Manager 9Jun10

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Present: David, Judy, Suzi, Rama, Pascale, Emily

Minutes: Emily

PAINT gene association files

1. Appropriate DB:Reference display.

-- Annotation groups need a valid reference type to display for each annotation they integrate.

-- Suzi: Panther reference ids should become a valid Reference type, alongside PMIDs, GO_REFs and DOIs. This would mean that a Panther id would be used to generate a resolvable URL that can supply an abstract describing the precise conditions used in generating the annotation.

-- Suzi: However, software development work will be needed to put in place this system.

-- In the meantime, GO_REF:0000033 will be added into the DB:Reference field for each PAINT annotation, to allow GO annotation groups to load PAINT annotations.

-- Groups however will need to swtich from GO_REF:33 to these Panther IDs when the system is in place.

ACTION: PAINT group to supply their gene association files with GO_REF:0000033 in the db_reference field.

2. Appropriate with field display.

-- Groups are concerned with the length of the with field that appear for some PAINT annotations. This is a particular concern when trying to display PAINT annotations in a MOD GO annotation browser.

-- Pascale/Suzi: All the information in this field is important, we are unwilling to reduce the contents of the with field

-- Browsers should work out a display mechanism that enables a neat display, and yet provides the option of displaying all of the ids that are provided in this field (this could be a truncation of the with field at a certain point, and then linking out/providing a pop-up box to provide the remainder of this data)

-- How groups approach this data display issue is up to them.

-- However, the Panther ID in the with field should be sorted so that it is displayed first.

ACTION: PAINT group to resort their with field, so that the Panther ID appears first in the list.

The AmiGO display of References

-- the current AmiGO display shows MOD internal reference identifiers for annotations.

-- however should the public reference (either the PMID or GO_REF) be considered the principal reference for an annotation?

-- there are advantages that the display of the MOD reference increases traffic to MOD databases (whereupon the PMID is displayed), and it may have been a consistency issue - as MODs will always display an internal reference, even if no public reference available.

ACTION: Rama to add this to the AmiGO working group agenda to discuss further.

New Reference Genome targets

Pascale: annotation targets related to the Wnt pathway will be the next RefGen annotation project. Working with Varsha to get this list ready.