Version 8 (modified by rvos, 10 years ago)

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Open Bio* Workgroup

I would like to get an overview about current support and implementations of web services in every Open Bio* libraries (BioPerl, BioPython, BioRuby and BioJava) and hope to discuss the following:

  • What can be done with the Open Bio* projects to support interoperability?
    • Is it worth trying to mapping BioMOBY data objects (BioMOBY triplets) to Bio* library specific data strucuture?
    • Why not use complexType in SOAP to automate object creation?
    • Could a webservice be defined to allow Bio* interoperability? This would require a common exchange format. Possibly one of the XML formats used by NCBI or EBI or  nexml. Could a webservice backed with BioSQL provide and persistent objects in this format?
  • What part should be done on the web service provider's side and what is the part left best to be addressed in Open Bio* libraries?
    • Format exchange, job management, sequence manipulation ...
  • What fraction of the bioinfomatics field is covered by current Open Bio* library and what subset of those is covered by web services?
Category Perl/BioPerl Java/BioJava Ruby/BioRuby Python/BioPython
BioMOBY o o x x
WSRF o o x x
EBI SOAP ? ? o ?
NCBI SOAP ? ? x ?
KEGG API ? ? o ?
DDBJ XML ? ? o ?
PDBj ? ? x ?
BioSQL o ? o ?