Changes between Version 29 and Version 30 of WikiStart

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2007/12/10 22:34:48 (10 years ago)
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anonymous
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  • WikiStart

    v29 v30  
    77 * [wiki:Objectives_in_Japanese] 
    88 
    9 == Goals == 
    10  
    11  * What is the best solution for integration of the web services? 
    12   * Is the list of BioMOBY objects is clean enough to treat with the client program? How about the inheritance? 
    13   * Why BioMOBY doesn't use SOAP's complexType instead of the BioMOBY triple (original XML) data structure? 
    14   * Is there any performance bottleneck in the current system of the BioMOBY? 
    15  * How to integrate arising new data structures such as pathways, metabolomics, and proteomics? 
    16  * What can be done with the Open Bio* projects to support interoperability? 
    17  * How to integrate non-MOBY web service providers (Japanese DDBJ, KEGG, PDBj, CBRC services + EBI, NCBI services) 
    18  
    199== Summary == 
    2010 
     
    2414Moreover, these services are often not usable by specific languages 
    2515(partly, due to the lack of compliance of the SOAP/WSDL specification in the langauge's library). 
     16 
    2617This situation prevents these services to be popularized for and used in combination by end users as a infrastructure of the daily research. 
    2718The BioMOBY project has been tried to overcome the circumstances by defining ontologies for data types and methods used in the services. 
    28 But the set of data types and methods gathered in BioMOBY looks redundant and complicated to generate typical workflows for end users. 
    29 Besides, some of the major service providers are not included in the BioMOBY framework yet. 
    30 In DBCLS, we are trying to develop a new proxy server which translates user's request for the appropriate web service provider. 
    31 The server will also converts the query and result to the simplified/unified data types, say "50 basic bioinformatics data types" (might be a subset of BioMOBY). 
    32 Anyway, interoperability can be significantly improved if all Bio* libraries supports them and we just need a practical environment for bioinformatics. 
    33 Thus, we believe gathering all web service providers and Open Bio* library developers to disucuss about the standardization of objects and methods among web services and programming languages must benefit usability and interoperability for the life science in the next era. 
     19However, there are many major service providers are not yet participated in the BioMOBY framework. 
     20Especially, there are several web service providers in Japan such as DDBJ, KEGG, PDBj and CBRC but none of them are not integrated in any context. 
    3421 
    35  * Utilizing every bioinformatics web services by 4 major computer languages 
    36  * Standardizing the objects and methods in bioinformatics web services 
    37  * Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries 
     22Thus, at [http://www.dbcls.jp/en/ DBCLS], we started to develop a new proxy server which translates user's request for the appropriate web service provider. 
     23If all [http://www.open-bio.org/ Open Bio*] libraries support BioMOBY and other service providers, interoperability of these services can be significantly improved. 
     24Here, we need agreement for the future web services with every web service providers and client developers. 
     25 
     26We believe gathering all web service providers to disucuss about the standardization of objects and methods among web services, 
     27and Open Bio* library developers from different programming languages to discuss about the implementation of the common infrastructure, 
     28must benefit usability and interoperability for the life science in the next era. 
     29 
     30For this purpose, we hope to organize a BioHackathon specialized for the web services in 2008. 
     31 
     32 * Standardizing the objects and methods in bioinformatics web services (BioMOBY) 
     33  * Discuss about the best solution of the framework and ontologies for the future in life science 
     34 * Utilizing every bioinformatics web services by 4 major computer languages (Perl, Python, Ruby, Java) 
     35  * Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries 
    3836 * Providing various clients to create and execute bioinformatics workflows 
    39  * Connecting seamlessly: Web service - Grid, Remote - Local, SOAP/WSDL - REST, Async - Sync 
     37  * Connecting seamlessly: Web service - Grid, Remote - Local, SOAP/WSDL - REST, Async - Sync 
     38 * Encourage independent service providers to join the movement of integration and interoperability 
     39  * How to increase the number of SOAP compliant services (tools/databases) 
    4040 
    4141== Topics == 
     
    4747 * [wiki:Workflow_workgroup] 
    4848 * [wiki:ServiceProvider_workgroup] 
    49  
    50 === BioMOBY === 
    51  
    52 I would like to ask Dr. Mark Wilkinson to give us a lecture for the following objectives: 
    53  
    54  * to make every web service providers understand what does the BioMOBY is 
    55  * current status of the BioMOBY project and how the sites integrated by BioMOBY works 
    56  * current status of the semantic MOBY and its practical usages or goals 
    57  
    58 and I would like to discuss about: 
    59  
    60  * what kind of efforts have been made to popularize BioMOBY 
    61   * why all web services are not compatible with BioMOBY yet? 
    62   * what is the strength of BioMOBY compared with non-BioMOBY web services? 
    63   * what kind of improvements can be made from now? 
    64   * which languages can be used to create BioMOBY clients (only Perl and Java for now?) 
    65     * refine the ontology for data types and methods 
    66     * implement BioMOBY client library in every Bio* projects 
    67     * utilize BioMOBY in NCBI, EBI, KEGG, DDBJ etc. or to create a proxy server  which converts these services compatible with BioMOBY 
    68  
    69 === Open Bio* === 
    70  
    71 to be written... 
    72  
    73 === Clients (Taverna, G-language etc.) === 
    74  
    75 to be written... 
    76  
    77 === Web Service providers === 
    78  
    79 to be written... 
    80  
    81  * How to increase the number of SOAP compliant services (tools/databases) 
    8249 
    8350== Venue ==