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 | ? |
