Bioinformatics: building bridges to biology information

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Bioinformatics building bridges to biology
information

• Biology Information Access
• Genome Information Systems
• Bio-Grids and Bio-Directories

Don Gilbert, gilbertd_at_bio.indiana.edu November
2002
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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
• Bioinformatics services
• http//sunflower.bio.indiana.edu/bioweb/ --
  molecular biology program use via web
• Bio-Data Grids
• http//iubio.bio.indiana.edu/grid/ --
  experimental distributed computing

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BioData

• BioData size, contents, dispersion, uses
• Genome data
• very important, highly complex, harder to find,
  long lived
• Literature (abstracted and curated), Sequence and
  feature analyses, maps, controlled
  vocabulary/ontologies, people, biologics,
  contacts, etc.
• BioData access
• Need to find and use best data
• New data kinds and sources - bio-information is
  very fluid
• Need current data update monthly, weekly, daily
• Distributed widely in world among 1000s of
  national, regional centers labs

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Bio Databanks, EBI, Sept. 2002
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Constellation of Bio-Data (SRS - Lion Bioscience)
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FlyBase and euGenes
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Genome Databases

• 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/Locu
  sLink/
• Human GeneCards http//bioinfo.weizmann.ac.il/car
  ds/
• Various eukaryotes Ensembl http//www.ensembl.org
  /
• Various eukaryotes euGenes http//eugenes.org/
  (Indiana Univ.)
• Many new organism genome systems for Daphnia,
  insects, vertebrates, others with complete genome
  data

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FlyBase.net

• Distributed project (4 sites, 6 PIs, 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

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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

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Genome Data Objects

Drosophila genome, FlyBase, Sept. 2002
8 eukaryote genomes, euGenes, July 2002
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Genome attributes in euGenesJuly 2002
Genes as extracted from genome project sources.
These differ from true gene numbers by orphan
gene records, prediction artifacts, unmerged
predicted/expt. records, and unfinished
sequencing gaps.
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Anatomy of genome database info system
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FlyBase/euGenes Query System
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FlyBase Query Results
FlyBase Genes query results Query   (
libsFBgn PFgn-allwing or libs-synwing )
and libs-orgDmel,  No. matches 1437 Bookmark
FBquery ( libsFBgn PFgn-allwing
libs-synwing ) libs-orgDmel
Symbol Name  Map Alleles Stocks Refs DNA Date
1 18w 18 wheeler 56F11 16 2 56 13 31 May
02 2 2R-F - - 2 1 3 - 31 May 02 ...
19 Act42A Actin 42A 42A2 2 - 73 23 31 May
02 20 Act5C Actin 5C 5C7 14 1 129 43 31 May
02 ------------------- Page and Sort results
------------------ Batch Download Fetch items x
All Items   Format Spreadsheet 
Report content Summary  Report only Select
fields Field list Refine query or find
items in related data Refine query ( libsFBgn
PFgn-allwing or libs-synwing ) and
libs-orgDmel and other fields matches
.. Search Genes , retrieve Related Data
Classes (alleles, aberrations, transcripts,
insertions, sequences )
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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

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Bio-grids - what might they be ?

• transparent use of available workstations
  commodity grid resources (commercial, academic)
• find biodata, computing resources easily and
  automatically via directories
• personal/project resources and peer-peer sharing
• less reliance, less cost for centralized services
  or building local IT centers
• Power grid - plug in your toaster, ignore the
  power sources and grid. Bio grid - plug in
  workstation, ignore where data and compute power
  comes from -- eventually!

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EU DataGrid Interfacesfrom Bob Jones, CERN
Computing Elements
Mass Storage Systems HPSS, Castor
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BioGrid Schematic

• Grid-aware client software
• Data and software resource directories
• Grid of processing computers

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Directories of Genome Data

• For genome data, "broad and shallow" directories
  federate the "narrow and deep" data-bases
• BioData access tools
• SRS - Sequence Retrieval System Entrez AceDB
• RDBMS Ensembl IBM DiscoveryLink BioSQL
  BioDAS
• Directory services - Data tools LDAP , Web
  Services
• LDAP mature, efficient for high volumes, allows
  federated queries over distributed directories,
  and works well for SRS databanks and genome
  annotations
• Web Services new, simple complex for XML
  messages over Web has wide industry support ,
  but its many standards are in flux

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Bio-directories Technology

• Technology for finding bio-data
• Current Web pages Web Indexers (Google) FTP
  servers
• Sometimes CORBA Java RMI
• Usable Lightweight Directories - LDAP
• Developing Web Services (XML on Web SOAP, WSDL,
  UDDI, ...)
• Related BioDAS BioMoby Life Sciences ID
  (LSID)

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SRS - LDAP WebXML gateways

• Sequence Retrieval System (SRS) knows millions of
  bio-objects good start for bio-directories
• OpenLDAP server combined with SRS6
• WebService SOAP server/client with SRS6
• SRS-LDAP-SOAP software is available at
  http//iubio.bio.indiana.edu/biogrid/directories/
• Compare LDAP, SOAP, Wgetz, FTP for Grid uses
• LDAP is 5x faster than SOAP, Wgetz

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BioDirectory tests for Grid
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Using Bio Directories

• Simple client software
• Automated use
• People use
• Discovery
• Search by many criteria
• Retrieve bulk subsets

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Genome Feature Directory

• Genome objects fit in directories, search
  retrieve as annotated sequence (like BioDAS)
• Same directory methods work for objects,
  databases, software and other resources

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BioGrid Runner
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Wrap up

• Future of Bio-data distribution
• Computationally find and use dispersed, complex
  data
• Best methods for Bio-data Grids
• High volume and complex data
• Efficient selection and transport to grid
  computers
• LDAP works well Web-XML is usable
• Community needs and uses
• Shared data descriptions, schema, ontologies
  (Semantic web)
• Simple, practical, flexible grid methods use
  existing dbs
• Use common developing standards

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Thanks to the work, help and support of these
folks and others IUBio Archive -- Danfeng Yao,
Paul Poole Bio-Mirrors --Yoshihiro Ugawa, Tin
Tan Wee, Markus Buchhorn, Akira Mizushima,
Juncai MA, and others. FlyBase -- Victor
Strelets, Gary Grumbling, Nihar Sheth, Manish
Anand, Edwin Wang, Thom Kaufman, Kathy
Matthews, and a crowd at other sites euGenes
-- original idea of and work with Bill Gelbart
and others Bioinformatics web -- Sue Olson
Eugenes fulgens (Magnificent Hummingbird, Costa
Rica)