Germplasm data exchange, CGIAR SINGER (2009)


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CGIAR SINGER planning meeting on network infrastructure. At USDA GRIN, Washington, 25th August 2009. Dag Endresen (Bioversity/NordGen)

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  • IMAGE: [Creative Commons License:]
  • TAPIR(2004 ->) (International Crop Information System): http://www.icis.cgiar.orgBioMOBY (2001), (2002, not active)http://digir.sourceforge.netBioCASE (2003, PyWrapper v2)http://www.biocase.orgEURISCO (2003, tab delimited text)http://eurisco.ecpgr.orgPyWrapper 3 (2006, not active)http://trac.pywrapper.orgTapirLink (2007) Provider Toolkit (2009)
  • Germplasm data exchange, CGIAR SINGER (2009)

    1. 1. Data exchange alternatives<br />GBIF Tools and Darwin Core germplasm extension<br />Cartoon by Sasha Kopf (Creative Commons)<br />SINGER GPG2 Consultation Meeting, USDA, Washington DC<br />Dag Terje Filip Endresen, Nordic Genetic Resources Center, NordGen (Sweden)<br />
    2. 2. GBIF IPT<br />Home:<br />Primary developers: Markus Döring, Tim Robertson<br />Source code: Java Released: 2009<br />Alternatives:<br />-------<br /><ul><li> TAPIR (2004 ->)</li></ul>-------<br /><ul><li>DiGIR(PHP, 2001-2006)
    3. 3. TapirLink(PHP, 2007 ->)</li></ul>-------<br /><ul><li>BioCASE(Python, 2001-2008)
    4. 4. PyWrapper3 (Python, 2006-2008)</li></ul>-------<br /><ul><li> EURISCO (tab-delimited, 2003) </li></ul>-------<br /><ul><li> ICIS (Java, 1996 ->)</li></ul>-------<br /><ul><li>BioMOBY(Perl, 2001 ->)</li></ul>DEMO at<br />2<br />
    5. 5. GBIF IPT<br />The GBIF IPT service comes with a graphical interface to explore the datasets published.<br />The visitor may explore the dataset from the map, different pie charts, or the right side context menu (taxonomy and geography).<br />3<br />
    6. 6. IPT<br />Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF&apos;s work.<br />The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community (GBIF, TDWG).<br />4<br />
    7. 7. GBIF IPT<br />GBIF IPT implements the Darwin Core Standard; and provides an interface to easily build extensions to the core Darwin Core terms.<br />The draft germplasm extension is one example of how-to extend the Darwin Core terms for the GBIF IPT.<br /><br /><br />5<br />
    8. 8. Darwin Core<br />A new version of Darwin Core is up for public review.<br /><br />TDWG 2009, Montpellier, November 9 -13<br />DRAFT Germplasm extension<br /><br />Please consider to contribute!<br />RDF, LSID, ontology friendly<br />6<br />
    9. 9. GBIF PGR Network 2<br />PGR GBIF network<br />Use of GBIF technology and integration of PGR collection data into GBIF allows PGR users to simultaneously search PGR collections and other biodiversity collections, and to get access to the data (and possibly the material) of relevant biodiversity collections.<br />[]<br />7<br />
    10. 10. GBIF GBRDS<br /><br />8<br />Slide prepared by GBIF (SamyGaiji)<br />
    11. 11. GBIF GBRDS<br /><br />9<br />Slide prepared by GBIF (SamyGaiji)<br />
    12. 12. GBIF IPT<br /><ul><li> The GBIF IPT is an open source, Java (TM) based web application that connects and serves primary biodiversity data.
    13. 13. The data registered in the IPT is connected to the GBIF distributed network and made available for public access.
    14. 14. Designed to decentralize and speed up the process of indexing (large) biodiversity occurrence datasets.
    15. 15. IPT also provides a local tool for data quality assessment to data publishers.
    16. 16. The data publisher can easily monitor data access and use.</li></ul>10<br />
    17. 17. Special thanks to<br /><ul><li>GBIF, Global Biodiversity Information Facility
    18. 18. TDWG, Biodiversity Information Standards
    19. 19. BioCASE, The Biological Collection Access Service for Europe. </li></ul><br /><ul><li>Bioversity International </li></ul><br />Things can happen in a band, or any type of collaboration, that would not otherwise happen. (Jim Coleman, Musician)<br />11<br />