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ENABLE project notes

ENABLE project notes Don Gilbert, gilbertd@indiana.edu Sept 2003 Biology information access projects Bio-info archiving and distribution IUBio Archive, http://iubio.bio.indiana.edu/ -- public molecular biology data / software archive

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ENABLE project notes

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  1. ENABLE project notes Don Gilbert, gilbertd@indiana.edu Sept 2003

  2. Biology information access projects • Bio-info archiving and distribution • IUBio Archive, http://iubio.bio.indiana.edu/ -- public molecular biology data / software archive • Bio-Mirrors, http://www.bio-mirror.net/ -- Sequence and related biology databanks • Genome information systems • FlyBase, http://flybase.bio.indiana.edu/ -- genome infosystem of Drosophila fruitfly • euGenes, http://eugenes.org/ -- infosystem for 8 important eukaryotes with 180,000 genes • Bio-Data Grids • http://iubio.bio.indiana.edu/grid/ -- experimental distributed computing

  3. FlyBase and euGenes

  4. ENABLE: data sets & access • Data sets and access to data • Back-end architecture and protocols • Bio-Grids and Bio-Directories

  5. Major Bio Databanks from EBI (www.ebi.ac.uk), Sept. 2002

  6. Constellation of Bio-Data (SRS - Lion Bioscience)

  7. ENABLE access architecture

  8. 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 (105 objects; >1 GB sizes)

  9. 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

  10. Directory components

  11. Bio 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

  12. Directory Standards • Open Grid Services Architechture (OGSA) • SOAP based; query support for XML-SQL, Xpath, Xquery. • Data Access project: http://www.ogsa-dai.org.uk/ • 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

  13. 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 • Tests in progress for IUBio, FlyBase

  14. Directory Tests

  15. ENABLE biodata access issues • Basic Web-Services and LDAP access working in testing form; not stable nor finalized • Bio-Data categorization, schema, and meta-data for directories needs work • Grid (OGSA), OAI, other interfaces to be developed Directory tests at http://iubio.bio.indiana.edu/biogrid/directories/

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