News

ReachPathways – A free application to retrieve processes a protein functions in

Athulaprabha Murthi

Reachpathway
Reachpathway  

ReachPathways developed by the team of Babylakshmi M., Harsha Gowda and Joji Kurian at the Institute of Bioinformatics (IOB), Bangalore (http://​www​.ibioin​for​mat​ics​.org/) won the second prize in the competition Code for Science India (CFS) conducted by Elsevier. ReachPathways is a free application that can be downloaded from Science Direct (http://​www​.appli​ca​tions​.sci​verse​.com/​a​c​t​i​o​n​/​g​a​llery).

The application allows one to uncover all the pathways a protein/​gene might function in. Numerous papers are published in signaling on a regular basis and most proteins are involved in multiple pathways. But sometimes, proteins involved in say pathway A might be involved in say Pathway B only under certain conditions. It is hard to obtain such information via traditional Pubmed searches due to its unstructured format. The team of Babylakshmi M, Harsha Gowda and Joji Kurian Thomas felt that the Elsevier’s code for science competition provided the best platform to create an application that will structure and make sense of the plethora of information available for multiple genes and proteins.

ReachPathways, scans through research articles and identifies the names of proteins within the paper. It then extracts information from 5 different pathway resources – NetPath, Reactome, Wikipathways, STKE and NCI-PID. The pathways that your favourite gene/​protein functions in, is then reported in a tabular format. So instead of having to go through each of the resources available, a concise, summary of all the functionalities of the gene is provided enabling the researcher now to choose a process to concentrate on further.

IOB, where this team works, is a 10-year-old private institution that specializes in developing unique bioinformatics solutions. IOB developed the Human Protein Database – a comprehensive reference database widely used by those who work with human proteins (http://​www​.hprd​.org/FAQ). Based on their experience, they set upon an ambitious project of documenting each protein and linking it to the pathway it functions in, this database of pathways was named NetPath and it is one of the sources used by ReachPathways. At present, NetPath concentrates on Ligand Stimulated pathways such as the EGF pathway and has 25-curated signaling pathways (http://​www​.net​path​.org). The second phase is to involve functional pathways, such as glycolysis, fatty acid synthesis and similar ones, within the database.

At present, NetPath as well as ReachPathways only recognize protein names and essentially those that function in higher eukaryotes. The world of science though is not quite limited to these. Maybe, the team will consider in future to include the prokaryotic pathways. It would also be nice if RNA, especially the small-RNAs can be curated in terms of pathways – the world of small RNAs and their diverse functions are just as complex as those of the signaling molecules — a future direction perhaps.

Links:

Human Protein Database — http://​www​.hprd​.org/FAQ

ReachPathways — http://​www​.youtube​.com/​w​a​t​c​h​?​v​=​6​U​B​f​E​q​4Y7f8