title: BioDB extractor: customized data extraction system for commonly used bioinformatics databases.
abstract: BACKGROUND
  Diverse types of biological data, primary as well as derived, are available in various formats and are stored in heterogeneous resources. Database-specific as well as integrated search engines are available for carrying out efficient searches of databases. These search engines however, do not support extraction of subsets of data with the same level of granularity that exists in typical database entries. In order to extract fine grained subsets of data, users are required to download complete or partial database entries and write scripts for parsing and extraction.
  
  
  RESULTS
  BioDBExtractor (BDE) has been developed to provide 26 customized data extraction utilities for some of the commonly used databases such as ENA (EMBL-Bank), UniprotKB, PDB, and KEGG. BDE eliminates the need for downloading entries and writing scripts. BDE has a simple web interface that enables input of query in the form of accession numbers/ID codes, choice of utilities and selection of fields/subfields of data by the users.
  
  
  CONCLUSIONS
  BDE thus provides a common data extraction platform for multiple databases and is useful to both, novice and expert users. BDE, however, is not a substitute to basic keyword-based database searches. Desired subsets of data, compiled using BDE can be subsequently used for downstream processing, analyses and knowledge discovery.
  
  
  BACKGROUND
  BDE can be accessed from http://bioinfo.net.in/BioDB/Home.html.
authors.affiliation: Bioinformatics Centre, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007 Maharashtra India.
authors.forename: Rajiv
authors.initials: R
authors.lastname: Karbhal
authors.affiliation: Bioinformatics Centre, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007 Maharashtra India.
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Sawant
authors.affiliation: Bioinformatics Centre, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007 Maharashtra India.
authors.forename: Urmila
authors.initials: U
authors.lastname: Kulkarni-Kale
keywords: Bioinformatics; Biological databases; Customized data retrieval; Data integration; Database cross-linking