11 MAY 2010 RefGen Phone Conference (Archived): Difference between revisions
Jump to navigation
Jump to search
m (→Present) |
m (Pascale moved page 11 MAY 2010 RefGen Phone Conference to 11 MAY 2010 RefGen Phone Conference (Archived)) |
||
(20 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, Mary | * MGI: Li, Mary | ||
Line 6: | Line 7: | ||
* Flybase: Susan | * Flybase: Susan | ||
* dictyBase: Pascale | * dictyBase: Pascale | ||
* TAIR: | * TAIR: Donghui, Tanya | ||
* AgBase: Lakshmi | * 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: Doug | * ZFIN: Doug | ||
* PPOD: | * PPOD: Mike | ||
* Berkeley: Suzi | * 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 [ | # 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
- Regulation : Jane Lomax and Kimberly VanAuken (2010_GO_camp_Use_of_Regulation_issues)
- Downstream events: Rachael Huntley and Varsha Khodiyar (Wiki Page: 2010_GO_camp_downstream_effect)
- Protein binding: Ruth Lovering and Ursula Hinz ( Wiki Page: 2010_GO_camp_binding_documentation_issues
- Protein complexes: Pascale Gaudet and Bernd Roechert (Wiki page: 2010_GO_camp_Annotation_of_complexes_issues)
- Response to : Rebecca Foulger and Pascale Gaudet (Wiki Page: 2010_GO-camp_Response_to_terms_issues)
- Annotation Propagation: Alan Bridge and Paul Thomas (Wiki Page: 2010_GO_camp_Annotation_propagation_rules)
- HTP: Rama Balakrishnan (Wiki page: 2010_GO_camp_Annotation_of_HTP_data)