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

GBIF NODES9, GB14, Amsterdam, October 14 2007GBIF NODES9, GB14, Amsterdam, October 14 2007

Cover Cover slideslideGBIF Data

PortalUse 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 EndresenNordic Gene Bank (Sweden)Bioversity International (Italy)

CWR Global Portal, 2007-10-14, NODES9, AmsterdamCWR Global Portal, 2007-10-14, NODES9, Amsterdam 2

TOPICSTOPICS

Crop Wild Relatives Global Data Portal

External CWR datasets Use case: GBIF Portal web service interface


KeywordsKeywords

A portal to crop wild relatives genetic resources:

Taxonomy level metadata

Country level metadata Data exchange,

distributed data network


Project partnersProject 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 networkA distributed data network

ARM

LKA

BOL

MDG

UZB

National Datasetsare shared usingthe CWR GRIS system.

(Implementation of PyWrapper3 and Darwin Core (DwC)is in progress.)

The nationalCWR datasetsand other relevantInternational datasetsare indexed by theCWR data portal.

EURISCO

SINGER


Data Sharing SoftwareData 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, Distributed Generic Information Retrieval. [http://digir.net]


The data portal applicationThe 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 UNICODEאבדו ضاإطقكغب ששچپچ

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]


LoginLogin

Login for administrator permissions.


Import external Import external datasetdataset

The portal admin can import an external dataset:

1. Download dataset (if online)2. Unpack dataset (if zipped)3. Convert to tab-separated text4. Recode to Unicode (if needed)5. Convert to SQL INSERT script6. Import dataset to replace

previous version7. Update species and country

level metadata

Examples: FAO WIEWS, BGCI, IUCN, WDPA, EURISCO, SINGER.


GBIF PortalGBIF 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 GBIF Data Portal, web service interfaceinterface

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 = "http://data.gbif.org/ws/rest/occurrence/count?";

$rest_url .= "stylesheet="; // switch off stylesheet browser formatting

if ($taxon_name) : $rest_url .= "&scientificname=" . urlencode($taxon_name); endif;

if ($country_iso2) : $rest_url .= "&originisocountrycode=" . strtoupper($country_iso2); endif;

$rest_url .= "&georeferencedonly=" . $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 "<xmp>\n" . $file_content . "</xmp><hr />\n"; // 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 serviceGBIF Data Portal, web service


GBIF Data Portal, web serviceGBIF Data Portal, web service


GBIF Data PortalGBIF 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 PortalCWR Portal [http://cwrint.grinfo.net] [http://cwrint.grinfo.net]

T


CWR Portal - AboutCWR 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.


OutlookOutlook

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 toSpecial 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!

Technology

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