Pathway Curation: An Upcoming Area in Bioinformatics

With the current boom in information technology, we see its application in almost every aspect of our life. “Bioinformatics” is the subject, which deals with the application of information technology in the field of biology, for example usage of computing power for drug designing, protein modeling, sequencing genomes and proteins and so on. Pathway curation is one branch/part of bioinformatics. A pathway is a representation of a set of related reactions in a given context, i.e. glycolysis, Krebs cycle or apoptosis [1].

Because of extensive research, with tools like High-throughput genomics and DNA microarrays, researchers have accumulated high volumes of data that are often too large for manual assessment. Mathematical and statistical analysis can be done to structure the large data volumes. Based on various computational algorithms, the tool generates pathways along with pictorial representations for easy understanding.

Significant biological reactions are more lucid when projected on pathway diagrams rather than being represented in the form of a large set of tabular data. Generally a biological pathway diagram is used to describe molecular biology processes in a graphical way.

This new area of pathway representation has created the role of a “Biocurator”.

Biocurators (also called scientific curators, data curators or annotators) are also recognized as the "museum catalogers of the Internet age". As a Biocurator He/She should be able to capture and integrate the knowledge from various sources such as databases and scientific literature into a pathway. The Biocurator should also support the data with relevant annotations and make this scientific data accessible to the scientific community.

Multiple programs should be able to access the pathway diagrams and information in a sharable format to facilitate its use in research tool. Apart from this in a pathway diagram the pathway entities (like proteins, small molecules, lipid molecules etc) and the relation between the entities have to be made explicit. To make a pathway user friendly various proteins/metabolites involved in the pathway should be connected to a database entry. This entry should be linked to the experimental evidence from scientific literature which details about the function and interactions of these particular proteins/metabolites with other proteins in the pathway. The types of modifications (for e.g., phosphorylation, glycosylation, acetylation etc) taking place during any biological process can also be represented with proper experimental support from scientific literature. The pathway should be treated as an interacting network wherein the reactions between metabolites or gene products are represented. The pathway, in general shows various reactions taking place gradually in response to external stimuli. This ultimately leads to either activation or repression of a set of genes resulting into phenotypic changes which is of a common interest to researchers, academicians, doctors etc.

The collaboration between authors, journals and biocurators will facilitate the exchange of data between journal publications and databases and in turn make the signaling pathways, metabolic pathways, disease pathways etc a readymade tool to every biologist. Combined effort of Biocurators, researchers, academic institutions and funding agencies will promote Biocuration as a professional career. A better understanding of the pathways will help the pharmaceutical companies to design new drugs and academicians and research personals to carry out research in new areas.

References

[1] Waagmeester AS, Kelder T, Evelo CT. The role of bioinformatics in pathway curation. Genes & nutrition 2008 Dec;3(3-4):139-42.