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Distributed Annotation System Version 2

Distributed Annotation System Version 2. Allen Day, UCLA Anthony Cox, EBI Gregg Helt, Affymetrix Andrew Dalke, Dalke Scientific Lincoln Stein, CSHL. Annotation Server. Reference Server. Annotation Server. Annotation Server. AC003027. M10154. AC005122. WI1029. AFM820. AFM1126. WI443.

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Distributed Annotation System Version 2

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  1. Distributed Annotation SystemVersion 2 Allen Day, UCLA Anthony Cox, EBI Gregg Helt, Affymetrix Andrew Dalke, Dalke Scientific Lincoln Stein, CSHL

  2. Annotation Server Reference Server Annotation Server Annotation Server AC003027 M10154 AC005122 WI1029 AFM820 AFM1126 WI443 DAS/1 AC003027 M10154 AC005122

  3. EnsEMBL 1

  4. EnsEMBL 2

  5. Deficiencies of DAS/1 • Format for representing genomic features too rigid. • Description of genomic features too flexible. • No IDs for genomic features. • No write-back.

  6. DAS/2 • Less Rigid • Multiple formats for representing genomic features. • Arbitrary nesting of features.. • DAS/2 More Rigid • Uses Sequence Ontology (SO) for describing features • Ready to accept attribute ontologies • Add your own ontology, but publish it!

  7. REST-Style IDs • Addressing a Data Source • http://wormbase.org/das/genome/wormbase/1 • Addressing a Feature Type • http://wormbase.org/das/genome/wormbase/1/type/tRNA • Addressing a Feature • http://wormbase.org/das/genome/wormbase/1/feature/gene0038

  8. Write-Back • PUT http://wormbase.org/das/wormbase/1/genome/feature/M7.1 • Update identified feature • POST http://wormbase.org/das/wormbase/1/genome/feature • Create feature • DELETE http://wormbase.org/das/wormbase/1/genome/feature/M7.1 • Delete feature

  9. Progress • Draft spec up and ready for comments • http://www.biodas.org • Server prototype up and running • See Allen Day • Client prototype up and running • See Gregg Helt • Project still in flux

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