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[protege-discussion] NCBO Webinar: Knowledge Organization System for Biodiversity information resources - Oct. 17 at 10am PDT

Trish Whetzel plwhetzel at
Mon Oct 15 13:18:40 PDT 2012

The next NCBO Webinar will be presented by Dag Endresen and Éamonn Ó Tuama
from the Global Biodiversity Information Facility (GBIF) on "Knowledge
Organization System (KOS) for biodiversity information resources, GBIF KOS
work program" at 10:00am PDT, Wednesday, Oct. 17.  Below is information on
how to join the online meeting via WebEx and accompanying teleconference.
For the full schedule of the NCBO Webinar presentations see:

The Biodiversity Information Standards (TDWG) maintains standards for
biodiversity data. Many of these standards have in the past been expressed
using the XML schema language (XSD). With the advance of the semantic web
there is a growing interest in TDWG for expressing vocabularies as RDF
resources. The Global Biodiversity Information Facility (GBIF) has proposed
a Vocabulary Management Task Group (VoMaG) [1] to develop best practices
and guidelines for maintaining RDF vocabularies of terms and concepts from
biodiversity informatics. One of the first tasks for the vocabulary
management task group would be to evaluate software tools including the
ISOcat [2] and the Semantic MediaWiki [3] for collaborative development and
maintenance of vocabularies of fundamental concepts (declared here to be
re-used by other resources). The simple knowledge organization system
(SKOS) has been proposed for the declaration of the “concept vocabularies”.
SKOS vocabularies can be expressed using the resource description framework
(RDF). One of the uses for the concept vocabularies is as a repository of
terms for the data sharing profiles in use by the GBIF network. These data
sharing profiles include the Darwin Core "extensions" and the
"vocabularies" of controlled values that are declared for some of the terms
included in "extensions". The overall outline is that terms to be included
in the "extensions" and in the "vocabularies" would be drawn from the
fundamental concepts declared by the concept vocabularies. We have proposed
as a best practice to separate the declaration of standalone concepts from
the declaration of semantic relationships between these concepts. The
rationale is partly that the user-friendly declaration of standalone
concepts will maximize their reuse, and in part that we believe the
ontologies declaring semantic relationships between concepts will always
depend on the purpose and context of the ontology. We believe that
declaring fundamental concepts as part of rich ontologies will cause an
undesired limitation for the reuse of these concepts. The web ontology
language (OWL) has been proposed for the declaration of relationships
between concepts. OWL can be expressed using RDF. GBIF has published a
resources repository [4] for biodiversity vocabularies. The NCBO BioPortal
has been proposed as a more appropriate portal for the publication of
biodiversity ontologies and vocabulary resources. The BioPortal provides
tools for cross-mapping between vocabulary and ontology concepts. BioPortal
will therefore provide an efficient platform to build interoperability
between biodiversity information standards and the standards of the
biomedical community. The Darwin Core standard of the biodiversity
community was loaded to the BioPortal as a first test [5].


Dag Endresen is the Node manager for the Norwegian participant node of the
Global Biodiversity Information Facility (GBIF). Dag was previously the
Knowledge System Engineer at the GBIF secretariat between August 2001 and
September 2012. As a member of the research community for plant genetic
resources for food and agriculture, Dag contributed to the interoperability
of data standards for biodiversity information resources. He has also
contributed to the development and technical implementation of data sharing
protocols and software tools. Dag holds a Ph.D. in agriculture and ecology
from the University of Copenhagen with the focus on prediction modeling
targeting the identification of genotypes with desired trait properties.

Éamonn Ó Tuama is the senior programme officer for Inventory, Discovery,
and Access (IDA) at the Global Biodiversity Information Facility (GBIF)
secretariat in Copenhagen. Éamonn is responsible for data integration and
interoperability issues for biodiversity data at GBIF. He has a background
in marine science, holding a Ph.D. in zoology from the National University
of Ireland, and several years experience in teaching and research.

To start or join the online meeting
Go to

Meeting Number: 925 756 393
Meeting Password: ncbo

Audio conference information
To receive a call back, provide your phone number when you join the
meeting, or call the number below and enter the access code.
Call-in toll number (US/Canada): 1-650-429-3300
Global call-in numbers:

Access code:925 756 393
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