Database The Journal of Biological Databases and Curation

Publisher: Oxford Journals (Firm), Oxford University Press (OUP)

Current impact factor: 3.37

Impact Factor Rankings

2016 Impact Factor Available summer 2017
2014 / 2015 Impact Factor 3.372
2013 Impact Factor 4.457
2012 Impact Factor 4.2
2011 Impact Factor 2.071

Impact factor over time

Impact factor

Additional details

5-year impact 4.51
Cited half-life 3.20
Immediacy index 0.61
Eigenfactor 0.01
Article influence 1.68
Other titles Journal of biological databases and curation
ISSN 1758-0463
OCLC 319891682
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Oxford University Press (OUP)

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    • Creative Commons Attribution License
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    • Eligible authors may deposit in OpenDepot
    • Publisher will deposit on behalf of NIH, HHMI, UK MRC, Telethon and Wellcome Trust funded authors to PubMed Central and Europe PMC
    • All titles are open access journals
    • Progress of Theoretical and Experimental Physics is a participant in SCOAP3
    • This policy is an exception to the default policies of 'Oxford University Press (OUP)'
  • Classification

Publications in this journal

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The ever-growing amount of data in the field of life sciences demands standardized ways of high-throughput computational analysis. This standardization requires a thorough documentation of each step in the computational analysis to enable researchers to understand and reproduce the results. However, due to the heterogeneity in software setups and the high rate of change during tool development, reproducibility is hard to achieve. One reason is that there is no common agreement in the research community on how to document computational studies. In many cases, simple flat files or other unstructured text documents are provided by researchers as documentation, which are often missing software dependencies, versions and sufficient documentation to understand the workflow and parameter settings. As a solution we suggest a simple and modest approach for documenting and verifying computational analysis pipelines. We propose a two-part scheme that defines a computational analysis using a Process and an Analysis metadata document, which jointly describe all necessary details to reproduce the results. In this design we separate the metadata specifying the process from the metadata describing an actual analysis run, thereby reducing the effort of manual documentation to an absolute minimum. Our approach is independent of a specific software environment, results in human readable XML documents that can easily be shared with other researchers and allows an automated validation to ensure consistency of the metadata. Because our approach has been designed with little to no assumptions concerning the workflow of an analysis, we expect it to be applicable in a wide range of computational research fields.Database URL: © The Author(s) 2015. Published by Oxford University Press.
    Full-text · Article · Jun 2015 · Database The Journal of Biological Databases and Curation
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    ABSTRACT: CerebralWeb is a light-weight JavaScript plug-in that extends Cytoscape.js to enable fast and interactive visualization of molecular interaction networks stratified based on subcellular localization or other user-supplied annotation. The application is designed to be easily integrated into any website and is configurable to support customized network visualization. CerebralWeb also supports the automatic retrieval of Cerebral-compatible localizations for human, mouse and bovine genes via a web service and enables the automated parsing of Cytoscape compatible XGMML network files. CerebralWeb currently supports embedded network visualization on the InnateDB ( and Allergy and Asthma Portal ( database and analysis resources. Database tool URL: © The Author(s) 2015. Published by Oxford University Press.
    Full-text · Article · May 2015 · Database The Journal of Biological Databases and Curation
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    ABSTRACT: Besides its important significance in plant taxonomy and phylogeny, sacred lotus (Nelumbo nucifera Gaertn.) might also hold the key to the secrets of aging, which attracts crescent attentions from researchers all over the world. The genetic or molecular studies on this species depend on its genome information. In 2013, two publications reported the sequencing of its full genome, based on which we constructed a database named as LOTUS-DB. It will provide comprehensive information on the annotation, gene function and expression for the sacred lotus. The information will facilitate users to efficiently query and browse genes, graphically visualize genome and download a variety of complex data information on genome DNA, coding sequence (CDS), transcripts or peptide sequences, promoters and markers. It will accelerate researches on gene cloning, functional identification of sacred lotus, and hence promote the studies on this species and plant genomics as well. Database URL: © The Author(s) 2015. Published by Oxford University Press.
    Full-text · Article · Mar 2015 · Database The Journal of Biological Databases and Curation
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    ABSTRACT: Mulberry has been used as an economically important food crop for the domesticated silkworm for thousands of years, resulting in one of the oldest and well-known plant-herbivore interactions. The genome of Morus notabilis has now been sequenced and there is an opportunity to mine the transposable element (TE) data. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database, MnTEdb, was constructed. It was built based on a detailed and accurate identification of all TEs in mulberry. A total of 5925 TEs belonging to 13 superfamilies and 1062 families were deposited in this database. MnTEdb enables users to search, browse and download the mulberry TE sequences. Meanwhile, data mining tools, including BLAST, GetORF, HMMER, Sequence Extractor and JBrowse were also integrated into MnTEdb. MnTEdb will assist researchers to efficiently take advantage of our newly annotated TEs, which facilitate their studies in the origin, amplification and evolution of TEs, as well as the comparative analysis among the different species. Database URL: © The Author(s) 2015. Published by Oxford University Press.
    Full-text · Article · Feb 2015 · Database The Journal of Biological Databases and Curation