RefGenome12Aug08 Phone Conference (Archived)

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Present

  • David Hill MGI
  • Harold Drabkin MGI
  • Mary Dolan MGI
  • Judy Blake MGI
  • Seth Carbon NCBO
  • Pascale Gaudet dictybase
  • Siddhartha Basu dictyBase
  • Petra Fey dictyBase
  • Paul Thomas SRI
  • Ruth Lovering BHF-UCL
  • Emily Dimmer GOA
  • Rachael Huntley GOA
  • Kara Dolinsky Princeton
  • Victoria Petri RGD
  • Kimberly Van Auken WormBase
  • Tanya Berardini
  • Suzi
  • Chris
  • Stacia
  • Michael
  • Varsha Khodiyar BHF-UCL
  • Jim Hu EcoliWiki
  • Debby Siegele EcoliWiki

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

Added the unresolved items to Reference_Genome_Annotation_Project#Annotation_Consistency_Issues


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(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.(see below)

ACTION ITEM 8. (Stacia) Send around SGDs SOP for HTP annotation. (we'll discuss, see below); SOPs are here SGD_GO_HTP_guidelines

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

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 (we'll discuss, see below)

ACTION ITEM 11. (Pascale) Discuss IEP: Some people had annotated 'response to heat' by IDA for the heat shock protein; while what was measured was the level of transcript/protein. There are 38 genes annotated to 'response to heat shock' with IDA in the GO database. Those should be checked? (we'll discuss, see below)

  • Another question arising from this is how to you have an IDA to 'response to xx'?(we'll discuss, see below)

ACTION ITEM 12. Discuss xx binding in the context of gene product. In this case I (Pascale) think the 'coenzyme' rather refers to the gene product. Most/many people seem to use 'coenzyme binding' only to annotate proteins that bind a coenzyme for activity. However the definition does not specify that. (we'll discuss, see below)

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.

ACTION ITEM: (Pascale) schedule electronic meeting in October

Curation Targets

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.


Software update

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

PANTHR update

Discussions from electronic jamboree

We discussed some of those points without reaching a conclusion. We have decided to form small groups that would think about the issues and propose solutions to the rest of the group, and then to the entire consortium. See Reference_Genome_Annotation_Project#Annotation_Consistency_Issues

  • 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
  • (Pascale) IEP: Some people had annotated 'response to heat' by IDA for the heat shock protein; while what was measured was the level of transcript/protein. There are 38 genes annotated to 'response to heat shock' with IDA in the GO database. Those should be checked?
  • Another question arising from this is how to you have an IDA to 'response to xx'?
  • Discuss xx binding in the context of gene product. In this case I (Pascale) think the 'coenzyme' rather refers to the gene product. Most/many people seem to use 'coenzyme binding' only to annotate proteins that bind a coenzyme for activity. However the definition does not specify that.

Source Forge QC discussion

Stack tracker update

Siddhartha Current development status and roadmap

Next conference call

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

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