Data exchange alternatives, GIGA TAG (2009)

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)

Data exchange
2
Cartoon by Sasha Kopf (Creative Commons)

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
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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
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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/
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Data Provider Software
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EURISCO tab delimited upload
http://eurisco.ecpgr.org
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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

BioCASE 2.5
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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.

BioCASE 2.5
Configuration
Add datasource (dsa)
Database connection
Database table structure
Mapping of data model to standard schema
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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.
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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.
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Web configuration tool
PyWrapper graphical web based configuration tool
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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
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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!

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
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DEMO at http://atlas.nordgen.org/ipt/

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.
The data registered in the IPT is connected to the GBIF distributed network and made available for public consultation and use.
Designed to transfer big amounts of records. Decentralize and speed up the process of indexing biodiversity occurrence datasets.
IPT also provides a local tool for data quality assessment to data publishers.
The data publisher will easily monitor data access and use.
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GBIF IPT
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GBIF IPT
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IPT
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GBIF IPT
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Web service interface
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Example TAPIR service SEARCH request
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Example TAPIR service Search response
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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
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OAI-PMH requests are submitted using either the HTTP GET or POST methods.

Example of OAI-PMH service RESPONSE
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OAI-PMH responses formatted as HTTP.
With The Content-Type as text/xml.

GBIF PGR Network 2
[http://data.gbif.org/datasets/network/2]
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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

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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)

Special thanks to
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Bioversity International
http://www.bioversityinternational.org
GBIF, Global Biodiversity Information Facility http://www.gbif.org
BioCASE, The Biological Collection Access Service for Europe.
TDWG, Biodiversity Information Standards http://www.tdwg.org

Data portal example (2006)
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http://wwwdev.ngb.se/portal/index.php?scope=demo

Data Harvest
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GBIF GBRDS
http://gbrds.gbif.org
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GBIF GBRDS
http://gbrds.gbif.org
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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.
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Data exchange alternatives, GIGA TAG (2009)

by Dag Endresen

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