Transcript TDWG - SBIS2008

TDWG
Biodiversity Information Standards
http://www.tdwg.org
Renato De Giovanni
Member, TDWG Executive Committee
[email protected]
December 1st, 2008
Meeting?
TDWG - Biodiversity Information Standards
Previously: Taxonomic Databases Working Group
• International not-for-profit organization that develops
standards and protocols for sharing biodiversity data.
• All outcomes are freely available to the public.
• Anyone can participate in subgroup discussions – no
need to be a TDWG member, although membership
is always encouraged.
TDWG Mission
• Develop, adopt and promote standards and
guidelines for the recording and exchange of data
about organisms.
• Promote the use of standards through the most
appropriate and effective means.
• Act as a forum for discussion through holding
meetings and through publications.
History
• TDWG activities date from 1985, when a group of
botanists met at the Conservatoire et Jardin
Botaniques in Geneva.
• The aim was to explore ideas on standardization and
collaboration between projects and institutions that
were working with plant taxonomic databases.
• This was before the Internet became widespread!
• First meeting was probably very successful…
TDWG Annual Meetings
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1985
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Geneva, Switzerland (Conservatoire et Jardin Botaniques)
Pittsburgh, USA (Hunt Institute)
Edinburgh, Scotland (Royal Botanic Gardens)
St Louis, USA (Missouri Botanical Garden)
Las Palmas, Gran Canaria (Jardin Botanico)
Delphi, Greece (European Cultural Centre)
Canberra, Australia (Australian National Botanic Gardens)
Xalapa, Mexico (Instituto de Ecologia)
Washington, USA (Smithsonian Institute)
Paris, France (IUBS 25th General Assembly)
Madrid, Spain (Real Jardin Botanico - CSIC)
Toronto, Canada (Royal Ontario Museum)
Taipei, Taiwan (Academia Sinica - IUBS 26th General Assembly)
Reading, England (Centre for Plant Diversity and Systematics)
Harvard, Cambridge, USA (Harvard University Herbaria)
Frankfurt am Main, Germany (Senckenberg Museum)
Sydney, Australia (Royal Botanic Gardens)
Indaiatuba, Brazil (CRIA)
Oeiras, Portugal (Instituto Gulbenkian de Ciência)
Christchurch, New Zealand (Landcare Research)
St. Petersburg, Russia (Zoological Institute of the Russian Academy of Sciences)
St. Louis, USA (Missouri Botanical Garden)
Bratislava, Slovakia (Department of Zoology of the Comenius University)
Fremantle, Australia (Maritime Museum)
Participation in the last meetings
TDWG Annual Meeting
• Opportunity for TDWG to assess achievements, plan
the next activities, elect new officers, and to conduct
any other relevant business.
• Opportunity for the subgroups to make progress by
organizing specific face-to-face meetings.
• Opportunity for all participants to attend a
biodiversity informatics conference, present their
work, interact with other people, become current with
new technologies, and learn about other projects
across the globe.
TDWG Expansion
• In 1988 TDWG became affiliated to the International
Union of Biological Sciences (IUBS): Zoologists and
microbiologists started to participate.
• In the 1990s the Internet started to flourish: dream of
being able to aggregate knowledge on the world’s
biodiversity and bring it to every biologist’s desktop.
• In 2006 TDWG got a US$1.5 million grant from the
Moore Foundation: Major restructuring process.
• Currently, TDWG members are a mix of biologists,
ecologists, computer scientists, taxonomists, librarians,
geoscientists...
TDWG Types of Standards
• Technical Specification
• Protocol, service, procedure, format
• Applicability Statement
• How an existing technology can be applied (e.g.
LSIDs)
• Best Current Practice
• Description of good behavior
• Data Standard
• Content specification or controlled vocabulary
TDWG Standards
Retired/
Deprecated
Standards
-no champion
Current
Standards
Draft
Standards
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Users Guide to the DELTA System (1986)
Floristic Regions of the World (1986)
International Transfer Format for Botanic Garden Plant Records (1987)
Index Herbariorum. Part I: The Herbaria of the World (1990)
Botanico-periodicum-huntianum/supplementum (1991)
XDF – Language for Definition and Exchange of Biological Datasets (1991)
World Geographical Scheme for Recording Plant Distributions (1992)
Authors of Plant Names (1992)
Plant Names in Botanical Databases (1995)
Plant Occurrence and Status Scheme (1995)
Economic Botany Data Collection Standard (1995)
HISPID3 - Herbarium Information Standards and Protocols for Interchange of Data
(1996)
Access to Biological Collection Data (ABCD) (2005)
Structure of Descriptive Data (2005)
Taxonomic Concept Transfer Schema (2005)
Standards Documentation Specification (draft)
Life Sciences Identifiers (LSID) Applicability Statement (draft)
Natural Collections Descriptions (draft)
TDWG Access Protocol for Information Retrieval —TAPIR (in preparation)
DarwinCore (in preparation)
TDWG Infrastructure Project - Aims
• Devise a new long-term support model for the
organization.
• Develop appropriate procedural rules.
• Set up a new infrastructure to support all its activities.
• Make the organization and its scope known to the
public.
• Effectively disseminate its work products.
TDWG Infrastructure Project - Results
• A new constitution and standards development process
are now in place to ensure the quality of standards.
• All working groups have been reorganized and received
support to accomplish their tasks.
• A new integrated web environment is now available
(content management system, Wiki, mailing lists,
journal management and publishing system, and
version control system).
• A new group has been created to define a common
technical architecture for all TDWG standards.
Current Working Structure
• TDWG is governed by an Executive Committee
consisting of:
• Chair
• Secretary
• Treasurer
• Editor (journal and website)
• 6 Regional Secretaries (based on the regions
of the world)
• 2 Additional individuals may be appointed by
the officers
• Officers are elected by the membership during the
annual meeting.
• When voting is required, results are based on
simple majority. One vote for each member.
Standards Development Process
• Interest Groups provide a base for discussing
goals and strategies for data sharing in a
particular area.
• Task Groups are created within Interest Groups to
develop a specific product in a specific timeframe.
• Any TDWG member can petition for the
establishment of a new Interest Group by
submitting a charter to the Executive Committee.
• Both kinds of Groups are managed by Conveners
responsible for developing consensus, preparing
the standards specification and reporting back to
the Executive Committee annually.
Standards Development Process
New Standards License
• To be defined by the TDWG Standards
Documentation Specification (under final review).
• New standards will normally be released under
the Creative Commons “By Attribution” license,
which means that users will be free:
• To Share: to copy, distribute, and transmit the
work;
• To Remix: to make derivative works;
• Under the condition that users must attribute
the work to TDWG by citing the standard by
name and providing the URL to the original
document, but not in any way suggesting that
TDWG endorses the user or the use of the
work.
TDWG Interest Groups
• Biological Descriptions
• Species Profiles (being established)
• Geospatial
• Imaging & Multimedia
• Invasive Species
• Literature
• Natural Collections Descriptions
• Observation and Specimen Records
• Taxonomic Names and Concepts
• Technical Architecture
• Global Identifiers
• Access Protocol for Information Retrieval
• Phylogenetics (being established)
New TDWG Standards Architecture
•
Principle 1: TDWG standards apply to shared data
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Enables interoperability of providers and consumers with
radically different internal implementations.
Does not dictate internal structures on data providers or
consumers.
‘Format’ matters when data crosses boundaries.
Data Sharing Scenario
Typical scenario for complex biodiversity research
will require different kinds of data from multiple
sources to be combined:
Nomenclature
Geospatial
Taxonomy
Molecular
?
Description
Interaction
Occurrence
Literature
TDWG Architecture Requirements
•
Data providers will not know who will use their
data or how it will be combined with data from
other sources.
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Data consumers will need some level of
commonality across all data received so that it
can be combined for analysis without much pain
– even for new types of combinations.
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Providers and consumers need to be able to
reference pieces of data in a consistent and
reliable way.
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Data exchange needs to be facilitated by
adopting common rules.
New TDWG Standards Architecture
• Principle 2: Biodiversity data will be modelled as
graph of identifiable objects.
– Objects will be defined by an ontology: Understandable by
humans and computers.
– Globally unique identifiers will be used to link objects
across the network.
– A common exchange protocol will be available to search
and retrieve data.
TDWG Architecture Components
1. Ontology
2. Globally Unique Identifiers
3. Exchange Protocols
TDWG Ontology
Initial prototype available as a series of UML
diagrams and OWL/RDF vocabularies.
Global Identifiers
• The Global Identifier Task Group produced an
Applicability Statement for Life Science
Identifiers (LSIDs) which is under final review.
• GUID systems like LSID provide mechanisms to
identify and access data objects on the Web.
• Identifiers must be persistent (permanently
associated with a data object).
• Identifiers must be global in scope.
• Identifiers must allow clients to access the
underlying data object in a standard way.
Data Exchange Protocol
• The TDWG Access Protocol for Information
Retrieval (TAPIR) Task Group is finalizing the
specification. TAPIR :
• Is based on established Web standards like
HTTP, XML and XML Schema.
• Is independent of the data being exchanged
(can be used to access a wide range of data).
• Can return data in different formats.
• Has five operations to address basic needs of
federated networks: access to metadata and
capabilities of the service, preliminary data
discovery and data mining, searching, and
service monitoring.
TDWG Priorities for 2009
1. Promote standards through the TDWG process
(Standards Documentation Specification, LSID
Applicability Statement, DarwinCore and TAPIR) .
2. Foster the uptake of LSIDs using RDF
vocabularies.
3. Complete the core ontology and vocabularies.
4. Develop a strategy on metadata.
5. Reach out to the community for support and to
ensure TDWG standards address community
needs.
Membership
• We need more people and institutions to support the
development of more effective standards.
• Current membership is small considering the size of
the community and the international significance of
the work.
• Individual membership:
US$75 / year
• Institutional membership:
US$500 / year
(US$400 before March 30)
TDWG Challenges
• Developing effective standards is not easy
• Involves people with different interests and
perspectives – also need to deal with
conservatism, rivalries, egos...
• Involves complex areas of knowledge – trivial
issues are not trivial...
• Involves multiple disciplines – experts from
different areas need to understand each other
• Information Technology evolves very quickly –
standards can soon become obsolete!
• TDWG needs more resources to facilitate rapid
development of effective standards
TDWG Challenges
Some think that any competent individual could
probably develop a standard faster than a group...
Group outcomes can be odd – an amalgam of
different views: “A camel is a horse designed by a
committee” (unknown source)
“If you want to go fast around a well-prepared track,
get yourself a racehorse.
If you want to reliably reach a distant destination
across unknown terrain, you are probably better off
on a camel.” (M. Champion)
Thank you
http://www.tdwg.org