Changes between Version 8 and Version 9 of Report

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Timestamp:
2009/07/03 20:09:19 (12 years ago)
Author:
atsuko
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  • Report

    v8 v9  
    376376Manifest of Bio-Web Service (Bio-WS) guidelines 
    377377 
    378 A web service may be very helpful to process data from heterogeneous biological databases. However, several problems, such as the lack of documents for methods, the lack of compliance of the SOAP/WSDL specification in the language's library and various data formats, make users feel difficult to built a workflow by using web services. 
     378A web service may be very helpful to process data from heterogeneous biological databases. However, several problems, such as the lack of documents for methods, the lack of compliance of the SOAP/WSDL specification in the language's library and various data formats, make users feel difficult to build a workflow by using web services. 
    379379 
    380380TogoWS is designed to address such issues for the improved usability as follows. 
    381 (1) SOAP based web services ideally follow the open standard and they should be independent from computer languages, however, many services still require language specific hacks in practice. TogoWS proxies these services to make them available in any programming language without difficulty. 
    382 (2) Query mechanism and syntax differs service to service that requires user to learn each usage beforehand. TogoWS provides a simple REST interface to query and retrieve in a unified manner. 
    383 (3) Entries obtained from databases are needed to be parsed by the client program to be fully utilized. TogoWS embeds open source bioinformatics libraries like BioPerl and BioRuby (which we also developed) to provide functionalities for parsing and conversion of various biological data formats without any installation on user side.  
     381(1) SOAP based web services ideally follow the open standard and they should be independent from computer languages. However, many services still require language specific programming in practice. TogoWS proxies these services to make them available in any programming language without difficulty. 
     382(2) TogoWS provides a simple REST interface to query and retrieve in a unified manner. 
     383(3) Entries obtained from databases are needed to be parsed by the client program to be fully utilized. TogoWS provides functionalities for parsing and conversion of various biological data formats without any installation on user side. 
    384384  
    385 Although the TogoWS supports many biological databases and the number of available databases is increasing, it is not practical to proxy all the major biological databases by TogoWS because the number of biological databases is extremely large. Therefore, it is preferable that users could combine the original web services without effort under a direction. To do so, we would like to establish a guideline for designing web services on biological databases.    
    386  
    387 We first began by discussing among Japanese database providers including The University of Tokyo as the KEGG provider, Osaka University as the PDBj provider, Computational Biology Research Center, Biomedicinal Information Research Center and Database Center for Life Science to make the web services on the databases work together. Then, the first guildeline for designing web services was proposed in Japanese in October, 2008. We improved it to be applicable to variable databases and easy to understand even for a beginner of web services. After that, we translated it to English to sharpen at the BioHackathon 2009.  
    388  
    389  
    390  
     385Although the TogoWS supports many biological databases and the number of available databases is increasing, it is not practical to proxy all the major biological databases by TogoWS because the number of biological databases is extremely large. Therefore, it is preferable that users could combine the original web services without effort under a unified direction. To do so, we would like to establish a guideline for designing web services on biological databases. 
     386 
     387Before the BioHackathon started, we first began by discussing among Japanese database providers including The University of Tokyo as the KEGG provider, Osaka University as the PDBj provider, Computational Biology Research Center, Biomedicinal Information Research Center and Database Center for Life Science to make the web services on the databases work together. Then, the first guildeline for designing web services was proposed in Japanese in October, 2008. We improved it to be applicable to variable databases and easy to understand even for a beginner of web services. After that, we translated it to English to sharpen at the BioHackathon 2009.