Communication Between Online Heterogeneous Repositories: An Application of Simple Object Access Prot

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Communication Between Online Heterogeneous
Repositories An Application of Simple Object
Access Protocol (SOAP) for Rapid Knowledge
Discovery

• Amir F. Merican , Takeshi Sagara, Sarinder Kaur,
  Zahriah M Pilos
• Institute of Biological Sciences, University of
  Malaya, Malaysia
• Center of Spatial Information Science,
  University of Tokyo, Japan

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Contents

• Introduction
• What is DIGIR
• Implementation of DIGIR
• Data Exchange Format Communication Protocol
• MIMODS AND DARWIN CORE DATA STANDARD
• Installation of DIGIR provider (test database)
• Testing
• Installation of DIGIR provider (MIMODS) Testing
• Algae database
• Scan Operation
• Installation of Portal
• Portal Interface
• Query Results
• Achievements
• Discussion
• Suggestions For Future Work
• Conclusion

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Introduction

• This project is implemented to overcome the
  problem of distributed databases with different
  data formats.
• The SOAP was suggested as a communication
  protocol XML to create a common data format, at
  the beginning of the research.
• However, through this collaboration, we
  identified a new technology, DIGIR, which is more
  preferable and appropriate to overcome the
  problem.

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What is DIGIR?

• Distributed Generic Information Retrieval
• a protocol for retrieving structured data from
  multiple, heterogeneous databases
• uses open protocols and standards, such as HTTP,
  XML, and UDDI to leverage existing and emerging
  technologies
• Compatible with the Darwin Core data standard.

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Implementation of DIGIR
DIGIR PROVIDER
DIGIR PROVIDER
MIMODS database
MDODS database
Provider Services
Provider Services
UDDI
UDDI
DIGIR PORTAL
Query Engine
REGISTRY
REGISTRY
Request Marshaller
USER INTERFACE
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Data Exchange Format Communication Protocol
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MIMODS

• MIMODS - contains microbial data compiled from
  Malaysian indigenous microbes (algae, bacteria,
  fungi, protozoa and fungi)

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Darwin Core V2

• DwC v2 is a profile describing the minimum set of
  standards for search and retrieval of natural
  history collections and observation databases
• It expands the original DwC v1
• Required fields are
• DateLastModified
• InstitutionCode
• CollectionCode
• CatalogNumber
• ScientifName

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Installation of DIGIR provider (test database)

• Installation of PHP on the web server
• Installation of DiGIR provider distribution
• Editing of localconfig.php to reflect local
  installation choices
• Editing of providerMeta.xml to present
  appropriate metadata about the installation.
• Creating the database configuration file and
  saving it in the configuration folder
• Updating resources.xml to point to the new
  configuration file.

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Testing

• Scan Operation
• A scan was done to check the test database
  contents. The scan was invoked using the scan
  operation parameter. The results of the scan in
  XML format are displayed in the next slide.

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Testing

• Search Operation
• A simple search operation was run to check
  whether it extracts the correct data from the
  database. This simple search looks for the string
  "otus" in attribute 1 which maps to
  "darwinScientificName?". The query is dislayed
  in the following URL
• http//127.0.0.1/DiGIR/DiGIR.php?operationsearch
  resourcetestfilter_at_attr1122otus2522
• An XML format results were generated

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Installation of DIGIR provider (MIMODS) Testing

• DiGIR provider was installed in the
  Bioinformatics server to read MIMODS (algae
  database). Scan and search operations were done
  to see the responses from the database.

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Algae database
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Testing-Scan Operation
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Installation of Portal

• A simple portal was designed to search the MIMODS
  provider remotely.
• The portal in the next slide is installed on a
  remote machine, which is running on a Linux
  platform. The portal interface was designed using
  Ruby-programming language.

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Portal Interface
By entering an algae family name, the meta search
engine can extract relevant data from MIMODS
local algae database.
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Query Results
The results of the search are displayed in a
tabular form . The search option is currently
limited to microbial family name in the algae
database in MIMODS.
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Achievements

• This project has successfully
•  
• established a biological data server that follows
  global standard specification
• implemented the DiGIR architecture for data
  communication between on-line heterogeneous
  repositories
• First in Asia / World ?

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Discussion

• Using the DiGIR technology, we have succeeded in
  retrieving data from two heterogeneous databases
  (the test database and algae database in MIMODS),
  which follow the Darwin Core v2 data format.

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Suggestions For Future Work

• To introduce and implement the DiGIR architecture
  to other repositories in Malaysia and
  Asia-Pacific region.
• At the moment, the DIGIR protocol cannot be used
  for FileMaker databases as it uses Adodb database
  connectivity, which is not applicable to
  FileMaker databases.
• To develop own portal for microorganisms with
  unique features like strain, serotype, serovar
  etc
• To add image feature files in data server. The
  DIGIR protocol uses the Darwin Core standard and
  retrieval is limited to text. Since biological
  data may contain images, therefore, search would
  be limited using the DIGIR technology
• To tackle the data updates issues in DBMS.

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Conclusion

• The DIGIR technology is a new and current ground
  to explore and this was realized through this HRD
  project. Therefore, this project was successful
  in term of developing a mechanism for efficient
  and productive search retrieval.

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Acknowledgement

• APT (President, Imai, Rob)
• UM (ISB)
• CSIS
• NIES
• etc

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References

• http//digir.sourceforge.net/
• http//sourceforge.net/projects/digir/
• http//tsadev.speciesanalyst.net/documentation/ow.
  asp?pDarwinCoreV2revision6
• http//speciesanalyst.net/digirwiki/ow.asp?DiGIRPr
  oviderInstallNotes
• http//digir.sourceforge.net/port/digir_portal_ins
  tall.html
• Building a Better Metasearch Engine, O'Reilly
  Associates,Inc .http//www.xml.com/pub/a/1999/06/m
  etasearch/metasearch1.html
• XML-RPC(2001), Userland Software, Inc.,
  http//www.xmlrpc.com
• SOAP 1.1 (2000), W3C Note, http//www.w3.org/TR/SO
  AP/
• Bray, T., Paoli, J., Maler E.,(2000) Extensible
  Markup Language (XML) 1.0 (Second Edition), W3C
  Recommendation, http//www.w3.org/TR/2000/REC-xml-
  20001006
• Kurgan, L., Swiercz, W.,Cios, K.J. (2002),
  Semantic Mapping of XML tags using Inductive
  Machine Learning, The 2002 International
  Conference on Machine Learning and Applications.

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Thank You for your time.