Manager 01August2012

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  • Tour of GOMine beta:
    • 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.
  • Can we confirm the dates and times for Pasadena meeting are fixed enough so European folks can book flights?



  • Question: Is the plan to replace AmiGO or GOOSE with GOMine?
  • A: Neither, this is another way to query GO data. All 3 interfaces will be available.
  • PaulT: We have to make sure the GO enrichment is done right (uses the correct annotations for the background, what evidence code is used etc). We should do some rigorous testing.
  • PaulD: The interface is not user friendly. Did SGD customize the interface? Is InterMine amenable to changing the interface?
  • Rama: We are aware that the UI is not friendly. SGD so far has changed the color scheme to match its website and is looking into changing the UI also. ZFin is working on the UI as well. We should be able to change it.
  • Rama: The software is flexible in that if we have new data (col-16 for example) we can load it into GOMine easily and unlike AmiGO and GOOSE we don't have to wait for the data to make it to the database.
  • Suzi: Mentioned that there are lot of nice features in Intermine that will be beneficial to GO users (especially the Lists functionality) and GOMine will serve our users.
  • PaulT: When we have it integrated in the GOC website we should recruit users to test. We should also make videos to educate users (more like If you want to do X do this etc).
  • Plan: Rama will give a tour of GOMine during the next Annotation Call, she will recruit people to test data retrieval and on UI. We will then make links from the main GOC site/AmiGO.

GOC meeting

Oct 7-9 dates are set for the next GOC meeting (@CalTech). We can book tickets/make travel plans.

NIH progress reports

The GO PIs will work on the second quarter progress report.