A master student performed a problem exploration for the PayDIBI project. This is the report he wrote.
Integration of Biological Sources – Exploring the Case of Protein Homology
Tjeerd W. Boerman, Maurice van Keulen, Paul van der Vet, Edouard I. Severing (Wageningen University)
Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heterogeneous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioinformatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Uncertain databases are able to contain several possible worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration.
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I have a vacancy for a PhD position in a project called “Pay-As-You-Go Data Integration for Bio-Informatics” (PayDIBI). In short, the objective is to develop data coupling and integration technology to support bio-informatics scientists in quickly constructing targeted data sets for researching questions that require the combination of information from more than one biological database. More information and a webform to apply can be found here.