Title: Communication Between Online Heterogeneous Repositories: An Application of Simple Object Access Prot
1Communication 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
2Contents
- 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
3Introduction
- 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.
4What 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.
5Implementation 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
6Data Exchange Format Communication Protocol
7MIMODS
- MIMODS - contains microbial data compiled from
Malaysian indigenous microbes (algae, bacteria,
fungi, protozoa and fungi)
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9Darwin 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
10Installation 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.
11Testing
- 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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13Testing
- 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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15Installation 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.
16Algae database
17Testing-Scan Operation
18Installation 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.
19Portal Interface
By entering an algae family name, the meta search
engine can extract relevant data from MIMODS
local algae database.
20Query 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.
21Achievements
- 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 ?
22Discussion
- 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.
23Suggestions 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.
24Conclusion
- 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.
25Acknowledgement
- APT (President, Imai, Rob)
- UM (ISB)
- CSIS
- NIES
- etc
26References
- 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.
27Thank You for your time.