kgcl-rdflib
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INCATools
Tools for working with KGCL
Bumps [markdown-it-py](https://github.com/executablebooks/markdown-it-py) from 2.1.0 to 2.2.0. Release notes Sourced from markdown-it-py's releases. v2.2.0 What's Changed ⬆️ UPGRADE: Allow linkify-it-py v2 by @hukkin in #218 🐛 FIX: CVE-2023-26303 by @chrisjsewell in...
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Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.6.15 to 2022.12.7. Commits 9e9e840 2022.12.07 b81bdb2 2022.09.24 939a28f 2022.09.14 aca828a 2022.06.15.2 de0eae1 Only use importlib.resources's new files() / Traversable API on Python ≥3.11 ... b8eb5e9 2022.06.15.1...
For `def get_representation()` , `mode_term` for a URI can start with `http` as well. Currently it only checks for `
e.g: Both - `rename MONDO:0000087 from 'polymicrogyria' to 'polymicrogyria ABCD'` and - `rename MONDO:0000087 from 'foo bar' to 'polymicrogyria ABCD'` yield the correct result of renaming whatever label is for...
This library uses low-level rdflib/sparql operations which may be unaware of reification add a test for a synonym with reification and check that rdf:object is updated
```json { "id": "CHANGE:001", "old_value": "'foo'", "new_value": "'bar'", "about_node": "GO:1", "about_node_representation": "curie", "@type": "NodeRename" } ``` This is unneccessary - just as with jsonld we can leave as either CURIE...
Given `"rename GO:1 from 'foo' to 'bar'"` the parser returns ```jjson { "id": "CHANGE:001", "old_value": "'foo'", "new_value": "'bar'", "about_node": "GO:1", "about_node_representation": "curie", "@type": "NodeRename" } ``` The quoted value is...
Running obsolete on any term in the ontology ends up obsoleting all elements. The current tests don't test for this scenario
Obsoletion should not place things under oio:ObsoleteClass. See: http://wiki.geneontology.org/index.php/Obsoleting_an_Existing_Ontology_Term
If the input has xsd:strings on literals (as is common for many ontologies like GO): ```turtle "Bacteria"^^xsd:string . ``` then rename fails: it adds a new name but does not...