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Rafael C Jimenez rafael@ebi.ac.uk

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 primitive datatypes defined by open standards.

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Rafael C Jimenez rafael@ebi.ac.uk

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  1. DAS Workshop 2012 • February 27-29, 2012 Rafael C Jimenezrafael@ebi.ac.uk • DAS • Using DAS software, an introduction to some DAS implementations

  2. Split data and presentation • Databases serving data as primitive datatypes defined by open standards • Different front ends or components of front ends compete for users Representation Data

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

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

  5. Ways to share in DAS Lots of annots with IT support • myDAS, proserver Many annots without IT support • easyDAS Few annots • DAS WriteBack client

  6. Clients

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

  8. Protein sequence data pFam http://pfam.sanger.ac.uk/

  9. Protein sequence data DASher http://dasher.sbc.su.se

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

  11. Protein sequence data Jalview http://www.jalview.org/

  12. Protein sequence data STRAP http://www.bioinformatics.org/strap/

  13. Genome sequence data Ensembl http://www.ensembl.org/

  14. Genome sequence data Dalliance http://www.biodalliance.org/

  15. Genome sequence data myKaryoview http://mykaryoview.com/

  16. Genome sequence data WormBase http://www.wormbase.org/

  17. Protein structure data Spice-Sisyphus http://www.dasregistry.org/spice/index.shtml

  18. Sequence alignment data Pfam http://pfam.sanger.ac.uk/

  19. Summaries Pfam http://www.ebi.ac.uk/s4/

  20. 3D-EM Pepper http://biocomp.cnb.csic.es/das/pepper.jsp

  21. EMAP data • DAS reference server • EMAP - Ontology DAS annotation servers • EMAGE • GXD EMAP: The Edinburgh Mouse Atlas Project Gene expression databases (EMAGE & GXD) 19.09.2014 21

  22. Protein-protein interaction data iPfam http://ipfam.sanger.ac.uk/

  23. PSICQUIC for molecular interactions User View MIQL PSI-MI Query Interactions Input Output PSICQUIC Web Service System PSICQUIC Service A PSICQUIC Service B PSICQUIC Service C PSICQUIC Registry Data Provenance

  24. Thanks! Questions? Acknowledgements

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