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Web service technologies, at CGIAR ICT-KM workshop in Rome (2005)
 

Web service technologies, at CGIAR ICT-KM workshop in Rome (2005)

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Presentation of web services for the CGIAR ICT-KM training workshop on information interoperability, 13th June 2005, at IPGRI Rome Italy. Dag Endresen (Nordic Gene Bank).

Presentation of web services for the CGIAR ICT-KM training workshop on information interoperability, 13th June 2005, at IPGRI Rome Italy. Dag Endresen (Nordic Gene Bank).

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  • * Spiders-web, photographer: Ian-Britton [http://www.freefoto.com/preview.jsp?id=01-17-1&k=Spiders+Web]
  • Photo: IRRI genebank. Los Banos, Philippines [http://www.cgiar.org/images/irrigenebank1.jpg], VIR seed collection. St. Petersburg. Photographer Eva Thörn (NGB Picture Archive, image 001319).
  • The text formulation above is edited from various sources – on search hits with google.
  • * W3C Web Services Glossary. W3C Working Group Note 11 February 2004 [http://www.w3.org/TR/ws-gloss/] * Spiders-web, photographer: Ian-Britton [http://www.freefoto.com/preview.jsp?id=01-17-1&k=Spiders+Web] * Copyright statement “feel free to use any of the images on the site if you are a private individual and your use is not commercial” [http://www.freefoto.com/browse.jsp?id=99-5-0]
  • Some examples to use...? * http://www.xmethods.com * http://www.xmethods.com/ve2/ViewListing.po;jsessionid=tYR5gLa3iESq9FYCW1m1IqHo(QHyMHiRM)?key=uuid:57D835E5-B4A5-4C4A-38E8-37E964100CF8 * http://services.bio.ifi.lmu.de:1046/prothesaurus/
  • Perhaps this slide is too much ... ? * WS-Security : The Web Services Security protocol has been accepted as an OASIS standard. The standard allows authentication of actors and confidentiality of the messages sent. (taken out to simplify the slide...)
  • Slide by Samy Gaiji, from presentation on: “ Information Networking - Challenges for the Plant Genetic Resources Communities, 2004.
  • Slide by Samy Gaiji, from presentation on: “ Information Networking - Challenges for the Plant Genetic Resources Communities, 2004.
  • * IRRI genebank. Los Banos, Philippines [ http://www.cgiar.org/images/irrigenebank2.jpg] * Text formulation source [http://www.bgbm.org/TDWG/CODATA/ABCD-Evolution.htm] wording above is modified.
  • * The mapping of MCPD to ABCD was started in 2004 by Helmut Knüpffer and Walter Berendsohn, and finalized by Javier de la Torre and Dag Terje Filip Endresen in 2005. [ http://ww3.bgbm.org/MCDPH]
  • * Multi-crop Passport Descriptors (MCPD) [http://www.ipgri.cgiar.org/publications/pdf/124.pdf] F AO (Food and Agricultural Organization of the United Nations) - IPGRI (International Plant Genetic Resources Institute). This is a revised version (December 2001) of the 1997 MCPD List. * FAO World Information and Early WarningSystem ( WIEWS) [http://apps3.fao.org/wiews/] * 19 Plant Uses Categories based on categories developed for the Working Group on Taxonomic Databases (TDWG) (Cook, Frances E.M., 1995. Economic Botany: Data Collection Standard. Royal Botanic Gardens Kew). [ http://www.ecpgr.cgiar.org/epgris/Training/MCPD-1998.doc] * The mapping of MCPD to ABCD was started in 2004 by Helmut Knüpffer and Walter Berendsohn, and finalized by Javier de la Torre and Dag Terje Filip Endresen in 2005. [ http://ww3.bgbm.org/MCDPH]
  • * IPGRI Descriptors lists [http://www.ipgri.cgiar.org/system/page.asp?frame=programmes/inibap/home.htm] (119 descriptor lists, 2005) * MCPD [http://www.ipgri.cgiar.org/publications/pdf/333.pdf] * UPOV - International Union for the Protection of New Varieties of Plants (UPOV) [ http://www.upov.int/] * UPOV - The International Union for the Protection of New Varieties of Plants or UPOV (French: Union internationale pour la protection des obtentions végétales) is an intergovernmental organization with headquarters in Geneva, Switzerland. [http://en.wikipedia.org/wiki/UPOV] * COMECON - The Council for Mutual Economic Assistance (COMECON / Comecon / CMEA / CEMA), 1949 – 1991, was an economic organisation of communist states and a kind of Eastern European equivalent to the European Economic Community. The military counterpart to the Comecon was the Warsaw Pact. [http://en.wikipedia.org/wiki/Comecon]
  • Major contributors to DiGIR is the MaNIS project (University of California, Berkeley) and GBIF.
  • BioCASE development is coordinated by the Botanischer Garten und Botanisches Museum Berlin-Dahlem – BGBM.
  • Photo: PICT0173.jpg Sub-section from Whale Safari to Kaikoura New Zealand. Photo Dag Terje Filip Endresen [http://r142b.ngb.se/ngb/2004-10-New-Zealand-Australia/index.php?offset=79&size=medium&stp=1]
  • * Illustration: Tapir - © 1999-2005 www.barrysclipart.com (Licence “Feel free to use Barrys Clipart Server content in personal/ non profit projects to create webpages…”) [http://www.barrysclipart.com/barrysclipart.com/showphoto.php?photo=13376&papass=&sort=1&thecat=149] Not Quality counts: Chemist Gary List checks soybeans. Photo by Keith Weller. [ http://www.ars.usda.gov/is/graphics/photos/k5256-2.htm]

Web service technologies, at CGIAR ICT-KM workshop in Rome (2005) Web service technologies, at CGIAR ICT-KM workshop in Rome (2005) Presentation Transcript

  • 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
  • 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.
  • 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]
  • 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]
  • Some web service keywords
    • 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.
  • 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 ]
  • Example of a web service call
    • 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.
  • 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
  • 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]
  • 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/]
    • 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]
  • 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/]
  • PGR sub-unit of ABCD
    • 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
  • 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).
    • 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]
  • 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/]
  • 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/]
  • 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]
    • Thank you for listening!