International Council for Science : Committee on Data for Science and Technology

< home > < newsletter > < discussion list > < data science journal > < contact > < members area >
C O D A T A

Approved by the CODATA 23^rd General Assembly in Montréal 2002
Renewal approved by the CODATA 24th General Assembly, Berlin 2004
Renewal approved by the CODATA 25th General Assembly, Beijing 2006

http://www.bgbm.org/TDWG/CODATA/

The objective of the ABCD task group is to foster accessibility of existing and emerging biological collection data banks at the international level by developing ad-coordinating proposals for data and metadata standards and standard protocols.

Biological collections exist in different scientific sub-disciplines: zoological, botanical, and palaeontological natural history collections, living collections like botanical and zoological gardens and microbial strain and tissue collections, and data collections stemming from surveys of objects in the field (like floristic and faunistic mapping, inventories). They represent an immense knowledge base on global biodiversity. Field and research notes contain detailed data on the locality, time, and often appearance of organisms; the collected object itself can be a physical resource for research and industry. The preserved object also presents a falsifiable source of information, i.e. it can be re-observed to verify a scientific hypothesis based on it. Between 2 and 3 billion objects exist in natural history collections alone. Currently, this knowledge base is largely under-utilized, because its highly distributed, heterogeneous, and complex scientific nature obstructs efficient information retrieval. Data basing and networking is now seen as the key to employ the potential value of biological collections for science, government, education, the public, and businesses, operating in the environmental sector, in biotechnology, or in biodiversity research. International collaboration on the standardization of information models and standard data used in collection databases will enhance the efficiency of this process.

Recent Task Group Activities

ABCD content definition schema: The Subgroup members met in September 2005 in St. Petersburgh to discuss further proceedings. ABCD version 2.06 was accepted as a standard by the Taxonomic Databases Working Group’s meeting in St. Petersburg, and it also passed the subsequent mail ballot of the membership, so it is now a recognized TDWG Standard (TDWG is the IUBS commission for taxonomic databases, the standardization body for biodiversity informatics). See http://www.bgbm.org/TDWG/CODATA/Schema/default.htm.

A comprehensive documentation has been prepared on a wiki site (with detailed documentation of all elements, see http://ww3.bgbm.org/abcddocs/ and a printed documentation primer (Introduction to ABCD schema) is in preparation.

Follow-up activities will include the updating of the existing standard according to experience made by the reference implementations (ABCD is used by the portal of the Global Biodiver­sity Information Facility, by the Biological Collection Information Service for Europe, and soon by the Australian Virtual Herbarium project). In parallel to this effort, the successor version is already under discussion. As we envision it now, it will use a more object-oriented approach, defining a suite of objects representing the major data areas within the collection domain, linked to objects defined by other domains (geography, taxonomy, bibliography, molecular data), and made accessible with emerging web services and integrated with semantic networks in general biology and ecology. Work on this scheme is supposed to start with a workshop early in 2006.   

TAPIR protocol: With support from the Global Biodiversity Information Facility, a common data access protocol has been developed based on the DiGIR and BioCASe protocols currently in use. TAPIR incorporates advanced features and builds upon the experience gained with the DiGIR and BioCASe reference implementations (the GBIF network alone provides access more than 86 Million primary biodiversity collection records from 158 providers representing 636 collections world wide, using DiGIR and BioCASe protocols, and DwC and ABCD 1.2 as data definitions). A comprehensive documentation was delivered (see http://ww3.bgbm.org/tapir) with funding obtained from the GBIF Secretariat. The protocol is currently undergoing further tests. 

The results of the reference implementations of the protocol will be documented and and submission for recognition as a TDWG standard will take place either in 2006 or 2007.

DRAFT ABCD Group Meeting Report
Access to Biological Collection Data – Comprehensive Content Definition (TDWG ABCD standard)
26th – 28th July 2006
Royal Museum For Central Africa, Tervuren, BELGIUM