Charles Tapley Hoyt

As a follow-up to #1537, this adds type annotations for torch. This is the most difficult step so far

PyKEEN 1.11.3 Release

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@mberr is there anything we should try getting into the next release? - [ ] Update PyKEEN to use cookiecutter-snekpack - [ ] #1220 - [ ] #1306

There are many scenarios in which triples themselves have weights, such as chemical-protein interactions, which have an activity value associated with them. This has been requested in several places, so...

⚗️🐄 Add proteochemometrics case study

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This PR adds the proteochemometrics case study, which can be run with `uv run --script notebooks/proteochemometrics.py` from the root folder. It automatically download a few resources then start training It...

What are GAID references?

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As a specific part of #2205, can someone help me understand what GAID references are? Here's a listing of usages across ontologies indexed in the Bioregistry: https://biopragmatics.github.io/oquat/unknowns/prefix/gaid e.g., [`UBERON_0001508` (arch...

Include assessment of conflicts with Identifiers.org/Bioregistry for new submissions

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I've had a nice discussion with @hoganwr [here](https://github.com/ufbmi/geographical-entity-ontology) about how the Geographical Entity Ontology has been registered in OBO Foundry (and subsequently included in the Ontology Lookup Service) under the...