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