Resolving Taxonomic Names · Kylepedia

Resolving Taxonomic Names

Details

Title: The taxonomic name resolution service: an online tool for automated standardization of plant names

Citation: Boyle, Brad, et al. “The taxonomic name resolution service: an online tool for automated standardization of plant names.” BMC bioinformatics 14.1 (2013): 16.

Web interface: http://www.iplantcollaborative.org/ci/tnrs

Source code: https://github.com/iPlantCollaborativeOpenSource/TNRS/

Overview

This tool looks to be very promising for resolving the incorrect taxonomic names in the 16S databases that we are using. It was created to resolve plant names, but the source code is available on Github. The authors stress repeatedly that it could be adapted for non-plant taxonomies. Furthermore, the algorithm looks to be quite robust, and uses multiple methods of identifying and correcting errors.

Description

Types of resolved problems

Supports the combining of different external taxonomic sources. We might consider doing this to resolve differences between rRNA dbs (eg: SILVA, Greengenes), but the authors advise against this. They recommend assigning a priority to one source over another.

NOTE: The authors advise against using the NCBI taxonomy due to poor quality1

Technical Details

Database

Algorithm

Pre-Processing

Name parsing

Fuzzy Matching

Post-Processing

Interface

Other Tools

Tropicos

Catalog of Life

Global Names Resolver

Software Requirements

Some Thoughts

This looks very promising for our purposes. I think we could adapt this to be used for bacteria. A potential problem could be the different languages used. I haven’t used Java recently, and am unfamilar with PHP and Ruby. I took a databse course in college, but we only covered basic SQL commands, so I haven’t actually created a database myself

1: iPhylo

2: sourcecode