super_curator

Video Tip of the Week: Complex Portal with Super Curators

From the same team that brings us the IntAct database for protein interaction data, the Complex Portal offers insights for additional levels of protein interactions that are organized around a biological function. Although there are various resources that store individual interactions between proteins, collecting additional interactions in units of a complex are specially challenging for various reasons–both technical and computational.

The introduction part of this recent webinar from the Complex Portal team establishes definitions for PPI (protein-protein interactions) and PPIN (protein-protein interaction networks) and explores the difficulty of assessing and capturing information about which ones are part of complexes. In the Complex Portal database, the entries may consist of numerous individual studies of PPI that amalgamate into one set. About 6min they define complexes as “A stable set of (2 or more) interacting protein molecules which can be co-purified and have been shown to exist as a function unit in vivo.” Small molecules or nucleic acids might also be included if they are integral as well. Their complex calls are based on experimental evidence or they may be curator inferred.

super_curatorThey have a lot of source databases and curators from different groups, besides the IntAct data–most of them are familiar names such as MINT, SGD, Reactome, UniProt, etc. And most of their complex entries end up being the result of many papers. At ~5min, they describe their curation process. Their diagram includes my new favorite hero, “Super curator“. (We have always been huge fans of curators–the most undervalued resource in bioinformatics. Well, maybe trainers are too. Sometimes they are the same people.)

The species of focus are human, mouse, yeast, and E. coli, but they may have data on others as well. In the video they also talk about future plans if you want to know about other things they are doing. And they want to hear from you if there are complexes you think they should look at.

Additional training materials, and their paper (below), can help you to understand how to get the most out of their resources. I found the demo piece at the end helpful to locate specific examples of the features that were covered quickly in the slides, so be sure to hang on to the end of this video for that.

Quick links:

Complex Portal: http://www.ebi.ac.uk/intact/complex/

IntAct: http://www.ebi.ac.uk/intact/

Reference: 

Meldal, B., Forner-Martinez, O., Costanzo, M., Dana, J., Demeter, J., Dumousseau, M., Dwight, S., Gaulton, A., Licata, L., Melidoni, A., Ricard-Blum, S., Roechert, B., Skyzypek, M., Tiwari, M., Velankar, S., Wong, E., Hermjakob, H., & Orchard, S. (2014). The complex portal – an encyclopaedia of macromolecular complexes Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku975