27 February 2012

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,
gene, pseudogene, probeset, QTL, …)
• UCSC
• ENSEMBL
• ArrayExpress
• …
– Protein (domain, PTM, literature,
expression, variants, … )
• UniProt
• Pfam
• CBS
• …
Data Representation
• Applications
– 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. 6
Protein sequence dataDasty
www.ebi.ac.uk/dasty

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

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

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

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

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

12. Genome sequence dataEnsembl
http://www.ensembl.org/

13. Genome sequence dataWormBase
http://www.wormbase.org/

14. Genome sequence dataDalliance
http://www.biodalliance.org/

15. Protein structure dataSpice-Sisyphus
http://www.dasregistry.org/spice/index.shtml

16. Sequence alignment dataPfam
http://pfam.sanger.ac.uk/

17. 3D-EMPepper
http://biocomp.cnb.csic.es/das/pepper.jsp

18. 13.12.18 18
EMAP data
EMAP: The Edinburgh Mouse Atlas Project
Gene expression databases (EMAGE & GXD)

DAS reference server

EMAP - Ontology
DAS annotation servers

EMAGE

GXD

19. Protein-protein interaction dataiPfam
http://ipfam.sanger.ac.uk/

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

21. Thanks!
Questions?
Acknowledgements