Data Integration using the Distributed Annotation System (DAS) - - PowerPoint PPT Presentation

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Data Integration using the Distributed Annotation System (DAS) - - PowerPoint PPT Presentation

Mar 22, 2023 681 likes •1.02k views

Data Integration using the Distributed Annotation System (DAS) Andreas Prli , Ewan Birney, Tony Cox, Thomas A. Down, Rob Finn, Stefan Grf, David Jackson, Andreas Khri, Eugene Kulesha, Roger Pettett, James Smith, Jim Stalker, Tim J. P

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Data Integration using the Distributed Annotation System (DAS)

Andreas Prlić, Ewan Birney, Tony Cox, Thomas A. Down, Rob Finn, Stefan Gräf, David Jackson, Andreas Kähäri, Eugene Kulesha, Roger Pettett, James Smith, Jim Stalker, Tim J. P . Hubbard

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  • what is DAS
  • what do we do with it
  • DAS registration server
  • latest developments
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Text Integration of personal data into bioinf. resources

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  • Integration of annotations from external

sources into local applications

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  • online access to most recent data versions
  • no need for local installations
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DAS, how it works

Dowell, Jokerst, Allen, Eddy, Stein BMC Bioninformatics 2001

XML response http:// request

DAS Server DAS Server DAS Server Client

get sequence get features

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a few principles...

  • Clients are “intelligent” (few)
  • Servers are simple and easy to set up (many)
  • (most of) data is precalculated
  • libraries for server and client
  • multiple programming languages
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SLIDE 8

http://www.ensembl.org

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  • > 20 vertebrates / model organism
  • 5 mill. page impressions / week
  • 100 mirrors/internal installations worldwide
  • open source
  • used for other species as well
  • MySQL
  • 5-10 G / species + 100 G multi species data
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SLIDE 10

Add your own uses Registry

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Text Linking protein structure to e! Peptide view

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http://www.efamily.org.uk/software/dasclients/spice SPICE browser

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Click See exon structure mapped

  • nto 3D
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Show SNPs

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Zoom RASMOL commands

interact with Menu & RASMOL

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Structure Sequence Features Alignment DAS commands

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SPICE DAS registry Java Web Start auto install latest version send arguments

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SPICE DAS registry Meta information about DAS servers

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The DAS registration server

http://das.sanger.ac.uk/registry/

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DAS registration server

  • allows to “publish” DAS servers & share

with community

  • communicates with clients
  • regularly checks servers, sends notification
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What is the glue?

  • “Coordinate Systems”
  • Authority
  • Type of data
  • Version
  • Organism (optional)
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  • Ensembl - most of the views can display DAS

sources from multiple CS

  • SPICE - PDB, UniProt, Ensp
  • Dasty - UniProt

Clients and Coordinate Systems

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the DAS - SOA

DAS registration server a DAS source e.g. Ensembl, SPICE DAS

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111 DAS sources 26 institutions 12 countries + others

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DAS - issues

  • inconsistent implementations
  • no consistent use annotation types
  • error handling
  • searches not possible - in DAS/1
  • open sharing of data - low security
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SLIDE 28

http://sisyphus.mrc-cpe.cam.ac.uk

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  • Alignment DAS:
  • rotation matrices, shift vectors
  • range information (optional)
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SLIDE 32

http://www.jalview.org A. Waterhouse, J. Procter, G. Barton

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  • T. Down, T. Hubbard
  • Web Team, E. Kulesha, R. Pettett, T. Cox
  • eFamily Project
  • S. Gräf, A. Kahari, BioSapiens
  • A. Murzin, A. Andreeva
  • R. Finn, H.Hotz, A.Ahmed
  • Jmol, Biojava, MSD, everybody who sets up

DAS servers

Acknowledgments