Published March 15, 2023
| Version v0.2.3
Software
Open
INCATools/ontology-access-kit: v0.2.3
Authors/Creators
- 1. Lawrence Berkeley National Laboratory
- 2. Harvard Medical School
- 3. @jhu-bids
- 4. LBNL
- 5. Leibniz-Institut für Katalyse e.V. (LIKAT)
- 6. SIB Swiss Institute of Bioinformatics
- 7. semanticly Ltd
- 8. @det-lab @tis-lab @monarch-initiative
- 9. Queen Mary University of London
- 10. Lawrence Berkeley National Lab
Description
Highlights
Relationship Type support
This adds full support for treating certain axioms in the "RBox" as edges - i.e it allows you to visualizing relationship type hierarchies, as well as inverse edges, and domain/range links between relations and classes:
Example:
ro relationships RO:0002211 --direction both
| subject | subject_label | predicate | predicate_label | object | object_label |
|---|---|---|---|---|---|
| RO:0002211 | regulates | rdfs:subPropertyOf | None | RO:0002411 | causally upstream of |
| RO:0002211 | regulates | owl:inverseOf | None | RO:0002334 | regulated by |
| RO:0002211 | regulates | rdfs:domain | None | BFO:0000015 | process |
| RO:0002211 | regulates | rdfs:range | None | BFO:0000015 | process |
| RO:0002212 | negatively regulates | rdfs:subPropertyOf | None | RO:0002211 | regulates |
| RO:0002213 | positively regulates | rdfs:subPropertyOf | None | RO:0002211 | regulates |
| RO:0002578 | directly regulates | rdfs:subPropertyOf | None | RO:0002211 | regulates |
| RO:0012012 | indirectly regulates | rdfs:subPropertyOf | None | RO:0002211 | regulates |
Visualize:
ro viz RO:0002211 --down
<img width="534" alt="image" src="https://user-images.githubusercontent.com/50745/225152396-20631343-d628-4cec-aabb-e8e11490b4b0.png">
SQL Alchemy 2.0 supportOAK now works with SQLA 2.0
What's Changed- Ensure sqldb is sqlalchemy-2.x compatible. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/463
- Adding extract operation by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/464
- Adding rbox support for sql_implementation. by @cmungall in https://github.com/INCATools/ontology-access-kit/pull/466
- update bioregistry dependency to fix downstream dependency errors by @sierra-moxon in https://github.com/INCATools/ontology-access-kit/pull/468
Full Changelog: https://github.com/INCATools/ontology-access-kit/compare/v0.2.1...v0.2.3
Files
INCATools/ontology-access-kit-v0.2.3.zip
Files
(12.4 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:2605e7dcd0d20ed34640ee2e630ebe4a
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Additional details
Related works
- Is supplement to
- https://github.com/INCATools/ontology-access-kit/tree/v0.2.3 (URL)