Web services for sharing germplasm data sets, at FAO in Rome (2006)


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Sharing of Germplasm datasets with web services. Food and Agriculture Organization of the United Nations (FAO) 20th February 2006.

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  • * Spiders-web, photographer: Ian-Britton [http://www.freefoto.com/preview.jsp?id=01-17-1&k=Spiders+Web]
  • Photo: IRRI genebank. Los Banos, Philippines [http://www.cgiar.org/images/irrigenebank1.jpg], VIR seed collection. St. Petersburg. Photographer Eva Thörn (NGB Picture Archive, image 001319).
  • * IRRI genebank. Los Banos, Philippines [ http://www.cgiar.org/images/irrigenebank2.jpg] * Text formulation source [http://www.bgbm.org/TDWG/CODATA/ABCD-Evolution.htm] wording above is modified.
  • * Multi-crop Passport Descriptors (MCPD) [http://www.ipgri.cgiar.org/publications/pdf/124.pdf] F AO (Food and Agricultural Organization of the United Nations) - IPGRI (International Plant Genetic Resources Institute). This is a revised version (December 2001) of the 1997 MCPD List. * FAO World Information and Early WarningSystem ( WIEWS) [http://apps3.fao.org/wiews/] * 19 Plant Uses Categories based on categories developed for the Working Group on Taxonomic Databases (TDWG) (Cook, Frances E.M., 1995. Economic Botany: Data Collection Standard. Royal Botanic Gardens Kew). [ http://www.ecpgr.cgiar.org/epgris/Training/MCPD-1998.doc] * The mapping of MCPD to ABCD was started in 2004 by Helmut Knüpffer and Walter Berendsohn, and finalized by Javier de la Torre and Dag Terje Filip Endresen in 2005. [ http://ww3.bgbm.org/MCDPH]
  • * IPGRI Descriptors lists [http://www.ipgri.cgiar.org/system/page.asp?frame=programmes/inibap/home.htm] (119 descriptor lists, 2005) * MCPD [http://www.ipgri.cgiar.org/publications/pdf/333.pdf] * UPOV - International Union for the Protection of New Varieties of Plants (UPOV) [ http://www.upov.int/] * UPOV - The International Union for the Protection of New Varieties of Plants or UPOV (French: Union internationale pour la protection des obtentions végétales) is an intergovernmental organization with headquarters in Geneva, Switzerland. [http://en.wikipedia.org/wiki/UPOV] * COMECON - The Council for Mutual Economic Assistance (COMECON / Comecon / CMEA / CEMA), 1949 – 1991, was an economic organisation of communist states and a kind of Eastern European equivalent to the European Economic Community. The military counterpart to the Comecon was the Warsaw Pact. [http://en.wikipedia.org/wiki/Comecon]
  • * Illustration: Corn earworm pupae that will be used to produce control parasites for release in the field. Photo by Scott Bauer. [http://www.ars.usda.gov/is/graphics/photos/k5554-2.htm] * UBIF is an attempt to define a common foundation for several TDWG/GBIF standards like SDD (see SDD WIKI), ABCD (see ABCD content schema homepage) or TaxonConceptNames (see Taxonomic Concept Transfer Schema WIKI). * Unified Biosciences Information Frameword (UBIF) XML schema for data exchange and integration across knowledge domains. The schema has been design for biological data, but is applicable to other knowledge areas as well. It is based on work of the TDWG SDD and ABCD subgroups and currently jointly authored by the SDD, ABCD, TaxonName subgroups and by GBIF (Global Biodiversity Information Facility). The framework may be used without changes for new schemata, no registration is necessary. * Complex Types are part of the UBIF infrastructure (TDWG common complex type for several schemas, ABCD, SDD, TCS, Lnnean Core, etc.)
  • Photo: PICT0173.jpg Sub-section from Whale Safari to Kaikoura New Zealand. Photo Dag Terje Filip Endresen [http://r142b.ngb.se/ngb/2004-10-New-Zealand-Australia/index.php?offset=79&size=medium&stp=1]
  • Slide by Samy Gaiji, from presentation on: “ Information Networking - Challenges for the Plant Genetic Resources Communities, 2004.
  • Slide by Samy Gaiji, from presentation on: “ Information Networking - Challenges for the Plant Genetic Resources Communities, 2004.
  • Web services for sharing germplasm data sets, at FAO in Rome (2006)

    1. 1. Sharing of germplasm data with Web Services February 20, 2006 FAO, Rome, Italy Dag Endresen The Nordic Gene Bank, IPGRI
    2. 2. TOPICS <ul><li>Germplasm data </li></ul><ul><li>Data Standards </li></ul><ul><li>Data exchange </li></ul>
    3. 3. Germplasm data <ul><li>The Germplasm data describe very similar data objects as the natural history museums and the botanical gardens. </li></ul><ul><li>Preserved reference 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. </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>[http://www.bgbm.org/TDWG/CODATA/ABCD-Evolution.htm]
    4. 4. <ul><li>Data Standards </li></ul>
    5. 5. MCPD M ulti C rop P assport D escriptors <ul><li>The MCPD is designed to be compatible with the IPGRI crop specific descriptor lists and the FAO World Information and Early Warning System ( WIEWS ). </li></ul><ul><li>The MCPD descriptor list is compatible with ABCD (2.06). </li></ul>
    6. 6. IPGRI Crop Specific Descriptors <ul><li>The IPGRI crop descriptors (as well as other networks) expand the MCPD List to meet specific needs for these crops. </li></ul><ul><li>The International Union for the Protection of New Varieties of Plants ( UPOV ) maintains crop descriptors for protection of intellectual property right (since 1961). </li></ul><ul><li>The COMECON descriptor lists came even earlier, and was the result of a cooperation of the Eastern European Genebanks in PGR documentation (1949 –1999). </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://darwincore.calacademy.org/] </li></ul><ul><li>Access to Biological Collection Data (ABCD) 2.06 - 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://www.bgbm.org/TDWG/CODATA/Schema/] </li></ul><ul><li>ABCD 2.06 is compatible with MCPD. </li></ul>
    8. 8. PGR sub-unit of ABCD <ul><li>PGR </li></ul>
    9. 9. Generation Challenge Programme <ul><li>In the context of the GCP (Generation Challenge Programme), the GCP_Passport data exchange schema was developed. </li></ul><ul><li>Similar XML schema are under development for Phenotype (trait data) and Genotype </li></ul>
    10. 10. <ul><li>Biodiversity informatics </li></ul><ul><li>data exchange tools </li></ul>
    11. 11. Data Provider Software <ul><li>Distributed network of data providers retrieving structured data from multiple, distributed, heterogeneous databases across the Internet. </li></ul><ul><li>DiGIR , Di stributed G eneric I nformation R etrieval. [http://digir.net] </li></ul><ul><li>BioCASE , The Biological Collection Access Service for Europe. </li></ul><ul><li>[http://www.biocase.org/] </li></ul>
    12. 12. BioCASE Bio logical C ollection A ccess for E urope <ul><li>BioCASE data provider software has been implemented at (almost) all the CGIAR germplasm centers during the autumn of 2005. </li></ul><ul><li>Several genebanks have installed the GBIF web service technology. Nordic Gene Bank, IPK Gatersleben, IHAR (DiGIR), USDA GRIN, CGN, more to follow soon. </li></ul>[www.biocase.org/]
    13. 13. BioMOBY <ul><li>BioMOBY is an international research project on methodologies for biological data representation, distribution, and discovery. </li></ul><ul><li>BioMOBY is chosen as the web service framework for the Generation Challenge Program </li></ul><ul><li>[http://www.biomoby.org/] </li></ul><ul><li>Work is in progress to develop BioMOBY and BioCASE interoperability. </li></ul>
    14. 14. <ul><li>Biodiversity informatics workflow tools </li></ul>
    15. 15. Workbench <ul><li>Bioinformatics analyses often involve combining the use of databases and analysis programs which are linked in a specific order to form a workflow process. </li></ul><ul><li>Flow of data from one analytical step to another can be captured in a formal workflow language. </li></ul>
    16. 16. Taverna workflow <ul><li>The Taverna Workbench allows users to construct complex analysis workflows from components located on both remote and local machines, run these workflows on their own data and visualize the results. </li></ul><ul><li>BioMOBY objects can be connected in a workflow. </li></ul><ul><li>[http://taverna.sourceforge.net/] </li></ul>
    17. 17. <ul><li>Web service technology </li></ul>
    18. 18. Some web service keywords <ul><li>Application-to-application </li></ul><ul><li>Platform independent </li></ul><ul><li>Programming language independent </li></ul><ul><li>Object model independent </li></ul>
    19. 19. Example of a service call <ul><li>All exchanged data is formatted with XML tags. </li></ul>
    20. 20. Example of a service response
    21. 21. Data warehouse model (Slide by Samy Gaiji, IPGRI)
    22. 22. Decentralized model (Slide by Samy Gaiji, IPGRI)
    23. 23. Data flow from genebanks to EURISCO and ECCDBs
    24. 24. Decentralized model
    25. 25. Demo Data Portal <ul><li>A demo data portal was developed, providing live access to the BioCASE data providers. </li></ul>
    26. 26. Germplasm data harvest <ul><li>We are now building data harvest methodologies for access to global germplasm data. </li></ul><ul><li>This is planned to build a Germplasm Clearing House Mechanism. </li></ul><ul><li>In cooperation with GBIF, which themselves harvest global biodiversity data from a similar approach. </li></ul>
    27. 27. Thank you for listening!