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					                 DAS Workshop 2012
                      February 27-29, 2012
                   Rafael C Jimenez
                          rafael@ebi.ac.uk




DAS
Using DAS software, an introduction
to some DAS implementations
         Split data and presentation
•   Databases serving data as       • Different front ends or
    primitive datatypes defined by     components of front ends
    open standards                    compete for users




          Data                      Representation
          Tools for data handling
• Frameworks               • Libraries
   – MyDAS (Java)             – JDAS (Java)
   – Dazzle (Java)            – Dasobert (Java)
   – Proserver (Perl)         – Bio::Das::Lite (Perl)
   – LDAS (Perl)              – jsDAS (Javascript)

• Application
   – EasyDAS (Proserver)

       Data                Representation
                               Applications
•   Sources                                •   Clients
     – Genome (gene, pseudogene,                –   Dalliance
        transcript, phenotype, SNP, CNV,
        probeset, QTL, …)                       –   IGV
          •   UCSC                              –   Ensembl
                                                –   Gbrowse
          •   ENSEMBL
                                                –   IGB
          •   ArrayExpress                      –   SPICE
          •   …                                 –   Dasty
     – Protein (domain, PTM, literature,        –   Jalview
        expression, variants, … )
                                                –   PeppeR
          •   UniProt
                                                –   DASher
          •   Pfam                              –   EpiC
          •   CBS                               –   STRAP
          •   …                                 –   EBI search


              Data                             Representation
Ways to share in DAS
             Lots of annots
                   with     • myDAS, proserver
               IT support




              Many annots
                without • easyDAS
               IT support




                  Few     • DAS WriteBack
                 annots     client
Clients
Protein sequence data
        Dasty




           7     www.ebi.ac.uk/dasty
Protein sequence data
        pFam




               http://pfam.sanger.ac.uk/
Protein sequence data
        DASher




                 http://dasher.sbc.su.se
Protein sequence data
           Spice




    http://www.dasregistry.org/spice/index.shtml
Protein sequence data
        Jalview




                  http://www.jalview.org/
Protein sequence data
        STRAP




         http://www.bioinformatics.org/strap/
Genome sequence data
       Ensembl




                 http://www.ensembl.org/
Genome sequence data
       Dalliance




                   http://www.biodalliance.org/
Genome sequence data
       myKaryoview




                     http://mykaryoview.com/
Genome sequence data
       WormBase




                  http://www.wormbase.org/
Protein structure data
        Spice-Sisyphus




    http://www.dasregistry.org/spice/index.shtml
Sequence alignment data
         Pfam




                http://pfam.sanger.ac.uk/
Summaries
   Pfam




          http://www.ebi.ac.uk/s4/
  3D-EM
    Pepper




http://biocomp.cnb.csic.es/das/pepper.jsp
                          EMAP data
                                             DAS reference server
                                                EMAP - Ontology




                                          DAS annotation servers
                                             EMAGE

                                             GXD




EMAP: The Edinburgh Mouse Atlas Project
 05.04.2013                        21
Gene expression databases (EMAGE & GXD)
Protein-protein interaction data
              iPfam




                      http://ipfam.sanger.ac.uk/
PSICQUIC for molecular interactions
                                                                    User View

                  MIQL                      PSI-MI
                   Query                     Interactions




                     Input                       Output


                                PSICQUIC

                                                            Web Service System




      PSICQUIC      PSICQUIC         PSICQUIC                 PSICQUIC
      Service A     Service B        Service C                Registry

                                                              Data Provenance
 Thanks!
Questions?

   Acknowledgements

				
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posted:4/5/2013
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