Service provider Workgroup

Here, we gather the major web service providers including BioMOBY projects and Japanese providers such as DDBJ, KEGG, PDBj, CBRC and other foreign providers like EBI and NCBI.

• Discuss current problems existing in each services:
  • Language dependencies
  • Naming conventions
  • Returned data type
  • Returned data size
  • Job managements
  • WSDL syntax violations
  • Timeouts
  • Sync and async
  • MIME attachments
  • Not implemented yet

• How to integrate non-MOBY web service providers?
  • What kind of effort is needed to compromise with BioMOBY framework?

• How to improve interoperability among the services?
  • Do you need proxy server to translate objects among services?
  • Object identity matching problem (LSID, BioMOBY)

• How to treat the needs for the REST services?
  • PDBj's REST API (prototype):  http://doc.pdbj.org/help.cgi?REST%20API
  • DDBJ's REST API:  http://www.xml.nig.ac.jp/tutorial/rest/index.html
  • EBI's REST API  http://www.ebi.ac.uk/Tools/webservices/tutorials/rest

Attending Service Providers

• STRING/STITCH,  http://string.embl.de /  http://stitch.embl.de (Michael Kuhn)
  • scope of database: protein-protein and protein-chemical interaction networks
  • existing web-services: rudimentary/broken SOAP interface to retrieve network via PSI-MI
  • plans for API: query for the network (return PSI-MI 2.5), query for protein by identifier, synonym or sequence, retrieve orthologs/homologs, retrieve synonyms for protein, retrieve abstracts mentioning a protein
  • open questions:
    • Which ontologies should be used for the input (i.e., how to represent a protein or chemical so that other web services can deal with it)?

• Ontology Lookup Service  http://www.ebi.ac.uk/ols (Richard Cote)
  • scope of database: ontology and controlle vocab term queries
  • existing web-services: AXIS 1.4 SOAP interface to query on term name, identifier, synonyms, relationships to other terms
  • plans for API: port to JAX-WS 2.x
  • open questions: since we're planning on porting it, what new functionality would be useful?

• Protein Identifier Cross Reference (PICR),  http://www.ebi.ac.uk/Tools/picr (Richard Cote)
  • scope of database: protein identifier cross reference queries by sequence and identifier across all databases and releases loaded into the UniProt? Archive (UNIPARC)
  • existing web-services: JAX-WS SOAP and REST interfaces
  • plans for API: currently in maintenance mode
  • open questions: what new functionality would be useful?

• DATABASE,  http:// ()
  • scope of database:
  • existing web-services:
  • plans for API:
  • open questions: