Action items from previous calls
- David, Tanya, Jane: Compose wiki documentation for ontology editors, with step-by-step instructions on making cross-products - in progress
- Jen: Draft wiki page to summarize motivation for MF-BP links - in progress
- Managers: Comment on draft proposal that Suzi will circulate (content meetings, RefGen annotations, etc.) - not sent
- Pascale: Confirm date of Geneva annotation camp - 14th-17th June at SIB - sent to GO-Top and only Judy responded. GO-Top to confirm.
- Midori, Jane, David, Tanya, Chris: Midori to resend draft (DONE), others to comment - sent - some comments received. In progress.
New last time
- Chris filter IEAs from GAF inference. do we need more detailed evidence codes - e.g. IC-derived-from-ISS - in progress
- Chris report on aligning Reactome and GO - in progress
Emily - GAF 2.0 gene association file format
At the Cambridge GO Consortium meeting, I believe it was decided that the GOC would start converting gene association files into the GAF2.0 format from January 2010; and that this would become the primary GAF format of files provided in: ftp://ftp.geneontology.org/pub/go/gene-associations/. I have this noted down as an outcome from this meeting, however is this still true?
GOA would like to start producing both GAF1.0 and GAF2.0-formatted files. We had been planning to provide both GAF1.0 and GAF2.0 formatted files for 4 months from December until March 2010, when we would provide just the GAF2.0 format and then advise our users to find GOA GAF1.0 files in the GOC submissions folder.
We were thinking of announcing this intended format change in November, however I was uncomfortable in announcing this change without having a page on the GO Consortium website to direct users to; I feel the GOC website should provide the primary source of gene association file format information and any confirmed changes.
Shouldn't there be some documentation on GAF2.0 that is visible from: http://www.geneontology.org/GO.current.annotations.shtml ?
Similarly, would an email be going out on the gofriends list to alert users to this change before GAF2.0 becomes the primary association file format in January?
A/ Is there something on the wiki already?
If Emily is happy to write the docs then that would be great.
If there is documentation written already then we can add the links that she requests. There should also be a README.
Should this be on the web, the wiki, or both? David - it should be on the website.
This is what we have already: http://wiki.geneontology.org/index.php/GAF_2.0
Action: We can use this text http://wiki.geneontology.org/index.php/GAF_2.0 to make documentation of GAF 2.0 for the website. Perhaps Emily and Amelia would like to work together on that.
Action: Send a mail to GO-friends to advertise GAF 2.0 and to show the docs.
(Carried over from last time) I'm concerned that we're not able to capture information about decisions we make about ontology structure at the level of terms and relations. We're relying a lot on collective memory which is going to become increasingly difficult as staff change! Example is thylakoid. Do we have a long-term plan. Is there anything we can do in the interim? [Jane]
A/Should we label those terms in the ontology that are correct and should not be edited, and those that are so bad that they should not be used as a template for new terms?
A/Would having the GO in a database help?
A/Can we afford to have duplication of roles so there are always two people who know all the information?
A/ Very hard problem!