BioCASE web services for germplasm data sets, at FAO, Rome (2006)
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Sharing of biodiversity data with web services - demonstration of the BioCASE software. Food and Agriculture Organization of the United Nations (FAO) 2nd March 2006.
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BioCASE web services for germplasm data sets, at FAO, Rome (2006)
- 1. Sharing of biodiversity data with Web Services Demonstration of BioCASE
- 21. BioCASE protocol stack
- 27. Example of a service response
- 30. TAPIR service response singer:/sourcename singer:/taxonomy/genus singer:/taxonomy/species singer:/taxonomy/subspecies singer:/holding/ID singer:/holding/name singer:/origin/collecting/countrysource singer:/origin/collecting/countrysourceID singer:/status/biologicalstatus singer:/status/biologicalstatusID ...
- 32. Data warehouse model (Slide by Samy Gaiji, IPGRI)
- 33. Decentralized model (Slide by Samy Gaiji, IPGRI)
- 34. Data flow from genebanks to EURISCO and ECCDBs
- 38. BioCASE and germplasm data [http://chm.grinfo.net/index.php?app=data_providers]
- 40. Thank you for listening!
Notes de l'éditeur
- * Text formulation source [http://www.bgbm.org/TDWG/CODATA/ABCD-Evolution.htm] wording above is modified. * Photo (top): Beetle collection in Benin, West Africa (March 24 2004). Photographer Dag Endresen. [http://r142b.ngb.se/ngb/2003-03_Cotonou_Benin/index.php?offset=85&size=medium&stp=1]
- Photo (top) * Seed storage in Benin, West Africa (March 24 2004). Photographer Dag Endresen. [http://r142b.ngb.se/ngb/2003-03_Cotonou_Benin/index.php?offset=108&size=medium&stp=1] Photo (below)* VIR seed collection. St. Petersburg. Photographer Eva Thörn (NGB Picture Archive, image 001319).
- Photo: Field been from Boreal, accession NGB11518, 2005-03-05, Dag Endresen [http://r142b.ngb.se/ngb/2005-03--the-making-of-seeds-pictures/index.php?offset=19&size=medium&stp=1]
- * 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] * 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 continued by Javier de la Torre and Dag Terje Filip Endresen in 2005. [ http://ww3.bgbm.org/MCDPH] [ http://www.bgbm.org/TDWG/CODATA/Schema/Mappings/EURISCO-2-ABCD.pdf ]
- * 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.)
- * The mapping of MCPD to ABCD was started in 2004 by Helmut Knüpffer and Walter Berendsohn, and continued by Javier de la Torre and Dag Terje Filip Endresen in 2005. [ http://ww3.bgbm.org/MCDPH] [ http://www.bgbm.org/TDWG/CODATA/Schema/Mappings/EURISCO-2-ABCD.pdf ]
- GCP_Passport v 1.03 [http://tor.ngb.se/dev/temp/gcp_passport_01_03.xsd]
- * Demo Data Portal [http://geifir.ngb.se/abcdproto/default.jsp] The work on the demo portal has been replaced by routines to harvest and index remote data. The live remote access proved to slow and unreliable. See the Germplasm Clearing House Mechanism for more info [http://chm.grinfo.net/].
- * Illustration: Tapir - © 1999-2005 www.barrysclipart.com (Licence “Feel free to use Barrys Clipart Server content in personal/ non profit projects to create webpages…”) [http://www.barrysclipart.com/barrysclipart.com/showphoto.php?photo=13376&papass=&sort=1&thecat=149] Not Quality counts: Chemist Gary List checks soybeans. Photo by Keith Weller. [ http://www.ars.usda.gov/is/graphics/photos/k5256-2.htm]
- 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]
- [http://www.biocase.org/index.shtml]
- BioCASE development is coordinated by the Botanischer Garten und Botanisches Museum Berlin-Dahlem – BGBM.
- http://www.biocase.org/whats_biocase/unit_net.shtml
- http://www.biocase.org/whats_biocase/unit_net.shtml
- http://tapir.grinfo.net/queryforms/qf_tapir.cgi?url=http://tapir.grinfo.net//pywrapper.cgi?dsa=SINGER
- http://tapir.grinfo.net/queryforms/qf_tapir.cgi?url=http://tapir.grinfo.net//pywrapper.cgi?dsa=SINGER <?xml version='1.0' encoding='UTF-8'?> <request> <header /> <inventory count='true' start='0' limit='40' xmlns:singer='http://singer.grinfo.net/schema/SINGER-1.0' > <concepts> <concept path='singer:/sourcename'/> <concept path='singer:/taxonomy/genus' /> <concept path='singer:/taxonomy/species' /> <concept path='singer:/taxonomy/subspecies' /> <concept path='singer:/holding/ID' /> <concept path='singer:/holding/name' /> <concept path='singer:/origin/collecting/countrysource' /> <concept path='singer:/origin/collecting/countrysourceID' /> <concept path='singer:/status/biologicalstatus' /> <concept path='singer:/status/biologicalstatusID' /> </concepts> <filter> <like> <concept path='singer:/taxonomy/genus' /> <literal value='cice*' /> </like> </filter> </inventory> </request>
- http://tapir.grinfo.net/queryforms/qf_tapir.cgi?url=http://tapir.grinfo.net//pywrapper.cgi?dsa=SINGER http://apps3.fao.org/wiews/wiews.jsp
- 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.
- http://apps3.fao.org/wiews/wiews.jsp
- Photo (top) IRRI genebank. Los Banos, Philippines [ http://www.cgiar.org/images/irrigenebank1.jpg] Photo (below) CIP genebank. Lima, Peru [http://www.cgiar.org/images/cipgenebank.jpg]
- http://chm.grinfo.net/index.php?app=data_providers