Annotation Conf. Call, August 14, 2012

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Present

Rama, Dianna, Rachael, Prudence, Li, Midori, Doug, Becky, Chris, Antonia, Ruth, Kalpana (SGD developer)

Agenda

1. GO Mine presentation (Rama)

  • Tour of GOMine beta: http://gomine.stanford.edu:8080/gomine/templates.do
    • GOmine is powered by InterMine developed by Gos Micklem.
    • Stores data in denormalized precomputed tables (postgreSQL)
    • It allows to search and retrieve GO data using a query interface. You don't need to know formal sqlplus language to query.
    • Easy to make lists, results can be customized
    • For the beta release, GO annotations from the GAF files have been loaded.

Discussion

  • Chris- Is it possible to traverse through the ECO and retrieve all Experimental annotations?
    • Kalpana, Rama- We haven't loaded the ECO yet. All the data come from the GAF. But this should be possible as long as there is a way to map the codes.
  • Chris- Can Col-16 data be loaded? Yes, it can be. The current GO loading parser has to be fixed to load col-16. It can be done.
    • Kalpana will look into modifying the script.
    • Doug- Can the modified script be made available to the ModMines also? Yes, Kalpana can change the script and check it in.
  • Rama will contact curators at individual groups to test GOMine.
  • YeastMine/SGD made several 2 min video tutorials to educate users (http://www.yeastgenome.org/help/video-tutorials/yeastmine). Since the basic concept of using templates/lists are the same between YeastMine and GOMine, curators can see these videos to get familiar with GOMine features.