Web services for sharing germplasm data sets, at FAO in Rome (2006)

The Nordic Gene Bank, NGB, Alnarp, SwedenThe Nordic Gene Bank, NGB, Alnarp, Sweden

Sharing of germplasm data with Web Services

February 20, 2006FAO, Rome, Italy

Dag EndresenThe Nordic Gene Bank, IPGRI

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TOPICSTOPICS

Germplasm data

Data Standards Data exchange

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Germplasm dataGermplasm data

The Germplasm data describe very similar data objects as the natural history museums and the botanical gardens.

Preserved reference collections, such as those in museums and herbaria.

Living collections, like botanical and zoological gardens, aquaria, seed banks, microbial strain cultures and tissue collections.

Data collections, from surveys of objects in the field, such as observations.

These collections have most of their attributes in common, although the terminology used to describe them may differ substantially.[http://www.bgbm.org/TDWG/CODATA/ABCD-Evolution.htm]

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Data Standards

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MCPDMCPD MMulti ulti CCrop rop PPassport assport DDescriptorsescriptors

The MCPD is designed to be compatible with the IPGRI crop specific descriptor lists and the FAO World Information and Early Warning System (WIEWS).

The MCPD descriptor list is compatible with ABCD (2.06).

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IPGRI Crop Specific IPGRI Crop Specific DescriptorsDescriptors

The IPGRI crop descriptors (as well as other networks) expand the MCPD List to meet specific needs for these crops.

The International Union for the Protection of New Varieties of Plants (UPOV) maintains crop descriptors for protection of intellectual property right (since 1961).

The COMECON descriptor lists came even earlier, and was the result of a cooperation of the Eastern European Genebanks in PGR documentation (1949 –1999).

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Taxonomic Database Working Taxonomic Database Working GroupGroup

Standards development and Standards development and maintenancemaintenance

Darwin Core 2 - Element definitions designed to support the sharing and integration of primary biodiversity data". [http://darwincore.calacademy.org/]

Access to Biological Collection Data (ABCD) 2.06 - An evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data)“.[http://www.bgbm.org/TDWG/CODATA/Schema/]

ABCD 2.06 is compatible with MCPD.

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PGR sub-unit of ABCDPGR sub-unit of ABCD

PGR

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Generation Challenge Generation Challenge ProgrammeProgramme

In the context of the GCP (Generation Challenge Programme), the GCP_Passport data exchange schema was developed.

Similar XML schema are under development for Phenotype (trait data) and Genotype

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Biodiversity informatics

data exchange tools

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Data Provider SoftwareData Provider Software

Distributed network of data providers retrieving structured data from multiple, distributed, heterogeneous databases across the Internet.

DiGIR, Distributed Generic Information Retrieval. [http://digir.net]

BioCASE, The Biological Collection Access Service for Europe.

[http://www.biocase.org/]

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BioCASE data provider software has been implemented at (almost) all the CGIAR germplasm centers during the autumn of 2005.

Several genebanks have installed the GBIF web service technology. Nordic Gene Bank, IPK Gatersleben, IHAR (DiGIR), USDA GRIN, CGN, more to follow soon.

BioCASEBioCASEBioBiological logical CCollection ollection AAccess for ccess for EEuropeurope

[www.biocase.org/]

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BioMOBYBioMOBY

BioMOBY is an international research project on methodologies for biological data representation, distribution, and discovery.

BioMOBY is chosen as the web service framework for the Generation Challenge Program[http://www.biomoby.org/]

Work is in progress to develop BioMOBY and BioCASE interoperability.

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Biodiversity informatics workflow

tools

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WorkbenchWorkbench

Bioinformatics analyses often involve combining the use of databases and analysis programs which are linked in a specific order to form a workflow process.

Flow of data from one analytical step to another can be captured in a formal workflow language.

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Taverna workflowTaverna workflow

The Taverna Workbench allows users to construct complex analysis workflows from components located on both remote and local machines, run these workflows on their own data and visualize the results.

BioMOBY objects can be connected in a workflow.

[http://taverna.sourceforge.net/]

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Web service

technology

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Some web service keywordsSome web service keywords

Application-to-application

Platform independent

Programming language independent

Object model independent

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Example of a service callExample of a service call

All exchanged data is formatted with XML tags.

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Example of a service Example of a service responseresponse

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Data warehouse modelData warehouse model(Slide by Samy Gaiji, IPGRI)(Slide by Samy Gaiji, IPGRI)

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Decentralized modelDecentralized model(Slide by Samy Gaiji, IPGRI)(Slide by Samy Gaiji, IPGRI)

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Data flow from genebanks to Data flow from genebanks to EURISCO and ECCDBs EURISCO and ECCDBs

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Decentralized modelDecentralized model

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Demo Data PortalDemo Data Portal

A demo data portal was developed, providing live access to the BioCASE data providers.

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Germplasm data harvestGermplasm data harvest

We are now building data harvest methodologies for access to global germplasm data.

This is planned to build a Germplasm Clearing House Mechanism.

In cooperation with GBIF, which themselves harvest global biodiversity data from a similar approach.

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Thank you for listening!