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YAML subsets not correct #192

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lpalbou opened this issue Nov 13, 2019 · 7 comments
Closed

YAML subsets not correct #192

lpalbou opened this issue Nov 13, 2019 · 7 comments

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@lpalbou
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lpalbou commented Nov 13, 2019

I was looking at the YAML version of the subsets and except a header, they are all empty:

http://current.geneontology.org/ontology/subsets/goslim_agr.yaml

http://current.geneontology.org/ontology/subsets/goslim_aspergillus.yaml

They are referenced from the website: http://geneontology.org/docs/download-ontology/

@kltm @dougli1sqrd ?

@kltm
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kltm commented Nov 13, 2019

No idea where those files come from. Maybe @balhoff ?

@balhoff
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balhoff commented Nov 15, 2019

No idea here either. All I can find in the ontology makefile is this: https://github.com/geneontology/go-ontology/blob/7f02b38f9c51e11a24fc04cf7d246bf9f045cb8c/src/ontology/Makefile#L240-L241

@cmungall
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The yaml files are not empty, they are doing precisely what they are intended to do which is to provide metadata abut the subset

The source is here:

https://github.com/geneontology/go-ontology/blob/master/src/ontology/subsets/goslim_agr.yaml

You will find the contents at URLs like this:

http://current.geneontology.org/ontology/subsets/goslim_agr.obo
http://current.geneontology.org/ontology/subsets/goslim_agr.json
http://current.geneontology.org/ontology/subsets/goslim_agr.owl

@cmungall cmungall reopened this Nov 15, 2019
@cmungall
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Reopening as the action is to change the download page so it doesn't mislead

@pgaudet
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pgaudet commented Nov 21, 2019

I think we should remove the yaml definitions. OK ?

@pgaudet pgaudet transferred this issue from geneontology/go-site Nov 21, 2019
@lpalbou
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lpalbou commented Nov 22, 2019

Agreed, the references to yaml files should be removed as they are meta data and not the subsets themselves. Those files could be used in #102.

The PR to remove them can be approved here: #194

@lpalbou
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lpalbou commented Nov 22, 2019

Just saw #193, I approved it.
Closing #194 and this ticket.

@lpalbou lpalbou closed this as completed Nov 22, 2019
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