A Taxonomic Search Engine: federating taxonomic databases using web services

BMC Bioinformatics. 2005 Mar 9:6:48. doi: 10.1186/1471-2105-6-48.

Abstract

Background: The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.

Results: The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name.

Conclusion: The Taxonomic Search Engine is available at http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

MeSH terms

  • Classification
  • Computational Biology / methods*
  • Computer Communication Networks
  • Database Management Systems
  • Databases as Topic
  • Databases, Factual*
  • Databases, Genetic
  • Databases, Protein
  • Information Dissemination
  • Information Services
  • Information Storage and Retrieval
  • Information Systems
  • Internet
  • Medical Informatics
  • National Institutes of Health (U.S.)
  • National Library of Medicine (U.S.)
  • Sequence Analysis, Protein
  • Software
  • Software Design
  • Systems Integration
  • Unified Medical Language System
  • United States
  • User-Computer Interface