basic module to write nxo features for efo #1
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nxontology_ml/features.py
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| class NodeFeatures: | ||
| def __init__(self, info: Node_Info[T_Node]) -> None: | ||
| self.info = info |
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Instead of a separate NodeFeatures class that embeds a node info object, I think a subclass of Node_Info could be nice. This would make it really easy for us to promote methods from nxontology_ml to nxontology, and it would allow us to benefit from the caching infrastructure provided by nxontology.
Basic approach in related-sciences/nxontology#26, but timeline on getting that working with typing and reviewing its desirability is TBD.
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As of 208bee7, generated features look like:
@eric-czech soft review request. Will add more features and move to a more disciplined feature naming convention in future PRs, but any feedback on whether this is what you have in mind is helpful. |
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Will merge now rather than continuing to make this PR larger. Review still welcome. |
| # https://python-poetry.org/docs/versions/ | ||
| [tool.poetry.dependencies] | ||
| bioregistry = "^0.8.3" | ||
| fire = "^0.5.0" | ||
| ipykernel = "^6.24.0" |
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Should the jupyter libs be tool.poetry.dev-dependencies?
This PR provides some basic code to features describing each ontology node (i.e. term/class). Currently includes only features that are provided by nxontology.