Exjobbsförslag från företag

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Förslaget inkom 2002-12-18

A REST-style Web service for Gene Ontology data

The Gene Ontology Consortium (GO) (www.geneontology.org) is creating an organized set of keywords or phrases (GO terms) for use in describing genes and gene
products (proteins) in a more consistent way. Such a controlled vocabulary is useful for computational analysis and comparison of genomics and functional genomics data. Web services is an approach to using the Web for communication between applications. Resources (data and computation) are made available on the Web in such a way that external software can access the resource and use it for its own needs. The XML family of technologies and standards are seen as the building blocks for these
developments, for example XML, XLink and SOAP (Simple Object Access Protocol). REST (Representational State Transfer) is a style for designing Web services different from the SOAP approach, which arguably fits better with the basic components and architecture of the Web (see articles by Paul Prescod and Roger L. Costello).
This project has the following goals:
Design an XML format for Gene Ontology data that is appropriate for the Web services architecture.
Design an interface for a Web service accessible from a server at SBC. The data must be available as both XML (for applications) and HTML (for human browsing). Design and implement the Web service:
Download the data from the Gene Ontology Consortium web sites as it is updated.
Store the data in an appropriate way (MySQL or other DBMS).
Create software to make the data available through the interface.
Good working knowledge about programming the Web (HTML, CGI, script languages such as Perl or Python) is necessary.
MySQL or other DBMS system experience is very good, but can probably be learned as part of the project.
Knowledge about biology and Gene Ontology is good, but is not necessary.
Final result A Web service available to the public, making Gene Ontology data available.
A paper for publication describing the architecture and experience of setting up the Web service.


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