Poster. 1 May 2013

1. EMBL-EBI Tel. +44 (0) 1223 494 444
Wellcome Trust Genome Campus comms@ebi.ac.uk
Hinxton, Cambridgeshire, CB10 1SD, UK www.ebi.ac.uk
Challenges in protein networks
representation and integration
the EMBL-EBI complexes project and the PSI-MI standards
Pablo Porras and Rafael C Jimenez
EMBL-EBI, Hinxton, Cambridge, CB10 1SD, United Kingdom
Data standardization with PSI-MI and
integration through PSICQUIC
Client
Query Interactions
PSICQUIC
Registry
PSI-MIMIQL
Input Output
PSICQUIC
Service A
PSICQUIC
Service B
PSICQUIC
Service C
User View
Web Service System
The production and study of molecular interaction networks is nowadays
a popular tool used to gain insight into cellular organization and as a
mean to add biological context and meaning to both small and large
scale data obtained through experimentation. However, the production
and visualization of biological interaction networks is challenged by
fundamental problems that have no easy solution.
Among the challenges that the study of interaction networks faces, we
can highlight the problem to produce an effective visualization of multi-
molecular entities such as protein complexes. Formed by several protein
subunits physically interacting between themselves, the researcher
faces the dilemma of having to represent either an oversimplification of
the complex renouncing to the detailed information about its constituent
parts or representing each subunit as a different entity and this way
increasing the already overwhelming complexity of a biological network.
At the EMBL-EBI we are working on a unified database of protein
complexes which will help to identify, represent and reference these
entities, providing a midway solution to this dilemma.
Another major problem the researcher faces when building molecular
interaction networks is the integration of data from different sources. We
are also working with the community on the PSI-MI standards to facilitate
access and integration of molecular interaction data. We provide an
ontology (PSI-MI CV), several formats (PSI-MI XML and PSI-MITAB),
minimun information guidelines (MIMIx and IMEx) and a common query
interface for computational access to molecular-interaction data
resources (PSICQUIC). Text, Arial 31pt
Work supported by
NHLBI Proteomics Center Award (HHSN268201000035C)
http://www.nhlbi-ucla.org/
https://code.google.com/p/psicquic/
Main challenges representing protein complexes
Other challenges representing protein interactions and complexes
• Data integration from other related domains
• Present protein domain interactions
• Visualize dynamic interactions
• Visualize the internal topology of a complex
• Present the interaction the complex in the context of a protein interaction network
• Subcomplexes