rafael c jimenez [email protected]
DESCRIPTION
DAS Workshop 2012 February 27-29, 2012. Rafael C Jimenez [email protected]. DAS. Using DAS software, an introduction to some DAS implementations. Split data and presentation. Databases serving data as primitive datatypes defined by open standards. - PowerPoint PPT PresentationTRANSCRIPT
Rafael C [email protected]
DAS
DAS Workshop 2012 February 27-29, 2012
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
Data Representation
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)
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
Ways to share in DASLots of annots
withIT support
Many annotswithout
IT support
Fewannots
• easyDAS
• myDAS, proserver
• DAS WriteBack client
Clients
7
Protein sequence dataDasty
www.ebi.ac.uk/dasty
http://pfam.sanger.ac.uk/
pFamProtein sequence data
DASherProtein sequence data
http://dasher.sbc.su.se
http://www.dasregistry.org/spice/index.shtml
SpiceProtein sequence data
http://www.jalview.org/
JalviewProtein sequence data
http://www.bioinformatics.org/strap/
STRAPProtein sequence data
Genome sequence dataEnsembl
http://www.ensembl.org/
Genome sequence dataDalliance
http://www.biodalliance.org/
Genome sequence datamyKaryoview
http://mykaryoview.com/
Genome sequence dataWormBase
http://www.wormbase.org/
Protein structure dataSpice-Sisyphus
http://www.dasregistry.org/spice/index.shtml
Sequence alignment dataPfam
http://pfam.sanger.ac.uk/
SummariesPfam
http://www.ebi.ac.uk/s4/
3D-EMPepper
http://biocomp.cnb.csic.es/das/pepper.jsp
21.04.23 21
EMAP data
EMAP: The Edinburgh Mouse Atlas Project
Gene expression databases (EMAGE & GXD)
DAS reference serverEMAP - Ontology
DAS annotation serversEMAGEGXD
Protein-protein interaction dataiPfam
http://ipfam.sanger.ac.uk/
PSICQUIC
Query Interactions
PSICQUICRegistry
PSI-MIMIQL
Input Output
PSICQUICService A
PSICQUICService B
PSICQUICService C
User View
Web Service System
Data Provenance
PSICQUIC for molecular interactions
Thanks!
Questions?
Acknowledgements