11 MAY 2010 RefGen Phone Conference (Archived): Difference between revisions

From GO Wiki
Jump to navigation Jump to search
mNo edit summary
 
(21 intermediate revisions by 6 users not shown)
Line 1: Line 1:
[[Category:Reference Genome]][[Category:Archived]]
==Present==
==Present==
* GOA: Rachael
* GOA: Rachael, Yasmin
* BHF-UCL: Ruth
* BHF-UCL: Ruth
* MGI: Li,  
* MGI: Li, Mary
* RGD: Stan
* RGD: Stan
* Flybase: Susan
* Flybase: Susan
* dictyBase: Pascale
* dictyBase: Pascale
* TAIR:  
* TAIR: Donghui, Tanya
* AgBase: Lakshmi Pillai
* AgBase: Lakshmi  
* SGD: Rama, Julie
* SGD: Rama, Julie
* pombe
* pombe: Val
* Ecoli:  
* Ecoli:  
* Wormbase:  Ranjana Kishore, Kimberly Van Auken  
* Wormbase:  Ranjana Kishore, Kimberly Van Auken  
* ZFIN:  
* ZFIN: Doug
* PPOD:  
* PPOD: Mike
* Berkeley: Suzi, Seth
* Berkeley: Suzi


----
----
Line 22: Line 23:


http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/submission/paint/
http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/submission/paint/
'''ACTION ITEMS''': Software/PAINT groups to look into the following points brought up by curators:
* Issue (Doug): many IDs in the 'with' column - this creates a display problem
* Issue: (Ranjana, Doug): hard to manage downloading all the individual families; especially once we'll have many families
* Databases must make sure that they accept and display annotations here data_source =ref genome
* Where will the reference be displayed from?
* For the cvs repository: it would be helpful if there was a file  that would contain ALL annotations (not just by family) with only the 12 MODs
* GO ref genome xref description should be expanded on the webpage.
* Need to also confirm that ref_genome is the correct string for this column.


==Preparation of GO camp==
==Preparation of GO camp==
* Progress by each working group - 5-10 minute summary
* Progress by each working group - 5-10 minute summary
# Regulation : Jane Lomax and Kimberly VanAuken
# Regulation : Jane Lomax and Kimberly VanAuken ([[2010_GO_camp_Use_of_Regulation_issues]])
# Downstream events: Rachael Huntley and Varsha Khodiyar
# Downstream events: Rachael Huntley and Varsha Khodiyar (Wiki Page: [[2010_GO_camp_downstream_effect]])
# Protein binding: Ruth Lovering and Ursula Hinz [http://wiki.geneontology.org/index.php/2010_GO_camp_binding_documentation_issues#Discussion_30-04-2010 binding discussion]
# Protein binding: Ruth Lovering and Ursula Hinz ( Wiki Page: [[2010_GO_camp_binding_documentation_issues]]
# Protein complexes: Pascale Gaudet and Bernd Roechert
# Protein complexes: Pascale Gaudet and Bernd Roechert (Wiki page: [[2010_GO_camp_Annotation_of_complexes_issues]])
# Response to : Rebecca Foulger and Pascale Gaudet
# Response to : Rebecca Foulger and Pascale Gaudet (Wiki Page: [[2010_GO-camp_Response_to_terms_issues]])
# Annotation Propagation: Alan Bridge and Paul Thomas
# Annotation Propagation: Alan Bridge and Paul Thomas (Wiki Page: [[2010_GO_camp_Annotation_propagation_rules]])
# HTP: Rama Balakrishnan
# HTP: Rama Balakrishnan (Wiki page: [[2010_GO_camp_Annotation_of_HTP_data]])

Latest revision as of 11:20, 16 January 2018

Present

  • GOA: Rachael, Yasmin
  • BHF-UCL: Ruth
  • MGI: Li, Mary
  • RGD: Stan
  • Flybase: Susan
  • dictyBase: Pascale
  • TAIR: Donghui, Tanya
  • AgBase: Lakshmi
  • SGD: Rama, Julie
  • pombe: Val
  • Ecoli:
  • Wormbase: Ranjana Kishore, Kimberly Van Auken
  • ZFIN: Doug
  • PPOD: Mike
  • Berkeley: Suzi

PAINT-generated GAF file

Samples are avilable for download here:

http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/submission/paint/

ACTION ITEMS: Software/PAINT groups to look into the following points brought up by curators:

  • Issue (Doug): many IDs in the 'with' column - this creates a display problem
  • Issue: (Ranjana, Doug): hard to manage downloading all the individual families; especially once we'll have many families
  • Databases must make sure that they accept and display annotations here data_source =ref genome
  • Where will the reference be displayed from?
  • For the cvs repository: it would be helpful if there was a file that would contain ALL annotations (not just by family) with only the 12 MODs
  • GO ref genome xref description should be expanded on the webpage.
  • Need to also confirm that ref_genome is the correct string for this column.

Preparation of GO camp

  • Progress by each working group - 5-10 minute summary
  1. Regulation : Jane Lomax and Kimberly VanAuken (2010_GO_camp_Use_of_Regulation_issues)
  2. Downstream events: Rachael Huntley and Varsha Khodiyar (Wiki Page: 2010_GO_camp_downstream_effect)
  3. Protein binding: Ruth Lovering and Ursula Hinz ( Wiki Page: 2010_GO_camp_binding_documentation_issues
  4. Protein complexes: Pascale Gaudet and Bernd Roechert (Wiki page: 2010_GO_camp_Annotation_of_complexes_issues)
  5. Response to : Rebecca Foulger and Pascale Gaudet (Wiki Page: 2010_GO-camp_Response_to_terms_issues)
  6. Annotation Propagation: Alan Bridge and Paul Thomas (Wiki Page: 2010_GO_camp_Annotation_propagation_rules)
  7. HTP: Rama Balakrishnan (Wiki page: 2010_GO_camp_Annotation_of_HTP_data)