poetry.group.dev.dependencies`**. The former is Po...
cmungall closed a pull request on linkml/linkml-map
Clean up dependency specifications
Fixes #43 The changes in `pyproject.toml` do the following: * Remove unused dependencies, including `linkml-model` which (correctly) is used via `linkml_runtime.linkml_model` imports. * Dec...
cmungall created a tag on cmungall/chemessence
v2024-12-20 - EXPERIMENTAL extraction of essence from CHEBI
cmungall published a release on cmungall/chemessence
v2024-12-20
**Full Changelog**: https://github.com/cmungall/chemessence/compare/v2024-11-18...v2024-12-20
cmungall created a comment on an issue on microbiomedata/issues
I am working on a modified FAIR evaluation we can link to: https://docs.google.com/spreadsheets/d/1ck9YzSQchadygA_JZJmgrEQtE0tD_7FllD1CcPWINWE/edit?gid=127295437#gid=127295437
cmungall created a comment on an issue on geneontology/go-releases
> Other changes are OK, but for these organisms, it seems that we should not release the changes. ZFIN is particularly disturbing, since it’s a MOD. agreed > What are our options anyway? Can ...
cmungall created a comment on an issue on EnvironmentOntology/envo
> How bad is it to have the same term for two different classes, i.e. radiation as a process and radiation as a material entity? If it's in two ontologies that are not intended to be combined in...
cmungall created a comment on an issue on oborel/obo-relations
Thanks for setting this up, laying it out cleanly, and linking to the relevant ticket. My preference is: **remove** the property chain in both places. While in the past I have been an advocat...
cmungall created a comment on a pull request on OBOAcademy/obook
I’d be surprised if closures aren’t sufficient… On Thu, Dec 19, 2024 at 1:05 AM Nico Matentzoglu ***@***.***> wrote: > ***@***.**** approved this pull request. > > Thank you Chris! While i...
cmungall opened a pull request on OBOAcademy/obook
Add documentation on subset to module extraction docs
See https://github.com/EnvironmentOntology/envo/pull/1588#issuecomment-2552318990
cmungall created a branch on OBOAcademy/obook
cmungall-patch-1 - OBO Organized Knowledge: Training materials for becoming an OBO engineer
cmungall created a comment on a pull request on EnvironmentOntology/envo
> I'm not sure why the make process for PATO generates an OWL file with so much CHEBI in it. See: https://oboacademy.github.io/obook/tutorial/project-ontology-development/?h=slme#extracting-modu...
cmungall created a comment on an issue on geneontology/go-annotation
The NOT is from the 2nd publication https://amigo.geneontology.org/amigo/reference/PMID:31653696 _The apparent deglycase activity of DJ-1 results from the conversion of free methylglyoxal pre...
cmungall opened an issue on geneontology/go-ontology
Automate deepening of BPs using RHEA; example from lactate biosynthetic process
"lactate biosynthesis" is a broad term that IMO should be do-not-annotate. In general both the form (L/D) and the mechanism are well known. Here is the current distribution of annotations * [...
cmungall opened an issue on geneontology/go-annotation
Propagate uniprot caution warnings to GO annotations (example from PARK7 gene)
**Example**: the PARK7 gene has been implicated in many things: https://www.uniprot.org/uniprotkb/Q99497/entry If we look at one publication, it suggests lactate biosynthesis via the methylg...
cmungall created a comment on an issue on geneontology/go-annotation
For my own notes: This was spotted using an automated QC procedure that aligns GO BP, MF annotations, RHEA mappings, RHEA to CHEBI, and GO BP logical definitions: <img width="1083" alt="image...
cmungall opened an issue on geneontology/go-annotation
Incorrect annotations to CHAC1 and CHAC2 from Reactome annotation
CHAC1 and CHAC2 have confusing seemingly conflicting stories when Reactome annotations are combined from elsewhere: https://www.uniprot.org/uniprotkb/Q9BUX1/entry MF: <img width="955" alt=...
cmungall created a review on a pull request on linkml/linkml-runtime
Can we extend the test to also make sure that no premature exceptions are raised when using schemaview to cycle through all slots and do a lookup (or to ensure that randomAttribute is not returned ...