Rafael C Jimenez [e-mail]

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DAS Workshop 2012 February 27-29, 2012
Rafael C Jimenezrafael_at_ebi.ac.uk
DAS
Using DAS software, an introduction to some DAS
implementations
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Split data and presentation

• Databases serving data as primitive datatypes
  de?ned by open standards

• Different front ends or components of front ends
  compete for users

Data
Representation
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Tools for data handling

• Frameworks
• MyDAS (Java)
• Dazzle (Java)
• Proserver (Perl)
• LDAS (Perl)
• Application
• EasyDAS (Proserver)

• Libraries
• JDAS (Java)
• Dasobert (Java)
• BioDasLite (Perl)
• jsDAS (Javascript)

Data
Representation
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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

Data
Representation
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Ways to share in DAS
Lots of annots with IT support

• myDAS, proserver

Many annots without IT support

• easyDAS

Few annots

• DAS WriteBack client

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Clients
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Protein sequence data
Dasty
www.ebi.ac.uk/dasty
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Protein sequence data
pFam
http//pfam.sanger.ac.uk/
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Protein sequence data
DASher
http//dasher.sbc.su.se
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Protein sequence data
Spice
http//www.dasregistry.org/spice/index.shtml
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Protein sequence data
Jalview
http//www.jalview.org/
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Protein sequence data
STRAP
http//www.bioinformatics.org/strap/
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Genome sequence data
Ensembl
http//www.ensembl.org/
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Genome sequence data
Dalliance
http//www.biodalliance.org/
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Genome sequence data
myKaryoview
http//mykaryoview.com/
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Genome sequence data
WormBase
http//www.wormbase.org/
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Protein structure data
Spice-Sisyphus
http//www.dasregistry.org/spice/index.shtml
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Sequence alignment data
Pfam
http//pfam.sanger.ac.uk/
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Summaries
Pfam
http//www.ebi.ac.uk/s4/
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3D-EM
Pepper
http//biocomp.cnb.csic.es/das/pepper.jsp
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EMAP data

• DAS reference server
• EMAP - Ontology
• DAS annotation servers
• EMAGE
• GXD

EMAP The Edinburgh Mouse Atlas Project Gene
expression databases (EMAGE GXD)
21.05.2016
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Protein-protein interaction data
iPfam
http//ipfam.sanger.ac.uk/
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PSICQUIC for molecular interactions
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Thanks! Questions?
Acknowledgements