December 15, 2010

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item 1 - BioGRID
What BioGRID is doing.
Standardization and usage of terms to describe interactions

item 2 - Database Display Changes For Interactions
Current changes?
See attached .ppt slides 1-3 in documents distributed section
Future Changes?
Remove interaction based phenotypes from existing tables-→ new table

item 3 - Interaction Model (slides 4-5, attached .ppt in documents distributed section)
What do we need to capture that we don’t??? ----Missing tag?
Easy change ---→ other_interactor tag w/ text field
Complicated changes???????

Documents Distributed



item 1 – BioGRID
  1. Gary S named as contact person for BioGRID curators.
  2. Chris and Gary will try to map WormBase interaction types to BioGRID interaction types and figure out what the difficulties will be.

item 2 - Database Display Changes For Interactions

Gary will submit a BitBucket ticket (submitted on 12/16/10 – Issue 471) that will outline the changes we initially want to make to the web display of interactions.

The changes are as follows:

  1. Changes to Interaction Summary (Table linked from Gene Page)
    • Reorder the current columns and include a column for phenotypes.
    Currently it lists the following in the following order : interaction ID / type / interactor 1 / interactor 2 / Effector to effected
    We would like it to have to following in the following order: interactor 1 / interactor 2 / Effector to effected/ type / Interaction based phenotype / interaction ID.
    Many interactions currently will not have a phenotype attached, but this will change in the near future.
    • Currently the table is listed in numerical order according to ID.
    We would like to have all the predicted interactions listed last and all other types preceding them. The order of the other types is not so important, but it would be nice if all of a similar type were grouped (i.e. all genetic ints are together, all suppression ints are together etc.)
  2. Interaction Summary for WBInteractionobjects
    • We would like to add the following information to the “interaction summary” section: Remark and RNAi ID.
    • We would like the phenotype to be displayed and not just listed as “interaction_phenotype”
    • In addition we would like to re-order this section as follows:
RNAi Report:

item 3 - Interaction Model (slides 4-5, attached .ppt in documents distributed section)
  1. No model changes proposed at this time to deal with interaction objects that cannot be assigned a WBGene ID. These are things like transgenes that contain human genes that are used in an experiment. They cannot get an “interactor” tag as a ?Gene is necessary. For now we will enter these into the Ontology Annotator (OA) for interactions into a new field called Effected/Effector Other (for more details, please refer to ggi_OA). These will be dumped into the remark section for the interaction object. When we accumulate enough of these, we can figure out what model changes need to be made to accommodate them to make them “real” database objects.