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.

News from the EMBL-European Bioinformatics Institute: Enzyme Portal Launches

We received the following press release today from the European Bioinformatics Institute announcing the launch of their Enzyme Portal, a freely available resource for people who are interested in the biology of enzymes and proteins with enzymatic activity:

"Enzymes catalyse the myriad reactions that take place in living organisms, allowing chemical changes to occur that would otherwise need conditions that are incompatible with life. Until now, information about enzymes was scattered throughout many different resources. This meant that you had to know exactly what you were looking for, which could be a real barrier to discovery.

The Enzyme Portal mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature. It summarises information in the UniProt knowledge base; the Protein Data Bank in Europe; Rhea, a database of enzyme-catalysed reactions; Reactome, a database of biochemical pathways; IntEnz, a resource with enzyme nomenclature information; ChEBI and ChEMBL, which contain information about small-molecule chemistry and bioactivity; and CoFactor and MACIE for highly detailed, curated information about cofactors and reaction mechanisms.

The Enzyme Portal covers a large number of species, including the key organisms used in biological research, and makes it simple to compare the characteristics of equivalent enzyme activities in different organisms.

“The Enzyme Portal will serve researchers interested in the native metabolism of organisms as well as those working in drug discovery or chemical biology,” explained Dr Christoph Steinbeck, Head of Cheminformatics and Metabolism at EMBL-EBI. “The resource seamlessly bridges the various enzyme-related aspects of these areas, all the way from the small molecules – which may occur naturally in the organism of study or be introduced  – to the 3D structure of the enzymes affected and the genomic information coding for those.”

The design of the Enzyme Portal was based entirely on user demand and feedback. “We didn’t come in with preconceived ideas of what it should be; it was designed by users, for users,” said Cheminformatics Coordinator Paula de Matos. “We had enough data, but it was distributed over 10 different resources. Now, we have a central place where they can access and explore all of it – including information about disease.”

“The Enzyme Portal takes the researcher’s perspective,” added User Experience Analyst Jenny Cham. “We leveraged user-testing feedback to create it, making it the first EMBL-EBI resource to have a fully user-centred design from scratch. This approach was not only cost-effective; it made decision making and communication much easier – particularly in terms of design and technology choices.”

www.ebi.ac.uk/enzymeportal"

To download images, please visit: http://www.ebi.ac.uk/Information/News/press-releases/press-release-22022012-Enzyme_portal.html

To watch a short video about the Enzyme Portal on our YouTube channel, visit: http://youtu.be/Kldp0WXcxUM

Closure of the NCRI Informatics Initiative - ONIX source code avaiable

Sad to hear from our colleagues at the National Cancer Research Institute that their Informatics Initiative is closing down in March next year.

Good news, however, in that the source code which supports their award-winning Oncology Information Exchange (ONIX) platform freely available to the community including their APIs to e.g. Entrez and various other databases.

It will be available under Creative Commons licences which will allow re-use, development and extension of the software – but no one organization will have exclusive rights to publish the resource and derivations will need to recognize the original development work as an output of NCRI Informatics.

If you think your organisation would be interested let us know here at bioinformaticsolutions @ gmail . com or email them directly (finlay.macdougall @ ncri.org .uk).

ONIX currently offers a number of functions which may be useful to bioinformaticians:

·         The Resource Catalogue: a tool that brings together and describes a diversity of biomedical resources which include databases, analytical tools, projects, initiatives and research technologies. This information has either been entered directly to ONX forming the ONIX Catalogue or is contained in one of the other catalogues searchable from the Resource Catalogue:

o    caBIG - the list of grid services currently available from the US National Cancer Institute's caBIG^® programme

o    BioCatalogue - A curated registry of biological Web Services. It provides an open platform for biological Web Services registration, annotation and monitoring

o    NCRI Cancer Biosample Directory - A directory of biosamples (tissue, blood and other biological samples, including extracted derivatives) held in the UK in cancer biobanks. Searchable by a variety of parameters, the directory provides information about how to contact custodians and how access may be possible

o    NCRI Cancer Clinical Trials Biosample Directory - A directory of biosamples (tissue, blood and other biological samples, including extracted derivatives) held in the UK from cancer clinical trial collections. Searchable by a variety of parameters, the directory provides information about how to contact custodians and how access may be possible.

o    NHS IC DoCDat - DoCDat is an information resource for all those involved in clinical audit, clinical governance, health services management and health services research. It provides information about databases containing patient level and administrative data concerned with clinical care in the UK

·         The Quick Search (with advanced options): searches simultaneously across a range of biomedical databases from genetics to clinical trials and access a diversity of types of information from publications to biological images

·         The Cancer InfoMatrix (CIM): the InfoMatrix provides information about work being conducted to support good data management in cancer research through the development of data standards. Biomedical domains are arranged across the horizontal axis of the CIM while on the vertical axis are broad areas of data management that enable data sharing, access and exchange. Clicking on a cell within the CIM will take you to a list describing each initiative in that area as well as other relevant information. The cells in the Cancer InfoMatrix are colour coded using a "traffic-light-battery system" to indicate the degree of progress in each area

NEW Science Council Report - The current and future UK science workforce

We were researching issues facing the medical research enterprise in the UK and came across this report from the Science Council published on the 5th September this year.

From their executive summary: "The objectives of this research were to explore the potential for expanding registration to technician and intermediate levels by developing comprehensive data on the current UK science workforce, understanding the profile of employment across the skills levels and providing a view on the future workforce and where demand is likely to be the highest"

Let us know what you think....

Also, let us know what you think of our VERY draft text which, only just begun and in need of much work! currently reads:

In their report of September 2011 Building the Ideal Environment for Medical Research, Cancer Research UK looked at means by which the government might encourage ‘the best scientists to stay in science’ as they noted various pushes and shoves which might lead talent to exit the industry:

“At various stages along the science career path, a proportion of high quality scientists leave research to pursue other careers^xiii The skills that researchers are equipped with during their undergraduate and postgraduate degrees are seen as being highly transferable to other sectors, including finance, banking and education.^xiv

It is widely recognised that researcher salaries are not as competitive as those for other careers that would require a similar level of training or skill, and this can be seen as a considerable disadvantage at the early stages of a scientific career.^xv This is compounded by the fact that competition for jobs and funding is increasingly fierce.^xvi”[1]

They noted that career progression within science can be unstable and unpredictable, an observation that they elicited in conversation with researchers. The structure of careers in research leads to a high level of competition for Group Leader positions and “the transition from post-doctoral research to running a research group... has been described as the most brutal step in career progression. The skills that are needed to conduct high quality research in order to gain support for a research career are not necessarily the same skills required to manage other people, to write grant applications or to meet teaching responsibilities.”[2]

Scientists, however, do not constitute the whole research workforce. There are many different roles and types of expertise required for research projects to function.

The report Managing Clinical Research in the UK highlighted a shortage of experienced trial managers and monitors and these personnel prove difficult to recruit and retain. However, the report observes that “these are the people who know how to make the systems work in practice.”[3]

One of the recommendations of the report Managing Clinical Research in the UK is that “clearer career trajectories in clinical research could help to narrow the skills gaps experienced in this sector”[4]. They call for a UK-wide strategy to identify such trajectories and for career profiles of the range of roles engaged in clinical research to be developed.

The MRC also make recommendations for skills development in their document A Strategic Framework for Health Informatics in Support of Research which addresses human capital capacity building. They state as aims:

·         “To develop a cadre of researchers and information scientists who are familiar with the research potential offered by electronic health records and are confident with new technologies and services provided

·         To ensure provision of training delivered at a range of levels: from building awareness and informal training through to professional qualifications and the development of a formal career structure.”[5]

---

[1] Cancer Research UK: Building the Ideal Environment for Medical Research (September 2011) http://info.cancerresearchuk.org/prod_consump/groups/cr_common/@nre/@pol/documents/generalcontent/cr_076936.pdf:

xiii The Scientific Century, The Royal Society, 2010, p14.

xiv What do researchers do? First destinations of doctoral graduates by subject, Vitae, 2009. http://www.vitae.ac.uk/CMS/files/upload/Vitae-WDRD-by-subject-Jun-09.pdf

xv Careers of Doctorate Holders: Employment and mobility patterns, Auriol, L., OECD, 2010. http://www.oecd.org/dataoecd/46/43/44893058.pdf

xvi Education: The PhD Factory, Nature, Cyranoski, D., Gilbert, N., Ledford, H., Nayar, A., Yahia, M., 2011, vol 472, 276. http://www.nature.com/news/2011/110420/full/472276a.html

[2] Ibid.

[3]Write-up by The Institute of Clinical Research: discussion of report by Warwick Business, School Managing Clinical Research in the UK http://www.icr-global.org/crfocus/2009/20-10/managing-clinical-research-in-the-uk/

[4] Managing Clinical Research in the UK: Evidence on the challenges of conducting clinical research projects in the UK. December 2009, Warwick Business School.

[5] MRC: A Strategic Framework for Health Informatics in Support of Research

Industry and academic reports - New page

We're getting there - 15 documents so far - suggestions welcome!

These are the better known documents from a trawl covering the spectrum of web-pages, journal articles and major reports – these include several reports from the Academy of Medical Sciences, DoH white papers, reports from or commissioned by the Research councils, strategic plans from funders of research in the UK, the Health Survey for England, reviews on data sharing, reviews of patient and professional perspectives on the use of personal information in medical research and statements regarding the economic importance of biomedical research from both government ministries and independent commentators.

We already have a few more lined up to go on today - let us know your views - see the new page above Useful Industry Reports.

Industry and academic reports - New page

During the course of the day we will be adding (and potentially cutting down the descriptive text as the list grows!) a list of academic, industry and government reports of relevance to those working in biomedical research.

Many of these have been referenced in our soon to be published environmental scan of biomedical research in the UK.

They can be found on our new page 'Useful industry reports' above - please let us know of any others you suggest would be of value to our readers.

UK universities are at the 'bleeding edge' of medical research

This article in online journal The Engineer gives a few examples of the multidisciplinary research conducted in UK universities which is keeping the UK at the forefront in this field and a link to the report from the Research Councils:

Linked again here: Medical Research

NHS HE Forum slides online

Malcolm Teague (NHS-HE Co-ordinator) puts the updates from the Forum on 24th May much better:

Thank you to all of you who made it to the last NHS-HE Forum meeting on 24th May 2011 and made it such a useful day. Thank you again particularly to all those who presented. The agenda, attendee list and copy of the presentations are available here.

Following introductions from Ted, we started the day with Mike Denis who with some very fortunate timing was presenting on the same day as his public announcement and press release on a major development at South London and Maudsley NHS Foundation Trust which will positively impact on patient empowerment and research. The press release “ Microsoft and Maudsley join up to develop a world first for mental health care” is therefore included. Presentation. Press release.

Kerrie Woods then gave us an update on the Research Capability Programme and the development of a Health Research Support Service (HRSS). There is currently a process of “due diligence” on the way forward for the overall development and we look forward to further news on this once this is complete. In the meantime it was good to hear of the progress being made with the pilot HRSS.

Mark Blakeman followed giving us an update on the NHS-HE Connectivity Best Practice Working Group which he chairs. No mean feat given the Working Group had met for the second major time the previous day. A number of strands and actions are being taken forward with the aim of learning to live better with reality!

After lunch we had a dual presentation – Ian Wilcox gave us an update on the Public Sector Network developments, the Government’s strategic plan for inter-Department and inter-sector connectivity. Max Finch then told us about the latest position on the more immediate work to improve NHS-HE connectivity solutions through the N3 JANET Gateway Phase II project under 5 main headings where initial workshops have happened or are about to.

It was two for the price of one after that as Suzanne Hardy updated the Forum on two projects that we are following closely, both of which are now well established and progressing i.e. Reusing Healthcare Recordings and also the Pathways to Open Resource Sharing through Convergence in Healthcare Education (PORSCHE). You may also want to note the e-learning in health conference on 27th & 28th June and a workshop on PORSCHE on.

Finally Betsy Anagnostelis briefed us on a step towards potentially major development in shared content licensing. Betsy described the pilot in 2011 with 5 major publishers and the 5 Academic Health Science Centres where there will be a pilot for one year where the content purchased by the University partners in each AHSC will be extended to the NHS partners at no extra cost. The information gained from this exercise during 2011 will be used to develop sustainable models for enhanced provision of access to high quality e-content across NHS and academic staff.

Ted rounded off the day by thanking everyone and asking for views on what should be included next time. The Information Governance Toolkit and NHS Statement of Compliance from a University perspective was suggested, plus a view on the DH’s Information and Technology Strategies that should be available by then. If anyone has further suggestions then please let Ted or I know.

In any case the next NHS-HE Forum is planned to be in November 2011 although a date has not yet been agreed. There will be a Scotland NHS-HE Forum in Edinburgh on 20th September as well but I will send a separate announcement on that in case not everyone has reached this far.

NHS HE Forum

Late link to the output from a very interesting day at the NHS Higher Education Forum - Mike Denis (CIO at South London and Maudsley NHS Foundation Trust)filled in the key-note slot in exemplary fashion delivering a really engaging talk on the SLAM BRC Case Register and the use of patient health records in patient empowerment.

See Mike's slides (and the others from the day)and a press release from the South London and Maudsley NHS Foundation Trust here.

And the E-Health Insider story on the Trust's use of Microsoft Health Vault here