Biomedical Research Insider

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Friday, February 8, 2013

Recent Examples of Infrastructure (Databases and Analytics) Engagements in Healthcare (IBM, Truven, Oracle, ATG)

For those of you who enjoyed our reports on informatics platform development in the UK (use the search feature on the blog to look for posts referencing 'NOCRI'), we're going to be focusing again on enterprise platforms which support service delivery and research with a global lens in the coming months. To whet your appetite for upcoming posts here's a selection of projects we've come across in the last week:
 From HealthDataManagement.comTruven Health Analytics has introduced a new suite of products for statewide health information exchanges, called HIE Advantage Analytics
The suite is designed to enable public health officials to access and analyze operational and clinical statistical data in a state’s HIE. The West Virginia Health Information Network is an early adopter.
HIE Advantage uses near real-time clinical data from providers, claims data from the Centers for Medicare and Medicaid Services, and data from other sources that are stored in state HIE repositories. The goal is to monitor community health status while improving outcomes, according to Truven Health, previously the health care business of Thomson Reuters.
Reports analyze prevalence, process of care and outcome metrics for specific diseases, as well as rates of screening and preventive care to identify communities at higher risk for poor health status. More information is available here.
From Investors.comThe University of Texas MD Anderson Cancer Center Selects Oracle Applications and Technology as Part of Platform to Help Transform Cancer Care
·         MD Anderson, one of the world's most respected centers devoted exclusively to cancer patient care, research, education and prevention, has selected Oracle Health Sciences applications and Oracle technology as the foundation for an organization-wide analytics initiative designed to enable a new generation of personalized cancer treatment that improves outcomes. The platform will also support the center's renowned Moon Shots Program, an unprecedented effort to dramatically accelerate the pace of converting scientific discoveries into clinical advances that reduce cancer deaths.
·         Oracle applications and technology will power the enterprise analytics initiative, one of the program's platforms. The new platform will bring together clinical, genomic, financial, administrative and operational information from internal and external sources to yield insights that drive care innovation and optimize operational efficiency.
·         To achieve its goals, the center, ranked first for cancer care in U.S. News & World Report's "Best Hospitals" survey for seven of the last nine years, will deploy a wide range of Oracle solutions, including Oracle Enterprise Healthcare Analytics and Oracle Translational Research Center
·         MD Anderson, which sees data growth of 30 percent to 40 percent annually, is also deploying Oracle Database and Oracle Business Intelligence Enterprise Edition.

From Executive Biz IBM to Provide Int’l Medical Research Facility with IT Infrastructure, Application Support
IBM and the Dmitry Rogachev Clinical Center have entered into a contract of agreement to deploy PureFlex integrated systems in the Clinic’s facilities to bolster IT support, according to an IBM statement.
“By 2015, we expect to increase the volume of clinical tests five times and to be able to cover 5,000 primary patients generating over a petabyte of medical data,” said Igor Pyatnitsa, head of operations at the Russian Federal Scientific-Clinical Center of Pediatric Hematology, Oncology and Immunology.
“This is valuable data which we must effectively store and manage for medical and legal reasons. IBM’s PureFlex systems help us to do this effectively while controlling costs and ensuring the highest levels of data security,” he added.
The agreement is an extension of an existing contract for the IBM PureSystems roll out.
The center focuses on finding treatment for blood disorders, cancer, immune system diseases, and other diseases. It is a part of the Russian Ministry of Health and a chief collaborator on more than 400 projects, 100 clinical trials and 20,000 medical tests per year.
This will be the first time PureFlex will be used in Russia. PureFlex technology will assist the center with installing fast systems and critical medical applications.
It will also help in organizing their extensive medical data repository through an automatic locator using existing applications. The hospital hopes that this will lead to better collaboration and field research.
Andrey Filatov, Director, IBM Systems and Technology Group for IBM in Russia and the CIS said the PureFlex Systems is meant to provide a platform for Russian healthcare and medical research development.
The offering is tuned for cloud computing and can consolidate more than 100 databases on a single system and helps to rapidly deploy medical applications.

From Executive BizAllied Technology Designing, Analyzing Army Medical Research Projects [Databases, Analytics]
Maryland-based information technology and engineering provider Allied Technology Group has won a five-year contract to help a U.S. Army medical research facility in Silver Spring design, analyze and report on projects.
ATG says its statisticians and public health analysts work with the Walter Reed Army Institute of Research ("the largest and most diverse biomedical research laboratory in the Department of Defense") to include and exclude criteria, select study subjects, develop analytic databases and analyze statistics.
The company will provide the institute a team of epidemiologists, biostatisticians and administrative personnel for analysis, collecting and entering data, managing databases and programming computers.
Since 2007, ATG says staff members have authored and co-authored articles for 30 peer-reviewed publications and 34 scientific presentations on their work at the institute.

    Monday, December 3, 2012

    European data assets catalogue & eHealth Infrastructure - analyses of progress

    We'll be looking at access to European patient-level data for research purposes over the next few months and have hit on a couple of online resources we thought worth sharing with you.

    The first is a listing of data assets by country (and some international assets) with clear concise descriptions of their content.This is a great starting place for anyone looking to understand the large-scale datasets which might support various kinds of clinical, epidemiological and commercial research. The below is an excerpt, the entry for the Netherlands, to whet your appetite:

    Health records
    • Integrated Primary Care Information (IPCI) information from electronic patient records of 150 GPs covering more than 1 000 000 patients
    • Pharmo Independent research organization for drug use and outcomes (including cardiovascular, metabolic disease, oncology and autoimmune disease, respiratory disease, and mother and child health). Overall it covers 2 million residents in the Netherlands and around 200 000 patients linked to GP patient records. Other data includes:
      • Community Pharmacy database (CPD)
      • Clinical Laboratory File (CLF)
      • General Practitioner database (GPD)
      • Dutch Pathology Registers (PALGA)
      • Hospital Pharmacy database (HPD)
      • Dutch mortality statistics (CBG)
      • National Dutch Hospital Registration (LMR)
      • Perinatal Registry (PRN)
      • Eindhoven Cancer registration (IKZ)
    Health statistics
    • GIP database from Health Care Insurance Board (Free online) covering outpatient drug utlization for 85% of population
    The second resource is a series of reports by country, together with a summary across the continent, of eHealth Infrastructure initiatives in Europe. The final report is dated January 2011 but the speed with which these state and EU funded initiatives are able to progress is such that we suspect these analyses still stand and can be considered fairly current. The summary report is a good document to start with to understand the scope and purpose of the analysis but the individual country briefs are invaluable in their discussion of, for example, the data integration issues thrown up by Spain's regional administration, or the legal impediments to cross-border data sharing.

    Monday, August 27, 2012

    ELIXIR - 'A sustainable infrastructure for managing biological information in Europe' - One year on

    It's been nearly a year since we last wrote about Elixir, the European research infrastructure project looking to support life-science information. Our friends at the European Bioinformatics Institute made us aware at the time that a pan-European project was under way to build and operate a sustainable infrastructure for managing and safeguarding biological information including genetic, protein and complex network analysis outputs.

    So what's been happening in the intervening period?

    Another seven countries have signed the Memorandum of Understanding in that time, broadening the remit and support-base for the initiative. The wider this base the better in light of the organisation's assertion that "the collection, curation, storage, archiving, integration and deployment of biomolecular data is an immense challenge that cannot be handled by a single organisation or by one country alone, but requires international coordination."

    The European Commission's Community Research and Development Information Service (CORDIS) page on the project indicates that the first phase of funding is due to come to an end in December 2012 having run for five years. The project's aims over that period were all directed at gaining the widest possible support for the initiative by means of Memoranda of Understanding and included defining:
    • The scope of the infrastructure, its role and benefits
    • An appropriate governance and legal structure
    • A long term funding structure to provide a sustainable infrastructure
    • The requirements for the European Data Centre in the next 5-10 years
    • The critical interdisciplinary links that need to be forged between the biological and related scientific disciplines, including medicine, agriculture and the environment
    • The needs of related European industries
    • A training strategy to ensure that Europe effectively exploits all the available information
    In carrying out this work Elixir assert that they were committed to involving all relevant stakeholders including users, data providers, tools providers to ensure that the infrastructure designed would be fit for purpose and exploring interoperability and supporting standards facilitating the between integration between core and specialised data resources.

    Back in November 2011, we were anticipating the the Interim Board's announcement of the first phase of construction, however, we should point out that this period in Elixir's development is still the Preparatory Phase which title may make sense of the difficulty we've had finding concrete outputs from the project - the website for the Preparatory Phase is a little low-tech and also a little out of date - for more up-to-the-minute news see the Press Releases page on the main Elixir site from which you can see that much of the recent news involves the 'on-boarding' of various different European states but also covers the inception of their newsletter and, of most interest to us, the start of a new initiative co-ordinted by Elixir: BioMedBridges.

    In their own words: "BioMedBridges is a joint effort of ten biomedical sciences research infrastructures on the ESFRI roadmap. Together, the project partners will develop the shared e-infrastructure—the technical bridges—to allow interoperability between data and services in the biological, medical, translational and clinical domains and thus strengthen biomedical resources in Europe. Launched in January 2012, the four-year initiative has been financed with €10.6 million by the European Commission’s Seventh Framework Programme."

    Thursday, July 12, 2012

    UK's e-infrastructure for research needs development

    It may be too late to respond to the consultation (e-infrastructure for innovation and growth?) issued by the UK's research and education computer network JANET - but we'll be keeping an eye out for the results.

    Their consultation was issued after JANET were asked to sit on the E-Infrastructure Leadership Council which has been created (in March 2012), co-chaired by David Willetts, Minister of State for Universities and Science, to co-ordinate the future governance and effective development of the UK’s research e-infrastructure.

    It's worth checking out the consultation to see the kind of areas for development which JANET have in mind and for the link to the influential 2011 report 'A Strategic Vision for UK e-Infrastructure – A Roadmap for the Development and Use of Advanced Computing, Data and Networks'.

    Wednesday, July 11, 2012

    Cancer Research UK turns to the cloud to support Race For Life site demand

    We know a couple of the guys who worked on the revamp of Cancer Research UK's Race for Life site, we watched them passing a toy fish round their scrum meetings and tolerated their thieving of desk-space and chairs from our team - but we didn't know that they had been using cloud-based services to support the massive demand for access to their new site - read more at the Cloudcircle.

    Saturday, June 23, 2012

    Tableau - data analysis and visualisation made awesome

    Another inspiring pair of presentations last week covering data analysis using Tableau, a new-ish (it's on version 7, so the analytics community have had their input into the development process) Business Intelligence product developed and commercialised by techies from MIT. First impressions? Tableau is awesome.

    Having said that Google's BigQuery could save on the painful set-up and optimisation which facilitates data analysis of vast datasets using traditional database solutions - if you are prepared to or have already gone through the pain and are satisfied with the performance of your kit, this analytics tool will take care of the other pain of producing comprehensible and easily customisable analytics including any map-based representations you require as it has its own inbuilt WMS. The demos we saw using the Olympics travel disruption data and some healthcare financials were equally jaw-dropping - no coding required after you've pointed Tableau at your datasource (every conceivable variant of SQL database, or simple Excel and .csv files; online, offline, Tableau compresses extracts of big-ish datasets down to in-memory usable size - we wonder if you could, in fact, point it at BigQuery?), the whole demo was done using just a mouse, dragging, dropping and clicking - no function is meant to be more than six clicks away, most far lest than that - representing a massive time-saving.

    And it's not just super-smart, it's pretty too - Stephen Few, the Visual Business Intelligence guru, helped to design the charting/representation options, and they really do create an impact.

    You can find out more at both Concentra's blog where they demonstrate Tableau's web-plugin, showing off the mapping capabilities in regard of Clinical Commissioning Groups data and the Tableau home page - check out the free trial and also the various uses of Tableau server including Sharepoint integration.

    Thursday, June 21, 2012

    Google BigQuery - Hospital Episode Statistics data analysis made easy (ish)

    We had a visit from PA consulting last week, who were very excited about their application of Google's new Big Data solution, BigQuery, to the vast dataset which is the UK's Hospital Episode Statistics (HES).

    We've had to wrestle with HES data before and come off the worse for it - and that was looking only at one year's Inpatient data - about 18 million lines of data. We encountered all kinds of issues in the setup of our bespoke database, created to hold and analyse this data, starting with the published data dictionary's divergence from the fields in our extract, taking in the discovery of duplicated unique episode identifiers (see our post on the response from the NHS Information Centre) and ending with our discovery that the processing power required to run some of our composite queries in a timely fashion was beyond our meagre infrastructure (this was at the now defunct National Cancer Research Institute's Informatics Initiative).

    We could really have used the facility which BigQuery is set to provide. The guys from PA described how they had obtained the entire start-to-finish HES dataset across all three areas of collection (inpatient, outpatient and A&E) and loaded this into BigQuery (this being the most arduous part of the process, the data arriving on 27 DVDs and taking a couple of weeks to upload) prior to demonstrating the speed with which it was able to provide answers and how the data could be linked to google maps and google docs' spreadsheet application to dynamically produce visual and graphical analyses.

    BigQuery dynamically calls in servers to assist in the running of a query based on the processing power required and then releases them once the query has been executed. The result of being able to access Google's immense army of servers is that without any of the usual time-consuming optimisation (indexing etc.) which supports enhanced performance on traditional database technologies, the user can execute a query against billions of data points in seconds. If you're working to some degree 'in the dark', uncertain of how you wish to structure your data and what analyses you will require it to support, you can experiment on vast datasets without waiting hours for queries to produce results (or fail!) - a facility which would have delivered huge time-savings to us in our HES analysis.

    PA have a video describing their work and approach here and Google provide further information about BigQuery here.

    Monday, June 11, 2012

    Clinical data - toward a single dataset supporting Research, Service Delivery and Performance Management

    We were lucky enough last month to discuss with the Finance Director of a major London healthcare service, the use of enterprise data, from clinical to financial, to support performance management - and were struck by the extent to which the processes which support performance management analytics mirror those which support clinical research.

    We were put in mind of our conversations earlier this year with Oracle and other vendors whose healthcare data warehouse platforms and attendant applications were being demonstrated as solutions to both research and performance measurement problems - this in turn called to mind the comments we had heard from data experts coming into healthcare from other industries who could not understand why information of all kinds pertinent to the administration of healthcare, from genomic analyses to staff costs, were not seen as belonging to a single and vitally important information asset.

    The concerns of this London hospital in getting a handle on their data were strikingly similar to those of the research institutes we have spoken with - and indeed what they describe as performance management is really research by another name - when they correlate outcomes with treatment modalities and different packages of care, they are using their Business Intelligence architecture in many ways like a clinical research engine but with the addition of financial data .

    Their core issue is data quality - they currently have four main clinical IT systems - one for each borough subsumed into their organisation. Trying to use these to derive information even at the level of 'number of patient encounters' has not been straightforward. Although they didn't go into it, we should imagine that supporting those clinical systems must be an array of systems capturing e.g. pathology, radiology, cytology data at a more granular level.

    In addition, their financial data resides in three ledgers each with different coding - a 'consolidation nightmare' was how they described the move to a single ledger; painful but essential as they attempt to get a grip on expenditure.

    The introduction of Service Line Reporting of income and expenditure (in order to assess profit by service) is driving their data validation and data quality improvement - but their clinical operations requirement to deliver an integrated service, developing 'packages of care' rather than looking at individual activities related to the same condition in isolation, is also dependent on quality and timely data - both financial and clinical performance management require the facility to benchmark accurately.

    Touching on other IT issues their organisation faces, they mentioned that the mobile workforce are not well supported by technology - "it's still a surprise that no-one has developed a good mobile working solution for healthcare in the UK". Their words, not ours! They did suggest complications which we hadn't thought of hitherto, coming from a tertiary care background as we do, for example nurses on home visits may not be able to work online, thus need data stored locally to upload later which means on-device storage of personal identifiable data. We can't believe that is still an issue from a technological perspective, however, we can imagine that risk-aversion in respect of personal data in the healthcare industry is dampening demand for solutions - anyone care to offer a more informed opinion?All comments welcome!

    We were really interested to hear how they addressed the development of their Business Intelligence capabilities - developing KPIs to meet significant and varied requirements from different commissioners. Their previous dashboards had been provided by NHS London - their goal at that time had been to ensure compliance with standards and regulations but as they have matured they now have to develop their own dashboards to meet more complex internally-driven reporting requirements. To do this, they have their own Performance and Information team who work on data collation and aggregation - creating Performance Packs - which provide detail by Service line under headings such as Operations, Quality, Finance, Workforce etc. supported by detailed analysis across the board from hard to soft data.

    The capacity to present a performance summary across directorates has led to internal competition which is already leading to performance improvements. Their next steps?

    the P&I teams are looking to automate the production of their performance packs and to create an overall dashboard for the organisation, leading in turn to a Balanced Scorecard.

    Having realised that their previous KPIs and the systems which provided the data were inadequate, they embarked on a redesign of their processes by, and in this order!:

    • Defining the goals / purpose / vision of the organisation

    • Asking what information they need to support the delivery of these

    • Asking what KPIs would adequately measure their delivery

    • Then developing the systems which support the provision of the answers to the above

    They are no longer looking simply at meeting regulatory reporting requirements - but at using their data internally to drive their performance - they are setting up data quality fora - having an external data quality audit and linking their output data to their income - and beginning to realise the benefits of placing data at the heart of the organisation.

    Monday, May 14, 2012

    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!

    Monday, May 7, 2012

    Managing Research Data - the Joint Information Systems Committee Programme

    In covering the BRISSkit vision for a cloud-based open-source "research application as a service" at the end of last year, we mentioned the Joint Information Systems Committee's (JISC)  Managing Research Data workstream about which we've been hearing a lot more recently and thought we should pass on the basics and a link for your own browsing:

    JISC are a non departmental public body who support higher education and research in the UK by providing advice on the use of ICT - their Managing Research Data workstream supports both good data management and the sharing of data "for the benefit of UK Higher Education and Research". Their work in this area focuses on infrastructure, practice and skills:

    • piloting essential research data management infrastructures within institutions and for distributed research groups
    • improving practice in research data management planning
    • developing tools to help institutions plan their research data management practice
    • encouraging the publication of research data and demonstrating the benefits of improved methods for citing, linking and integrating research data
    • and, stimulating the acquisition of appropriate skills, among academics and research support staff in Universities
    Follow this link to their page which contains further information about their internationally recognised Digital Curation Centre and more information on the five strands of the programme which include projects, planning, tools and training.

    Monday, April 16, 2012

    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.

    Wednesday, April 4, 2012

    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 ( 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.

    Wednesday, March 21, 2012

    Clinical Practice Research Datalink edges nearer

    We were interested to find today this URL for the new Clinical Practice Research Datalink about which we have blogged much in the past. Click on it and you will see the screen below (click the picture to zoom in) and thus be able to sign up for news of it's development. April seems pretty close now though we were aware that the Department of Health had set out some pretty aggressive deadlines - we hope to be surprised (pleasantly) come April Fools [note also that the MHRA appear to be hiring now for data specialists...]

    Tuesday, March 20, 2012

    Allied health professionals (AHP) Qality Improvement (QIPP) toolkits

    Courtesy of the King's Fund:

    The Department of Health has identified potential savings and the opportunity to provide better care by involving more AHPs in patient care. This series of online tools aims to help the NHS identify how therapists can intervene at different stages of a patient's condition to improve patient care whilst saving on costs. This first set of toolkits covers how AHPs can help to improve care for stroke; oral nutritional support; musculoskeletal care; cancer; and diabetes.