Changes between Version 91 and Version 92 of WikiStart

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2008/02/07 19:59:34 (10 years ago)
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pjotr2007
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minor grammar fixes

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    99The number of web service providers in the field of bioinformatics is increasing every year. 
    1010In theory, these services are interoperable and independent of specific computer languages. 
    11 However, each service uses their own definition of the data types and naming conventions for the methods. 
     11However, each service uses its own definition of data types and 
     12method naming conventions. 
    1213Moreover, these services are often not usable by specific languages 
    1314(partly, due to the lack of compliance of the SOAP/WSDL specification in the language's library). 
    1415 
    15 This situation prevents these services from becoming popular among and used by end users and developers alike as an infrastructure of their daily research. 
     16This lack of interoperability prevents these services from becoming 
     17popular among end users and developers alike and they are under 
     18utilised as an infrastructure of their daily research. 
     19 
    1620The [http://www.biomoby.org/ BioMOBY] project has tried to overcome these problems by defining ontologies for data types and methods used in the services. 
    1721However, there are many major service providers which are not yet participating in the BioMOBY framework. 
    1822For example, there are several web service providers in Japan such as [http://www.xml.nig.ac.jp/ DDBJ], [http://www.genome.jp/kegg/soap/ KEGG], 
    19 [http://www.pdbj.org/ PDBj] and [http://www.cbrc.jp/ CBRC] but none of them are integrated in any way. 
     23[http://www.pdbj.org/ PDBj] and [http://www.cbrc.jp/ CBRC] but none of these are integrated in any way. 
    2024 
    21 Thus, 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 providers. 
    22 If all [http://www.open-bio.org/ Open Bio*] libraries support BioMOBY and other service providers, interoperability among these services can be significantly improved. 
    23 Here, we need agreement about the future direction of web services by every web service provider and by client developers. 
     25For this reason, at [http://www.dbcls.jp/en/ DBCLS], we started to 
     26develop a new proxy server which translates user requests for the 
     27appropriate web service providers.  If all [http://www.open-bio.org/ 
     28Open Bio*] libraries were to support BioMOBY and other service providers, 
     29interoperability among these services are significantly improved. 
     30To achieve this we need agreement about the future direction of web services by 
     31every web service provider and by client developers. 
    2432 
    25 We believe gathering all web service providers to discuss the standardization of objects and methods among web services, 
    26 and Open Bio* library developers from different programming languages ([http://www.bioperl.org/ BioPerl], [http://www.biopython.org/ BioPython], 
    27 [http://www.bioruby.org/ BioRuby], and [http://www.biojava.org/ BioJava]) to discuss the implementation of the common infrastructure, 
    28 must benefit usability and interoperability for the life science in the next era. 
     33We believe that getting all web service providers together, to discuss the 
     34standardization of objects and methods among web services, with Open 
     35Bio* library developers from different programming languages 
     36([http://www.bioperl.org/ BioPerl], [http://www.biopython.org/ BioPython], [http://www.bioruby.org/ BioRuby], and 
     37[http://www.biojava.org/ BioJava]) will benefit usability and 
     38interoperability of services for the life sciences in the next era. 
    2939 
    30 For this purpose, we hope to organize a !BioHackathon focusing on web services from four different domains. 
     40For this purpose, we organize a !BioHackathon focusing on web services from four different domains. 
    3141 
    3242 * Web service providers 
    3343  * Encourage independent service providers to join the movement of integration and interoperability 
    34    * Increasing the number of SOAP compliant services (tools/databases) 
     44   * Increase the number of SOAP compliant services (tools/databases) 
    3545 * Open Bio* developers 
    36   * Utilizing every bioinformatics web service by 4 major computer languages (Perl, Python, Ruby, Java) 
    37    * Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries 
     46  * Utilize every bioinformatics web service by 4 major computer languages (Perl, Python, Ruby, Java) 
     47   * Create compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries 
    3848 * Workflow client developers 
    39   * Providing various clients to create and execute bioinformatics workflows 
    40    * Connecting seamlessly: Web service - Grid, Remote - Local, SOAP/WSDL - REST, Sync - Async 
     49  * Provide various clients to create and execute bioinformatics workflows 
     50   * Connect seamlessly: Web service - Grid, Remote - Local, SOAP/WSDL - REST, Sync - Async 
    4151 * BioMOBY project developers 
    42   * Standardizing the objects and methods in bioinformatics web services via BioMOBY 
    43    * Discussing the best solution of the framework and the ontologies for life science 
     52  * Standardize the objects and methods in bioinformatics web services via BioMOBY 
     53   * Discuss the best solution of the framework and the ontologies for the life sciences 
    4454 
    4555== Presentations and Open Space topics ==