Species

ABCD: Access to Biological Data Collections

kstocks — Wed, 31 Oct 2007 09:33:00 -0700

Description

The Access to Biological Collections Data (ABCD) is an XML-based common data specification for biological collection units, including living and preserved specimens, along with field observations that did not produce voucher specimens. As stated on the ABCD website: "The purpose of the ABCD Task Group is to foster accessibility of existing and emerging biological collection data banks at the international level by developing and maintaining a comprehensive and commented schema for biological collection records (ABCD Schema).

Advancing ecological research with Ontologies (a review paper)

kstocks — Fri, 08 Aug 2008 10:00:15 -0700

Joshua S. Madin, Shawn Bowers, Mark P. Schildhauer and Matthew B. Jones. 2008. Advancing ecological research with ontologies. Trends in Ecology and Evolution 23(3): 159-168.

Animal Behavior Ontology

kwalz — Sun, 10 Feb 2008 17:55:00 -0800

(2011-04-14: Please note, the link at the bottom of the page seems to be no longer valid.

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Biodiversity Information Standards (TDWG): Vocabularies and Ontologies

kwalz — Thu, 28 May 2009 20:15:03 -0700

Description

Biodiversity Information Standards (TDWG) is an international not-for-profit group that develops standards and protocols for sharing biodiversity data. They have a detailed collection of vocabularies and ontologies for studies of biological organisms.

Type

Vocabulary/Ontology
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Biodiversity Resource Information Ontology

kwalz — Sun, 10 Feb 2008 17:55:00 -0800

Biodiversity resource information ontology - introduced species, taxonomic information, geographic location.

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COBrA

kwalz — Thu, 31 Jan 2008 05:50:00 -0800

COBrA allows the user to manually create links between terms in two ontologies. For example, links between tissues in an anatomy and the cell types of the tissues can be recorded and stored: these links are referred to as mappings.

Has the following features:
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MESH: Mapping European Seabed Habitats

graybeal — Fri, 11 Jan 2008 23:22:00 -0800

The MESH program goal is to develop international standards and protocols for seabed mapping studies. The end products will include a meta database of mapping studies, and guidance for marine habitat mapping including protocols and standards.
In the basic search page, there is a list of pointers to different habitat mapping vocabularies.
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OBO: Open Biological Ontologies

graybeal — Fri, 11 Jan 2008 21:45:00 -0800

From the site: "This site contains ontologies and points to some other efforts within the community. Ideally we see a range of ontologies being designed for biological domains. Some of these will be generic and apply across all organisms and others will be more restricted in scope, for example to specific taxonomic groups."
The site is not simply a compendium of ontologies. It has inclusion criteria which are fairly strict, in order to facilitate interoperation of the multiple ontologies listed.
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Plazi.org - the digital repository for species descriptions

kwalz — Thu, 19 Jun 2008 09:51:44 -0700

Information from their web site:
Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To this end Plazi will:
* Maintain a digital taxonomic literature repository to enable archiving of taxonomic treatments.
* Enhance submitted taxonomic treatments by creating taxonx XML versions.
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