ontobio
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biolink
python library for working with ontologies and ontology associations
- [ ] command line tool that takes two gpad files and produces a "diff" report between them. - [ ] high level summary statistics generated, ie: N genes had...
Using this notebook as an example: https://nbviewer.org/github/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb I am having trouble with this import: w = GraphRenderer.create('png') which gives error: ModuleNotFoundError: No module named ‘ontobio.graph_io’ Context: I did pip install...
When trying to obtain the GO subgraph for 800 input terms, as here: https://github.com/kbaseIncubator/KE_KG/blob/main/src/embeddings/GO_ontobio.ipynb I am running into the recursion limit RecursionError: maximum recursion depth exceeded. I can set the...
It's not clear from the README of this repo (nor the PyPI page) what this repo is for. The readme should have some examples of use cases/examples so people know...
Originating from https://github.com/geneontology/pipeline/issues/242#issuecomment-861114921. Use case here is converting a GPAD, which lacks aspect column, into GAF. For most annotations the null aspect is correctly filled in from the ontology term...
To generate the Alliance gene descriptions, I'm loading GO obo file and the GAF files for the MODs with ontobio, but GO rule 26 is skipping IBA annotations. Is there...
Hello Ontobio team, I have a simple RDF Turtle file `test.ttl` that I want to load using Ontobio: ``` @prefix skos: . @prefix owl: . @prefix rdfs: . @prefix xsd:...
I came across this processing the cell ontology. The class 'naive B cell' provides an example. As you can see in the screenshot, the two synonyms without xsd:type string declarations...
The RDF GO-CAM generation from association code in assoc_rdfgen does not handle NOT annotations. Currently there are GO Rules that refer to annotations being `NOT` annotations. But this is not...
