dustine32

EcoMap should parse eco.owl as ontology

1

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...

Run GO rule 20 (obsolete term repair) before GO rule 28 (term aspect check)

2

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...

GoRule 57 update and test for issue #473

5

@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 ```

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...

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...

OntologyFactory should handle propertyChainAxioms

2

It would be nice if I could use propertyChainAxioms in certain ontologies (e.g. RO) to connect certain terms. Example use case is deriving "causally upstream of or within, positive effect"...

Parse Annotation_Properties column with GpadParser

1

I noticed that some new annotation properties key-values I was looking for weren't available via GpadParser. [Here's](http://www.geneontology.org/specifications/gpad/gpad-1_2.md) _one_ of the GPAD specs that describes the `annotation_properties` column. For an example,...

Double-quote issue in DO file breaks xref and synonym parsing

1

Sorry, I can add more detail later (after I reproduce it). The latest DO file [here](https://raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/834f2cacd7876b74915928cafdcaf663ac5f089f/src/ontology/doid.obo) has double-quotes somewhere in the header that's allegedly breaking the parsing of cross-refences and...

Generate closure of ontology for use in writing slim

2

Sorry if there's already functionality like this in ontobio: Use case is generating a new Panther slim from an Ontology object. We first load the whole GO, run some heuristic...