Bio Web Service Resources
BioInformatics
Bioinformatics is an emerging scientific discipline that uses information technology to organize, analyze, and distribute biological information in order to answer complex biological questions.
Bioinformatics is an interdisciplinary research area, which may be broadly defined as the interface between biological and computational sciences.
It involves the solution of complex biological problems using computational tools and systems.
It also includes the collection, organization, storage and retrieval of biological information from databases.
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Web Services
The Web services are a type of service that can be shared by and used as components of distributed Web-based applications.
They commonly interface with existing back-end applications, such as customer relationship management systems, order-processing systems, and so on.
Web services are defined to share the following properties that make them easily accessible from heterogeneous environments:
1. Web services are accessed over the Web.
2. Web services describe themselves using an XML-based description language.
3. Web services communicate with clients (both end-user applications or other Web services) through XML messages that are transmitted by standard Internet protocols, such as HTTP.
Weblogic's tutorial on Web Services
Sun's Java Tutorial on Web Services
Web Services for Bioinformatics
In order to facilitate universal access to bioinformatics data and analysis software,
Web sevices have much to offer (see the article by
Licoln Stein ).
A number of online bioinformatic databases and services are currently available or in the works.
Web services that are currently in place allow programmatic access to data.
There are many different ways to do this, but the typical approach would include writing one script to fetch the data from the provider's Web site, another one to parse the file format, a third to move the data into a private database.
In a true Web services model, the data providers would register their services in a formalized service registry, and researchers' scripts would no longer need to be concerned with the interface details of the different databases.
For example, the OmniGene project from MIT aims to create an open source Web Services platform for bioinformatics.
To mention, BioMOBY and Distributed Annotation Service are the other related projects in progress.
Major benefits of this kind of true Web services include:
1. Interoperability among distributed applications that span diverse hardware and software platforms.
Interoperability could be interms of providing distributed access to multiple bioinformatic services,aggregating data from multiple sources, providing a centralized registry for finding new services etc.
2. Easy, widespread access to applications through firewalls using Web protocols
3. A cross-platform, cross-language data model (XML) that facilitates developing heterogeneous distributed applications
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XML and Bioinformatics
Biology is a complex discipline and a wide variety of data resources and repositories have been developed to support biological research.
Many of these are interrelated, but it is currently difficult to identify or use these in relationships computationally because the different data sources use incompatible formats and semantics.
XML offers a way to serve and describe data in a uniform and automatically parseable format.
XML also provides an open source solution for data migration between programming languages. Using modules such as XML::Parser, it is possible to move a structured data object between C/C++, java, and PERL without having to worry about the encoding/decoding details.
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