Presentation of Web Services for the Training Workshop on interoperability June 13, 2005 – IPGRI, Rome Dag Terje Filip Endresen – The Nordic Gene Bank

TOPICS for this talk Web Services Biodiversity data Standards Data exchange

Web Services

Biodiversity data

Standards

Data exchange

Simplicity and global standards Important factors behind the success of the web is simplicity and global standards. A service provider with a web site can reach the global community. Web services is about expanding the Web as a platform not only to information but also to services.

Important factors behind the success of the web is simplicity and global standards.

A service provider with a web site can reach the global community.

Web services is about expanding the Web as a platform not only to information but also to services.

Web Service definition – W3C A Web service is a software system identified by a URI, whose public interfaces and bindings are defined and described using XML. Its definition can be discovered by other software systems. These systems may then interact with the Web service in a manner prescribed by its definition, using XML based messages conveyed by Internet protocols. W3C, Web Services Glossary [http://www.w3.org/TR/ws-gloss]

A Web service is a software system identified by a URI, whose public interfaces and bindings are defined and described using XML.

Its definition can be discovered by other software systems.

These systems may then interact with the Web service in a manner prescribed by its definition, using XML based messages conveyed by Internet protocols.

W3C, Web Services Glossary

[http://www.w3.org/TR/ws-gloss]

Web Service definition - Wikipedia A web service is a collection of protocols and standards used for exchange of data between applications. Web services provide interoperability between various software applications running on disparate platforms. Interoperability (e.g., between Java and Python, or Windows and Linux applications) is due to the use of open standards . Web services easily allow software and services from different companies and locations to be combined to provide an integrated service . [http://en.wikipedia.org/wiki/Web_services]

A web service is a collection of protocols and standards used for exchange of data between applications.

Web services provide interoperability between various software applications running on disparate platforms.

Interoperability (e.g., between Java and Python, or Windows and Linux applications) is due to the use of open standards .

Web services easily allow software and services from different companies and locations to be combined to provide an integrated service .

[http://en.wikipedia.org/wiki/Web_services]

Some web service keywords Application-to-application Platform independent Programming language independent

Application-to-application

Platform independent

Programming language independent

Combination of services Web services can be combined to create new services. Seed bank Accession Inventory Weather Info Service GIS Species Occurrences Service New service to plan collecting missions for under-collected species to a period of good weather.

Web services can be combined to create new services.

Some Web Service standards XML : All exchanged data is formatted with XML, eXtensible M arkup L anguage. The message is transmitted through a transport protocol such as SOAP or RPC. WSDL : The public interface to the web service is described by W eb S ervices D escription L anguage (WSDL). This is an XML-based service description on how to communicate with the web service. UDDI : The web service information is published using this protocol. It enables applications to look up web services information in order to determine whether to use them. [ http://en.wikipedia.org/wiki/Web_services ]

XML : All exchanged data is formatted with XML, eXtensible M arkup L anguage. The message is transmitted through a transport protocol such as SOAP or RPC.

WSDL : The public interface to the web service is described by W eb S ervices D escription L anguage (WSDL). This is an XML-based service description on how to communicate with the web service.

UDDI : The web service information is published using this protocol. It enables applications to look up web services information in order to determine whether to use them.

[ http://en.wikipedia.org/wiki/Web_services ]

Example of a web service call All exchanged data is formatted with XML.

All exchanged data is formatted with XML.

Example of a service response

Message transport protocols * The message (XML) is transmitted through a service transport protocol such as SOAP or RPC. * And wrapped in a common internet transport protocol like HTTP, FTP, SMTP ... for transport through the internet.

* The message (XML) is transmitted through a service transport protocol such as SOAP or RPC.

* And wrapped in a common internet transport protocol like HTTP, FTP, SMTP ... for transport through the internet.

Regular SOAP message Information intended for the recipient is written in the body . Such as Remote Procedure Call information, XML messages, or error messages. The header contains additional information on the SOAP message . Such as digital signature information, transaction information, and routing information. The SOAP envelope consists of a header and a body.

Communication protocol Although SOAP does not depend on the underlying communication protocol, HTTP is usually used. Because of this, it is possible to communicate with Web services protected by firewalls.

Data warehouse model (Slide by Samy Gaiji)

Decentralized model (Slide by Samy Gaiji)

Network data flow The Data Provider is the web service package (wrapper) installed at the data source. The Data Portal is a gateway to data published from the data provider nodes. Provider wrapper software Provider etc... DB User Database Portal

The Data Provider is the web service package (wrapper) installed at the data source.

The Data Portal is a gateway to data published from the data provider nodes.

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

Biodiversity collections data have most of their attributes in common , although the terminology used to describe them often differ substantially .

TDWG T axonomic D atabases W orking G roup TDWG Mission: To provide an international forum for biological data projects To develop and promote the use of standards To facilitate data exchange . The TDWG web site is hosted by The Natural History Museum in London, UK. [http://www.tdwg.org/]

TDWG Mission:

To provide an international forum for biological data projects

To develop and promote the use of standards

To facilitate data exchange .

The TDWG web site is hosted by The Natural History Museum in London, UK.

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

Biodiversity informatics standards

Biodiversity informatics standards

Darwin Core 2 (DwC2) The Darwin Core 2 is a simple set of data element definitions designed to support the sharing and integration of primary biodiversity data. The Darwin Core is not a sufficient model or data structure for managing primary data, such as a collection database. Darwin Core can be compared to the MCPD of the PGR community as a minimum common descriptor list. [http://darwincore.calacademy.org]

The Darwin Core 2 is a simple set of data element definitions designed to support the sharing and integration of primary biodiversity data.

The Darwin Core is not a sufficient model or data structure for managing primary data, such as a collection database.

Darwin Core can be compared to the MCPD of the PGR community as a minimum common descriptor list.

[http://darwincore.calacademy.org]

ABCD A ccess to B iological C ollection D ata ABCD is a common data specification for data on biological specimens and observations (including the plant genetic resources seed banks). The design goal is to be both comprehensive and general (about 1200 elements). Development of the ABCD started after the 2000 meeting of the TDWG. ABCD was developed with support from TDWG/CODATA , ENHSIN, BioCASE, and GBIF. The MCPD descriptor list is now completely mapped and compatible to ABCD 2.0. [http://www.bgbm.org/TDWG/CODATA/Schema/]

ABCD is a common data specification for data on biological specimens and observations (including the plant genetic resources seed banks).

The design goal is to be both comprehensive and general (about 1200 elements).

Development of the ABCD started after the 2000 meeting of the TDWG.

ABCD was developed with support from TDWG/CODATA , ENHSIN, BioCASE, and GBIF.

The MCPD descriptor list is now completely mapped and compatible to ABCD 2.0.

[http://www.bgbm.org/TDWG/CODATA/Schema/]

PGR sub-unit of ABCD PGR

PGR

MCPD M ulti C rop P assport D escriptors MCPD is developed jointly by IPGRI and FAO as an international standard for germplasm passport data exchange. 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 was first released in 1997. [http://www.ipgri.cgiar.org/publications/pdf/124.pdf] The MCPD descriptors are compatible with ABCD 2.0

MCPD is developed jointly by IPGRI and FAO as an international standard for germplasm passport data exchange.

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 was first released in 1997.

[http://www.ipgri.cgiar.org/publications/pdf/124.pdf]

The MCPD descriptors are compatible with ABCD 2.0

IPGRI Crop Specific Descriptors The IPGRI crop descriptors expand the MCPD to meet crop specific needs. As long as these crop descriptors allow for an easy conversion to the format proposed in the multi-crop passport descriptors, basic passport data can be exchanged worldwide in a consistent manner. 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).

The IPGRI crop descriptors expand the MCPD to meet crop specific needs. As long as these crop descriptors allow for an easy conversion to the format proposed in the multi-crop passport descriptors, basic passport data can be exchanged worldwide in a consistent manner.

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).

Biodiversity informatics data exchange tools

Biodiversity informatics data exchange tools

DiGIR Di stributed G eneric I nformation R etrieval Distributed - a protocol for retrieving structured data from multiple, heterogeneous databases across the Internet. Generic - a protocol independent of the data retrieved and of the software to retrieve it. The DiGIR protocol uses the Darwin Core as its data definition. [http://digir.net] [https://sourceforge.net/projects/digir]

Distributed - a protocol for retrieving structured data from multiple, heterogeneous databases across the Internet.

Generic - a protocol independent of the data retrieved and of the software to retrieve it.

The DiGIR protocol uses the Darwin Core as its data definition.

[http://digir.net]

[https://sourceforge.net/projects/digir]

BioCASE Biological Collection Access for Europe BioCASE establish web-based unified access to biological collections in Europe while leaving control of the information with the collection holders. ABCD is the main data definition used by BioCASE. Designed generic to handle any schema and connect to any SQL capable database. BioCASE provide full access to its registry for GBIF . Being a BioCASE provider thus means being a GBIF provider. [http://www.biocase.org/]

BioCASE establish web-based unified access to biological collections in Europe while leaving control of the information with the collection holders.

ABCD is the main data definition used by BioCASE.

Designed generic to handle any schema and connect to any SQL capable database.

BioCASE provide full access to its registry for GBIF . Being a BioCASE provider thus means being a GBIF provider.

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

BioMOBY BioMOBY i s an international research project on methodologies for biological data representation, distribution, and discovery. MOBY-S is a web service based interoperability solution. S-MOBY is a Semantic Web-based interoperability solution. [ http://www.biomoby.org/]

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

MOBY-S is a web service based interoperability solution.

S-MOBY is a Semantic Web-based interoperability solution.

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

Protocol integration - TAPIR There is a need to integrate the current protocols in use by different biodiversity informatics community networks. During the TDWG meeting in 2004, the unified protocol was presented and named TAPIR . The T DWG A ccess P rotocol for I nformation R etrieval. It was agreed to start testing the protocol by rewriting the data provider software of the existing BioCASE and DiGIR implementations. Will TAPIR also help us to integrate GBIF with the BioMOBY community?? [http://ww3.bgbm.org/tapir]

There is a need to integrate the current protocols in use by different biodiversity informatics community networks.

During the TDWG meeting in 2004, the unified protocol was presented and named TAPIR . The T DWG A ccess P rotocol for I nformation R etrieval.

It was agreed to start testing the protocol by rewriting the data provider software of the existing BioCASE and DiGIR implementations.

Will TAPIR also help us to integrate GBIF with the BioMOBY community??

[http://ww3.bgbm.org/tapir]

Thank you for listening!

Thank you for listening!