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Tools list Tools/Algorithms

Tools, algorithms and services developed by uBio.

Much of our recent (2005) development has focused on automated and machine-enhanced methods for locating, identifying, parsing, and mapping names and relationships among them. Some of these are listed below. Please refer to our tools menu and NameBank Admin Panel for additional links.

Dynamic Linking - automatically link names in your site to authoritative databases.

LinkIT is a tool that allows you to build automated link outs from names in your own pages, databases, and texts to expert systems. Links are created dynamically and only build links if the referenced system has information. Documention.

Name Recognition Tool - findIT identifies scientific names in any text. Documentation.

FindIT is available via both a web application and as a SOAP method for embedding name-recognition into your own applications. One of findiTs rulesets is based on an analysis of scientific name suffixes. Read the WSDL file.

The Author Abbreviation Resolver is a thesaurus for resolving abbreviations of author names in scientific nomenclature. It is available as a SOAP method. Documentation

Checking classifications

The TNS Name Mapper superimposes lists of names against multiple checklists and classifications.

Deconstruct a scientific name

ParseIT - This tool accepts a complex scientific name and breaks it into it's component parts. This tool is useful for identifying different forms of the same name, especially in combination with the author abbreviation service and findiT SOAP. Documentation.

CanonizeIT - This function complements the parser by deconstructing a scientific name into is canonical (or simplest) form. Documentation.

Find all the names in a web site.

CrawLIT can locate all the names within a collection of content and match the results against NameBank and various authority lists. The index of names can be linked to different name concepts to increase access to your content. We have several versions. The MRIB crawler was built for the USGS. Another version reconciles the crawled site to a classification such as ITIS or Species 2000.

Deconstruct a checklist

This application parses various standard checklist formats into a single normalized form. Documentation.

Build your own identification keys

X:ID is identification key software for the creation and display of interactive taxonomic keys. It is written entirely in OpenSource code and is XML-based. It uses XSLT to allow provide multiple display options for a given key.


CompareIt takes a URL or a list of names as input and compares the taxon names with a current taxonomy such as Species 2000 or ITIS and reports on the current status of the name and other metrics. URL input is first piped to FindIt so a web page with names can be checked against a current taxonomy.

A set of ITIS-centric applications including a custom LinkIt application an ITIS comparison tool and others.

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