Difference between revisions of "RefGenome8Jul08 Phone Conference (Archived)"

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[[Category:Reference Genome]][[Category:Archived]]
 
Tuesday July 8, 2008, 1 PM CDT, 11 AM PDT, 7 PM BST
 
Tuesday July 8, 2008, 1 PM CDT, 11 AM PDT, 7 PM BST
  
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* Stacia SGD
 
* Stacia SGD
  
==Electronic jamboree==
+
==[[Electronic jamboree_july18-2008 |Electronic jamboree]]==
 
+
* select genes or papers? and annotate together
 +
* US people should annotate on Thursday and UK people on Friday; we'd all meet Friday (8 AM in California; 4 PM in UK)
 +
* topics: elongation factors or housekeeping genes
 +
* Emily will put together a suggestion list for genes to annotate
 +
* we'll do this by webex and phone conference
  
 
==Review old/ongoing action items==
 
==Review old/ongoing action items==
Line 34: Line 39:
 
see also [[Annotation_QC]] for some general documentation and previous issues
 
see also [[Annotation_QC]] for some general documentation and previous issues
 
# 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.
 
# 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.
 
 
# All (ongoing): Develop annotation SOPs
 
# All (ongoing): Develop annotation SOPs
 
There are some wiki pages about that on the ref genome main page's annotation section:  
 
There are some wiki pages about that on the ref genome main page's annotation section:  
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[Action item] : All : fill the old Google spreadsheets so that Mary can generate the ortho sets for making the graphs.
 
[Action item] : All : fill the old Google spreadsheets so that Mary can generate the ortho sets for making the graphs.
 
[Action item]: Discuss use of binding/regulation terms (GOC meeting)
 
[Action item]: Discuss use of binding/regulation terms (GOC meeting)
 
  
 
==PPOD update==
 
==PPOD update==
Line 50: Line 53:
  
 
==Software==
 
==Software==
 +
===Integrating ref genomes in AmiGO===
 +
(Seth) As discussed on the call last month, I wanted to give links to the
 +
current implementation of the Ref Genome information that we're going to
 +
be putting into AmiGO. The page explaining the current state is at:
 +
 +
[[RG:_Software#Summary_and_Graph_Views |RG:_Software#Summary_and_Graph_Views]]
 +
 +
I also have setup a wiki page to help keep track of the development of
 +
and feedback for the Ref Genome in AmiGO. You might want to take a look
 +
at it before commenting:
 +
 +
[[RG:_Software_:AmiGO |RG:_Software_:AmiGO]]
 +
 +
This is still a work in progress, so there may be downtime and sudden
 +
changes. Thank you in advance for any feedback.
  
 
==Source Forge QC discussion==
 
==Source Forge QC discussion==
Line 58: Line 76:
 
discussion; Susan : This raises the question of how best to handle paralogs. The 3 human genes TNNT1,2,3 cluster in InParanoid with a single fly troponin protein (encoded by up). up has the best InParanoid score with TNNT3 so this was what I declared as ortholog in the spreadsheet (pending the review of ortholog determination). However, this is probably misleading:  from a tree (e.g. treefam) it is clear that the duplication in human occurred after the fly/human divergence. Is it better to enter in the fly gene multiple times in the spreadsheet for gene human paralog?
 
discussion; Susan : This raises the question of how best to handle paralogs. The 3 human genes TNNT1,2,3 cluster in InParanoid with a single fly troponin protein (encoded by up). up has the best InParanoid score with TNNT3 so this was what I declared as ortholog in the spreadsheet (pending the review of ortholog determination). However, this is probably misleading:  from a tree (e.g. treefam) it is clear that the duplication in human occurred after the fly/human divergence. Is it better to enter in the fly gene multiple times in the spreadsheet for gene human paralog?
 
* (Pascale: Note that Kara's ortho MCL analysis puts 'up' with TNNT2)
 
* (Pascale: Note that Kara's ortho MCL analysis puts 'up' with TNNT2)
 +
* Maybe the tree view will solve this
  
 
==ACVR1B==
 
==ACVR1B==
 
Ranjana
 
Ranjana
[[http://sourceforge.net/tracker/index.php?func=detail&aid=1944446&group_id=36855&atid=1040173]]
+
[http://sourceforge.net/tracker/index.php?func=detail&aid=1944446&group_id=36855&atid=1040173 SF tracker]
 
+
[http://www.geneontology.org/images/RefGenomeGraphs/91.html Graph]
==EIF2B2==
+
* Annotations to xx binding can be ISS'ed
Stacia
+
* wormbase happy to keep IEAs for things like 'protein kinase activity'; unsure that function is conserved
[[http://sourceforge.net/tracker/index.php?func=detail&aid=1904301&group_id=36855&atid=1040173]]
+
* transferring CC annotation?
 +
* transferring Processes by ISS can be tricky
  
  

Latest revision as of 08:27, 16 January 2018

Tuesday July 8, 2008, 1 PM CDT, 11 AM PDT, 7 PM BST

Present

  • Pascale dictyBase
  • Kimberly wormbase
  • Ranjana wormbase
  • Kara ppod
  • Mike SGD
  • Ruth
  • Tanya TAIR
  • Donghui TAIR
  • Emily GOA
  • Petra dictybase
  • Jim Hu
  • Seth
  • Victoria RGD
  • Susan flybase
  • Judy MGI
  • Stacia SGD

Electronic jamboree

  • select genes or papers? and annotate together
  • US people should annotate on Thursday and UK people on Friday; we'd all meet Friday (8 AM in California; 4 PM in UK)
  • topics: elongation factors or housekeeping genes
  • Emily will put together a suggestion list for genes to annotate
  • we'll do this by webex and phone conference

Review old/ongoing action items

DONE:

  1. Seth: send URL sometime to the prototype of the ortholog tool this week (will do!)
  2. [Action item]: MGI: verify GRIN1 annotation binding/complex

Ongoing:

  1. 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

  1. 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.
  2. 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

[Action item] : All : fill the old Google spreadsheets so that Mary can generate the ortho sets for making the graphs. [Action item]: Discuss use of binding/regulation terms (GOC meeting)

PPOD update

Our programmer is back from leave and will be rolling out several new features to the PPOD web interface as soon as tomorrow.

I need to check in with Paul to see where they are, and whether we should start a new OrthoMCL and Jaccard run from the gp2protein/fasta files that he has used for PANTHER analysis.


Software

Integrating ref genomes in AmiGO

(Seth) As discussed on the call last month, I wanted to give links to the current implementation of the Ref Genome information that we're going to be putting into AmiGO. The page explaining the current state is at:

RG:_Software#Summary_and_Graph_Views

I also have setup a wiki page to help keep track of the development of and feedback for the Ref Genome in AmiGO. You might want to take a look at it before commenting:

RG:_Software_:AmiGO

This is still a work in progress, so there may be downtime and sudden changes. Thank you in advance for any feedback.

Source Forge QC discussion

General points

discussion; Susan : This raises the question of how best to handle paralogs. The 3 human genes TNNT1,2,3 cluster in InParanoid with a single fly troponin protein (encoded by up). up has the best InParanoid score with TNNT3 so this was what I declared as ortholog in the spreadsheet (pending the review of ortholog determination). However, this is probably misleading: from a tree (e.g. treefam) it is clear that the duplication in human occurred after the fly/human divergence. Is it better to enter in the fly gene multiple times in the spreadsheet for gene human paralog?

  • (Pascale: Note that Kara's ortho MCL analysis puts 'up' with TNNT2)
  • Maybe the tree view will solve this

ACVR1B

Ranjana SF tracker Graph

  • Annotations to xx binding can be ISS'ed
  • wormbase happy to keep IEAs for things like 'protein kinase activity'; unsure that function is conserved
  • transferring CC annotation?
  • transferring Processes by ISS can be tricky


Next conference call

Tuesday August 12, 2008, 10 AM CDT (8 AM PDT, 4 PM BST)

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