Genecode/Ensembl name space and release version

[shawntanzk]

From Brian Aevermann:

Also we should be tracking the annotations spaces used within the onotology. is that part of the imported ontology make file?

Gencode and Ensembl mostly merged a few years back, but gencode maintains a larger annotation system of hypothetical and putative genes. The most important thing is to maintain a record somewhere in the ontology the actual annotation system used during the data analysis steps as this will be an important distinction when interpreting the results in the future.

[shawntanzk]

Also we should be tracking the annotations spaces used within the onotology. is that part of the imported ontology make file?

I think our import file automatically updates right?

The most important thing is to maintain a record somewhere in the ontology the actual annotation system used during the data analysis steps as this will be an important distinction when interpreting the results in the future.

Not sure how to handle this, but we should have a record of this

[dosumis]

@jeremymiller - can we get details of ENsembl version for the mouse reference we're using?

[shawntanzk]

Current status:

• we have gotten a gtf file from Ray - they are working on getting a fixed link for this (it is too big to put into github)
• For now @shawntanzk has converted it into simple files using a dirty R code (see: https://github.com/obophenotype/brain_data_standards_ontologies/tree/gene-curation/src/templates)
• Have changed the taxonomy_details.yaml file to point to the correct files (I think, needs double checking from @hkir-dev) here: f93478d
• Still requires implementation and checks

[shawntanzk]

version metadata should live in taxonomy nodes from #191