Welcome to the TaxonProfile web

Project overview

Many taxonomic communities have taken on the task of creating a unitary taxon profile with the goal of providing taxonomists and users of taxonomic information with a structure to store data.

Existing schemas (see below) may be more useful if there was consensus on what the terms mean. Providing a collaborative web environment will enable taxonomists to discuss and sort out what is really meant when we use terms such as "habitat".

The issue is that "habitat" has a variety of meanings, depending upon context; the habitat of an ant, a fish or a bacteria are different. Not being an expert in any of these areas, I can't say whether i would even use the term "habitat", in preference to "environment".

Why is this important?

Taxon Profile information is stored in databases around the would, but each database is independant from all the others and structured differently, so it is difficult to share this information to assess the biodiversity of a region.

Consensus on the meaning of each term (e.g. "habitat", "distribution") in a taxon profile will achieve what taxonomists have been trying to resolve for years; a better understanding of the earth's biodiversity and the interrelationships between all organisms.

TRIN aims to encourage taxonomists to participate in a discussion on the meaning of each term used in the taxon profiles they author and, if synonyms exists, provide those too.

Examples of organisations working with taxon profile information.

• Creating a Taxonomic e-Science - the Cate Project
• European Distributed Institute of Taxonomy (EDIT) - are working on a Platform for CyberTaxonomy and have in mind a Common Data Model
• Pan-European species directories Infrastructure working with the Natural History Museum

Tasks

1. List stakeholder's (ALA, TRIN, ABRS, CHAH, CHAFC, CHAEC) requirements
2. List fields and focus area of the TDWG specifications StructuredDescriptiveData (SDD), SpeciesProfileModel (SPM) and DarwinCore? (DwC?).
3. List other commonly used specifications? used in the storage and dissemination of biodiversity information (Habitat, soil types, etc. )
4. List existing nomenclature? and TaxonomyDataStores (AFD, APNI, etc.)
5. List existing multimedia? and ImageDataStores? (APII, etc.) Build and load descriptive data store

Creating a New Taxon Profile

Use this form to create a taxon profile using the TRIN set of Terms

TaxaCreator application is a tool that assists taxonomists to create taxon profiles based on a predefined template.

Define a new Taxon Profile Term

Terms which make up a Taxon profile can be entered and defined using established standards like Dublin Core. This form is intended to be used to add elements or classes to a taxon profile. A more detailed set of instructions is being drafted.

Past and Future Taxon Profiles

Taxon profiles of past may have described the daily activities of animals as manners, today (13 July 2009) we might describe these same activities as animal behaviour. The definition of manners has changed, possibly due to using that same terms to describe ever expanding groups on organisms, but society and culture also play a part in the language used. Species descriptions today are connected in various ways to institutions, whether it in by the publisher, the author's employer or the organisation receiving a mention in the description text, eg. via legislation or being listed on an endangered species list. Links or connections that provide context:

• A koala profile could be linked to related legislation on Austlii when the profile is migrated to electronic format
• The distribution could be defined by a WWF region

The structure of the TaxonProfile wiki

The structure of the TaxonProfile wikiWeb, webTopics and how they relate to the Mangrove Species Profile structure.

Example Taxon Profiles

Documenting of taxon profiles and carry out an analysis of the requirements for taxon profiles.

Provide a proof of concept using the mangroves project as a starting point in creating sample pages towards and inter-relatable taxon profile

Several target profiles from the mangroves? will be listed here and expanded as the project continues.

Taxon	Existing WikiTopic	Taxon Profile
Amphibians	/Mangroves/Amphibians	Amphibians?
Birds	/Mangroves/Birds	Birds
Crustaceans	/Mangroves/Crustaceans	Crustaceans?
Fish	/Mangroves/Fish	Fish?
Fungi	/Mangroves/Fungi	Fungi?
Insect - Ants	/Mangroves/Insects-Ants	Insect - Ants
Lichens	/Mangroves/Lichens	Lichens?
Molluscs	/Mangroves/Molluscs	Molluscs?
Plants - Vascular	/Mangroves/Plants	Plants - Vascular
Plants - Bryophytes	Mangroves/Plants-Bryophytes	Plants - Bryophytes
Polychaetes	/Mangroves/Polychaetes	Polychaetes?
Reptiles	/Mangroves/Reptiles	Reptiles?
River Red Gum	RiverRedGum	RiverRedGum

Overview of the relevant standards (eg. TDWG) and the methods or storage and access to taxon profiles

Taxon Profiles created by the herbarium interns TaxaCreator.

Resources

Altova XmlSpy and oXygen are tools for manipulating and creating XML files and Altova also produce a tool called SemanticWorks which can be used to produce Ontologies (%CALLMACRO{topic=AcronymMacro term="OWL"}%) and Data Description files (%CALLMACRO{topic=AcronymMacro term="RDF"}%).

There is a discussion of these file formats and these tool in the ToolsPage

TaxaCreator application is a tool that assists taxonomists to create taxon profiles based on a predefined template.

Glossary

Habitat Glossary (Handbook of Australian, New Zealand & Antarctic Birds Vol 1)

Thesaurus

Terms used when discussing organism descriptions:
species profile, species account, taxonomic treatment, taxon profile and taxonomic arrangement

Habitat section of the thesaurus tree from the (Zoological Record Markup Guide)

How might Taxon Profiles be represented

Strategies
Analysis of the various fields/terms/elements/properties of a taxon profile could be grouped into several methods,

1. List all the known fields then group them by similarity (ie. have similar meaning or same ontology)
2. Atomise the fields, define a shared meaning using ontologies

I see a problem with atomising fields where the depth of detail is not restricted. This may be more of a problem when talking about diagnosis, because by definition the diagnosis documents the comparision of one species with another, highlighting the differences and common characteristics.

Thought: Might it be enough to list the fields without making a textual comparison, especially where the fields are the same or similar(i.e. Ceyx pusilla.distribution compared to Alcedo azurea.distribution). Distribution may not be an ideal term on which to make a comparison, but Length and Weight would be a more suitable candidate field for diagnosis. ( Ceyx pusilla.size compared to Alcedo azurea.size)

TaxonProfile Web Utilities

• - advanced search
• WebTopicList - all topics in alphabetical order
• WebChanges - recent topic changes in this web
• WebNotify - subscribe to an e-mail alert sent when topics change
• WebRss, WebAtom - RSS and ATOM news feeds of topic changes
• WebStatistics - listing popular topics and top contributors
• WebPreferences - preferences of this web

• Cropped version of the TRIN logo, i.e. the @ symbol: