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BioDB extractor: customized data extraction system for commonly used bioinformatics databases
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, d...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624652/ https://www.ncbi.nlm.nih.gov/pubmed/26516349 http://dx.doi.org/10.1186/s13040-015-0067-z |
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author | Karbhal, Rajiv Sawant, Sangeeta Kulkarni-Kale, Urmila |
author_facet | Karbhal, Rajiv Sawant, Sangeeta Kulkarni-Kale, Urmila |
author_sort | Karbhal, Rajiv |
collection | PubMed |
description | 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. AVAILABILITY: BDE can be accessed from http://bioinfo.net.in/BioDB/Home.html. |
format | Online Article Text |
id | pubmed-4624652 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-46246522015-10-30 BioDB extractor: customized data extraction system for commonly used bioinformatics databases Karbhal, Rajiv Sawant, Sangeeta Kulkarni-Kale, Urmila BioData Min Research 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. AVAILABILITY: BDE can be accessed from http://bioinfo.net.in/BioDB/Home.html. BioMed Central 2015-10-28 /pmc/articles/PMC4624652/ /pubmed/26516349 http://dx.doi.org/10.1186/s13040-015-0067-z Text en © Karbhal et al. 2016 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Karbhal, Rajiv Sawant, Sangeeta Kulkarni-Kale, Urmila BioDB extractor: customized data extraction system for commonly used bioinformatics databases |
title | BioDB extractor: customized data extraction system for commonly used bioinformatics databases |
title_full | BioDB extractor: customized data extraction system for commonly used bioinformatics databases |
title_fullStr | BioDB extractor: customized data extraction system for commonly used bioinformatics databases |
title_full_unstemmed | BioDB extractor: customized data extraction system for commonly used bioinformatics databases |
title_short | BioDB extractor: customized data extraction system for commonly used bioinformatics databases |
title_sort | biodb extractor: customized data extraction system for commonly used bioinformatics databases |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624652/ https://www.ncbi.nlm.nih.gov/pubmed/26516349 http://dx.doi.org/10.1186/s13040-015-0067-z |
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