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)

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Data exchange

Cartoon by Sasha Kopf (Creative Commons)

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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

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

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BioCASE 2.5• 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

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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 TorreSource code: Python

14/07/2008 - Development stalledWe 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 0.6.1Home: http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLinkPrimary developers: Renato De Giovanni, Dave VieglaisDownload: http://sourceforge.net/project/showfiles.php?group_id=38190Source code: PHP

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!

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GBIF IPTHome: http://code.google.com/p/gbif-providertoolkit/ Primary developers: Markus Döring, Tim RobertsonDownload: http://code.google.com/p/gbif-providertoolkit/downloads/list Source code: Java

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

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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

http://an.oa.org/OAI-script?verb=GetRecord&identifier=oai:arXiv.org:hep-th/9901001&metadataPrefix=oai_dc

OAI-PMH requests are submitted using either the HTTP GET or POST methods.

Request types:IdentifyListMetadataFormatsListSetsGetRecordListIdentifiersListRecords

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EXAMPLE OF OAI-PMH SERVICE RESPONSE

OAI-PMH responses formatted as HTTP.With The Content-Type as text/xml.

GBIF PGR Network 2

[http://data.gbif.org/datasets/network/2]26

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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)

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Special thanks to

• Bioversity International http://www.bioversityinternational.org

• GBIF, Global Biodiversity Information Facility http://www.gbif.org

• BioCASE, The Biological Collection Access Service for Europe. http://www.biocase.org

• TDWG, Biodiversity Information Standards http://www.tdwg.org

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Data portal example (2006)

31http://wwwdev.ngb.se/portal/index.php?scope=demo

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Data Harvest

GBIF GBRDS

http://gbrds.gbif.org 37

GBIF GBRDS

http://gbrds.gbif.org 38

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Fallacies of Distributed Computing

1. The network is reliable.2. Latency is zero.3. Bandwidth is infinite.4. The network is secure.5. Topology doesn't change.6. There is one administrator.7. Transport cost is zero.8. The network is homogeneous.

This list of fallacies came about at Sun Microsystems around 1994.