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W3C Workshop on Semantic Web for Life Sciences

From: SUGAWARA Hideaki <hsugawar@genes.nig.ac.jp>
Date: Tue, 28 Sep 2004 13:44:31 +0900
Message-Id: <6.0.0.20.2.20040928133300.02cc9d70@genes.nig.ac.jp>
To: public-swls-ws@w3.org
Cc: richard.scott@denovopharma.com, hsugawar@genes.nig.ac.jp

Dear Sir/Madam,

I am involved in LSR DTF of OMG and would like to also participate
in the W3C Workshop on Semantic Web for Life Sciences. In the meantime,
the co-chair of LSR (Dr. Richard K. Scott) informed us that W3C had
extended the position paper submission deadline for LSR DTF attendees.

I send the position paper in ASCII text in the following and would
like to register to your meeting.
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 From Web Services towards Semantic Web in a Public Data Bank

Hideaki Sugawara
Japan Biological Information Consortium
5F Grande Building, 2-26-9 Hacchobori,
Chuo Ward,Tokyo 104-0032
Japan
Center for Information Biology and DNA Data Bank of Japan
National Institute of Genetics
1111 Yata, Mishima, Shizuoka 411-8540
Japan

Introduction

The International Nucleotide Sequence Databases (INSD) is composed of DNA 
Data Bank of Japan (DDBJ), EMBL Nucleotide Database at the European 
Bioinformatics Institute and GenBank at the National Center for 
Biotechnology Information in US and has accumulated nucleotide sequences 
and their biological meaning (annotation).  The size of INSD exceeded 30 
millions entries and 30 billions nucleotides in 2003. It is obvious that 
data processing by hand is not feasible any more. Therefore, DDBJ has 
developed Web services to provide users with programmatic interfaces and to 
improve the interoperability in bioinformatics

Categories of Web services provided by DDBJ

DDBJ has provided search engines and data analysis tools that are 
accessible by E-mails and Web browsers. Most of these services are now 
available as Web services: blast, fasta, ClustalW and retrieval by 
accession numbers and key words; secondary databases of microbial genomes, 
comprehensively predicted secondary structures of ORFs, an integrated 
database of SNPs data, and a unified taxonomy file. The URL address of the 
Web services is http://www.xml.nig.ac.jp/

Linkage with other Web services

Web services in bioinformatics are available at several sites like European 
Bioinformatics Institute and it will be possible for us to construct 
workflow that dynamically combine methods of Web services in multiple 
sites. In order to develop the dynamic workflow, standards for the 
description of semantics including ontology of services are required. It is 
also critical for the success of the dynamic workflow that standards are 
accepted and actually implemented by providers and users of Web services. 
For example, the Global Biodiversity Information Facility 
(http://www.gbif.org/) need a system to assign unique identifier to all the 
biological specimens in natural history museum and other biological 
resource centers, but LSID is not readily accepted by the GBIF communities. 
Therefore, W3C and OMG are expected to expand the public relations about 
the standardization.
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Received on Tuesday, 28 September 2004 05:05:37 GMT

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