Import of IMEx interactions into BioGRID REST Service.
1. PSI-MI2.5 XML files are downloaded from the three major IMEx partners, IntAct, MINT and DIP (ftp://ftp.ebi.ac.uk/pub/databases/IntAct/current/psi25 ftp://mint.bio.uniroma2.it/pub/release/psi/current/psi25/dataset/full.psi25. http://dip.doe-mbi.ucla.edu/dip/File.cgi?FN=2008/imex/dip_imex20081221CT2008.xml). Datasets are downloaded from IntAct and MINT monthly. The publicly available IMEx data at DIP was downloaded manually as login is required.
2. In order to map IMEx interactions to BioGRID evidence codes, the interactionDetectionMethod (MI:0001) field of the IMEx records was examined. Since there are hundreds of possible MI terms for this field we counted the frequency each term is used in the IMEx interactions and performed mapping for those terms with 20 or more interactions (from files downloaded on June 17, 2010) to BioGRID evidence codes; the mapping file is here. For some interactionDetectionMethod values an alternative BioGRID mapping is used if interactionType (MI:0190) is ‘direct interaction’ (MI:0407). For those interactionDetectionMethods which map to the Biogrid evidence code ‘Biochemical Activity’, a ‘Modification’ is also provided.
3. The rules used to create Biogrid binary interactions are as follows: For each interaction having an experimental method mappable to a BioGRID evidence code, one or more binary interactions are created according to the rules outlined in the table below.
|Biochemical Activity||Binary interactions are created between the interactor with biologicalRole “enzyme” (MI:0501) and each other interactor.|
|Affinity Capture-*||Binary interactions are created between the interactor with experimentalRole “bait” (MI:0496 ), and each other interactor. The evidence code is appended with the appropriate prey detection according to the value of participantIdentificationMethod (MI:0002) and the mapping here.|
|Others||Binary interactions are created between the interactor with experimentalRole “bait” (MI:0496 )or “fluorescence donor” (MI:0583), and each other interactor. If no interactor has one of these experimentalRoles, an arbitrary interactor is chosen as the bait.|
4. Imported IMEx interactions have been merged with Biogrid interaction data (in the BioGRID REST Service only, not in BioGRID download files) as follows: 1) If the IMEx interaction has the same Interactor A (bait), Interactor B (prey), Experimental System, Modification and Pubmed Id as an existing BioGRID interaction, the database containing the IMEx interaction is included in the Source Databases field of the BioGRID interaction. 2) If the IMEx interaction does not match an existing BioGRID interaction an interaction is created with a new Biogrid Interaction ID. Interactions not curated by BioGRID begin at Biogrid Interaction ID 20,000,000 and the interaction’s unique combination of values (Interactor A, Interactor B, Experimental System, Modification and Pubmed Id) is guaranteed always to have the same stable Biogrid Interaction ID (from 20,000,000). If , in a subsequent release of BioGRID, a BioGRID interaction matching one of the imported IMEx interactions is added, the imported interaction will be removed, and its source database and source database ID will be added to the appropriate field of the new BioGRID interaction.