TDWG and GBIF, at European genbank network meeting (Bonn, April 2004)


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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.

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  • The COMECON descriptor list came earlier than Multi-Crop, it was the result of a cooperation of the Eastern European Genebanks in PGR documentation.
  • TDWG and GBIF, at European genbank network meeting (Bonn, April 2004)

    1. 1. Presentation of TDWG and GBIF for the ECP/GR D&I Network meeting April 11, 2005 – ZADI, Bonn Dag Terje Filip Endresen – The Nordic Gene Bank
    2. 2. TOPICS for this talk <ul><li>GBIF </li></ul><ul><li>TDWG </li></ul><ul><li>Darwin Core and DiGIR </li></ul><ul><li>ABCD and BioCASE </li></ul><ul><li>TAPIR </li></ul>
    3. 3. Global Biodiversity Information Facility GBIF <ul><li>GBIF, the G lobal B iodiversity I nformation F acility is a mega-science project with the aim &quot;to make the world's primary data on biodiversity freely and universally available via the Internet&quot; </li></ul>
    4. 4. GBIF Work Programmes <ul><li>NODES – Data providers </li></ul><ul><li>ECAT – Electronic Catalogue of Names of Known Organisms </li></ul><ul><li>DIGIT – Digitisation of Natural History Collections </li></ul><ul><li>OCB – Outreach and Capacity Building </li></ul><ul><li>DADI – Data Access and Database Interoperability </li></ul>
    5. 5. Taxonomic Databases Working Group - TDWG <ul><li>TDWG Mission </li></ul><ul><li>To provide an international forum for biological data projects; </li></ul><ul><li>To develop and promote the use of standards ; and </li></ul><ul><li>To facilitate data exchange . </li></ul><ul><li>The TDWG web site is hosted by The Natural History Museum, London. </li></ul><ul><li>http:// / </li></ul>
    6. 6. Biodiversity collections data <ul><li>Biodiversity collections from different scientific sub-disciplines: </li></ul><ul><li>Preserved collections , such as those in museums and herbaria </li></ul><ul><li>Living collections, like botanical and zoological gardens, aquaria, seed banks , microbial strain cultures and tissue collections </li></ul><ul><li>Data collections , from surveys of objects in the field, such as observations, floristic and faunistic mapping and inventories </li></ul><ul><li>These collections have most of their attributes in common, although the terminology used to describe them may differ substantially. </li></ul><ul><li>Source: </li></ul>
    7. 7. Taxonomic Database Working Group Standards development and maintenance <ul><li>Darwin Core 2 - element definitions designed to support the sharing and integration of primary biodiversity data&quot;. http:// / </li></ul><ul><li>Access to Biological Collection Data (ABCD) 2.0 </li></ul><ul><li>an evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data)“ </li></ul><ul><li>http:// /TDWG/CODATA/Schema/ </li></ul><ul><li>Structure of descriptive data (SDD) 1.0 http:// </li></ul><ul><li>Taxonomic Concept Transfer Schema (TCS) 1 </li></ul><ul><li>development of a Taxon Name/Concept resolution service </li></ul><ul><li>http:// </li></ul>
    8. 8. Darwin Core 2 (DwC2) <ul><li>The Darwin Core 2 is a simple set of data element definitions designed to support the sharing and integration of primary biodiversity data </li></ul><ul><li>The Darwin Core is intended to be simple ; simplicity reduces the barriers for data providers </li></ul><ul><li>The Darwin Core is not a sufficient model or data structure for managing primary data, such as a collection database </li></ul><ul><li>Darwin Core can be compared to the MCPD of the PGR community </li></ul><ul><ul><li>http:// </li></ul></ul>
    9. 9. DiGIR Di stributed G eneric I nformation R etrieval <ul><li>Distributed - a protocol for retrieving structured data from multiple, heterogeneous databases across the Internet </li></ul><ul><li>Generic - a protocol independent of the data retrieved and of the software to retrieve it </li></ul><ul><li>The DiGIR protocol uses the Darwin Core as its data definition </li></ul><ul><li>http:// </li></ul><ul><li> </li></ul><ul><li>A major contributor to DiGIR is the MaNIS project. Mammal Networked Information System (University of California, Berkeley) </li></ul>
    10. 10. Access to Biological Collection Data ABCD Schema <ul><li>ABCD is a common data specification for biological collection units, including living and preserved specimens </li></ul><ul><li>The design goal of the data specification is to be both comprehensive and general </li></ul><ul><li>Development of the ABCD content definition started after the 2000 meeting of the TDWG </li></ul><ul><li>ABCD was developed by a CODATA/TDWG Task group </li></ul><ul><li>ABCD was developed with major input from BioCASE </li></ul><ul><li>GBIF accepted the draft ABCD schema in 2002 as a future collection data standard </li></ul><ul><li> </li></ul><ul><li>ZADI is a member of the ABCD task group </li></ul>
    11. 11. PGR sub-unit of ABCD <ul><li>PGR </li></ul>
    12. 12. Biological Collection Access for Europe BioCASE <ul><li>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 </li></ul><ul><li>ABCD is the data definition used by BioCASE </li></ul><ul><li>BioCASE and GBIF have overlapping objectives and close cooperation </li></ul><ul><li>BioCASE will provide full access to its registry for GBIF . Being a BioCASE provider thus means being a GBIF provider </li></ul><ul><li>BioCASE is also related to the European Network for Biodiversity Information ( ENBI ) </li></ul><ul><li>http:// / </li></ul><ul><li>BioCASE is coordinated by the Botanischer Garten und Botanisches Museum Berlin-Dahlem – BGBM </li></ul>
    13. 13. BioCASE (ABCD) and DiGIR (Darwin Core) <ul><li>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. </li></ul><ul><li>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. </li></ul><ul><li>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 . </li></ul>
    14. 14. Protocol integration - TAPIR <ul><li>There is a need to integrate the current protocols being used by different networks from the biodiversity informatics community. </li></ul><ul><li>During the TDWG meeting in Christchurch, NZ in October 2004, the presented unified protocol under development was named TAPIR . The T DWG A ccess P rotocol for I nformation R etrieval. It was agreed to start testing the protocol by rewriting the data provider software of the existing BioCASE and DiGIR implementations. </li></ul>
    15. 15. <ul><li>Thank you for listening! </li></ul>