Andy Jenkinson Bosc Das 2008

BioDAS Andy Jenkinson

BioDAS – Andy Jenkinson 7/20/08 2

BioDAS

BioDAS •  an Open Bio project •  oversees the DAS protocol

DAS •  distributed data integration platform •  for visual display


BioDAS


DAS Architecture

Web service protocol •  client-server model •  client executes commands on the server

Defines 3 constraints •  communication method (HTTP) •  query model (REST) •  data model (XML schema)


DAS Design Principles

Principally for display •  should be responsive (fast) •  targeted queries •  lightweight infrastructure

Use existing technologies •  don’t reinvent the wheel


DAS Design Principles

Data remains distributed •  “live” data •  data providers retain responsibility •  good for private/changing data •  spreads resources

Easy for data providers to implement •  simple protocol •  “dumb server, clever client”


DAS Software

Server implementations •  Dazzle, ProServer (and others) •  pluggable architecture •  “standard” plugins provided

Client libraries •  Dasobert, Bio::Das::Lite •  core communication/parsing only


DAS Extensions

Originally designed for genomics

DAS… extended •  additional data types •  discovery functionality •  feature ontology •  advanced stylesheets

1.53E specification


Additional data types

•  Protein sequences

•  Protein 3D structures

•  Alignments

•  Molecular interactions

•  3D-EM volume maps


Discovery

Public DAS registry •  documents capabilities & coordinate systems •  servers can be registries •  registry can “mirror” servers

Client

Server

Registry

Server


Ontology integration

DAS enforces no semantics •  minimal effort for data providers •  limits programmatic analysis

Optional ontology for features •  adopted by BioSapiens NoE •  incorporates SO; PSI-MOD; ECO •  fully backwards compatible


DAS/2

History •  bifurcation of DAS project •  aim to expand features (e.g. writeback)

Currently •  initial grant now expired •  lacks features from DAS/1 •  minimal adoption, especially outside US


DAS/2

Lessons •  backwards compatibility essential •  geographical divide a challenge

Options •  adopt a single realistic strategy •  attempt to merge back •  incorporate ideas from DAS/2 into DAS/1


DAS/1 Future

Improve cohesion •  better documentation •  uniform software implementation

Continue to expand •  Authentication •  Small molecule DAS •  Searches? •  Writeback?


DAS adoption

Registered public DAS sources

•  401 servers •  53 institutions •  18 countries


Acknowledgements

OBF

Ensembl

BioSapiens

DAS data providers!

Andreas Prlic Rob Finn Eugene Kulesha Hagen Blankenburg Gabby Reeves Henning Hermjakob Tim Hubbard Ewan Birney


More info

http://biodas.org/ http://www.dasregistry.org/

http://www.biojava.org/wiki/Dazzle http://www.sanger.ac.uk/Software/analysis/proserver/

[email protected]

[email protected]

Andy Jenkinson Bosc Das 2008

Technology

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