recently , more and more genomes have been sequenced and annotated , and the data of proteins and gene interactions are accumulating .
biological data are mostly digital and stored in a wide variety of formats in heterogeneous systems .
biological data exist all over the world as various web services , which provide biologists with much useful information .
however , when users actually make use of them , they need to access to web services ( databases ) one by one . if they want to compare many different kinds of data , they need to do cumbersome task .
actually , a large part of the work of biologists today consists in distributing local data , querying multiple remote heterogeneous data source , and integrating retrieved data manually .
therefore , distributing and integrating biological data is a very important task and has been recognized as a key component of today s genome biology research .
many communities have devoted to a large amount of work on the exchange and integration of biological data ( 1 ) .
the difficulties in dealing with the bioinformatics data exchange and integration come from the following technical issues:1)the volume of biological data grows at an exponential rate.2)data are disseminated in a myriad of different databases and managed by different database management system ( dbms).3)biological data from different sources have heterogeneous formats ( 2).4)the platforms or systems for distributing data are different , and the interaction and independence is lacked among these platforms or systems.5)hypertext markup language ( html ) , as a language used widely for database browsing , data publishing , gathering , submission and analysis , is not suitable for extracting and integrating data .
data are disseminated in a myriad of different databases and managed by different database management system ( dbms ) .
the platforms or systems for distributing data are different , and the interaction and independence is lacked among these platforms or systems .
hypertext markup language ( html ) , as a language used widely for database browsing , data publishing , gathering , submission and analysis , is not suitable for extracting and integrating data .
data integration consists in wrapping data sources and either loading retrieved data into a data warehouse or returning it to the user .
nowadays , database federation is a main technology for solving data integration problem ( 3 ) .
database federation offers the promise of a unified view of these disparate data and detailed query through a single easy - to - use interface available via the world wide web .
there are two approaches for implementing database federation : concrete and virtual ( or loose ) federation .
some systems such as entrez , srs , discoverylink , and dbget ( 4 ) , have been designed for the specific integration of biomolecular data . however , there are some shortcomings by using database federation technology for integrating data
. first , the retrieved data by concrete federation are not always the latest and greatest .
second , because the retrieved data by virtual federation are web pages ( html format ) , it is an arduous task to parse the result documents .
third , a client of virtual federation must be tied to the upstream web service directly .
web services , a kind of service - oriented architecture , have been used worldwide to exchange and integrate data in e - commerce .
actually , the shortcomings described above are addressed in part by web services and xml ( extensible markup language ) technologies . the flat file format ( ff format )
however , it is very difficult to parse the ff format for extracting the interesting information .
xml provided a generic way to represent structured and typed data , which makes it easy to write a script for parsing an xml document .
a web service is a unit of business logic , located somewhere on the internet , which is accessible through standard - based internet protocols such as http or simple message transfer protocol ( smtp ) .
the core of today s web services technology is made up by soap ( simple object access protocol ) , wsdl ( web service description language ) and uddi ( universal , description , and discovery integration ; figure 1 ) .
web services have some features for solving the problems of information exchange , data integration and distributed application:1)web service is xml - based .
all of web services use xml as the data representation layer.2)web service is loosely coupled .
a client of a web service is not tied to the web service directly.3)web service is coarse - grained .
the technology provides a natural way of defining coarse - grained services that access the right amount of business logic.4)web service supports remote procedure calls ( rpcs ) .
it allows clients to invoke procedures , functions , and methods on remote object using xml - based protocol.5)web service supports a transparent exchange of documents to facilitate data and documents integration .
the technology provides a natural way of defining coarse - grained services that access the right amount of business logic .
it allows clients to invoke procedures , functions , and methods on remote object using xml - based protocol .
xml is a markup language that specifies neither the tag set nor the grammar for that language , and is a meta language used to define other language .
xml allows one to define his own markup language , which consists of his own tags .
furthermore , the meaning of tags is essentially different between xml and html . unlike html , the tags defined in xml indicate the semantics of a document rather than display a document .
the set of tags and grammar , or schema , for an xml language , describing admissible combinations of tags in a document , can be formalized and enforced by standard parsing tools .
it is clear that xml has some interesting features addressing the problems of data exchange and integration introduced above . for one thing
, xml makes it very advantageous to exchange data among data sources if all of them adopt the same standardization in xml documents .
thirdly , it is convenient to extract interesting information from xml documents , which helps to data integration . in life science
, many commercial and academic communities are now adopting xml as a standard for their genome biology data management ( http://scbi.scu.edu.cn/xml/ ) .
a web service is a unit of business logic , located somewhere on the internet , which is accessible through standard - based internet protocols such as http or simple message transfer protocol ( smtp ) .
the core of today s web services technology is made up by soap ( simple object access protocol ) , wsdl ( web service description language ) and uddi ( universal , description , and discovery integration ; figure 1 ) .
web services have some features for solving the problems of information exchange , data integration and distributed application:1)web service is xml - based .
all of web services use xml as the data representation layer.2)web service is loosely coupled .
a client of a web service is not tied to the web service directly.3)web service is coarse - grained .
the technology provides a natural way of defining coarse - grained services that access the right amount of business logic.4)web service supports remote procedure calls ( rpcs ) .
it allows clients to invoke procedures , functions , and methods on remote object using xml - based protocol.5)web service supports a transparent exchange of documents to facilitate data and documents integration .
the technology provides a natural way of defining coarse - grained services that access the right amount of business logic .
it allows clients to invoke procedures , functions , and methods on remote object using xml - based protocol .
xml is a markup language that specifies neither the tag set nor the grammar for that language , and is a meta language used to define other language .
xml allows one to define his own markup language , which consists of his own tags .
furthermore , the meaning of tags is essentially different between xml and html . unlike html
, the tags defined in xml indicate the semantics of a document rather than display a document .
the set of tags and grammar , or schema , for an xml language , describing admissible combinations of tags in a document , can be formalized and enforced by standard parsing tools .
it is clear that xml has some interesting features addressing the problems of data exchange and integration introduced above .
for one thing , xml provides an open framework for standard specifications in managing bioinformatics data .
, xml makes it very advantageous to exchange data among data sources if all of them adopt the same standardization in xml documents .
thirdly , it is convenient to extract interesting information from xml documents , which helps to data integration . in life science
, many commercial and academic communities are now adopting xml as a standard for their genome biology data management ( http://scbi.scu.edu.cn/xml/ ) .
using web services , soap and xml , a simple web service client was constructed to retrieve xml nucleotides data .
the extensible stylesheet language ( xsl ) was used to transform xml data into html form .
the web service client is available at http://scbi.scu.edu.cn / webservices/. the new and exciting web services and xml technologies are drastically changing the way people conduct business , vastly altering the competitive landscape of information technology industries , and significantly improving enterprise efficiency .
the influences of the web services and xml technologies are becoming increasingly visible , and their momentum will greatly become more significant over the next several years . under the web services ,
a single application can tap into the services of millions of applications scattered throughout the internet .
the promise of web services is to enable a distributed environment in which any number of applications , or application components , can interoperate seamlessly among and between organizations in a platform - neutral , language - neutral fashion .
the interoperation brings heterogeneity to the world of distributed computing . nowadays , web services are revolutionizing the internet , and are used in e - commerce worldwide . as a promising standard ,
web services and xml technologies will undoubtedly be a chance to exchange and integrate biological data on the bioinformatics community .
it supports an integrated view for managing remote or local heterogeneous biological data sources with advanced data accessing .
we propose to replace the flat file format by xml and to distribute data by web services , which would provide the programmers a uniform access to the biological data and a standardized interface for interoperable applications . in this paper
, the author examined only a simple application for integrating biological data using web service client and xml technologies , but an architecture of web services is obviously more complex than the application that makes the web service call directly ( figure 2 ) .
our service client is implemented by the hardware of pentium iv 1.8  g with 512  mb memory and 18  g hard disk .
the set of software is redhat linux 8.0 , jakarta tomcat 4.1.24 , java ( j2sdk1.4.1_02 ) , apache axis 1.1 , and apache 1.3.27 .
apache axis ( apache extensible interaction system , http://ws.apache.org/axis/ ) is an open - source implementation of the soap submission to w3c .
it is essentially a soap engine  a framework for constructing soap processors such as clients , servers , gateways , etc . the current version of axis is written in java
the server provides various servers , including blast , fasta , clustalw , and so on ( 6 ) .
the getentry is one of the appropriate servers for getting entries by specifying accession number . using soap message
, our service sends a request into the getentry server to call the method getxml_ddbjentry .
the information of the getentry server is obtained from the wsdl document ( http://xml.nig.ac.jp/wsdl/getentry.wsdl ; fig .
consider , for example , that the same xml document may need to be displayed in html , pdf , and postscript form respectively . without xsl , the xml document would have to be manually duplicated , and then converted into each of these three formats .
instead , xsl provides a mechanism of defining stylesheets to accomplish these types of tasks . rather than having to change the data because of a different representation , xsl provides a complete separation of data , or content , and presentation . to transform xml documents into html form , an xsl file named 
it is a key advantage of xml to bioinformatics data integration that xml documents are parsed easily .
sax ( the simple api of xml ) , dom ( the document object model ) and jaxp ( java api for xml parsing ) are three major apis ( application programming interface ) to parse xml documents . by parsing xml documents ,
data extracted from various xml documents can be dumped into a database , or integrated into an xml document , which is the major task of bioinformatics data integration ( figure 5 ) . moreover ,
application interoperability , standardizing the interfaces between stand - alone applications such as the data generated from one application flow as the input to another application , will be convenient .
the server provides various servers , including blast , fasta , clustalw , and so on ( 6 ) .
the getentry is one of the appropriate servers for getting entries by specifying accession number . using soap message
, our service sends a request into the getentry server to call the method getxml_ddbjentry .
the information of the getentry server is obtained from the wsdl document ( http://xml.nig.ac.jp/wsdl/getentry.wsdl ; fig .
consider , for example , that the same xml document may need to be displayed in html , pdf , and postscript form respectively . without xsl , the xml document would have to be manually duplicated , and then converted into each of these three formats .
instead , xsl provides a mechanism of defining stylesheets to accomplish these types of tasks . rather than having to change the data because of a different representation , xsl provides a complete separation of data , or content , and presentation . to transform xml documents into html form , an xsl file named 
it is a key advantage of xml to bioinformatics data integration that xml documents are parsed easily .
sax ( the simple api of xml ) , dom ( the document object model ) and jaxp ( java api for xml parsing ) are three major apis ( application programming interface ) to parse xml documents . by parsing xml documents ,
data extracted from various xml documents can be dumped into a database , or integrated into an xml document , which is the major task of bioinformatics data integration ( figure 5 ) . moreover ,
application interoperability , standardizing the interfaces between stand - alone applications such as the data generated from one application flow as the input to another application , will be convenient .
 it is widely recognized that exchange , distribution , and integration of biological data are the keys to improve bioinformatics and genome biology in post - genomic era . 
 however , the problem of exchanging and integrating biological data is not solved satisfactorily . the extensible markup language ( xml ) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the world wide web ( www ) . 
 web service is the next generation of www and is founded upon the open standards of w3c ( world wide web consortium ) and ietf ( internet engineering task force ) . 
 this paper presents xml and web services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration . 
Introduction
Web Services
eXtensible Markup Language (XML)
Results and Discussion
Methods
Retrieving XML nucleotides documents
Transforming XML documents into HTML form
Extracting information from XML