RefGenome12Aug08 Phone Conference (Archived)

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Present

Review old/ongoing action items

  1. [Action item]: DONE. MGI: verify GRIN1 annotation binding/complex. Chris helped with a query to find all those, see Misused_terms
  2. All (ongoing): Annotation Quality control: Please pick an ortholog set from the Curation Targets table [1] see also Annotation_QC for some general documentation and previous issues
  3. All (ongoing): Annotation Quality control: Have a look at the SF items and see if the ortholog from your organism is correctly annotated ("comprehensive"). Let lead curator for that set know that you're done.
  4. All (ongoing): Develop annotation SOPs. There are some wiki pages about that on the ref genome main page's annotation section: Reference_Genome_Annotation_Project#Gene_Annotation
  5. [Action item] : All : fill the old Google spreadsheets so that Mary can generate the ortho sets for making the graphs.
  6. [Action item]: Discuss use of binding/regulation terms (GOC meeting) (moved to GOC meeting agenda)


Action items from electronic jamboree

ACTION ITEM 1. (Debby) Put in a SourceForge request that definitions of terms for oligomerization, dimerization, protein complex assembly etc. should be clarified as to their use and annotations using these terms be checked and, if necessary, changed.

ACTION ITEM 2. Emily will make a SourceForge request to get the mappings for GO:0006556 S-adenosylmethionine biosynthetic process changed.

ACTION ITEM 3. Put “Process IC or IDA?” On agenda for consortium meeting. (Done)

ACTION ITEM 4. (Petra) Make SourceForge item for making membrane fraction a child of insoluble fraction//done(22-JUL-2008 pf)

ACTION ITEM 5. (Susan) Request new term for Regulation of GTP Cyclohydrolase I activity.

ACTION ITEM 6. (Victoria) Make a SourceForge request to clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’.

ACTION ITEM 7. Discuss microarray data further, possibly GOC meeting item.

ACTION ITEM 8. (Stacia) Send around SGDs SOP for HTP annotation.

ACTION ITEM 9. (Pascale) Make HTP annotation a topic for a Reference Genome call.

ACTION ITEM 10. (Becky) Move discussion to email on whether we need more terms under protein binding to describe protein binding as a target for a process

Electronic jamboree

  • Was pretty useful!
  • Email: consensus was to hold this quarterly. I suggest we have another in early October, so some issues that come up could perhaps be discussed at the GOC meeting.

PPOD update

(Email from Kara, Aug 1, 2008) We've added links from PPOD pages to the MGI GO Graphs for the set of ~ 150 clusters that had entries for all 12 organisms, for example:

http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO0/ORTHOMCL755

It's the "MGI GO" link at the top of the page (thanks Mary for helping us set up the links)--the links only show up when a graph exists.

We've also added disease info (from OMIM and SGD, available via the "Disease Info" link at the top) and curated functional conservation info (the "Functional Conservation" link at the top) from the literature, where we recorded cases from the literature that tested functional conservation (eg. human gene complements the corresponding yeast mutation). There are examples of this info on the page above.

We plan to add AmiGO links for each protein record very soon (thanks Mike C and Seth for help with this).

Also, Paul and I checked in with each other--the Panther stuff is coming along well and they are QC'ing what they have thus far. They used pg2protein files that were generated after we did the current PPOD analysis, so we are a bit out of sync. Of course, we will be synchronized at some point. My question to the group is when we want to do that. Paul said that they are considering this a beta version and after getting feedback from everyone, they would be happy to re-run the analysis if necessary using the even newer and more improved gp2protein files that are (or will soon be? I remember Judy mentioning a new mouse set, but can't remember if those are up now or will be shortly) available. So, options from the PPOD front are:

1) Sit tight with the current version until the Panther stuff has been tested, at which time we (and Panther people) can re-run our analyses using the latest/greatest sets.

2) Re-run the analysis now with the set that Panther used for the beta version about to be send around. We can re-run a 2nd time if need be, if/when Panther does another run based on feedback and the improvements to the gp2protein files.

To me, it makes a little more sense to do 1) (won't be changing the sets that everyone is currently working on only to possibly have to change them again after Panther testing), but it is little work (just compute time) on our end to do 2), so if there is some reason to do that, let us know. We can also discuss this on the next conference call, if that's easier for everyone.


Paul and Suzi agreed to do option 1. Are there comments, questions or objections?

PANTHR update

Discussions from electronic jamboree

  • HTP annotation: does this need to be captured in the annotations?
  • Microarray: did we decide NOT to annotate data from microarray experiments?
  • (Becky): Do we need more terms under protein binding to describe protein binding as a target for a process

Source Forge QC discussion

Next conference call

Tuesday September 9, 2008, 1 PM CDT (11 AM PDT, 7 PM BST)

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