biolink-model

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add 'url' property with a description that was difficult to write in …

7

…the context of the existing xref property for your review @codewarrior2000 fixes #https://github.com/biolink/biolink-model/issues/1486

sierra-moxon

Generated Python/Pydantic Models as Package?

1

**Question:** I see that the LinkML generators have been used to generate Python and Pydantic dataclasses, but I'm unclear as to whether these have been published as a pip installable...

riyavsinha

I'm not sure if these belong all the way up on Association, or if they should be more applied to more specific associations

kevinschaper

Prediction Qualifiers

2

**Question:** We are looking to include predictive associations in a knowledge graph using the BioLink model. Are there currently qualifiers to specify `is_predicted` with a boolean value and/or `predicted_by_model_type` with...

riyavsinha

**Describe the bug** Almost all the files in the `project/` directory are generated from the Biolink model files in `src/` _except_ for [project/prefixmap/biolink_model_prefix_map.json](https://github.com/biolink/biolink-model/blob/fb9f849022602aaeed2e98bb27881d4923ad904c/project/prefixmap/biolink_model_prefix_map.json), which appears to be edited manually. **To...

gaurav

update predicate mapping to refer to qualified predicates for regulates

3

fixes https://github.com/NCATSTranslator/Feedback/issues/744 outstanding questions for discussion at DM call: - Should “object_aspect_qualifier=’activity_or_abundance’” be required? - Should “object_direction_qualifier=’downregulated’” or “object_direction_qualifier=’upregulated’” be required? - New associations help define these requirements, what does...

sierra-moxon

sierra-moxon

**Question:** In the Biolink YAML, version 4.2.1, the list of PREFIXES has "mirbase" as the id_prefix for microRNA (miRNA) identifiers. But why does elsewhere in the YAML, the id_prefixes for...

codewarrior2000

Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. Release notes Sourced from jinja2's releases. 3.1.4 This is the Jinja 3.1.4 security release, which fixes security issues and bugs but does not otherwise...

dependabot[bot]

Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.66.1 to 4.66.3. Release notes Sourced from tqdm's releases. tqdm v4.66.3 stable cli: eval safety (fixes CVE-2024-34062, GHSA-g7vv-2v7x-gj9p) tqdm v4.66.2 stable pandas: add DataFrame.progress_map (#1549) notebook: fix...

dependabot[bot]