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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 primitive datatypes defined by open standards.
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DAS Workshop 2012 • February 27-29, 2012 Rafael C Jimenezrafael@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 • Different front ends or components of front ends compete for users Representation Data
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
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
Ways to share in DAS Lots of annots with IT support • myDAS, proserver Many annots without IT support • easyDAS Few annots • DAS WriteBack client
Protein sequence data Dasty www.ebi.ac.uk/dasty 7
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 Gene expression databases (EMAGE & GXD) 19.09.2014 21
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 Service A PSICQUIC Service B PSICQUIC Service C PSICQUIC Registry Data Provenance
Thanks! Questions? Acknowledgements