All binary interactions evidences in the IntAct database, including those generated by Spoke expansion of co-complex data, are clustered to produce a non-redundant set of protein pairs. Each binary pair is then scored, using a simple addition of the cumulated value of a weighted score for the interaction detection method and the interaction type for each interaction evidence associated with that binary pair. Only experimental data is scored, inferred interactions, for example, would not be scored, and any low confidence data, or data manually tagged by a curator for exclusion from the process, are also not scored. Isoforms and post-processed protein chains are regarded as individual proteins for scoring purposes. Score weightings were determined using the PSI-MI CV.
Once the interactions have been scored, a cut-off filter of 9 has been established, below which the interaction is not exported to UniProtKB and to the Gene Ontology annotation files. Additional rules ensure that any protein pair scoring above 9 must also include at least one evidence of a binary pair, excluding spoke expanded data, before export to UniProtKB/GOA.
These criteria ensure that:
* Only experimental data is used for making the decision to export the protein pair to UniProtKB/GOA as a true binary interacting pair
* The export decision is always based on at least two pieces of experimental data. A single evidence cannot score highly enough to trigger an export
* An export cannot be triggered if the protein pair only ever co-occurs in larger complexes, there must be at least one evidence that the proteins are probably in physical contact.
IMEx will only call an interaction 'direct' when performed with 2 purified molecules in vitro so any method using whole cells or cell lysates would not be regarded as direct. The described methodology will give you binary i.e. either direct or involved in the same small complex.For more details, please see the corresponding entry on the the IntAct FAQ page.