How suitable is BioPAX for database integration?

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has title::How suitable is BioPAX for database integration?
status: finished
Master: project within::Bioinformatics
Student name: student name::Hester Stekelenburg
Start start date:=2011/08/01
End end date:=2011/11/30
Supervisor: Andrew Gibson
Second reader: has second reader::Sanne Abeln
Company: has company::UvA/ AMC
Thesis: has thesis::Media:Thesis.pdf
Poster: has poster::Media:Media:Posternaam.pdf

Signature supervisor



Headline text


Biological pathways are an important part of systems biology, and many databases exist which contain pathway information. Bioinformatics analysis which involves pathways may need pathway information from more than one database, so data integration can be a problem. BioPAX is a standard language based on semantic web standards. It facilitates analysis of pathway data, and data integration between biological databases. PeroxisomeKB is a knowledge base which contains information about human pathways that rely on metabolic processes located in the peroxisome. The hypothesis is that BioPAX is a good format for semantic web based data integration, and should be applied to PeroxisomeKB. The goal of the project is to evaluate BioPAX and find out how to exchange data of different databases, and to build a program on the PAXTools API to make BioPAX pathway data easier to create. The programming language will be java.

There are several ways of assessing the suitability of the BioPAX standard. The following approaches will be accomplished to reach this. Peroxisomal data will be exchanged between the databases WikiPathways and Reactome. Some guidelines shall be accessed to make working with the BioPAX Standard easier. Moreover, a program will be build for helping users to follow the guidelines.


The internship will take from 1 August until 30 November. A global timeline is displayed here:


Background reading, exchange data between WikiPathways and Reactome


Exchange data between WikiPathways and Reactome, accessing guidelines


Building the programm, writing "introduction" and "methods" for report


Finishing the report

--Hsg600 11:23, 11 August 2011 (UTC)