[[PageOutline(1-3)]] = 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 == * [wiki:AsynchronousServicesFirstDay Asynchronous services first day notes] == 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 ([http://www.phylo.org/rest/rest_api.php 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?