Value-adding, Access, and Use: Biological Databases as a Case Study

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Value-adding, Access, and Use Biological
Databases as a Case Study
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Genes..
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.make proteins
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Proteins form complex 3D structures
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Molecules interact
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the right molecules need to bepresent at the
right time
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EMBL-BankDNA sequences
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EMBL-BankDNA sequences
SWISS-PROT TrEMBL InterPro
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EMBL-BankDNA sequences
SWISS-PROT TrEMBL InterPro
EnsEMBL Metazoan Genome Gene Annotation
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EMBL-BankDNA sequences
SWISS-PROT TrEMBL InterPro
EnsEMBL Metazoan Genome Gene Annotation
Array-Express Microarray Expression Data
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EMBL-BankDNA sequences
SWISS-PROT TrEMBL InterPro
EnsEMBL Metazoan Genome Gene Annotation
Array-Express Microarray Expression Data
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EMBL-BankDNA sequences
SWISS-PROT TrEMBL InterPro
EnsEMBL Metazoan Genome Gene Annotation
Array-Express Microarray Expression Data
EMSD Macromolecular Structure Data
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EMBL-BankDNA sequences
SWISS-PROT TrEMBL InterPro
EnsEMBL Metazoan Genome Gene Annotation
Array-Express Microarray Expression Data
EMSD Macromolecular Structure Data
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EMBL-BankDNA sequences
EnsEMBL
Array-Express Microarray Expression Data
SWISS-PROT TrEMBL InterPro
IntAct Protein Protein Interaction Data
EMSD Macromolecular Structure Data
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Integr8
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EMBL-BankDNA sequences
EnsEMBL
Array-Express Microarray Expression Data
SWISS-PROT TrEMBL InterPro
IntAct Protein Protein Interaction Data
EMSD Macromolecular Structure Data
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EMBL-BankDNA sequences
SWISS-PROT TrEMBL InterPro
IntAct Protein Protein Interaction Data
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Running a database project
Database design
End Users
Service Tools
Service DB
Genomes Genes Patents Updates
Submitters
Add value (computation)
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Database design
End Users
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submitters
Add value (computation)
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Database design
End Users
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submission tools
Submitters
Add value (computation)
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Database design
End Users
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submission tools
Submitters
Add value (computation)
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Database design
End Users
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submission tools
Submitters
Add value (computation)
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Database design
End Users
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submission tools
Submitters
Add value (computation)
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Database design
End Users
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submission tools
Submitters
Data Distrib.
Add value (computation)
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Other archives
Database design
End Users
Data exchange
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submission tools
Submitters
Data Distrib.
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Other archives
Database design
Development DB
End Users
Data exchange
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submission tools
Submitters
Data Distrib.
Releases Updates
Q/C etc
Add value (review etc.)
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Running a database project
Other archives
Database design
Development DB
End Users
Data exchange
Service Tools
Production DB
Service DB
Genomes Genes Patents Updates
Submission tools
Submitters
Data Distrib.
Add value (computation)
Releases Updates
Q/C etc
Add value (review etc.)
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EMBL nucleotide sequence database
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Dataflow
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EMBLFlat File
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EMBL Relational Schema
Sequence Info
Reference Info
Location Info
Taxonomy Info
Feature Info
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Data Access and Use

• Network services
• Sequence Retrieval System (SRS) integrating and
  linking the main nucleotide and protein databases
  plus many specialized databases
• Database releases are produced quarterly- via
  FTP (inc. mirror sites) and CD-ROM
• Daily and cumulative updates via FTP
• Sequence search servers

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April 2003 TrEMBL 23.4 SWISS-PROT 41.2

• 829,111 TrEMBL entries
• 123,721 SWISS-PROT entries
• weekly production of a non-redundant and
  comprehensive protein sequence database
  consisting of SWISS-PROT, TrEMBL, and TrEMBLnew
  ftp.ebi.ac.uk/pub/databases/sp_tr_nrdb/

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Goals

• High level of annotation
• Minimal redundancy
• High level of integration with other databases
• Complete and up-to-date
• Availability

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Automatic annotation of TrEMBL

• Data-mining to extract conditions from InterPro
• Extract SWISS-PROT reference entries fulfilling
  the conditions
• Extract common annotation
• Store conditions and common annotation in
  RuleBase
• Group TrEMBL by conditions
• Add common annotation to TrEMBL

InterPro
SWISS-PROT
TrEMBL
RuleBase
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Cross-references
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Funding

• EMBL
• European Commission
• NIH
• Industrial licenses
• MRC
• IUPHAR

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SWISS-PROT, TrEMBL, InterPro, etc, at EBI and SIB

• Group leaders Rolf Apweiler, Amos Bairoch
• Co-ordinatorsWolfgang Fleischmann, Henning
  Hermjakob, Michele Magrane, Maria-Jesus Martin,
  Nicola Mulder, Claire ODonovan, Manuela Pruess
• Annotators/curators Philippe Aldebert, Andrea
  Auchincloss, Kirsty Bates, Marie-Claude Blatter
  Garin, Brigitte Boeckmann, Silvia Braconi
  Quintaj, Paul Browne, Evelyn Camon, Danielle
  Coral, Elisabeth Coudert, Tania de Oliveria
  Lima, Kirill Degtyarenko, Sylvie Dethiollaz, Ann
  Estreicher, Livia Famiglietti, Nathalie
  Farriol-Mathis, Stephanie Federico, Serenella
  Ferro, Gill Fraser, Raffaella Gatto, Vivienne
  Gerritsen, Arnaud Gos, Nadine Gruaz-Gumowski,
  Ursula Hinz, Chantal Hulo, Janet James, Florence
  Jungo, Vivien Junker, Youla Karavidopoulou, Maria
  Krestyaninova, Kati Laiho, Minna Lehvaslaiho,
  Karine Michoud, Virginie Mittard, Madelaine
  Moinat, Sandra Orchard, Sandrine Pilbout, Sylvain
  Poux, Sorogini Reynaud, Catherine Rivoire, Bernd
  Röchert, Michel Schneider, Christian Sigrist,
  Andre Stutz, Shyamala Sundaram, Michael Tognolli,
  Sandra van den Broek, Bob Vaughan, Eleanor
  Whitfield
• Programmers Daniel Barrell, David Binns, Michael
  Darsow, Ujjwal Das, Eduardo de Castro, Alexander
  Fedotov, Astrid Fleischmann, Elisabeth Gasteiger,
  Alain Gateau, Andre Hackmann, Ivan Ivanyi, Eric
  Jain, Alexander Kanapin, Paul Kersey, Ernst
  Kretschmann, Corinne Lachaize, Chris Lewington,
  Xavier Martin, John Maslen, Peter McLaren,
  Rupinder Singh Mazara, Lorna Morris, John
  ORourke, Isabelle Phan, Astrid Rakow, Kai Runte,
  Florence Servant, Allyson Williams, Dan Wu
• Research staff Kristian Axelsen, Pierre-Alain
  Binz, Nicolas Hulo, Anne-Lise Veuthey
• Clerical/secretarial assistance Veronique
  Mangold, Claudia Sapsezian, Margaret Shore-Nye,
  Veronique Verbegue
• Students Pavel Dobrokhotov, Alexandre Gattiker,
  various MCF, etc