tdwg and gbif, at european genbank network meeting (bonn, april 2004)
DESCRIPTION
Presentation of TDWG and GBIF for the ECP/GR D&I Network meeting at ZADI Bonn Germany 11th April 2005. Dag Endresen (Nordic Gene Bank). TDWG is a standardization body for Biodiversity Information Standards; GBIF is a Global Biodiversity Information Facility for free and open access to biodiversity data.TRANSCRIPT
The Nordic Gene Bank, NGB, Alnarp, SwedenThe Nordic Gene Bank, NGB, Alnarp, Sweden
Presentation of TDWG and GBIF
for theECP/GR D&I Network
meetingApril 11, 2005 – ZADI, Bonn
Dag Terje Filip Endresen – The Nordic Gene Bank
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
TOPICS for this talkTOPICS for this talk
GBIF TDWG Darwin Core and
DiGIR ABCD and
BioCASE TAPIR
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Global Biodiversity Information Global Biodiversity Information FacilityFacility
GBIFGBIF
GBIF, the Global Biodiversity Information Facility is a mega-science project with the aim "to make the world's primary data on biodiversity freely and universally available via the Internet" www.gbif.org
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
GBIF Work ProgrammesGBIF Work Programmes
NODES – Data providers ECAT – Electronic Catalogue
of Names of Known Organisms
DIGIT – Digitisation of Natural History Collections
OCB – Outreach and Capacity Building
DADI – Data Access and Database Interoperability
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Taxonomic Databases Working Group - Taxonomic Databases Working Group - TDWGTDWG
TDWG Mission
To provide an international forum for biological data projects;
To develop and promote the use of standards; and
To facilitate data exchange.
The TDWG web site is hosted by The Natural History Museum, London.
http://www.tdwg.org/
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Biodiversity collections dataBiodiversity collections data
Biodiversity collections from different scientific sub-disciplines:
Preserved collections, such as those in museums and herbaria
Living collections, like botanical and zoological gardens, aquaria, seed banks, microbial strain cultures and tissue collections
Data collections, from surveys of objects in the field, such as observations, floristic and faunistic mapping and inventories
These collections have most of their attributes in common, although the terminology used to describe them may differ substantially.Source: http://www.bgbm.org/TDWG/CODATA/ABCD-Evolution.htm
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Taxonomic Database Working GroupTaxonomic Database Working Group Standards development and maintenanceStandards development and maintenance
Darwin Core 2 - element definitions designed to support the sharing and integration of primary biodiversity data". http://darwincore.calacademy.org/
Access to Biological Collection Data (ABCD) 2.0 an evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data)“http://www.bgbm.org/TDWG/CODATA/Schema/
Structure of descriptive data (SDD) 1.0 http://wiki.cs.umb.edu/twiki/bin/view/SDD/CurrentSchemaVersion
Taxonomic Concept Transfer Schema (TCS) 1development of a Taxon Name/Concept resolution servicehttp://tdwg.napier.ac.uk
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Darwin Core 2 (DwC2)Darwin Core 2 (DwC2)
The Darwin Core 2 is a simple set of data element definitions designed to support the sharing and integration of primary biodiversity data
The Darwin Core is intended to be simple; simplicity reduces the barriers for data providers
The Darwin Core is not a sufficient model or data structure for managing primary data, such as a collection database
Darwin Core can be compared to the MCPD of the PGR community
http://darwincore.calacademy.org
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
DiGIRDiGIRDiDistributed stributed GGeneric eneric IInformation nformation RRetrievaletrieval
Distributed - a protocol for retrieving structured data from multiple, heterogeneous databases across the Internet
Generic - a protocol independent of the data retrieved and of the software to retrieve it
The DiGIR protocol uses the Darwin Core as its data definition
http://digir.nethttps://sourceforge.net/projects/digir
A major contributor to DiGIR is the MaNIS project. Mammal Networked Information System (University of California, Berkeley)
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Access to Biological Collection DataAccess to Biological Collection DataABCD SchemaABCD Schema
ABCD is a common data specification for biological collection units, including living and preserved specimens
The design goal of the data specification is to be both comprehensive and general
Development of the ABCD content definition started after the 2000 meeting of the TDWG
ABCD was developed by a CODATA/TDWG Task group
ABCD was developed with major input from BioCASE
GBIF accepted the draft ABCD schema in 2002 as a future collection data standardhttp://www.bgbm.org/TDWG/CODATA/Schema/default.htmZADI is a member of the ABCD task group
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
PGR sub-unit of ABCDPGR sub-unit of ABCD
PGR
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Biological Collection Access for Biological Collection Access for EuropeEurope
BioCASEBioCASE The BioCASE project establish a web-based
information service providing researchers with unified access to biological collections in Europe while leaving control of the information with the collection holders
ABCD is the data definition used by BioCASE
BioCASE and GBIF have overlapping objectives and close cooperation
BioCASE will provide full access to its registry for GBIF. Being a BioCASE provider thus means being a GBIF provider
BioCASE is also related to the European Network for Biodiversity Information (ENBI)
http://www.biocase.org/
BioCASE is coordinated by the Botanischer Garten und Botanisches Museum Berlin-Dahlem – BGBM
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
BioCASEBioCASE (ABCD) and (ABCD) and DiGIRDiGIR (Darwin Core) (Darwin Core)
DiGIR and the Darwin Core schema is the main data provider supported by GBIF. GBIF has developed a separate Phyton Provider package as an easier-to-install alternative to the original PHP DiGIR wrapper.
In 2002 the ABCD Schema was accepted by GBIF, and in October 2003, GBIF decided to integrate the BioCASE network into the GBIF network along with the DiGIR protocol and Darwin Core.
The primary difference between the two standards is that DiGIR handles only flat schemas, such as Darwin Core, whereas the BioCASE protocol can handle structured schemas, such as ABCD.
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Protocol integration - TAPIRProtocol integration - TAPIR
There is a need to integrate the current protocols being used by different networks from the biodiversity informatics community.
During the TDWG meeting in Christchurch, NZ in October 2004, the presented unified protocol under development was named TAPIR. The TDWG Access Protocol for Information Retrieval. It was agreed to start testing the protocol by rewriting the data provider software of the existing BioCASE and DiGIR implementations.
ECP/GR D&I meeting April 11, 2005, ZADI, BonnECP/GR D&I meeting April 11, 2005, ZADI, Bonn
Thank you for listening!