ontobio
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biolink
python library for working with ontologies and ontology associations
@dougli1sqrd I'll probably need to update the [mgi.yaml](https://github.com/geneontology/go-site/blob/master/metadata/datasets/mgi.yaml) and [wb.yaml](https://github.com/geneontology/go-site/blob/master/metadata/datasets/wb.yaml) files in [go-site](https://github.com/geneontology/go-site/tree/master/metadata/datasets) as well, right? Example: ``` filter_for: provided_by: - MGI ```
Arrange unit and integration tests separately.
Make sure notebooks are run/tested to ensure that they don't break between releases.
Use proper paths for resources instead of relative paths in tests. For example, ```py cwd = os.path.abspath(os.path.dirname(__file__)) resource_dir = os.path.join(cwd, '../resources') target_dir = os.path.join(cwd, '../target') ```
This ticket is to indicate that GPI 2.0 needs to be read along with parsing GPAD 2.0. Currently only GPI 1.2 is accepted. See https://github.com/biolink/ontobio/pull/509
I'm using OntoBio to process the Cell Line Ontology. This ontology attaches multiple rdfs:label annotations to classes. In many cases one label will be in Chinese and one will be...
ontobio validate.py should not grab the "compression" value from the dataset metadata without guards
Line 138 of validate.py we have `dataset_metadata["compression"] == "gzip"` when grabbing compression info for a dataset source. If the `compression` field is not present -- which is valid by the...
ontobio-parse-assocs.py `convert` command needs a version option to select what version output for a file type.