Glasgow Taxonomic Name Server

Developed by Rod Page

Home

Queries

• Find a name
• Find from id
• List synonyms
• Show classification
• Check names

Source

Links

Web service

Portal

Resolver buttons

Related projects

• ITIS
• Species2000
• uBio

Credits

Visualising big trees

• InfoVis 2003 Contest: Visualization and Pair Wise Comparison of Trees
• SpaceTree
• Tamara Munzner's H3Viewer

Tree queries in SQL

Miguel Sofer describes a clever way to combine SQL and string operations to query trees. You can get a copy of his notes and source from his web site, or download a local copy or read his draft manuscript. I use his approach in these queries.

Other links of interest

• Relational Modelling of Biological Data: Trees and Graphs (O'Reilly)
• Tree In Sql pattern
• Modelling Trees: Nested sets and adjacency lists

Approximate string matching

It would be nice to add a feature where if user type a taxon name and it is missplelt the database suggests an alternative (just like Google's "did you mean" feature). This can be done fairly simply by using agrep. Kevin A. McGrail's article "How-to build a better web-ring" suggests the following approach.

1. Create a text file list of names where each name is on the line corresponding to it's unique id in the database. If there is no name corresponding to a line number the line is blank.
2. Use agrep to search for names within some specified mismatch of the target name, and get agrep to output the line number of the hits, e.g. agrep -2 -n 'name' file.txt

These line numbers correspond to the id of the names in the database.

Agrep can be gotten by ftp from ftp://ftp.cs.arizona.edu/agrep/.