Database The Journal of Biological Databases and Curation

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

Current impact factor: 3.37

Impact Factor Rankings

2015 Impact Factor Available summer 2016
2014 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)

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author cannot archive a post-print version
  • Conditions
    • Creative Commons Attribution License
    • Pre-print on author's personal website, employers website or subject repository
    • Pre-print can only be posted prior to acceptance
    • Pre-print must be accompanied by set statement (see link)
    • Pre-print must not be replaced with post-print, instead a link to published version with amended set statement should be made
    • Post-print in Institutional repositories or Central repositories
    • Publisher's version/PDF must be used
    • Publisher's version/PDF on institutional repository or centrally organised repositories
    • Published source must be acknowledged
    • Must link to publisher version
    • Set phrase to accompany archived copy (see policy)
    • 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: 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.
    Database The Journal of Biological Databases and Curation 03/2015; 2015. DOI:10.1093/database/bav023
  • Source
    [Show abstract] [Hide abstract]
    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.
    Database The Journal of Biological Databases and Curation 02/2015; 2015. DOI:10.1093/database/bav004
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Spermatogenic failure is a major cause of male infertility, which affects millions of couples worldwide. Recent discovery of long non-coding RNAs (lncRNAs) as critical regulators in normal and disease development provides new clues for delineating the molecular regulation in male germ cell development. However, few functional lncRNAs have been characterized to date. A major limitation in studying lncRNA in male germ cell development is the absence of germ cell-specific lncRNA annotation. Current lncRNA annotations are assembled by transcriptome data from heterogeneous tissue sources; specific germ cell transcript information of various developmental stages is therefore under-represented, which may lead to biased prediction or fail to identity important germ cell-specific lncRNAs. GermlncRNA provides the first comprehensive web-based and open-access lncRNA catalogue for three key male germ cell stages, including type A spermatogonia, pachytene spermatocytes and round spermatids. This information has been developed by integrating male germ transcriptome resources derived from RNA-Seq, tiling microarray and GermSAGE. Characterizations on lncRNA-associated regulatory features, potential coding gene and microRNA targets are also provided. Search results from GermlncRNA can be exported to Galaxy for downstream analysis or downloaded locally. Taken together, GermlncRNA offers a new avenue to better understand the role of lncRNAs and associated targets during spermatogenesis. Database URL:
    Database The Journal of Biological Databases and Curation 01/2015; 2015:bav044-bav044. DOI:10.1093/database/bav044
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Compared with animal microRNAs (miRNAs), our limited knowledge of how miRNAs involve in significant biological processes in plants is still unclear. AtmiRNET is a novel resource geared toward plant scientists for reconstructing regulatory networks of Arabidopsis miRNAs. By means of highlighted miRNA studies in target recognition, functional enrichment of target genes, promoter identification and detection of cis- and trans-elements, AtmiRNET allows users to explore mechanisms of transcriptional regulation and miRNA functions in Arabidopsis thaliana, which are rarely investigated so far. High-throughput next-generation sequencing datasets from transcriptional start sites (TSSs)-relevant experiments as well as five core promoter elements were collected to establish the support vector machine-based prediction model for Arabidopsis miRNA TSSs. Then, high-confidence transcription factors participate in transcriptional regulation of Arabidopsis miRNAs are provided based on statistical approach. Furthermore, both experimentally verified and putative miRNA-target interactions, whose validity was supported by the correlations between the expression levels of miRNAs and their targets, are elucidated for functional enrichment analysis. The inferred regulatory networks give users an intuitive insight into the pivotal roles of Arabidopsis miRNAs through the crosstalk between miRNA transcriptional regulation (upstream) and miRNA-mediate (downstream) gene circuits. The valuable information that is visually oriented in AtmiRNET recruits the scant understanding of plant miRNAs and will be useful (e.g. ABA-miR167c-auxin signaling pathway) for further research. Database URL: © The Author(s) 2015. Published by Oxford University Press.
    Database The Journal of Biological Databases and Curation 01/2015; 2015. DOI:10.1093/database/bav042
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. The BioXpress database includes expression data from 64 cancer types, 6361 patients and 17 469 genes with 9513 of the genes displaying differential expression between tumor and normal samples. In addition to data directly retrieved from RNA-seq data repositories, manual biocuration of publications supplements the available cancer association annotations in the database. All cancer types are mapped to Disease Ontology terms to facilitate a uniform pan-cancer analysis. The BioXpress database is easily searched using HUGO Gene Nomenclature Committee gene symbol, UniProtKB/RefSeq accession or, alternatively, can be queried by cancer type with specified significance filters. This interface along with availability of pre-computed downloadable files containing differentially expressed genes in multiple cancers enables straightforward retrieval and display of a broad set of cancer-related genes. Database URL: © The Author(s) 2015. Published by Oxford University Press.
    Database The Journal of Biological Databases and Curation 01/2015; 2015. DOI:10.1093/database/bav019
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Functional annotation of genetic variants including single nucleotide polymorphisms (SNPs) and copy number variations (CNV) promises to greatly improve our understanding of human complex traits. Previous transcriptomic studies involving individuals from different global populations have investigated the genetic architecture of gene expression variation by mapping expression quantitative trait loci (eQTL). Functional interpretation of genome-wide association studies (GWAS) has identified enrichment of eQTL in top signals from GWAS of human complex traits. The SCAN (SNP and CNV Annotation) database was developed as a web-based resource of genetical genomic studies including eQTL detected in the HapMap lymphoblastoid cell line samples derived from apparently healthy individuals of European and African ancestry. Considering the critical roles of epigenetic gene regulation, cytosine modification quantitative trait loci (mQTL) are expected to add a crucial layer of annotation to existing functional genomic information. Here, we describe the new features of the SCAN database that integrate comprehensive mQTL mapping results generated in the HapMap CEU (Caucasian residents from Utah, USA) and YRI (Yoruba people from Ibadan, Nigeria) LCL samples and demonstrate the utility of the enhanced functional annotation system. Database URL: © The Author(s) 2015. Published by Oxford University Press.
    Database The Journal of Biological Databases and Curation 01/2015; 2015. DOI:10.1093/database/bav025