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

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

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

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

6. Clients

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

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

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

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

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

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

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. 23.04.201521 EMAP data EMAP: The Edinburgh Mouse Atlas Project Gene expression databases (EMAGE & GXD) DAS reference server EMAP - Ontology DAS annotation servers EMAGE GXD

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

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

24. Thanks! Questions? Acknowledgements