BBSRC Doctoral Training Partnership Studentship in Text Mining


Online applications are now being accepted for BBSRC Doctoral Training Partnership Studentships at the University of Manchester.

The following text mining project is among those proposed at

Title: Developing text mining capabilities to retrieve information on protein phosphatases

Summary: Protein phosphatases are crucial for many mechanisms regulating cell physiology, cell division and environmental adaptation. Their important roles in all living organisms are just being unravelled as more genome data becomes available. To understand their biological function, we must know their substrate preferences, cellular localisation and interacting partners at different cell life stages. Gathering and analysing manually this information from the literature is a daunting perspective for the researcher, with expanding numbers (currently >16,000) of citations to query. A more rational approach is to compile relevant information into publicly available resources for the scientific community, facilitating querying and organising the information in a relational manner. Our existing protein phosphatase resource, PhosphaBase (Wolstencroft et al., (2005) Bioinformatics, 21, 1685-92; Wolstencroft, et al., (2004) Proteins 58: 290-4.), contains genome and protein information on protein phosphatases. However, the main limitation on populating PhosphaBase from public databases is the lack of available information on particularly important topics, like regulation, substrates preference, binding partners, catalytic activity and other biochemical data. This project will address these limitations by customising and applying text mining methods to extract biologically relevant data from the literature and populate PhosphaBase. The main aim is to support curators in production of a comprehensive resource for the community, thus supporting experimental design to address important functional questions in biology.

Supervision team: John McNaught (Lead supervisor) (School of Computer Science & NaCTeM), Sophia Ananiadou (School of Computer Science & NaCTeM), Lydia Tabernero (Faculty of Life Sciences)

Applications must be made online. Deadline: Friday 25th November 2011.

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