Difference between revisions of "9 MAR 2010 RefGen Phone Conference (Archived)"

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[[Category:Reference Genome]][[Category:Archived]]
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==Present==
 +
* GOA:
 +
* BHF-UCL: Ruth, Varsha
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* MGI: Li, Mary
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* RGD: Stan
 +
* Flybase: Susan
 +
* dictyBase: Pascale
 +
* TAIR:
 +
* AgBase: Lakshmi Pillai
 +
* SGD: Rama, Julie
 +
* pombe
 +
* Ecoli:
 +
* Wormbase:  Ranjana Kishore, Kimberly Van Auken
 +
* ZFIN:
 +
* PPOD: Kara
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* Berkeley: Suzi, Seth
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 +
----
 +
 
==Action items - ALL==
 
==Action items - ALL==
 
# Please fill the wiki pages for curation progress of lung targets ([[9_MAR_2010_RefGen_Phone_Conference#Lung_targets:_progress]])
 
# Please fill the wiki pages for curation progress of lung targets ([[9_MAR_2010_RefGen_Phone_Conference#Lung_targets:_progress]])
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* Focused annotation topics:  
 
* Focused annotation topics:  
 
# Use of regulation
 
# Use of regulation
# Downstream effects /response to  
+
# Process beginning/end: Downstream effects /response to  
 
# Binding and complexes
 
# Binding and complexes
 
##Binding documentation
 
##Binding documentation
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'''Please add yourself to the working group(s) you would like to be part of. ''' So far everyone who voted for a topic is part of that group. This may be too many groups for everyone and too many members per group.
 
'''Please add yourself to the working group(s) you would like to be part of. ''' So far everyone who voted for a topic is part of that group. This may be too many groups for everyone and too many members per group.
 +
 +
==Ref.Genome in AmiGO==
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http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=live_search
 +
Seth has implemented some enhancements. Check it out.
 +
 +
* Example query: top and homolset:yes
  
 
==Ref genome progress report for April 2010 SAB==
 
==Ref genome progress report for April 2010 SAB==
 
[[Reference_Genome_SAB_04_2010]]
 
[[Reference_Genome_SAB_04_2010]]
  
 +
Please suggest edits if appropriate.
  
 
==Annotation status reporting tool : progress==
 
==Annotation status reporting tool : progress==
 +
Kara:
 +
 +
Sven Heinicke (developer at Princeton) is working through ID mapping issues:
 +
 +
of the 339448 proteins in the seq2pthr.gz file:
 +
 +
61123 exist in the gene_product table 5126 have entries in the dbxref table but not the gene_product table 273199 new rows in the dbxref table (and gene_product) will have to be created
  
Kara and her group have started to work on a tool that would display the annotation status of the Panther families. There will be a regularly updated web page that will show the following information:
+
the script to load these missing rows into the go database has been run.
  
# Panther family ID
+
Sven has just started to work on the web interface and is aiming to send something very simple around toward the end of the week.
# Date selected for concurrent annotation
 
# Date Panther family last annotated (tree annotations)
 
# Number of members
 
# Number of RefG members
 
# Number of members with EXP
 
# Date more recent member last annotated
 
# We could add 'date comprehensively annotated' for groups that can provide this information
 
  
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----
 
----
 
Back to Ref Genomes [[Conference_Calls]]
 
Back to Ref Genomes [[Conference_Calls]]

Latest revision as of 08:20, 16 January 2018

Present

  • GOA:
  • BHF-UCL: Ruth, Varsha
  • MGI: Li, Mary
  • RGD: Stan
  • Flybase: Susan
  • dictyBase: Pascale
  • TAIR:
  • AgBase: Lakshmi Pillai
  • SGD: Rama, Julie
  • pombe
  • Ecoli:
  • Wormbase: Ranjana Kishore, Kimberly Van Auken
  • ZFIN:
  • PPOD: Kara
  • Berkeley: Suzi, Seth

Action items - ALL

  1. Please fill the wiki pages for curation progress of lung targets (9_MAR_2010_RefGen_Phone_Conference#Lung_targets:_progress)
  2. Please add yourself to the working groups for the GO annotation camp (2010_GO_camp_Meeting_Logistics#Suggestions_for_annotation_issues_to_be_discussed)

Lung targets: progress

Li Ni: Please continue to fill wiki page for curation progress: Note that high priority genes are in red.


Next targets: heart development

Varsha Khodiyar, UCL


GO annotation camp

  • Please fill the attendees list of you already know whether you can attend or not. We'd like at least one person from each group to participate. the goal is to finalize annotation guidelines on several topics and we'd like all groups to participate in discussions and be aware of the finalized guidelines.
  • Focused annotation topics:
  1. Use of regulation
  2. Process beginning/end: Downstream effects /response to
  3. Binding and complexes
    1. Binding documentation
    2. Annotation of complexes

Please add yourself to the working group(s) you would like to be part of. So far everyone who voted for a topic is part of that group. This may be too many groups for everyone and too many members per group.

Ref.Genome in AmiGO

http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=live_search Seth has implemented some enhancements. Check it out.

  • Example query: top and homolset:yes

Ref genome progress report for April 2010 SAB

Reference_Genome_SAB_04_2010

Please suggest edits if appropriate.

Annotation status reporting tool : progress

Kara:

Sven Heinicke (developer at Princeton) is working through ID mapping issues:

of the 339448 proteins in the seq2pthr.gz file:

61123 exist in the gene_product table 5126 have entries in the dbxref table but not the gene_product table 273199 new rows in the dbxref table (and gene_product) will have to be created

the script to load these missing rows into the go database has been run.

Sven has just started to work on the web interface and is aiming to send something very simple around toward the end of the week.



Back to Ref Genomes Conference_Calls