Abstract
Owing to the recent advances in technology and to the growth in the number and size of projects tasked with collecting and assembling biological and genomic information, a highly heterogeneous collection of databases have become available to the community in the last two decades. As a consequence of rapid and distributed progress throughout the field, bioinformatics databases are provided in a variety of formats and specifications. This chapter discusses the most frequently encountered data formats in bioinformatics and the tools used to access these data.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aho A, Hopcroft JE, Ullman J (1986) Compilers: Principles, techniques, and tools. Addison-Wesley, Reading
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
Appel A (1998) Modern compiler implementation in C. Cambridge University Press, New York
BioPerl (http://www.bioperl.org)
Stajich et al (2002) The bioperl toolkit: Perl modules for the life sciences, Genome Res (12):1611–1618
Codd EF (1983) A relational model of data for large shared data banks. Commun ACM 26, 1 (Jan. 1983):64–69
The Document Object Model (http://www.w3c.org/DOM/)
Extensible Markup Language (XML) (2006) 1.0 (Fourth Edition). W3C Recommendation, March 2006 (http://www.w3.org/TR/REC-xml/)
The Gene Ontology Consortium (2000) Gene Ontology: Tool for the unification of biology. Nature Genet 25:25–29
GNU Bison (http://www.gnu.org/software/bison/)
Grune D, Jacobs CJH (1990) Parsing techniques – A practical guide. Ellis Horwood, Chichester, England (http://www.cs.vu.nl/∼dick/PTAPG.html)
Higgins DG, Sharp PM (1988) CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene 73:237–244
Hubbard TJP, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y et al (2007) Ensembl 2007. Nucleic Acids Res 35, Database issue:D610–D617
IUPAC-IUB Joint Commission on Biochemical Nomenclature (1984) Nomenclature and symbolism for amino acids and peptides. Recommendations. Eur J Biochem 138:9–37
OWL Web Ontology Language Reference (1999) W3C Recommendation November 1999 (http://www.w3.org/TR/owl)
Rice P, Longden I, Bleasby A (2000) EMBOSS: The European molecular biology open software suite. Trends Genet 16(6):276–277
The European Bioinformatics Institute (http://www.ebi.ac.uk/)
The UniProt Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res 36:D190–D195
The World-Wide-Web Consortium (http://www.w3c.com/)
XML (1999) Path Language (XPath). W3C Recommendation, November 1999 (http://www.w3.org/TR/xpath)
XQuery 1.0: An XML Query Language. W3C Recommendation January 2007 (http://www.w3.org/TR/xquery/)
XSL Transformations (XSLT) (1999) Version 1.0. W3C Recommendation November 1999 (http://www.w3.org/TR/xslt)
W3C Semantic Web Activity (http://www.w3.org/2001/sw)
Wall L, Christiansen T, Orwant J (2000) Programming Perl. O’Reilly & Associates, Inc.
Wilkinson M, Links M (2002) BioMOBY: An open source biological web services proposal. Brief Bioinformatics 3(4):331–341
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Damian, D. (2009). Data and Databases. In: Edwards, D., Stajich, J., Hansen, D. (eds) Bioinformatics. Springer, New York, NY. https://doi.org/10.1007/978-0-387-92738-1_18
Download citation
DOI: https://doi.org/10.1007/978-0-387-92738-1_18
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-92737-4
Online ISBN: 978-0-387-92738-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)