Germplasm data exchange, CGIAR SINGER (2009)
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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)

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

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  • IMAGE: http://blog.tapirtype.com/cartoons/ [Creative Commons License: http://creativecommons.org/licenses/by-nc-sa/3.0/us/]
  • TAPIR(2004 ->) http://www.tdwg.org/standards/449/ICIS (International Crop Information System): http://www.icis.cgiar.orgBioMOBY (2001)http://biomoby.org, http://en.wikipedia.org/wiki/BioMOBYDiGIR (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)http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLinkGBIF Provider Toolkit (2009)http://code.google.com/p/gbif-providertoolkit
  • http://ipt.nordgen.org/ipt/occResource.html?resource_id=45
  • http://ipt.nordgen.org/ipt/occTaxon.html?resource_id=45&id=41799http://ipt.nordgen.org/ipt/occDetail.html?guid=9099d7ce-8546-47d6-825b-eb599477dafd&resource_id=45http://ipt.nordgen.org/ipt/occ/9099d7ce-8546-47d6-825b-eb599477dafd/xml
  • http://atlas.nordgen.org/rs/ipt/ipt_germplasm.xmlhttp://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germplasm/dwc_germplasm.xsd
  • http://en.wikipedia.org/wiki/Darwin_Corehttp://rs.tdwg.org/dwc/terms/index.htmhttp://code.google.com/p/darwincore/http://code.google.com/p/darwincore/source/browse/#svn/trunk/xsd/profiles/germplasm

Germplasm data exchange, CGIAR SINGER (2009) Germplasm data exchange, CGIAR SINGER (2009) Presentation Transcript

  • Data exchange alternatives
    GBIF Tools and Darwin Core germplasm extension
    Cartoon by Sasha Kopf (Creative Commons)
    SINGER GPG2 Consultation Meeting, USDA, Washington DC
    Dag Terje Filip Endresen, Nordic Genetic Resources Center, NordGen (Sweden)
  • GBIF IPT
    Home: http://code.google.com/p/gbif-providertoolkit/
    Primary developers: Markus Döring, Tim Robertson
    Source code: Java Released: 2009
    Alternatives:
    -------
    • TAPIR (2004 ->)
    -------
    • DiGIR(PHP, 2001-2006)
    • TapirLink(PHP, 2007 ->)
    -------
    • BioCASE(Python, 2001-2008)
    • PyWrapper3 (Python, 2006-2008)
    -------
    • EURISCO (tab-delimited, 2003)
    -------
    • ICIS (Java, 1996 ->)
    -------
    • BioMOBY(Perl, 2001 ->)
    DEMO at http://ipt.nordgen.org/ipt/
    2
  • GBIF IPT
    The GBIF IPT service comes with a graphical interface to explore the datasets published.
    The visitor may explore the dataset from the map, different pie charts, or the right side context menu (taxonomy and geography).
    3
  • IPT
    Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.
    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).
    4
  • GBIF IPT
    GBIF IPT implements the Darwin Core Standard; and provides an interface to easily build extensions to the core Darwin Core terms.
    The draft germplasm extension is one example of how-to extend the Darwin Core terms for the GBIF IPT.
    http://atlas.nordgen.org/rs/ipt/ipt_germplasm.xml
    http://code.google.com/p/darwincore/source/browse/trunk/xsd/profiles/germplasm/dwc_germplasm.xsd
    5
  • Darwin Core
    A new version of Darwin Core is up for public review.
    http://rs.tdwg.org/dwc/terms/index.htm
    TDWG 2009, Montpellier, November 9 -13
    DRAFT Germplasm extension
    http://code.google.com/p/darwincore/source/browse/#svn/trunk/xsd/profiles/germplasm
    Please consider to contribute!
    RDF, LSID, ontology friendly
    6
  • GBIF PGR Network 2
    PGR GBIF network
    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.
    [http://data.gbif.org/datasets/network/2]
    7
  • GBIF GBRDS
    http://gbrds.gbif.org
    8
    Slide prepared by GBIF (SamyGaiji)
  • GBIF GBRDS
    http://gbrds.gbif.org
    9
    Slide prepared by GBIF (SamyGaiji)
  • GBIF IPT
    • The GBIF IPT is an open source, Java (TM) based web application that connects and serves primary biodiversity data.
    • The data registered in the IPT is connected to the GBIF distributed network and made available for public access.
    • Designed to decentralize and speed up the process of indexing (large) biodiversity occurrence datasets.
    • IPT also provides a local tool for data quality assessment to data publishers.
    • The data publisher can easily monitor data access and use.
    10
  • Special thanks to
    • GBIF, Global Biodiversity Information Facility http://www.gbif.org
    • TDWG, Biodiversity Information Standards http://www.tdwg.org
    • BioCASE, The Biological Collection Access Service for Europe.
    http://www.biocase.org
    • Bioversity International
    http://www.bioversityinternational.org
    Things can happen in a band, or any type of collaboration, that would not otherwise happen. (Jim Coleman, Musician)
    11