ontobio
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biolink
python library for working with ontologies and ontology associations
Networkx 2.4 has deprecated a few methods including `graph.node[]`. The recommendation is to use `graph.nodes[]`. All calls to `graph.node` --> `graph.nodes`
If owltools is not installed then this produces an exception: https://github.com/biolink/ontobio/blob/080eabca82e1d1de3f661e4d7996c543cfa700e9/ontobio/ontol_factory.py#L104-L106 ``` File "/home/lance/git/2019/January/wf2/venv/lib/python3.6/site-packages/ontobio/ontol_factory.py", line 106, in create_ontology cp = subprocess.run(cmd, check=True) File "/usr/lib/python3.6/subprocess.py", line 403, in run with Popen(*popenargs,...
For the MOD imports project we need to port over the ability to filter for only lines with particular Provided_by values (`MGI` for the MGI GPAD, `WB` for the WB...
From v1.15.4, after importing ontobio, calling `logging.basicConfig` doesn't configure the logging system, unless **force** is set to `True`. This is due to the changes introduced in c942c70 and 736694e, which...
The case we ran into here was parsing the goa_uniprot_all.gaf.gz file for the GO. Specifically: ```bash ontobio-parse-assocs.py -f /opt/go-site/annotations/goa_uniprot_all.gaf -F gaf -o /opt/go-site/annotations_new/goa_uniprot_all.gaf -I /opt/go-site/gaferencer-products/all.gaferences.json --report-md /tmp/report.md --report-json /tmp/report.json convert...
On line 163 of https://github.com/biolink/ontobio/blob/master/ontobio/ontol_factory.py, there is code for retrieving the ontology from a cache. Would it be possible to have an optional argument to the factory constructor (or the...
We should change how we support the Qualifier field. Currently it is a list. But actually qualifiers are always `NOT`, a single Relation, `NOT` and a Relation, or Empty (for...
Many of the methods in the Ontology class (ontol.py) have terse documentation that doesn't include a description of the argument-types. For example, `add_synonym` takes a single argument `syn` that is...
Ontobio needs to have a new command specifically to create graph models (TTL) from annotation lines (GPAD/GAF). (This is what gocamgen does) * Probably the command will be in `validate.py`,...
From @cmungall: - clarify which modules here are calculating natively vs calling owlsimX - general documentation
