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

Text Snippets are fetched from Wikipedia articles. 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

Wikimedia Commons is used to find up to five images for the query term.

Documents

Documents are retrieved from PubMed. The script retrieves up to ten references for the query term.

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 originally 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

• Version 1.00, 29th Jun 08: Initial public release
• Version 1.01, 6th Jul 08: Added spelling suggestion from Yahoo! Spelling Suggestion service to provide a suggested spelling correction for a given name.
• Version 1.02, 10th Jul 08: Improved handling of synonym status and fixed a bug in spelling suggestion.
• Version 1.03, 11th Jul 08: Added a method to class COLSearch to check for the existence of a taxon name.
• Version 1.04, 31th Jul 08: Added automated tagging from Yahoo! Term Extraction for Wikipedia snippet.
• Version 1.05, 1st Aug 08: Added a method to class NCBISearch to return a list of external information resources for search name.
• Version 1.06, 11th Aug 08 - Added a function to strip out markup tags from Wikipedia snippet.
• Version 1.07, 05th Sep 08 - Fixed a bug in handling Unicode characters in the author of a taxon name returned from CoL
• Version 1.08, 09th Sep 08 - Renamed class YahooSearchImage to YahooSearch and added functions spellingSuggestion (renamed to spellCheck) and termExtraction (renamed to termExtract) as new methods.
• Version 1.09, 21th Oct 08 - Removed dependency of Set module, using tuple instead, and fixed a problem with the display image thumbnails from Yahoo search.
• Version 1.10, 19th Mar 09 - Rewrote class GoogleScholarSearch to removedependency of BeautifulSoup module, using a HTMLParser instead, and included a default value for class YahooSearch number of results
• Version 1.11, 25th Mar 09 - Improved handling of returned references from Google Scholar and rewrote class WikipediaSearch to make use of Dapper
• Version 1.12, 20th Jul 09 - Added some JavaScript for client-side search form validation
• Version 1.13, 21th Jul 09 - Added stylesheet for better form display and minor fixes
• Version 1.14, 14th Apr 10 - Adjusted for changes in CoL webservice calls
• Version 1.15, 29th Jul 11 - Removed Yahoo search class because of useless calls to deprecated Yahoo web services and substituted GoogleScholarSearch for a new GoogleSearch class to search from both Google Scholar and Google Images
• Version 1.16, 2nd Aug 11 - Improved Google Images search
• Version 1.17, 14th Jul 12 - Fixed a bug query string variable in class CoLSearch and updated URL to the latest Annual Checklist version website
• Version 1.18, 20th Sep 13 - Added new routine for retrieving images from Google and other minor improvements
• Version 1.19, 16th Aug 14 - Substituted a FiveFilters proxy webservice for deprecated calls to Yahoo! Search
• Version 1.20  22th Sep 14 - Fixed the FiveFilters webservice URL
• Version 1.30  30th Jan 19 - Removed class GoogleSearch and replaced it for a PubMedSearch class to get bibliographic references from PubMed. Added a method for #    fetching images from Wikimedia Commons to class WikipediaSearch. Restored dependency to BeautifulSoup
  

Todo

• Make use of synonyms in the searches, merging the results from searches using different names, and present those together (as suggested by Rod Page in the iPhylo Blog).
• Allow searches using common names

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 Flávio 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