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

A Taxonomic Search Engine: federating taxonomic databases using web services

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A Taxonomic Search Engine: federating taxonomic databases using web services

Roderic D M Page. BMC Bioinformatics..

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.

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Figure 1
Figure 1
Architecture of the Taxonomic Search Engine.The user's query is passed to each database using either the HTTP GET protocol or SOAP, and the results (which may be in XML format, delimited text, or a SOAP data structure) are combined and returned as an XML document.
Figure 2
Figure 2
Screen shot of the Taxonomic Search Engine.The web browser displays the results of searching for a name in five external databases. For each database that returns a "hit" the page displays some information about that name. The user can click on the name to obtain further information about the name, including a link to the original database record, and a Life Science Identifier (LSID) for that record.
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References

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