Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add missing field and docs gaf-eco-mapping-derived.txt #249

Closed
cmungall opened this issue Feb 25, 2020 · 7 comments
Closed

Add missing field and docs gaf-eco-mapping-derived.txt #249

cmungall opened this issue Feb 25, 2020 · 7 comments

Comments

@cmungall
Copy link
Contributor

A while ago I worked with Marcus on this https://github.com/evidenceontology/evidenceontology/blob/master/gaf-eco-mapping.txt

This provides a mapping from a GAF code + GO_REF to an ECO class

There is a PURL for this, so that people can use a PURL rather than a github URL http://purl.obolibrary.org/obo/eco/gaf-eco-mapping.txt

all good

at some point some groups started needing a derived version of this so they didn't have to walk to the ECO graph

Here:
https://github.com/evidenceontology/evidenceontology/blob/master/gaf-eco-mapping-derived.txt

This essentially has materialized inferences

However, it lacks a GO_REF. It also lacks documentation at the start of the file

Can these be added? The docs should state exactly what the file is an how it's derived

I also recommend the PURL is advertised in the header:

http://purl.obolibrary.org/obo/eco/gaf-eco-mapping-derived.txt

cc @kltm
@mgiglio99
Copy link

Hi Chris
Thanks for alerting us to this. We'll work on getting it fixed.
Michelle

beckyjackson pushed a commit that referenced this issue Apr 21, 2020
Add header to derived mapping for #249
d5e03b2
@beckyjackson
Copy link
Member

@cmungall should the GO_REF just be included on the ECO IDs that currently have the GO_REFs in the non-derived mapping file, or should it be propagated to descendants?

@beckyjackson beckyjackson mentioned this issue Apr 22, 2020
Closed
@cmungall
Copy link
Contributor Author

Can you also add a link to this in the wiki page?

@cmungall
Copy link
Contributor Author

https://github.com/evidenceontology/evidenceontology/blob/master/gaf-eco-mapping-derived.txt resolves to HTML, it needs to resolve to the raw github URL

$ curl -L -s https://github.com/evidenceontology/evidenceontology/blob/master/gaf-eco-mapping-derived.txt | head






<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">

@beckyjackson
Copy link
Member

Hi @cmungall - I'm a bit confused by your last comment because that GitHub URL will always resolve to the HTML. The URL we use in the header of the file is http://purl.obolibrary.org/obo/eco/gaf-eco-mapping-derived.txt and resolves to the raw text file.

We are reviewing the Wiki and will update with this link shortly! Thanks!

@beckyjackson beckyjackson mentioned this issue May 15, 2020
Closed
@mgiglio99
Copy link

@nsuvarnaiari
Hi Suvvi - let's review this one to see if there is anything else to do - I think it can be closed.
Michelle

@nsuvarnaiari
Copy link
Contributor

All the issues have been resolved.
1)PURL has been added in the header of http://purl.obolibrary.org/obo/eco/gaf-eco-mapping-derived.txt file. The header also contains details on how the file is generated.
2)The file does not have mappings to GO:REFs (mapping from a GAF code + GO_REF to an ECO class is in https://github.com/evidenceontology/evidenceontology/blob/master/gaf-eco-mapping.txt).
3) The PURLs to 'gaf-eco-mapping.txt' and 'gaf-eco-mapping-derived.txt' have been added to wiki page (https://github.com/evidenceontology/evidenceontology/wiki/Gene-Ontology-GafEcoMapping)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
4 participants
@cmungall @nsuvarnaiari @mgiglio99 @beckyjackson