8 JUN 2010 RefGen Phone Conference (Archived)
From GO Wiki
- GOA: Emily, Yasmin
- BHF-UCL: Ruth, Varsha
- RGD: Stan
- dictyBase: Pascale
- AgBase: Lakshmi
- SGD: Rama, Julie
- Wormbase: Kimberly Van Auken, Ranjana Kishore
- PPOD: Mike
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)
- IMP experiments can be misinterpreted as regulation (because of the definition of regulation)
- Ontology needs to improve beginning and end points of pathways
- Older annotations sometimes need to be checked and removed
- 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)
- The documentation needs to distinguish between 'mediators' of the response and 'targets' of the response.
- Annotations to high level terms should be removed
- 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)
- Read SGD guidelines on the above wiki page
- Propose to use extended evidence codes 'reviewed' - ' unreviewed'
PAINT-generated GAF file
Samples are avilable for download here:
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.