[tdwg] Consolidating TDWG work

Eamonn O Tuama (GBIF) eotuama at gbif.org
Mon Apr 6 15:17:33 CEST 2009

Dear Donald, TDWG Members and Friends,


GBIF supports your drive to use the GISIN community’s requirements as a test
bed to demonstrate how the various TDWG standards can be applied to solve
their informatics issues. Last January, we convened a three day workshop for
the main Darwin Core (DwC) developers to enable them to make the final push
before submitting their work to the TDWG standards ratification process. The
proposed DwC standard, now submitted, provides a mechanism for extending its
base capabilities by adding new terms to the DwC vocabulary. The basic
technical solution for developing an extensible data encoding / transfer
schema is thus in place for invasive species data. 


In addition, GBIF has just released the first public version of the
Integrated Publishing Toolkit (IPT) v1.0
(http://www.gbif.org/News/NEWS1238568696) which was demonstrated to great
interest at the last TDWG Conference in Perth. The goal of the IPT is to
remove constraints to the publishing and flow across networks of
biodiversity data. It provides simple interfaces to transfer complete data
stores efficiently in order to simplify the publishing process and reduce
the latency between data publication and discoverability through the GBIF
indexes. Accommodating three main data types - taxon primary occurrence
data, taxonomic checklists and resource metadata - the IPT enables users to
publish data residing in local databases, upload existing files, and access
central services to make use of standardised controlled vocabularies. The
IPT uses a “star schema”, i.e., a one-to-many schema in which a core record
(expressed as DwC) can be linked to many additional descriptors. The DwC
record in IPT does not need to be an occurrence. For checklist publishing we
use the same DwC elements, but the record in that case represents a species
name, not an occurrence, and any star schema extensions would be linking to
species. For GISIN, those extensions can cover relevant areas such as
management, impact, descriptions, images, related documents, distributions,
dispersal, etc. The challenge for us is therefore to help the GISIN
community to define extensions to DwC and to develop customized (thematic)
portals that process and present the invasive species data according to
their particular requirements, e.g. tracking species movements. 


The IPT allows the sharing and use of specialist extensions amongst the
IPT-user community. It can also act as an outreach tool for the GISIN
community as it includes a web application that allows browsing and
searching of published data, along with basic mapping services including
Open Geospatial Consortium Web Map Service and Web Feature Service. 


We support the idea of a “cook book”  that helps communities use and, where
required, extend standards to enable sharing of biodiversity data.  GBIF,
through its Training portfolio will be able to contribute documentation and
training materials on many topics, e.g., the IPT, metadata, web services.


With regards,





Éamonn Ó Tuama, M.Sc., Ph.D. ( <mailto:eotuama at gbif.org> eotuama at gbif.org), 

Senior Programme Officer, Inventory, Discovery, Access (IDA), 

Global Biodiversity Information Facility Secretariat, 

Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK 
Phone:  +45 3532 1494; Fax:  +45 3532 1480






From: tdwg-bounces at lists.tdwg.org [mailto:tdwg-bounces at lists.tdwg.org] On
Behalf Of Donald.Hobern at csiro.au
Sent: 25 March 2009 00:43
To: tdwg at lists.tdwg.org
Subject: [tdwg] Consolidating TDWG work


Dear TDWG Members and Friends,


Those of you who attended the conference in Perth last year will remember
Annie Simpson's explanation of how hard it still is for a group like the
Global Invasive Species Information Network (GISIN) to take TDWG's work and
apply it directly to solve data integration issues in their community.


As I have previously suggested, I believe we should look closely at GISIN's
requirements and make sure that those in a similar situation have all the
tools and documentation required to start connecting data easily in ways
that are compatible with TDWG standards.  We have most of the pieces in
place.  We just need to organise and document them better.


Invasive species are of great significance to many countries.  This means
that addressing GISIN's requirements is directly relevant to a large number
of TDWG participants.  However their scenario is also a template for data
sharing in many other biodiversity-related projects.  They need to aggregate
information from many sources to populate several inter-related data models
(BioStatus, Occurrences, ProfileURLs, ImpactStatus, ManagementStatus and
DispersalStatus).  Several of these are very close to existing data models
based on TDWG standards (for example, the Occurrence model can be considered
to be extended Darwin Core).  Others are examples of the kind of
community-specific data which all biodiversity projects need to share.  


TDWG's goal should be to ensure that GISIN and similar groups can follow a
simple set of instructions (a "cook book") and use standard tools to build a
network of this kind, and that they can do so in a way which ensures that
related communities can also benefit from the data they share.  For example,
if GISIN members use the GISIN toolkit to share data, we ought to make sure
that no further steps are required for GBIF, OBIS and others to integrate
GISIN Occurrence data into their own indexes of species occurrences, or for
EOL, ALA and others to integrate GISIN ImpactStatus, ManagementStatus and
DispersalStatus data into their species profiles.


I am therefore writing this email as an appeal for TDWG members to step
forward and help to complete the work we have started.  I am setting a
challenge for us to do whatever still needs to be done to our standards,
tools and data sharing recommendations so that we can produce such a cook
book by the end of 2009.  I don't believe this is an unrealistic goal.  We
can start work now on identifying and resolving issues.  We can plan
activities at the 2009 TDWG conference in November to resolve any issues
still outstanding at that point and to hold hackathon activities to fill any
gaps in our tool set.  This work also aligns well with the e-Biosphere
conference's plan to develop a roadmap for biodiversity informatics for the
next 10 years.


We have added a page to the TDWG Invasive Species wiki to seed discussion of
what we need to do -
Please take the time to look at this page (and at the information on GISIN's
requirements at http://wiki.tdwg.org/twiki/bin/view/InvasiveSpecies/WebHome
ion.php).  Append comments and suggestions on what else we may need to do to
the wiki, or simply reply to this message.  In particular, if you are
interested in being involved with the relevant TDWG Interest Groups in
addressing some of the listed requirements, please contact me or the
relevant Interest Group leaders.


I believe this is the most significant thing that TDWG can do right now to
support the work of biodiversity informatics worldwide.  Please consider
making your own contribution to make it happen.


Best wishes,







Donald Hobern, Director, Atlas of Living Australia

CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601

Phone: (02) 62464352 Mobile: 0437990208 

Email:  <mailto:Donald.Hobern at csiro.au> Donald.Hobern at csiro.au

Web: http://www.ala.org.au/ 










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