uBio Taxonomic Name Server

uBio - Universal Biological Indexer and Organizer uses names and taxonomic intelligence to manage information about organisms.1

Description

uBio is an initiative within the science library community to join international efforts to create and utilize a comprehensive and collaborative catalog of known names of all living (and once-living) organisms. The Taxonomic Name Server (TNS) catalogs names and classifications to enable tools that can help users find information on living things using any of the names that may be related to an organism.2

Information about organisms is often linked to a name.

This can create problems in information retrieval because:

• One taxon can have many names.
• The same name can refer to many taxa.

uBio is working on tools for providers of biological information that address these problems.

The uBio Taxonomic Name Server acts as a name thesaurus.

Names have many different classes of relationships that can be used to organize and retrieve information that is annotated with names. These classes are divided into two inter-connected services.

NameBank is a repository of millions of recorded biological names and facts that link those names together.

ClassificationBank stores multiple classifications and taxonomic concepts that are the result of expert opinions. It extends the functionality of NameBank.

All data within these components are linked to mechanisms that provide credit and attribution to experts who provide name and linkage information within the TNS.

Lastly, NameBank promotes the emergence of a layered biological informatics infrastructure that allows different expert systems to share common information. This conserves scarce resources and enhances the means to support continued expert work.3

Some of the tools algorithms and services developed by uBio:4

• LinkIT - Dynamic Linking - automatically link names in your site to authoritative databases.
• FindIT - Name Recognition Tool - identifies scientific names in any text.
• Author Abbreviation Resolver is a thesaurus for resolving abbreviations of author names in scientific nomenclature.
• ParseIT - Deconstruct a scientific name This tool accepts a complex scientific name and breaks it into its component parts.
• CrawlIT -Find all the names in a web site.  Locate all the names within a collection of content and match the results against NameBank and various authority lists.
• X:ID - Build your own identification keys. This identification key software is for the creation and display of interactive taxonomic keys. It is written entirely in OpenSource code and is XML-based.
• 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.
• uBioRSS A taxonomically intelligent RSS aggregator. Two applications that draw upon text-matching algorithms in conjunction with RSS feeds provided by academic publishers.5

uBio has its origins in the MBLWHOI Library in Woods Hole, Massachusetts, part of the Marine Biological Laboratory. FishBase, AntWeb and botanicus are uBio-based Services.6

Function

• Taxonomy

Why use this tool?

Information in biology related to organisms is often annotated with a name. We refer to this content as name-bearing or biocentric, content.

Names would appear to be a logical candidate for keyword searches within data repositories. The only problem is that organism names are neither fixed, stable, or unique and employing them as query terms can result in receiving information that is not related to the organism you were looking for as well as missing information you wanted.7

Who will use this tool?

• Data creation
  • Experts - taxonomy
• Data capture
  • Curators – specimens, identification
• Data providers
  • Institutions
  • Private collections
• ALA infrastructure
• Data users
  • Expert
  • Interest groups

How will the tool be used?

NameBank data are accessed via methods defined in SOAP. The SOAP methods provide access to lists of languages, management taxonomy "packages", and name search interfaces. The primary output object is the NameBank object. The NameBank object contains version and source metadata, record confidence and namestring metadata, and arrays of associated nominal, nomenclatural and canonical group identifiers and name strings.

The next version of NameBank will move output formats to RDF/XML which will be resolved through LSIDs.8

The web services allows users to access uBio data as if it were a local resource. For example, a library may have a database of fish pictures it serves. Users may query by name to find pictures. The developer of this system could use NameBank to access additional names that can be used to ensure that name queries find the pictures even if the name wasn't originally attached to the picture.

A remote application uses uBio web services to add taxonomic intelligence to application. In this figure an application serving images annotated with scientific names uses uBio web services to allow users to find images when searching by common name.9

 Where in the data chain could this tool be used?

• Data source
• ALA central
• Pathways between these

When could this tool be used?

• Before data is made available to ALA
• As data is imported into ALA for storage
• While data is stored with ALA
• At the time of a user request

Availability

• uBio: http://www.ubio.org/
• Sample applications: http://www.ubio.org/index.php?pagename=sample_applications
• Tools and services: http://www.ubio.org/index.php?pagename=sample_tools
• uBio news RSS: http://www.ubio.org/apps/uBioNews/rss.php
• Software is copyright MBL/WHOI Library and licensed under the Academic Free License 10

Comments

• Used by the Biodiversity Heritage Library
• uBio has a strong North American representation, and may have fewer Australian species.