- From: SUGAWARA Hideaki <hsugawar@genes.nig.ac.jp>
- Date: Tue, 28 Sep 2004 13:44:31 +0900
- 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. ------------------------------------------------------------------ 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. --------------------------------------------------------------------------
Received on Tuesday, 28 September 2004 05:05:37 UTC