ontobio
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biolink
python library for working with ontologies and ontology associations
To move away from relying on [gaf-eco-mapping.txt](https://github.com/evidenceontology/evidenceontology/blob/master/gaf-eco-mapping.txt) and [gaf-eco-mapping-derived.txt](https://github.com/evidenceontology/evidenceontology/blob/master/gaf-eco-mapping-derived.txt) we should fetch and parse [eco.owl](http://purl.obolibrary.org/obo/eco.owl) into an `Ontology`. With the whole ontology, we can compute closures for ECO codes indirectly...
I'm trying to use ontobio behind a proxy but when importing package with ```python from ontobio.ontol_factory import OntologyFactory ``` I get the following error (note that I do no get...
Addresses issue #615. For the record, I don't know how long this has been broken or whether it's actually broken by all users of ontobio, or just in Monarch's SciGraph...
In `ontobio.model.nlp` (https://github.com/biolink/ontobio/blob/master/ontobio/model/nlp.py#L19) the field `category` is always empty, since SciGraph appears to the return the field as `categories`. I can't find precisely where or when in the SciGraph commit...
Following along with [this notebook](https://github.com/biolink/ontobio/blob/master/notebooks/Wikidata_Ontology.ipynb) for rendering subgraphs using GraphRenderer, when running: ```python nodes = ont.traverse_nodes(qids, up=False, down=True) from ontobio.io.ontol_renderers import GraphRenderer w = GraphRenderer.create('tree') w.write_subgraph(ont, nodes, query_ids=qids) ``` I...
To make this work we'd need to talk about adding a pypi API token to this repo (maintainers of ontobio on pypi can do that).
ogr bug?
Trying to use ogr from local install following examples from docs I consistently get errors like this: ``` $ venv/bin/python bin/ogr.py -r cl neuron /Users/davidos/Documents/GitHub/ontobio/venv/lib/python3.9/site-packages/rdflib_jsonld/__init__.py:9: DeprecationWarning: The rdflib-jsonld package has...
Once I've manipulated a graph in ontobio, can I write it back to obograph json? Surely this is possible, but I haven't found anything in the documentation or from exploring...
loading local OboGraph JSON files following [examples from the notebooks](https://nbviewer.org/github/biolink/ontobio/blob/master/notebooks/Intro_Local_Ontologies.ipynb) or using local obograph JSON files generated by ROBOT consistently => empty graphs eg. ```python from ontobio.ontol_factory import OntologyFactory ont...