Manager 3June2015: Difference between revisions
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* https://trello.com/c/holv0gEG/151-reference-proteome-should-be-default | * https://trello.com/c/holv0gEG/151-reference-proteome-should-be-default | ||
Human Refernece Proteome Set- http://www.uniprot.org/proteomes/UP000005640 | Human Refernece Proteome Set- http://www.uniprot.org/proteomes/UP000005640 | ||
ftp://ftp.ebi.ac.uk/pub/databases/reference_proteomes/ | |||
==GAF2.1 (addition of pipe/comma to With/From column) (Rama)== | ==GAF2.1 (addition of pipe/comma to With/From column) (Rama)== |
Revision as of 11:26, 3 June 2015
Agenda
Welcome to Melanie Courtot
- She is the new GO project lead at UniProt
Adding people to managers list
- Make sure Moni and Melanie or on the list
Update on GitHub Migration
- https://trello.com/c/nf1HDHwv/149-migrate-ontology-from-svn-sourceforge-to-github (Chris)
- This has become high priority
There are not 46k human genes
This is consistently confusing users and even us. Need to fix:
Human Refernece Proteome Set- http://www.uniprot.org/proteomes/UP000005640 ftp://ftp.ebi.ac.uk/pub/databases/reference_proteomes/
GAF2.1 (addition of pipe/comma to With/From column) (Rama)
- I have put together some specs to make this happen.
- http://wiki.geneontology.org/index.php/GAF_2.1_specs
- Documentation on the GOC website for GAF 2.1- http://geneontology.org/page/go-annotation-file-gaf-format-21
- Annotation guidelines for use of pipe and comma is pending
- test file for checking scripts is available in github
- protein2GO is almost ready to make this option public
- We want to announce this version on July 1st.
Are there any concerns?
Annotating Complexes with GO
IntAct folks are making GO annotations for complexes and they have sent us some questions about how to annotate tricky situations etc. Myself and Kimberly have gone through the proposal. We recommend forming a working group to discuss the issues and to come up with guidelines. Is Pro making GO annotations to complexes? Any thoughts?
Author feedback form
Motivation
- We have been asked several times about the quality of our annotations
- Paul T mentioned that, at the Synapse meeting, an author said the annotations made from his paper were not accurate.
- How about we send a form to authors and ask if the annotations made from their papers are correct or not?
http://wiki.geneontology.org/index.php/Proposal_for_Author_Feedback_for_annotations#Specifications
Master GAF file
- Many of our users who want all the annotations for all taxons grab the UniProt file. We should be providing a master GAF file with all annotations
No more merge ?
(Pascale email; see minutes from Ontology call http://wiki.geneontology.org/index.php/Ontology_meeting_2015-05-28