Bioinformatics for Genome data

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Bioinformatics for Genome data

• Genome databases / 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-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

Don Gilbert, gilbertd_at_bio.indiana.edu
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What is bioinformatics?

• Bioinformatics is the field of science in which
  biology, computer science, and information
  technology merge into a single discipline. The
  ultimate goal of the field is to enable the
  discovery of new biological insights as well as
  to create a global perspective from which
  unifying principles in biology can be discerned.
• There are three important sub-disciplines within
  bioinformatics
• development of new algorithms and statistics with
  which to assess relationships among members of
  large data sets
• analysis and interpretation of various types of
  data including nucleotide sequences and proteins
  gene and genome features and functions,
  expression in cells and through development and
  other biology data.
• development and implementation of tools that
  enable efficient access and management of
  different types of information.
• http//www.ncbi.nlm.nih.gov/Education/index.html
  w/ dgg edits

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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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Genome Data Objects

Drosophila genome, FlyBase, Sept. 2002
8 eukaryote genomes, euGenes, July 2002
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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 and euGenes
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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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Anatomy of genome database info system
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Anatomy of genome database

• Data components
• biosequences, literature, external data,
  expression info, pathways, maps, anatomy,
  populations, species, ecology, stocks, people
• Metadata about primary data (ID, dates, sources,
  evidence)
• Architecture
• Relational database for management
• Search and retrieval software for flat file data
• Backend (database, analyses piplelines) Frontend
  (public views and access web, ftp) Middleware
  ('glue' back and front)
• Flexible data schema changes common
• Performance constraints
• Internet-shared, standards-based, open-source
  preferred

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Anatomy of genome database, cont.

• Analysis software
• Project uses sequence analyses, external
  database comparisons
• Pipeline for automated analyses, rerun as needed
• Public uses (e.g. BLAST search)
• Editing / data management interface
• Interactive document editing
• Batch data updates

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Anatomy of genome database, cont.

• Publication interface
• Detailed biological object views (sequences,
  genes, etc.)
• Queries simple and frequent, ad-hoc and general
• Graphic viewers
• Data exchange
• Data definitions schema (XML)
• Controlled vocabularies of science terms,
  ontologies
• Minimal information for collaboration, sharing

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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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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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Efficiency of SRS versus RDB
Drosophila Genome Annotations SRS or Gadfly DB
relational database Web search time (shorter is
better two computers - O,F)
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Current System Dataflow
Master Genes File (rw)
People DB
Stock Center DB
Image Curation
Supplemental nightly update
Mol5 (rw)
Public (ro) /SRS
Web Browser
Dumper
Gene Loader
Gene -Seen applet
GenBank
Sequence Analysis Pipeline
gadfly (rw)
Apollo
gadfly scripts
gadfly x xml
From Stan Letovsky, FlyBase
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Ultimate System Dataflow?
Master Genes File (rw)
People DB
Stock Center DB
Image Curation
Public (ro) /SRS
IDB proto (rw)
Web Browser
XML Dumper
XML Loader
Error cleanup
XML?
Gene -Seen applet
Apollo
GenBank
Sequence Analysis Pipeline
From Stan Letovsky, FlyBase
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Single DB vs. Federated Info. S/R
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GMOD - 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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From Shawn Hoon, Fugu Informatics Group
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From Shawn Hoon, Fugu Informatics Group
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From Shawn Hoon, Fugu Informatics Group
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From Shawn Hoon, Fugu Informatics Group
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Bio-Grids
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Bio-Grids - what are they?

• 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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BioGrid Schematic

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

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From Shawn Hoon, Fugu Informatics Group