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
  • DAS/1 API  http://biodas.org/documents/spec.html

Notes ¶

• Asynchronous services first day notes
• Security issues and needs on web services first day notes
• Interaction networks

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?

• PDBj,  http://www.pdbj.org (Akira Kinjo, Daron Standley)
  • scope of database: Member of World Wide Protein Data Bank (WWPDB); serves as PDB data deposition and retrieval center for Asia and Oceania
  • existing web-services: Text-based query of PDB content (xPSSS), sequence search engine (Sequence Navigator), pairwise structure alignment (ASH), structure-based search engine (Structure Navigator)
  • plans for API: Improve for interoperability, at least with other nearby databases such as DDBJ, KEGG, and CBRC.
  • open questions: Register web services with BioMoby?? Should we support REST and SOAP for all services? How to improve usability?
  • PDBj-DDBJ-KEGG