Prototype Crop Wild Relatives Global Portal, GBIF GB14 nodes meeting (2007)
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Prototype Crop Wild Relatives Global Portal, GBIF GB14 nodes meeting (2007)

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Crop Wild Relatives Data Portal using web services from the GBIF infrastructure. GBIF Governing Board (GB14) NODES meeting in Amsterdam 14th October 2007.

Crop Wild Relatives Data Portal using web services from the GBIF infrastructure. GBIF Governing Board (GB14) NODES meeting in Amsterdam 14th October 2007.

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  • Some keywords; the main topics of the talk
  • Some keywords; the main topics of the talk
  • Image: Dioscorea in a bowl , Photo by Annie Lane
  • [http://www.biocase.org/index.shtml]
  • Image: Cotton , Uzbekistan , photo by Annie L ane .
  • Image: Cotton , Uzbekistan , photo by Annie L ane .
  • Image: Cotton , Uzbekistan , photo by Annie L ane .
  • http://commons.wikimedia.org/wiki/Image:Herfstprei_Tara.jpg http://data.gbif.org/ws/rest/occurrence/count?scientificname=Allium+porrum&georeferencedonly=true&stylesheet=
  • http://commons.wikimedia.org/wiki/Image:Allium_porrum_porrum_HabitusInflorescences_BotGardBln0906.JPG http://data.gbif.org/ws/rest/occurrence/count?scientificname=Allium+porrum&georeferencedonly=&stylesheet=
  • Image: Cotton , Uzbekistan , photo by Annie L ane .
  • Some keywords; the main topics of the talk
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Samy to provide more input...? Release in December 2006? With approximately 2.2 million accessions indexed. Helmut suggest to describe CHM
  • Solanum tuberosum L. Potato. Light sprout. Photographer NGB (NGB Picture Archive, image 001289).
  • Image: Spider in a spiderweb Image: Imke Thormann Image: Annie Lane Image: Allison Polous Image: Dag Terje Filip Endresen (in Benin)

Prototype Crop Wild Relatives Global Portal, GBIF GB14 nodes meeting (2007) Prototype Crop Wild Relatives Global Portal, GBIF GB14 nodes meeting (2007) Presentation Transcript

  • Cover slide GBIF Data Portal Use case of the Crop Wild Relatives Data Portal using web services from the GBIF Data portal Agenda item 6.1 Portal – examples and conclusions October 14, 2007, NODES 9, GB14, Amsterdam Dag Terje Filip Endresen Nordic Gene Bank (Sweden) Bioversity International (Italy)
  • TOPICS
    • Crop Wild Relatives Global Data Portal
    • External CWR datasets
    • Use case: GBIF Portal web service interface
  • Keywords
    • A portal to crop wild relatives genetic resources:
    • Taxonomy level metadata
    • Country level metadata
    • Data exchange, distributed data network
  • Project partners
    • International partners
      • Bioversity International
      • BLE , Federal Agency for Agriculture and Food, Germany
      • UNEP GEF , Global Environment Facility
      • UNEP WCMC , World Conservation Monitoring Centre
      • FAO , UN Food and Agriculture Organization
      • IUCN , The World Conservation Union
      • BGCI , Botanical Gardens Conservation International
    • National partners
      • Armenia , Ministry of Nature Protection of the Republic of Armenia
      • Bolivia , Ministerio de Desarrollo Rural, Agropecuario y Medio Ambiente
      • Madagascar , Centre National de la Recherche Appliquée au Développement Rural
      • Sri Lanka , Department of Agriculture
      • Uzbekistan , Plants Genetic Resources in Central Asia and Caucasus
  • A distributed data network ARM LKA BOL MDG UZB National Datasets are shared using the CWR GRIS system. (Implementation of PyWrapper3 and Darwin Core (DwC) is in progress.) The national CWR datasets and other relevant International datasets are indexed by the CWR data portal. EURISCO SINGER
  • Data Sharing Software
    • CWR GRIS v.1.0 is based on the GeoNetwork data management and data sharing software.
    • Other data sharing alternatives include PyWrapper3 (and perhaps DiGIR):
      • PyWrapper is based on the BioCASE Python wrapper software. [ http://www.pywrapper.org/]
      • DiGIR , Di stributed G eneric I nformation R etrieval. [http://digir.net]
  • The data portal application
    • [ http://cwrint.grinfo.net]
    • The data portal application is tested to work well with MS Windows, Mac OSX, Linux, FreeBSD...
    • The data portal is developed for the PostgreSQL database, but works well with many different database systems , through the ADODB database abstraction library.
    • The data portal is developed for UNICODE
    • ضاإطقكغب שּׁשׁﭻﭗﭼﱠ אָבּדּוּ
    • The data portal is Open Source and licensed as GPL 2 .
    • The data portal is developed with the PHP5 programming language, with some maintenance scripts developed with Perl .
    • [http://wwwdev.ngb.se/WebSVN/listing.php?repname=data_portal]
  • Login Login for administrator permissions.
  • Import external dataset
    • The portal admin can import an external dataset:
    • Download dataset (if online)
    • Unpack dataset (if zipped)
    • Convert to tab-separated text
    • Recode to Unicode (if needed)
    • Convert to SQL INSERT script
    • Import dataset to replace previous version
    • Update species and country level metadata
    • Examples: FAO WIEWS, BGCI, IUCN, WDPA, EURISCO, SINGER.
  • GBIF Portal The CWR Portal provides the summary number of records from the GBIF Data Portal on the CWR species list. This summary number of records is regularly indexed to speed up the loading of the CWR Portal pages for species level and country level metadata. Whenever displayed, this summary number of records provides a deep-link back to the GBIF Data Portal.
  • GBIF Data Portal, web service interface PHP Code: function gbif_count_occurrences ($taxon_name, $country_iso2, $georeferenced_only = 'false') { /** * function : gbif_count_occurrences * Connect to the GBIF Data Portal and calculate summary species level or country level record count * INPUT : Species name, Country ISO-2 Code, Georeferenced_only (true/false) */ $totalMatched = ''; // init variable if ($country_iso2) : $country_iso2 = strtoupper($country_iso2); endif; $rest_url = &quot; http://data.gbif.org/ws/rest/occurrence/count? &quot;; $rest_url .= &quot; stylesheet= &quot;; // switch off stylesheet browser formatting if ($taxon_name) : $rest_url .= &quot; &scientificname= &quot; . urlencode($taxon_name); endif; if ($country_iso2) : $rest_url .= &quot; &originisocountrycode= &quot; . strtoupper($country_iso2); endif; $rest_url .= &quot; &georeferencedonly= &quot; . $georeferenced_only; // switch for georeferenced ONLY on/off $file_content = file_get_contents($rest_url); // Read the GBIF Data Portal web service response as REST URL $xml = new SimpleXMLElement($file_content); $xml->registerXPathNamespace('gbif', 'http://portal.gbif.org/ws/response/gbif'); // Register namespace $result = $xml->xpath('//gbif:summary[1]'); foreach ($result as $data_node) { foreach ($data_node->attributes() as $key => $value) { if ($key == 'totalMatched') { $totalMatched = (string)$value; } // end if key totalMatched } // end foreach data_node attribute } // end foreach result data_node # echo &quot;<xmp> &quot; . $file_content . &quot;</xmp><hr /> &quot;; // DEBUG return $totalMatched; } Examples: http://data. gbif .org/ ws /rest/occurrence/count? scientificname = Allium + porrum & georeferencedonly =true& stylesheet = http://data. gbif .org/ ws /rest/occurrence/count? scientificname = Allium + porrum & georeferencedonly =& stylesheet =
  • GBIF Data Portal, web service
  • GBIF Data Portal, web service
  • GBIF Data Portal
    • http://data.gbif.org
    • http://data.gbif.org/tutorial/services
    • http://data.gbif.org/ws/rest/occurrence/
    • Plant Genetic Resources (GBIF Network)
    • http://data.gbif.org/datasets/network/2
  • CWR Portal [http://cwrint.grinfo.net] T
  • CWR Portal - About The CWR Global Portal has an “About” section. Here you will find information pages about the content of the CWR portal.
  • Search CWR species
    • The keyword search in the top menu is for taxon level metadata data.
    • The portal species metadata is based on the CWR species names provided from the national partners.
  • Search CWR species
    • The advanced search form is the same template for all the CWR data units.
    • Select descriptor from the select list to build a filter condition.
  • Search Results
    • You may modify the list of your search results to add descriptors…
  • Search Results
    • … or remove added descriptors using the “x” in the column title.
  • Search Results
    • You may modify how many hits to display per page .
    • When there are more search hits, the navigation controls are displayed.
  • Search Results
    • Click the column title to change the list order.
    • Select the same column again for reverse order.
    • Most column titles have a tip when you move the mouse over the title.
  • Search Results
    • The letterbar offer a fast way to filter results by the first letter of the sort order column.
    • You may filter by the first letter, the first two letters… etc.
  • Search results
    • The species list has a link to the “Taxon level metadata” page.
    • … the country list has a link to the “Country level metadata” page.
  • Species level metadata
    • Species and Country lists have a link to a summary CWR metadata page.
    • You will also find deep links to relevant online CWR resources.
  • Country level metadata
    • Country level summary CWR metadata:
  • Contact institutes and persons Institutes and persons as part of the CWR Network are listed.
  • A simple image gallery A simple image gallery for CWR resources is also part of the CWR portal.
  • Web mapping
    • A Web Mapping application is under development.
    • CWR occurrence data from the National Inventories will be displayed with the UMN MapServer and Mapbender .
  • Outlook
    • The compatibility of data standards between Plant Genetic Resources (PGR) and other biodiversity collections made it possible to integrate the worldwide ex situ germplasm collections into the biodiversity community.
    • 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 new distributed data network for Crop Wild Relatives (CWR) builds further on the experiences of the ex situ genebanks for keeping compatibility with the GBIF/TDWG technology and standards…
  • Special thanks to
    • Bioversity International [http://www.bioversityinternational.org]
    • GBIF, Global Biodiversity Information Facility [http://www.gbif.org]
    • TDWG , Taxonomic Database Working Group [http://www.tdwg.org]
  • Thank you for listening!