About e-Species

This is a pure Python CGI-based implementation of a taxonomically intelligent species search engine. It searches biological databases for a taxonomic name. The search is done "on the fly" using web services (SOAP/XML) or URL API's.

Classification

Synonyms and higher taxa for a taxon name are retrieved using the Catalogue of Life Web Service

Description

Display of snippets from Wikipedia articles makes use of a Dapper transform. A link to the original article is also displayed.

Keywords

Keyword extraction uses the Term Extraction service from FiveFilters.org for extracting terms from the contents of Wikipedia articles.

Genomics

Queries to NCBI are performed using the Entrez Programming Utilities. The ESearch tool is used to look up a taxon name and, if the name is found, the ESummary tool is called to get basic statistics on what NCBI holds for that taxon. Links to external information resources for the taxon are retrieved using the Elinktool.

Maps

Distribution maps for a taxon are retrieved from GBIF using code inspired in the Species Distribution Widget written by Tim Robertson and Dave Martin.

Images

Google Images is used to find up to five images for the query term.

Documents

Documents are retrieved from Google Scholar. The script extracts references by screen scraping, since Google has not released any API for Google Scholar.

Related Projects

Rod Page has written the original iSpecies taxonomically-based search engine, that also uses web services David Shorthouse has written an iSpecies Clone, that uses JSON.

Source Code

The e-Species search engine has been developed on an IBM-PC compatible machine running Linux Ubuntu 8.04 Hardy Heron and Python 2.5

The e-Species source code is released under the terms of the GNU General Public License, and is available from SourceForge.

News

Todo

Acknowledgements

Thanks to Rod Page for his implementation tips on the iSpecies Blog and overall inspiration, to Edinaldo Nelson dos Santos-Silva and Projeto Biotupé for continuing support, to Eduardo Dalcin for crash testing and pointing out several flaws, to Flavio Coelho and other members of the PyScience-Brasil discussion list for support and constructive comments, and to Douglas Soares de Andrade for providing patches and creating an svn trunk for the e-Species source code.

Contact

Send comments and suggestions to Mauro J. Cavalcanti