Document extending scispaCy with additional ontologies with PyOBO

[cthoyt]

Following these improvements in scispaCy:

• Enable creation of entity linker from a knowledge base #544
• Refactor KnowledgeBase constructor #547
• Implement TF-IDF cache loading #549
• Add scispaCy integration biopragmatics/pyobo#437

This PR adds documentation on to the README to showcase how arbitrary ontologies and databases can be loaded for use as a scispaCy entity linker via PyOBO. It does this by:

1. Adding an end-to-end example for annotating genes using HGNC
2. Adds a link to more example usage in the PyOBO docs at https://pyobo.readthedocs.io/en/latest/scispacy.html

This also closes #331. hgnc can be replaced with to to use the Plant Trait Ontology, however I wasn't able to construct a convincing use case, so that can be left to the issue submitter.

[cthoyt]

@dakinggg @DeNeutoy hi both, I think you will find this PR interesting. Happy to give some more context in what I'm interested in doing or hop on a call sometime to explain. Cheers!

[cthoyt]

@dakinggg thank you for being patient so far with all of my other PRs - now, this one is a lot smaller and more manageable. I updated the example in the PR description to be possible to run with uv run to demonstrate it working from scratch

[dakinggg]

Thanks for the PR! I left a few comments, but generally I'm a little bit hesitant to accept this PR because its taking a dependency on a new (to scispacy), not super well established library (as far as i can tell from github stars and pypi downloads, feel free to correct me). I maintain scispacy in my spare time and am not really adding major new features. That being said, pyobo seems quite useful and I'm not certain one way or the other.

What do you think about keeping a helper function (scispacy_linker_from_pyobo or similar) within pyobo for now? Your previous PRs have made the scispacy code much easier to extend, such that the helper can be easily kept in pyobo itself. I'd be happy to accept a PR adding a link to pyobo in the readme somewhere in that case.

[cthoyt]

@dakinggg I totally appreciate the situation you're in. I'm happy to maintain this on the PyOBO side, then help write documentation both from PyOBO and SciSpacy sides to help users who want to use the external tooling in combination

[dakinggg]

Thanks for understanding, and thanks for your contributions to OSS :)

[cthoyt]

hi @dakinggg. I made a new release of PyOBO based on the code originally in this PR, then reorganized this PR to just be a documentation improvement in the README that gives a short demo and links to further PyOBO docs. I also updated the description and title of the PR to reflect this.