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Applying Swanson's ABC model to stored interaction data, we produced new possible interaction candidates.
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An "interaction browser" lists DNA baits and TFs for which interactions are available and facilitates the retrieval of stored interactions.
By selecting 'all' in either both or only one of the gene selection boxes, users can search for all stored interactions either of the whole database or in which a specific gene of interest is involved.
This database stores interaction between atoms as structural interaction fingerprints as implemented by Deng et al.
Since then, a plethora of protein-ligand interaction databases has been developed not only to store the interaction data but also to enable scientists to mine it efficiently (7 9).
A triple was stored for each interaction, including both interacting nodes and the type of interaction between them.
Each edge contains a matrix that stores an interaction score for each combination of modes of its two incident nodes.
Other HUPO-PSI formats are PSI-MI [37] for storing molecular interaction data and PSI-PAR [38], a format for describing Protein Affinity Reagents.
A number of experiments which depict PPI networks of living organism have been finished and a number of datasets such as MINT [ 5], BIND [ 6], and DIP [ 7] have been built to store proteins interaction data.
At the same time, a number of databases, such as Gavin [ 7], Krogan [ 8], Collins [ 9], DIP [ 10], and BioGRID [ 11], have been created to store protein interaction information in structured and standard formats.
In addition to the default InterMine Interaction class that was employed for storing biomolecular interactions from the BioGRID database [44], we designed a new ProteinInteraction class to collate all interactions curated in PPIview, an integrated repository of human PPIs [45].
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