Clinical Practice Research Datalink courts potential users

We received on Friday our invitation to the Clinical Practice Research Datalink (CPRD) Users Meeting that will be held at the MHRA offices in London on 24th May 2012, consisting of a series of short presentations by representatives of CPRD and external partner organisations to give "further insight, and an opportunity for input, into the current and future aims of CPRD."

The background we have covered severally before (see here and here): "CPRD is the new English NHS observational data and interventional research service, jointly funded by the NHS National Institute for Health Research (NIHR) and the Medicines and Healthcare products Regulatory Agency (MHRA). It combines the piloting work of the Research Capabilities Programme (RCP) and the existing General Practice Research Database (GPRD)."

CPRD services are designed to maximise the way anonymised NHS clinical data can be linked to enable many types of observational research and deliver research outputs that are beneficial to improving and safeguarding public health. CPRD will act to provide services to a wide range of researchers and the aim of the Users Meeting will be to ensure that its plans meet the needs of the broad cross section of researchers in academia, the NHS and commercial companies both in the UK and globally.

The specific topics that will be covered on the day include:

• Pragmatic and Phase III - IV clinical trials
• Multidimensional data quality
• Hospital prescribing data
• Models for linkage
• Disease and patient group data marts

The day will provide "several opportunities for potential users to raise and discuss their priorities and requirements" to ensure CPRD meets researchers' needs.

It is possible that we won't be able to attend ourself so if any of our readers are planning on going along, let us know and we'll get in touch to see if you want to post some feedback on these pages!

Oncology Research Information System now live at King's

We've blogged in the past about the Oncology Research Information System as an enterprise-breadth platform to support personalised cancer medicine.

When the System was presented at the NOCRI Information Systems Workshop towards the end of last year we gave you this overview taken from Prof. Peter Parker's abstract:

"ORIS is an IT platform that enables the routine extraction of consented, structured clinical data (notes, images, etc), its pseudonymisation and export into a research data store, from which patient cohorts can be selected and their information linked to molecular data derived from research"

We received an update from IDBS who are leading on the implementation and who look to have countered suggestions that the project was slow to deliver: "As you know until now, cross-hospital translational medicine technology to consolidate data across different scientific domains has been the subject of some debate but we have seen little movement in the industry in terms of actually making it happen. It is very pleasing to have the ORIS platform now in production [in] just under a year from when we started... with a lot of work that is now in the product so as we implement now the time scales are much reduced."

They also sent us a link to the press-release which gives further information and includes a link to details of their Enterprise Translational Medicine Solution.

Clinical Practice Research Datalink is finally here - or is it?

The new Clinical Practice Research Datalink about which we have blogged much in the past has finally arrived (http://www.cprd.com/intro.asp) amid a certain amount of fanfare - see this from Pharma Times, this from PMLive and this from GP magazine.

 You may notice that the GPRD pages now redirect to this site and to a certain extent, this is largely a rebranding exercise at the moment. Behind the scenes a team at the DoH are trying to ensure that major data sources are willing and able to engage with this initiative but the speed at which they come online remains to be seen. We'll fill you in further on plans for a researchers data-catalogue interface as this project advances - and if CPRD are not offering that just yet, perhaps the MRC are - we'll get you up to date with the MRC's Data Support Service before the week is out.

How Computer Science Agents Can Help in Medical Informatics

We've been trying to sneak them under your radar, almost certainly without success, but here in broad daylight we declare: the last of our updates from the NOCRI Information Systems workshop - and we have mercifully little to say on the talks as Prof. Michael Luck's abstract says it all [Prof. Luck is the Head of the Department of Informatics at King's College London]. Our only comment is that it might be worth checking out the PDF "50 facts about agent-based computing", which Prof. Luck mentioned, to consider some current applications of computer agents across a variety of industries. His abstract is presented here:

“Agents are computer systems capable of flexible autonomous action in dynamic, unpredictable, typically multi-agent domains. In particular, in dynamic and open environments, heterogeneous systems must interact, span organisational boundaries, and operate effectively within rapidly changing circumstances and with dramatically increasing quantities of available information. Thus, the need for some degree of autonomy, to enable components to respond dynamically to changing circumstances while trying to achieve over-arching objectives. For example, in the domain of bioinformatics, determining protein function can involve multiple independent processes connected together, operating on multiple independent data sources, in some workflow. In this context, multi-agent systems, in which the various processes and data sources are encapsulated as agents that interact with each other, can provide a means to manage primary databases, perform sequence analyses (using existing tools), or store and present resulting information in a coherent fashion. In the domain of e-medical records, multi-agent systems may similarly provide the means to integrate disparate processes and data sources. Rather than offer new methods for performing these tasks, this instead organises existing methods for effective and flexible operation.”

That wraps up the NOCRI workshop except to say that the two concrete Next Steps to come out of it sound promising: the first being the organisation of a co-ordinating group to further knowledge sharing in informatics and the second being the creation of a web-resource for learning materials.

Electronic Medical Records for Research-Tackling Unstructured Data

Angus Roberts (Life Science Lead forGATE ,Sheffield University) & Dr. Robert Stewart (Clinical Informatics Lead, NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust & King’s College London) spoke about extracting structure from free text and using open source toolkits to do it, in particular UIMA and GATE (see this article on combining UIMA and GATE) – of note, training is available for the latter – as the GATE guys put it :”coaxing state-of-the-art performance (accuracy, speed) from these tools is still a fine art, and likely to remain so” – so a little training might come in handy.

In talking about the language engineering skills required to make effective use of these tools and the creation of pattern suites, the question which formed for us was “are you going to make the pattern suites you created for clinical data mining publicly available in pattern libraries?” We’ll get back to you when we have an answer. The abstract for their talk follows:

The South London and Maudsley NHS Foundation Trust Biomedical Research Centre (SLAM BRC) hosts Europe's largest psychiatric case register. This is updated daily from live electronic medical records, and made available to approved researchers via a clinical records interactive search system (CRIS): a web search interface, and other search tools. While the structured records in the case register are of great value, an estimated 80% of the value of the data lies in free text entries made by clinicians in day-to-day practice.

With over 180,000 records, automated information extraction or text mining is essential if we are to make use of this. GATE - a General Architecture for Text Engineering’ - has been integrated with CRIS, to give a text mining capability. Several GATE applications have already been built to extract specific variables from free text. Output from these applications is being used successfully in a number of research projects, and a number of new applications are currently under development. There is an increasing understanding of how to maximise the benefits of GATE given the particular characteristics of the data.”

BRISSkit - A Vision for Cloud-Based Open Source Research Applications as a Service

The marathon of updates from the NOCRI Information Systems workshops is nearly run - but we couldn't finish without covering a final champion of Open Source and caBIG resources.

Nick Holden, Systems and Database Architect at the Leicester NIHR Cardiovascular Biomedical Research Unit, gave us a vision as follows:

“The Biomedical Research Informatics Centre for Cardiovascular Science (BRICCS) uses open source applications from around the world to deliver an end-to-end informatics platform for research at the Leicester Cardiovascular BRU.

Now the BRISSkit project aims to build on BRICCS to offer the same applications in a software-as-a-service”

Nick opened by saying that though they wanted to use Open Source, they never wanted to be developers – and that there are downsides to OS in this regard – however, the positives of using open source software for Electronic Data Capture and tissue storage management (OBIBA – open-source biobanking, and caTISSUE, the most successful resource within the caBIG suite) include the potential for data sharing inherent in those platforms e.g. linking up to caGRID for federated secure data querying.

He spoke about the advantages of using these platforms on the cloud (using I2B2 for translational data management, C3PR from caBIG for participant registration) to provide cloud-based research applications as a service! We’d be interested to know if there is anyone out there who would want to take advantage of such a service...

Their project is now aligned to the JISC Managing Research Data workstream.

Continuing Use and Adoption of OpenClinica for Clinical Data Management

Tim Bradford, Bioinformatics and eSciences Manager at the Oxford NIHR Biomedical Research Council, was another proponent of open source, in particular OpenClinica which he noted is now implemented in production environments in 650 instances of which 34 are in the USA and 29 in Europe – he mentioned that 200 regulatory submissions are expected in 2012!

He also mentioned that Oxford do run training in OpenClinica if you’re interested in implementing but lacking the expertise... Tim’s team are aware of the shortcomings of the software and have experience adapting it to meet specific needs – to the extent that “Since adopting the technology 18 months ago it is being used live [by Oxford] in 46 studies across 30 sites and has recruited in excess of 6000 subjects”. He also mentioned that they are using MIRTHConnect  (more open source)

For tissue storage they are using Labvantage Sapphire and to mine clinical data from Cerner Millennium they are using Power Insight.

NOCRI Conference in partnership with the Association of British Pharmaceutical Industry and the BioIndustry Association - upcoming

We somehow managed to miss this last week - will be happening 24th November this year:

Health Research: Easier, Better, Faster National Institute for Health Research Office for Clinical Research Infrastructure conference in partnership with the Association of British Pharmaceutical Industry and the BioIndustry Association Royal College of Physicians 24 November 2011

The National Institute for Health Research Office for Clinical Research Infrastructure (NOCRI) announces a major, national conference featuring the UK’s leaders in translational research. The conference brings together inspirational speakers from industry, academia, the NHS and the public sector. They will discuss new strategic initiatives and provide key updates in relation to ‘Health Research: Easier, Better, Faster’.

The conference will showcase cutting edge translational research that world-leading clinical academics are carrying out today. It will highlight how the nation’s strengths and expertise is being harnessed to deliver benefits for industry, the NHS and patients.

Confirmed speakers include:

• Earl Howe, Parliamentary Under Secretary of State for Quality, Department of Health
• Professor Dame Sally C Davies, Chief Medical Officer and Chief Scientific Adviser, Department of Health
• Sir John Savill, Chief Executive and Deputy Chair, Medical Research Council
• Mark Samuels, Managing Director, NOCRI
• Dr Allison Jeynes-Ellis, Medical and Innovation Director, ABPI
• Nigel Gaymond, Chief Executive, BIA
• Professor Ratko Djukanovic, Director NIHR Southampton Respiratory Biomedical Research Unit
• Professor Peng Tee Khaw, Moorfields Eye Hospital/ UCL Institute of Ophthalmology NIHR Biomedical Research Centre

This exciting conference is for senior decision makers within the pharmaceutical and biotechnology industries, will consist of a series of plenary sessions and presentations, followed by panel discussions lead by recognised leaders in translational research. NOCRI is organising the conference in partnership with the ABPI and BIA.

For further information contact NOCRI@nihr.ac.uk or visit the BIA website at www.bioindustry.org/cgi-bin/events.pl?CD=4128

27 October 2011