パイプラインを実現する相互運用性cdaa.ppt

2006/10/23 Primary Biological Databases Quality of services of 　　　　　a primary nucleotide sequence database Hideaki Sugawara Center for Information Biology and DDBJ, National Institute of Genetics SOKEN-DAI. International Nucleotide Sequence Database Collaboration (INSDC) serves communities Infrastructure for the services Today I will introduce: Mash-up of biological data resources Web services for the biological problem solving environment We implemented a SOAP (Simple Object Access Protocol) server and Web services that provide a program-friendly interface. We propose standardization of bioinformatics services to improve the interoperability of desperately diverse biological data resources. The world of Web services XML Central of DDBJ: http://xml.nig.ac.jp/index.html Workflow composed of methods provided by Web services Easy to bind Web services methods from your program Workflow with Online Mendelian Inheritance in Man (OMIM) Access frequency of DDBJ Web services Web services in the world A simple derived database: subset of complete microorganisms genomes from INSDC Gene prediction programs used Annotation: description of products unknown hypothetical protein probable orf predicted protein putative protein hypothetical conserved protein uncharacterized protein conserved domain protein conseved hypthetical A derived database: contents of complete microorganisms genomes were evaluated Features of GTPS Simultaneous prediction and evaluation of all the possible protein coding genes (ORFs) in prokaryote genomes All the ORFs are graded The criteria and evidence data are available Web site http://gtps.ddbj.nig.ac.jp/ Updated once a year Short history of GTPS How many genes are out there? Summary It is the long term mission of the primary database to archive all the data published for the long term. At the same time, it is requested to provide objective/reliable data and tools for the mash-up. It proposes and maintains standards of biological data pr