BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform

J Integr Bioinform. 2018 Mar 16;15(3):20170072. doi: 10.1515/jib-2017-0072.

Abstract

BIOchemical PathwaY DataBase is developed as a manually curated, readily updatable, dynamic resource of human cell specific pathway information along with integrated computational platform to perform various pathway analyses. Presently, it comprises of 46 pathways, 3189 molecules, 5742 reactions and 6897 different types of diseases linked with pathway proteins, which are referred by 520 literatures and 17 other pathway databases. With its repertoire of biochemical pathway data, and computational tools for performing Topological, Logical and Dynamic analyses, BIOPYDB offers both the experimental and computational biologists to acquire a comprehensive understanding of signaling cascades in the cells. Automated pathway image reconstruction, cross referencing of pathway molecules and interactions with other databases and literature sources, complex search operations to extract information from other similar resources, integrated platform for pathway data sharing and computation, etc. are the novel and useful features included in this database to make it more acceptable and attractive to the users of pathway research communities. The RESTful API service is also made available to the advanced users and developers for accessing this database more conveniently through their own computer programmes.

Keywords: Computational Platform; Pathway Nomenclature and Ontology; Protein-Disease Mapping; Protein-Protein Interaction Data; RESTful API.

MeSH terms

  • Databases, Factual*
  • Gene Ontology
  • Genomics
  • Humans
  • Metabolic Networks and Pathways
  • Protein Interaction Mapping / methods*
  • Proteins / genetics
  • Proteins / metabolism
  • Software*
  • Systems Integration
  • User-Computer Interface

Substances

  • Proteins

Grant support

Dr. Ram Rup Sarkar is supported by grants from the Council of Scientific and Industrial Research, XII Five Year Plan Project “GENESIS” (Funder Id: 10.13039/501100001412) (BSC0121), “HOPE” (BSC0114) and the project from SERB, Ministry of Science and Technology, Government of India (Funder Id: 10.13039/501100001843, No. EMR/2016/000516 Dated 19-12-2016).