MetaBase—the wiki-database of biological databases

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.

[1]  David S. Goodsell,et al.  The RCSB Protein Data Bank: redesigned web site and web services , 2010, Nucleic Acids Res..

[2]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[3]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[4]  John P. Overington,et al.  ChEMBL: a large-scale bioactivity database for drug discovery , 2011, Nucleic Acids Res..

[5]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..

[6]  Kevin A. Smith,et al.  The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research , 2011, J. Biomed. Informatics.

[7]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[8]  Alessio Lomuscio,et al.  Editorial , 2005, J. Appl. Log..

[9]  Paolo Romano,et al.  Interoperability of CABRI Services and Biochemical Pathways Databases , 2004, Comparative and functional genomics.

[10]  Mingming Jia,et al.  COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer , 2010, Nucleic Acids Res..

[11]  Antje Chang,et al.  BRENDA, the enzyme information system in 2011 , 2010, Nucleic Acids Res..

[12]  Carole A. Goble,et al.  BioCatalogue: a universal catalogue of web services for the life sciences , 2010, Nucleic Acids Res..

[13]  Cynthia S. Gadd,et al.  The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System—a one-stop gateway to online bioinformatics databases and software tools , 2006, Nucleic Acids Res..

[14]  Terri K. Attwood,et al.  The EMBRACE web service collection , 2010, Nucleic Acids Res..

[15]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[16]  David Osumi-Sutherland,et al.  FlyBase: enhancing Drosophila Gene Ontology annotations , 2008, Nucleic Acids Res..

[17]  Giorgio Valle,et al.  The Gene Ontology in 2010: extensions and refinements , 2009, Nucleic Acids Res..

[18]  Ioannis Xenarios,et al.  DIP: The Database of Interacting Proteins: 2001 update , 2001, Nucleic Acids Res..

[19]  Byungkyu Brian Park,et al.  HPID: The Human Protein Interaction Database , 2004, Bioinform..

[20]  Tim J. P. Hubbard,et al.  Data growth and its impact on the SCOP database: new developments , 2007, Nucleic Acids Res..

[21]  Tin Wee Tan,et al.  Towards BioDBcore: a community-defined information specification for biological databases , 2010, Database J. Biol. Databases Curation.

[22]  Yasunori Yamamoto,et al.  OReFiL: an online resource finder for life sciences , 2007, BMC Bioinformatics.

[23]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[24]  Ian Sillitoe,et al.  Extending CATH: increasing coverage of the protein structure universe and linking structure with function , 2010, Nucleic Acids Res..

[25]  Ibrahim Emam,et al.  ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments , 2010, Nucleic Acids Res..

[26]  Robert M. Buels,et al.  The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl , 2010, Nucleic Acids Res..

[27]  Tin Wee Tan,et al.  Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi) , 2010, BMC Genomics.

[28]  Trias Thireou,et al.  MetaBasis: a web-based database containing metadata on software tools and databases in the field of bioinformatics. , 2006, Applied bioinformatics.

[29]  Tanya Z. Berardini,et al.  The Arabidopsis Information Resource (TAIR): gene structure and function annotation , 2007, Nucleic Acids Res..

[30]  Steve Pettifer,et al.  BioXSD: the common data-exchange format for everyday bioinformatics web services , 2010, Bioinform..

[31]  Michael Y. Galperin,et al.  The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection , 2011, Nucleic Acids Res..

[32]  J McEntyre,et al.  PubMed: bridging the information gap. , 2001, CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne.

[33]  R. KNÜPPEL,et al.  TRANSFAC Retrieval Program: A Network Model Database of Eukaryotic Transcription Regulating Sequences and Proteins , 1994, J. Comput. Biol..

[34]  Kimberly Van Auken,et al.  WormBase 2007 , 2007, Nucleic Acids Res..