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The need to manage, analyse and interpret the volumes of data and literature generated by modern high-throughput biology has become a major barrier to progress. Research at the University of Manchester on interoperability and advanced interfaces has resulted in innovative software (Utopia Documents) that links biomedical data with scientific literature. The software has been adopted by international publishing houses (Portland Press, Elsevier, Springer, etc.), allowing them to explore new business models, and by pharmaceutical companies (e.g. AstraZeneca, Roche), providing new opportunities to explore more efficient, cost-effective methods for exploiting and sharing in-house data and knowledge. The research also led to a spin-out company, Lost Island Labs, in 2012, which expects a profit [text removed for publication] in its first year.
The loss of biodiversity is an issue of global concern. This has prompted intergovernmental aims and global campaigns, administered by organisations such as the World Wide Fund for Nature and the International Union for Conservation of Nature, to halt the rate of species extinction. A major hurdle in these initiatives was the lack of any form of definitive list of the World's species. Species data was scattered across hundreds of local databases, created and interpreted differently by many scientists. No uniform, agreed catalogue existed. However, research produced at the School of Computer Science, at Cardiff University, resolved this. The use of data modelling, constraint checking techniques, protocols and processes to amend conflicts have enabled Species2000/ITIS to produce the Catalogue of Life: www.catalogueoflife.org. This federated database is the most complete set of species data anywhere in the world, comprised of 1.4 million entries. It is accessed by approximately 30,000 users worldwide, each month, and utilised by governments across the globe for nature conservation, import control and predicting the effects of climate change. Other users include charities, specialists, scientists, publishers, students and members of the public worldwide. Therefore the categories of impact claimed are threefold - environmental, economic and impact on society, culture and creativity.
Research at the University of Manchester (UoM) has changed the landscape of medical care and research in fungal infections internationally. The impacts include: the world's first commercialised molecular diagnostic products for aspergillosis and Pneumocystis pneumonia (£10m investment); pivotal contributions to the preclinical development (£35m investment), clinical developments and registrations of 3 new antifungals with combined market share of ~$2 billion; one (voriconazole, 2012 sales >$750m worldwide) now first line therapy for invasive aspergillosis with improved survival of 15-20%; and internationally validated methods to detect azole resistance in Aspergillus (an emerging problem partly related to environmental spraying of azole fungicides for crop protection).
Automation of genomic data analysis has become essential. High-throughput sequencing technologies are producing data faster than can be managed and interpreted, meaning that much biomedical information remains unused.
Research led by Attwood introduced a unique method for protein sequence characterisation and a derived database of diagnostic protein signatures (PRINTS). This led directly to the development of a new database (InterPro), now routinely used to annotate the world's largest protein sequence archive (UniProt), and complete genomes and metagenomes. The databases and their search tools have been exploited in the private sector (including SMEs and multi-national pharmaceutical and agrichemical companies), generating workflows that have yielded candidate drug targets and provided insights into disease mechanisms.
Targeted Projection Pursuit (TPP) — developed at Northumbria University — is a novel method for interactive exploration of high-dimension data sets without loss of information. The TPP method performs better than current dimension-reduction methods since it finds projections that best approximate a target view enhanced by certain prior knowledge about the data. "Valley Care" provides a Telecare service to over 5,000 customers as part of Northumbria Healthcare NHS Foundation Trust, and delivers a core service for vulnerable and elderly people (receiving an estimated 129,000 calls per annum) that allows them to live independently and remain in their homes longer. The service informs a wider UK ageing community as part of the NHS Foundation Trust.
Applying our research enabled the managers of Valley Care to establish the volume, type and frequency of calls, identify users at high risk, and to inform the manufacturers of the equipment how to update the database software. This enabled Valley Care managers and staff to analyse the information quickly in order to plan efficiently the work of call operators and social care workers. Our study also provided knowledge about usage patterns of the technology and valuably identified clients at high risk of falls. This is the first time that mathematical and statistical analysis of data sets of this type has been done in the UK and Europe.
As a result of applying the TPP method to its Call Centre multivariate data, Valley Care has been able to transform the quality and efficiency of its service, while operating within the same budget.
Researchers at the University of Manchester (UoM) characterised fatal childhood lysosomal storage diseases (LSDs) and developed new treatments. The research has led to the licensing of 6 drugs worldwide (of a total of 9 available) for LSDs including mucopolysaccharide disease I, II, IIIA, IVA, VI, Fabry, Pompe and Niemann Pick C. As a result, longevity and quality of life have improved for more than 800 LSD patients in England and more than 3000 worldwide. Home enzyme treatment has improved quality of life for the majority of LSD patients in the UK (>400). The research has broadened the scope of haematopoietic stem cell transplantation for LSDs and reduced mortality, benefiting more than 100 LSD patients worldwide.
The UoA research enabled a step increase in the technical and commercial capabilities of Atlantic Geomatics (UK) Ltd (AGUK, Cumbria) and the development of a postal addressing solution for the Government of Gibraltar (GoG). The beneficiaries and benefits included: AGUK who secured a contract safeguarding jobs and opening new international markets. Moreover, the GoG now have a definitive solution for legislation to replace their manual, multiple and inconsistent address lists by a spatially-based official address register (OAR) incorporating geographical information thereby enabling the people of Gibraltar to receive enhanced services (e.g. postal, emergency, utilities) from a centrally managed OAR.
Development of the human cell GADD45a assay enabled accurate identification of carcinogens in vitro, with a low rate of misleading positives. Through the spin-out company Gentronix, this research is reducing costs to industry and decreasing the use of animals in research. Industrial collaboration has enabled commercial adoption of the technology in many sectors. With a 10-fold increase in orders in 2012 versus 2008, Gentronix is a profitable business employing 17 people and with an annual turnover of £1.88m. During 2008-12, Gentronix released a series of new products, established testing services, and signed a product license agreement with GlaxoSmithKline. More than 100 companies worldwide are using Gentronix kits, including pharmaceutical, agricultural and health and beauty companies, along with manufacturers of food flavourings and household goods. The Gentronix assay is currently being reviewed by the European Centre for the Validation of Alternative Methods.
Research carried out at Birkbeck's Department of Computer Science and Information Systems since 2000 has produced techniques for the management and integration of complex, heterogeneous life sciences data not previously possible with large-scale life sciences data repositories. The research has involved members of the department and researchers from the European Bioinformatics Institute (EBI) and University College London (UCL) and has led to the creation of several resources providing information about genes and proteins. These resources include the BioMap data warehouse, which integrated the CATH database — holding a classification of proteins into families according to their structure, the Gene3D database — holding information about protein sequences, and other related information on protein families, structures and the functions of proteins such as enzymes. These resources are heavily utilised by companies worldwide to explore relationships between protein structure and protein function and to aid in drug design.