Genome Data Directories Don Gilbert, May 2003.

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Presentation transcript:

Genome Data Directories Don Gilbert, May 2003

Data Access Needs Computable genome data access -- Page scraping and bulk files not enough -- Internet search & retrieval of all genome objects distributed among many sources -- Simple, flexible client program model -- Efficient for high volumes (10 5 objects; >1 GB sizes)

Directories of Genome Data Directories are a necessary step for bio grids "broad and shallow" directories federate the "narrow and deep" databases Bio-Data Access Tools SRS, Sequence Retrieval System; Entrez ; AceDB; Genome relational databases (Ensembl, FlyBase, WormBase) ; IBM DiscoveryLink; BioDAS ; BioMoby Directory services for data access Layer onto access tools for common query/retrieval LDAP: mature, efficient for high volumes, query distributed directories ; works well with bio-access tools Web Services: XML messages over Web ; wide industry support, standards are in progress

Directory components

Genome Directory Needs Build on existing technology for finding distributed objects Efficient for millions of objects, by the gigabyte and terabyte Queries distributed across directories of collaborating services Support existing and new bioinformatics data access (relational dbs, object and XML dbs, SRS, Entrez, AceDB) Simple client program methods for computable use of directories Flexible, common schema for describing objects Replicate directories and objects among bioinformatics centers Peer-to-peer directories for collaborative projects Strong authentication and security for data access

Directory Standards Open Grid Services Architechture (OGSA) SOAP based; query support for XML-SQL and Xquery. Data Access project: Lightweight Directory Access (LDAP) Robust system for distributed search and retrieval Object-centric, optimized for efficient read operations Hierarchical, distributed and replicated in nature Life Sciences ID (LSID) new standard for bio-object naming, with LDAP and WebServices implementations Moby project web services repository system

Directory Tests Design and test distributed access with LDAP and Web Services SRS backend for efficient search/retrieval from GenBank, SwissProt/TrEMBL, LocusLink, Medline, many others Find & fetch 20,000 to 1.2 million objects LDAP is ~10x faster than WebServices Test in progress for FlyBase

Directory Tests

Genome Directory Issues Directory tests at

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