DAS Workshop 2012
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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.

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Rafael c jimenez rafael ebi ac uk

  • DAS Workshop 2012

  • February 27-29, 2012

Rafael C [email protected]

  • DAS

  • Using DAS software, an introduction to some DAS implementations


Split data and presentation

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

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

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

Ways to share in DAS

Lots of annots

with

IT support

  • myDAS, proserver

Many annots

without

IT support

  • easyDAS

Few

annots

  • DAS WriteBack client


Clients

Clients


Protein sequence data

Protein sequence data

Dasty

www.ebi.ac.uk/dasty

7


Rafael c jimenez rafael ebi ac uk

Protein sequence data

pFam

http://pfam.sanger.ac.uk/


Rafael c jimenez rafael ebi ac uk

Protein sequence data

DASher

http://dasher.sbc.su.se


Rafael c jimenez rafael ebi ac uk

Protein sequence data

Spice

http://www.dasregistry.org/spice/index.shtml


Rafael c jimenez rafael ebi ac uk

Protein sequence data

Jalview

http://www.jalview.org/


Rafael c jimenez rafael ebi ac uk

Protein sequence data

STRAP

http://www.bioinformatics.org/strap/


Genome sequence data

Genome sequence data

Ensembl

http://www.ensembl.org/


Rafael c jimenez rafael ebi ac uk

Genome sequence data

Dalliance

http://www.biodalliance.org/


Rafael c jimenez rafael ebi ac uk

Genome sequence data

myKaryoview

http://mykaryoview.com/


Rafael c jimenez rafael ebi ac uk

Genome sequence data

WormBase

http://www.wormbase.org/


Protein structure data

Protein structure data

Spice-Sisyphus

http://www.dasregistry.org/spice/index.shtml


Sequence alignment data

Sequence alignment data

Pfam

http://pfam.sanger.ac.uk/


Summaries

Summaries

Pfam

http://www.ebi.ac.uk/s4/


Rafael c jimenez rafael ebi ac uk

3D-EM

Pepper

http://biocomp.cnb.csic.es/das/pepper.jsp


Emap data

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

Protein-protein interaction data

iPfam

http://ipfam.sanger.ac.uk/


Rafael c jimenez rafael ebi 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


Rafael c jimenez rafael ebi ac uk

Thanks!

Questions?

Acknowledgements


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