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    Genome Database & Information System For Daphnia: @bio - Indiana.edu

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    sruthy
    This document discusses requirements for developing a genome database and information system for Daphnia. It outlines the key components needed, including data types, standardized schemas, software architecture, analysis tools, publication interfaces, and data management interfaces. Examples of existing genome databases like FlyBase and euGenes are provided to illustrate the anatomy and components of a successful genome information system.

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    Genome Database & Information System For Daphnia: @bio - Indiana.edu

    Uploaded by

    sruthy
    94 views14 pages
    This document discusses requirements for developing a genome database and information system for Daphnia. It outlines the key components needed, including data types, standardized schemas, software architecture, analysis tools, publication interfaces, and data management interfaces. Examples of existing genome databases like FlyBase and euGenes are provided to illustrate the anatomy and components of a successful genome information system.

    Original Description:

    bioinformatics

    Original Title

    genome-dbs-talk

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    This document discusses requirements for developing a genome database and information system for Daphnia. It outlines the key components needed, including data types, standardized schemas, software architecture, analysis tools, publication interfaces, and data management interfaces. Examples of existing genome databases like FlyBase and euGenes are provided to illustrate the anatomy and components of a successful genome information system.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    94 views14 pages

    Genome Database & Information System For Daphnia: @bio - Indiana.edu

    Uploaded by

    sruthy
    This document discusses requirements for developing a genome database and information system for Daphnia. It outlines the key components needed, including data types, standardized schemas, software architecture, analysis tools, publication interfaces, and data management interfaces. Examples of existing genome databases like FlyBase and euGenes are provided to illustrate the anatomy and components of a successful genome information system.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    of 14

    Genome database &

    information system for


    Daphnia
    • Don Gilbert, gilbertd@bio.indiana.edu October
    2002
    • Talk doc at http://iubio.bio.indiana.edu/daphnia/docs/
    genome-dbs-talk.doc, .ppt
    Genome database
    examples
    • Drosophila: FlyBase, http://flybase.net/ (Indiana Univ.)
    • C. elegans: Wormbase, http://www.wormbase.org/
    • Mouse: MGD, http://www.informatics.jax.org/
    • Saccaromyces: SGD, http://genome-
    www.stanford.edu/Saccharomyces/
    • Human: LocusLink, http://www.ncbi.nlm.nih.gov/LocusLink/
    • Human: GeneCards http://bioinfo.weizmann.ac.il/cards/
    • Various eukaryotes: Ensembl http://www.ensembl.org/
    • Various eukaryotes: euGenes http://eugenes.org/ (Indiana
    Univ.)
    • Many newly developing organism genome systems for
    Daphnia, insects, vertebrates, new full-genome organisms
    Anatomy of genome
    database & info system
    Anatomy of Genome
    DB/IS
    • Structure
    – Complex document structure; tabular data; etc.
    – Organize: Table of contents, Reports, Indexing
    – Browse contents; Search / retrieve from biological
    questions
    – Bulk data search / retrieve for bioinformatics

    • Content
    – Literature (abstracted and curated), Sequence and
    feature analyses, maps, controlled
    vocabulary/ontologies, people, biologics, contacts, etc.
    – Metadata describing primary data, along with
    protocols, notes, sources
    Anatomy of Genome
    DB/IS, 2
    • Data exchange
    – Data definitions & schema (XML)
    – Controlled vocabularies of science terms, ontologies
    – Minimal information for collaboration, sharing

    • Informatics / software
    – Backend database, data collection, management,
    analyses
    – Front-end services (hypertext web, search/retrieval);
    ease of understanding and usage (HCI)
    – Middleware software, interfaces
    – Genome specialized: maps, BLAST searches,
    ontologies
    GMOD - Generic genome
    database tools
    • Generic Model Organism Database
    Construction Set, http://www.gmod.org/
    • Database schemas
    • Literature curation tools
    • Gene ontology management tools
    • Visualization tools
    • Data processing pipelines
    FlyBase and euGenes
    FlyBase.net
    • Distributed project (4 sites, ~6 PI’s, ~15 curators,
    ~15 informaticians); 10 years old
    • Multiple databases; project data flow and
    exchange critical
    • Curated and computed data, from expt.
    literature, genome sequence
    • Integrated database modules (for generic use w/
    GMOD)
    – Genetics, Sequences, Maps, Expression
    – Controlled vocabularies & Ontologies
    – Computational analyses
    – Organism, taxonomy, phylogenetic/comparative
    – Publications, General
    euGenes.org
    • Automated genome summaries for Human,
    Fruitfly, Mouse, Mosquito, Arabidopsis, C.
    elegans, Saccharomyces, Zebrafish
    • 3 year, computational DB project, 1 part-time
    informatician (dgg )
    • genome maps, sequences, gene reports,
    external database links
    • cross-species comparisons: similar genes,
    genome features, gene function
    A genome web db for
    Daphnia
    Preliminary example
    • http://iubio.bio.indiana.edu/daphnia/
    • Sample data include microsatellite DNA of J.
    Colbourne, GenBank Daphnia seqs, Medline
    abstracts
    • Blast searches, reports
    • Text data searches
    Requirements for a
    genome db/ info system
    • Data components??
    – biosequence types, literature, external data (insects,
    others), expression info, pathways, maps, anatomy,
    populations, species, ecology, organismal, stocks,
    people
    – Standard data structure and exchange schema
    (sequences, XML)

    • Architecture
    – Internet-shared, standards-based, open-source preferred
    – Relational database for data management
    – Search and retrieval software for flat file data
    – Flexible – data schema changes common
    – Performance constraints
    Requirements for
    genome system, cont.
    • Analysis software
    – Project uses: sequence analyses, external database
    comparisons
    – One-time analyses, publishing results
    – Pipeline for automated analyses, rerun as needed
    – Public uses (e.g. BLAST search)

    • Publication interface
    – Detail biological object views (sequences, genes, etc.)
    – Queries: simple-common, ad-hoc/general
    – Graphic viewers

    • Editing / data management interface


    – Interactive – document editing
    – Batch data updates
    Compute parts of
    system
    • Web server (Apache) and modules
    • FTP server for bulk data exchange
    • Relational DBMS: PostgreSQL.org, MySQL.com,
    Oracle..
    • Analysis programs: BLAST, various
    bioinformatics tools
    • Perl, Java middleware for data access &
    analysis, search and report
    • Limited, secure access for project data
    management
    • Public access for released data (web, ftp)

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