ontobio
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biolink
python library for working with ontologies and ontology associations
`ogr.py -t tree -r cl CL:1001608 &>log` generate 3.2gb log of warnings before I gave up, first 10 lines are: ``` 2020-03-10 09:46:17 [WARNING] [PID:25137 TID:140260928632640] [ontol_renderers.py:256 in `_show_tree_node`] CYCLE:...
Not sure if this problem is restricted to the GO pipeline but the product is where I observed it: http://current.geneontology.org/annotations/mgi.gpad.gz It's also in the wb.gpad. I think something's up with...
I just installed ontobio (via pip) and am going through the documentation to familiarise myself with the tool. When I try: `ogr.py -r cl -p subClassOf -t tree neuron` as...
And other IRIs/curies where the behavior varies from other cases. For example in https://github.com/biolink/ontobio/blob/b47b05/ontobio/ontol.py#L401, parents() accepts subClassOf but not rdfs:subClassOf. Another improvement would be to have both work.
This is a broad ticket speaking to the need to center all parts of the ontobio parsing and validating system to use GoAssociation objects. Parsing should be a minimal layer,...
For https://github.com/biolink/ontobio/issues/402, https://github.com/biolink/ontobio/issues/403, and https://github.com/biolink/ontobio/issues/295, we will need to ensure that AssocParser is functional the entire way through, as well as the report systems. I suspect given how we've drawn...
The following code from http://nbviewer.jupyter.org/github/biolink/ontobio/blob/master/notebooks/Find_All_Paths.ipynb ``` from ontobio.io.ontol_renderers import GraphRenderer w = GraphRenderer.create('png') w.outfile = 'output/multipath.png' w.write(subont,query_ids=sample_path) ``` fails with the error message ``FileNotFoundError: [Errno 2] No such file or...
Occasionally the GO Rules runner engine in ontobio ends up skipping a rule for one reason or another. For example if a needed resource to perform a test is not...
Add a new similarity API based on the interfaces defined here: https://github.com/biolink/ontobio/blob/master/ontobio/sim/api/interfaces.py This is blocked by https://github.com/monarch-initiative/monarch-devops/issues/124
