Stephen A. Ramsey

For the reasoners- you may wish to examine licensing as a criteria for inclusion. You can request license evaluation if you are uncertain here: http://reusabledata.org/ https://github.com/reusabledata/reusabledata/issues/new GitHub Build software better,...

Align with ICD 11

14

Requesting support for ICD11 codes in MONDO. Thank you, @cmungall !

question about owl:DatatypeProperty

14

Hello Ontobio team, I have a simple RDF Turtle file `test.ttl` that I want to load using Ontobio: ``` @prefix skos: . @prefix owl: . @prefix rdfs: . @prefix xsd:...

On line 163 of https://github.com/biolink/ontobio/blob/master/ontobio/ontol_factory.py, there is code for retrieving the ontology from a cache. Would it be possible to have an optional argument to the factory constructor (or the...

question: convention for arc directions in underlying networkx.DiGraph

2

I notice that in the `ontobio` source code (e.g., in `obograph_util.py` line 62 and in `ontol.py` line 153), the convention in the underlying `networkx.DiGraph` data model *appears to be* that...

serializing to JSON leads to OutOfMemory exception

1

Hi, I have a 5.5 GB OWL file "umls.owl". When I run `robot convert --input umls.owl --output umls.json` on a machine with 392 GB of RAM (and with '-Xmx390G' passed...

update kgx-format.md to include node and edge attributes?

4

Hello KGX team: Just passing along a friendly suggestion: it would be helpful if [kgx-format.md](https://github.com/biolink/kgx/blob/master/specification/kgx-format.md) could be updated to show how attributes are to be represented in KGX JSON. JSON...

DRUGBANK:drug-interaction shouldn't be mapped to biolink:physically_interacts_with

3

**Describe the bug** The `biolink-model.yaml` file is currently recommending that the source relation `DRUGBANK:drug-interaction` should be mapped to the predicate `biolink:physically_interacts_with`. These seem rather semantically inequivalent. **To Reproduce** See the...

two suggested changes to infores_catalog.yaml

2

I would like to ask if the `xref` URLs can get updated for the entries for `infores:rtx-kg2` and `infores:arax` in `infores_catalog.yaml`. Per discussion in the Translator Data Modeling Committee on...

Remove DOID subclass_of edges during ingestion of DOID

2

See this issue for context: https://github.com/NCATSTranslator/Feedback/issues/422#event-11585511674