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Data exchange alternatives, GIGA TAG (2009)

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GIGA TAG meeting at Bioversity International, Rome, Italy 18th May 2009. Data exchange alternatives for the Global Information on Germplasm Accessions (GIGA) project. Dag Endresen …

GIGA TAG meeting at Bioversity International, Rome, Italy 18th May 2009. Data exchange alternatives for the Global Information on Germplasm Accessions (GIGA) project. 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/]
  • http://www.bigfoto.com/miscellaneous/photos-05/index.htm
  • Photo: PICT0173.jpg Sub-section from Whale Safari to Kaikoura New Zealand. Photo Dag Terje Filip Endresen, October 2004.
  • http://www.tdwg.org
  • More details see:GBIF NODES meeting 2007 in Amsterdam.Agenda 09 Technical Training session - TAPIR/PyWrapper3:http://circa.gbif.net/Public/irc/gbif/nodes/library?l=/meetings/2007_10_amsterdam/tapir_pywrapper3/_EN_1.0_&a=i
  • More details see:GBIF NODES meeting 2007 in Amsterdam.Agenda 09 Technical Training session - TAPIR/PyWrapper3:http://circa.gbif.net/Public/irc/gbif/nodes/library?l=/meetings/2007_10_amsterdam/tapir_pywrapper3/_EN_1.0_&a=i
  • IMAGE source: http://commons.wikimedia.org/wiki/Image:Handshake_(Workshop_Cologne_%2706).jpeg; Copyright: GNU Public Licence
  • 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
  • http://wwwdev.ngb.se/portal/index.php?scope=demohttp://chm.grinfo.net/index.php?app=data_providers
  • http://wwwdev.ngb.se/portal/index.php?scope=demohttp://chm.grinfo.net/index.php?app=data_providers
  • http://wwwdev.ngb.se/portal/index.php?scope=demohttp://chm.grinfo.net/index.php?app=data_providers
  • http://wwwdev.ngb.se/portal/index.php?scope=demohttp://chm.grinfo.net/index.php?app=data_providers
  • http://wwwdev.ngb.se/portal/index.php?scope=demohttp://chm.grinfo.net/index.php?app=data_providers
  • IMAGE source: http://commons.wikimedia.org/wiki/Image:Handshake_(Workshop_Cologne_%2706).jpeg; Copyright: GNU Public Licence
  • Image source: University of Ottawa, Distributed Computing Research Group: http://www.genie.uottawa.ca/research/rsrch_site.php?lang=e&id=90 (Google Images).See also: http://en.wikipedia.org/wiki/Fallacies_of_Distributed_Computing
  • Transcript

    • 1. Data exchange alternatives
      Global Information on Germplasm Accessions (GIGA, ALIS)
      2nd GIGA Technical Advisory Group Meeting
      Dag Terje Filip Endresen, Nordic Genetic Resources Center, NordGen (Sweden)
    • 2. Data exchange
      2
      Cartoon by Sasha Kopf (Creative Commons)
    • 3. Data Exchange Format
      MCPD (1997)
      Multi Crop Passport Descriptors
      Darwin Core (2001) **
      New version up for revision at TDWG2009
      http://rs.tdwg.org/dwc/index.htm
      ABCD (2001)
      Access to Biological Collections Data
      http://wiki.tdwg.org/twiki/bin/view/ABCD
      GCP Passport (2005)
      http://www.generationcp.org
      Ontology (including all above)
      perhaps develop a new GIGA ontology
      3
    • 4. Data Provider Software
      BioMOBY (2001)
      http://biomoby.org
      DiGIR (2002, not active)
      http://digir.sourceforge.net
      BioCASE (2003, PyWrapper v2)
      http://www.biocase.org
      EURISCO (2003, tab delimited text)
      http://eurisco.ecpgr.org
      PyWrapper 3 (2006, not active)
      http://trac.pywrapper.org
      TapirLink (2007)
      http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink
      GBIF Provider Toolkit (2009) **
      http://code.google.com/p/gbif-providertoolkit
      4
    • 5. Data Harvest Infrastructure
      GIGA Registry (UDDI)
      New GIGA registry for germplasm dataset?
      ICIS and CropForge tools
      http://cropwiki.irri.org/icis/
      https://cropforge.org/
      GBIF data portal and registry**
      http://data.gbif.org
      gbrds.gbif.org (registry)
      GBIF Indexing Toolkit (2009)
      http://code.google.com/p/gbif-indexingtoolkit/
      5
    • 6. Data Provider Software
      6
    • 7. EURISCO tab delimited upload
      http://eurisco.ecpgr.org
      7
    • 8. 8
      BioMOBY
      The BioMOBY project was initiated in 2001 (in Saskatchewan, Canada).
      Two branches, web service and semantic (MOBY-S).
      MOBY ontology-aware registry for discovery of both data and services.
      Works well with TAPIR and BioCASE.
      GCP have selected BioMOBY as the main web service technology.
      http://biomoby.org
    • 9. BioCASE 2.5
      9
      The BioCASE provider software is a product of the EU funded BioCASE project (2001-2004).
      Developed at BGBM in Berlin.
      Last updated in April 2008, with support for Python version 2.5
      Data formats include: ABCD 2.06, Darwin Core, GCP_Passport, MCPD.
      http://www.biocase.org
    • 10. BioCASE 2.5
      Configuration
      • Add datasource (dsa)
      • 11. Database connection
      • 12. Database table structure
      • 13. Mapping of data model to standard schema
      10
    • 14. TAPIR
      TAPIR - TDWG Access Protocol for Information Retrieval.
      During the 2004 TDWG meeting in Christchurch, NZ, work started on a unified protocol and named TAPIR.
      TAPIR is based on the protocol from the two data provider software, BioCASE and DiGIR.
      11
    • 15. PyWrapper3
      Home:http://trac.pywrapper.org/
      Primary developers: Markus Döring, Javier de la Torre
      Source code: Python
      14/07/2008 - Development stalled
      We are sorry to inform you that development of the TAPIR branch of PyWrapper has been stalled. The latest 3.1 alpha version is not stable and not recommended for production! (Message from the home page)
      PyWrapper is tested and verified to work fine with Windows, Mac OS X and Linux.
      12
    • 16. Web configuration tool
      PyWrapper graphical web based configuration tool
      13
    • 17. TapirLink 0.6.1
      Home: http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLink
      Primary developers: Renato De Giovanni, Dave Vieglais
      Download: http://sourceforge.net/project/showfiles.php?group_id=38190
      Source code: PHP
      14
      Test resource with client form:
      http://localhost/tapirlink/tapir_client.php
      The XML Client form is very illustrative for understanding exactly how the wrapper software works!
    • 18. GBIF IPT
      Home: http://code.google.com/p/gbif-providertoolkit/
      Primary developers: Markus Döring, Tim Robertson
      Download: http://code.google.com/p/gbif-providertoolkit/downloads/list
      Source code: Java
      15
      DEMO at http://atlas.nordgen.org/ipt/
    • 19. GBIF IPT
      • The GBIF IPT is an open source, Java (TM) based web application that connects and serves three types of biodiversity data: taxon primary occurrence data, taxon checklists and general resource metadata.
      • 20. The data registered in the IPT is connected to the GBIF distributed network and made available for public consultation and use.
      • 21. Designed to transfer big amounts of records. Decentralize and speed up the process of indexing biodiversity occurrence datasets.
      • 22. IPT also provides a local tool for data quality assessment to data publishers.
      • 23. The data publisher will easily monitor data access and use.
      16
    • 24. GBIF IPT
      17
    • 25. GBIF IPT
      18
    • 26. IPT
      19
    • 27. GBIF IPT
      20
    • 28. Web service interface
      21
    • 29. Example TAPIR service SEARCH request
      22
    • 30. Example TAPIR service Search response
      23
    • 31. Example of OAI-PMH service request
      Request types:
      Identify
      ListMetadataFormats
      ListSets
      GetRecord
      ListIdentifiers
      ListRecords
      http://an.oa.org/OAI-script?verb=GetRecord
      &identifier=oai:arXiv.org:hep-th/9901001
      &metadataPrefix=oai_dc
      24
      OAI-PMH requests are submitted using either the HTTP GET or POST methods.
    • 32. Example of OAI-PMH service RESPONSE
      25
      OAI-PMH responses formatted as HTTP.
      With The Content-Type as text/xml.
    • 33. GBIF PGR Network 2
      [http://data.gbif.org/datasets/network/2]
      26
    • 34. 27
      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
      RDF, LSID, ontology friendly
    • 35. 28
      Outlook
      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).
      Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.
      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.
      The establishment of new data portals and tools on a specific crop, a regional thematic network or similar subset of the total global biodiversity datasets; can be done with rather few efforts!
      Adopted from a slide by Helmut Knüpffer (IPK Gatersleben)
    • 36. Special thanks to
      29
      • Bioversity International
      http://www.bioversityinternational.org
      • GBIF, Global Biodiversity Information Facility http://www.gbif.org
      • 37. BioCASE, The Biological Collection Access Service for Europe.
      http://www.biocase.org
      • TDWG, Biodiversity Information Standards http://www.tdwg.org
    • Data portal example (2006)
      30
    • 38. 31
      http://wwwdev.ngb.se/portal/index.php?scope=demo
    • 39. 32
    • 40. 33
    • 41. 34
    • 42. 35
    • 43. Data Harvest
      36
    • 44. GBIF GBRDS
      http://gbrds.gbif.org
      37
    • 45. GBIF GBRDS
      http://gbrds.gbif.org
      38
    • 46. Fallacies of Distributed Computing
      The network is reliable.
      Latency is zero.
      Bandwidth is infinite.
      The network is secure.
      Topology doesn't change.
      There is one administrator.
      Transport cost is zero.
      The network is homogeneous.
      This list of fallacies came about at Sun Microsystems around 1994.
      39

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