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
  • CIPRES's REST API  http://www.phylo.org/rest/rest_api.php

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?

• GlycomeDB,  http://www.glycome-db.org/ (René Ranzinger)
  • scope of database: data integration of carbohydrate structures and their taxonomical annotations from all freely available carbohydrate structure databases (currently 8 databases)
  • existing web-services: REST interfaces
  • plans for API: enhancement of data retrieval functions (substructure search, composition search, search by mass, search by species)
  • open questions:
    • what other functionalities would be useful ?
    • how to make an standardized API to become compatible to other webservices (BioMoby?) ?
    • how to close the gap between protein and glycan databases ?

• CIPRES,  http://www.phylo.org (Rutger Vos)
  • scope of service: phylogenetic analysis, principally multiple sequence alignment and tree inference
  • existing web-services: REST front end for service architecture ( API)
  • plans for API: implement more algorithms, support more data formats
  • open questions:
    • How to integrate with ontology-mediated service architectures?

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