Executive Summary

As in many areas of collaborative research, collaboration on orthopaedic research is typically achieved by e-mailing word processed documents and large datasets from clinical trials. The Collaborative Orthopaedic Research Environment (CORE) project developed and deployed a set of Web services that enabled researchers to collaboratively: design an experiment; collate the data, analyse the data, and disseminate the results. The type of experiments the system aimed to support were multi-centred clinical trials that needed to be managed and co-ordinated for a geographically dispersed set of researchers. The investigation into the growth of bone and cartilage also required the use of the Grid, and hence the CORE projected investigated the use of Grid services, using a portal framework and the OMII middleware.

Final report (1M)

This page describes CORE, a 24-month project that will develop and deploy a service enabling researches to design collaboratively an experiment, collect the results and disseminate the results. The experiments will be multi-centred clinical trials that involve analysis of large data sets, the documentation needs to be written collaboratively and the experiments will need to be managed and co-ordinated for this geographically disperse set of researchers. The CORE project will develop a Grid/Web services based Virtual Research Environment (VRE) demonstrator for supporting the collation and analysis of experimental results, the organisation of internal project discussions and the production of appropriate documents for dissemination for the benefit of the Higher Education and Further Education communities. It builds on: a current and completed JISC-funded projects for the development of "e-prints" (Opsis project and Open Citation Project); the output from the JISC funded EBank UK project investigating the issues surrounding provenance and the use and re-use of original data; and on outputs from the EU-funded educational programme for the development of a Virtual University for Orthopaedics (VOEU). One of the deliverables of VOEU was the development of a Dynamic Review Journal, a tightly coupled system for aiding surgeons to write papers collaboratively. This project will bring together members of the clinical, computer science, digital libraries, and Grid communities through the development of the demonstrator and though the wider dissemination activities.

The project is to be undertaken at the University of Southampton. Funding is sought for £136,961 based on a start date of 1st October 2004. The project aims to fulfil the requirements of strand III of the JISC Circular 05/04.

The current vision for the Grid focuses only upon the immediate aspects of e-Science the experiments, analyses and meetings which occur over the duration of a project. As well as these synchronic aspects, any scientific effort (and e-Scientific efforts in particular) will have diachronic features. These are collaborative activities extending through time, enabling the influence of the project to carry on beyond its funded timescale and disseminating its knowledge beyond the boundaries of the original collaboration. These activities are a well-known part of the scientist's profession (publishing papers, publishing data, rerunning experiments and checking others' results, comparing approaches from different projects, generalising or specialising the work of others, and teaching). The current deployment of Web technologies increases the effectiveness of this loose-coupled collaboration and the role of the digital library is to focus the various channels (archives, publishers' Websites, and aggregation agents) into a single portal which mediates these strands of diachronic collaboration. There is also a looser coupling that exists between researchers-as-educators and their students, particularly in the context of higher education. The accepted picture of e-science could be enlarged (see figure 1) from its current focus on experimentation and analysis to feature these processes of wider significance, since without these aspects of diachronic collaboration there would be no ongoing science and, indeed, no scientists.

Lyon sees the digital library in the context of an information grid, consisting of a collection of resources for learning and teaching, data repositories for research purposes, or archives of diverse cultural heritage materials. In her proposed scenario, researchers would undertake experiments, deposit raw data, and produce pre-prints using Web services. Recent advances in Web and Grid technologies allow such concepts to be realised. A portal could be developed that would support the collaborative development and dissemination of documents by assisting authors' collation and analysis of experimental results, organising internal project discussions, and the production of papers. By bridging the gap between the undertaking of experimental work and the dissemination of its results through electronic publication, this work addresses the cycle of activity on which a digital library rests.

Figure 1: Complete cycle of E-science

The project aims to provide integrated computer support across the research and educational cycles. There are additional requirements on surgeons as these activities are intrinsically coupled as a part of the requirements of the surgeon's Continuing Professional Development. Research should be undertaken and papers published to achieve goals under the learning contracts with their Professional organisations.

The CORE VRE will be implemented as a Grid/Web-based environment for supporting a critical subset of the e-science cycle (Figure 1): the collation and analysis of experimental results, the organisation of internal project discussions, and the production of appropriate outline documents depending upon the requirements of conferences and journals selected for dissemination. The CORE will allow surgeons to:

• create technical material (non research material for education),
• analyse data (from their own trials or data entered from journals),
• investigate hypotheses (from their own work or as meta or thematic reviews),
• discuss the finding from their or others work,
• prepare and submit articles for review, using semantic Web services.

The end users for this VRE will be the higher surgical trainees, who are qualified surgeons training to be consultants and who undertake clinical trials (experiments) as part of their practice.

The aim of this workpackage is to ascertain the wider issues and requirements involved with providing Grid/Web services that relate to the storage, access, use and re-use, of research data in repositories, and information from digital libraries and its dissemination. The requirements will be elicited and gathered through a number of focus groups, interviews and literature reviews. These will draw on the experiences and views of researchers in the clinical domain (Orthopeadic surgery), i.e consultants, specialist registrars, surgical trainees and other associated clinicians. However the project will also consult librarians/information scientists, instructional designers/learning technologists, and content providers. The conclusions from this workpackage will result in the Requirements Specification which will inform the development of the VRE demonstrator.

To illustrate how a medical researcher may use the CORE; this section outlines the process of managing e-experiments from the perspective of a fictional surgeon, Sam. In Sam's view of the CORE user space, it shows Sam is currently working on three trials, undertaking a different role in each. Sam is the co-investigator in the "charcot joints" trial, Sam is writing a systematic review of experiments in the "rotator cuff" trial, and Sam is also peer reviewer of the "cuff tear size" trial. Sam has also entered several experimental records into the personal logbook (patient details, operative procedures, and assessment results), part of Sam's e-portfolio.

Formalising Trial Protocol - To initiate a new trial, Sam first selects the experimental protocol from the available experimental schemas. The CORE then uses this schema to generate a number of data entry forms in which Sam enters specifics of the experiment. Guidelines for completing these forms are presented as "stretch text links", which can be viewed/hidden as required. Sam specifies the associative investigators and peer reviewers who will assist him/her on the trial. When created, the new trial will appear in Sam's user space, and also in the user spaces of the associate investigators and peer reviewers.

Selecting a Dataset - To create a dataset for the new trial, Sam searches the data repository from previous trials for suitable cases or uploads the case from Sam's logbook. Since Sam has already specified the experimental schema, only those cases matching this schema will be selected. Sam and associates subsequently add a number of different experimental results to the trial, which can be viewed in tabulated form for visual comparison.

Analysing the Dataset - To perform analyses on the dataset, Sam and associates choose from statistical methods offered by a Distributed Analysis Engine. Using the experiment schemas and metadata from the Analysis Engine, the CORE is able to generate an entry form for each statistical method, which Sam can use to fine tune the analysis (specify test variables, groupings etc.). The Analysis Engine queues the requested analysis and notifies the CORE when results are available. These results then appear in Sam's user space, and can be viewed.

Discussing the Results - Having obtained some significant results from the statistical analyses, Sam then decides to create a pre-print for discussion by Sam's co-investigators on a discussion board created for the e-print. Sam, co-investigators, or a tutor can specify who is able to see the pre-print and comment on it. For the trial Sam can take the pre-print on to publication. In this case Sam selects the JBJS publication schema and the CORE generates a pre-print template using the information Sam entered in the trial protocol. Sam fleshes out this template, following the JBJS guidelines provided, and specifies which analysis results should be included in the pre-print. After previewing the pre-print, Sam submits it. Behind the scenes the CORE submits the pre-print and its associated metadata to the community E-prints server (where it subsequently becomes available to the community), and makes the paper available in the user space of Sam and associates.

The CORE VRE will take a Service Oriented Architecture (SOA) approach. The architecture for the CORE project will build on the lessons learnt from a number of recent projects, for instance Opsis, eEBank UK, myGrid, MIAKT, and Combechem . The ePrints UK project has an architecture that supports the harvesting of metadata from eprint archives in UK academic institutions using the OAI Protocol for Metadata Harvesting (OAI-PMH). The e-Bank UK project has augmented this work to provide storage for and metadata descriptions of the research data. The myGrid project is focusing on the basic issues of storage, computation, and resource management. The MIAKT project is developing ontology, annotation and enrichment, and Grid reasoning services to aid the triple assessment in symptomatic focal breast disease. The CORE will bring these lesson learnt and where possible the technologies developed into a SOA.

Figure 2: Overview of the proposed infrastructure

Figure 2 illustrates the CORE-Framework concept, in the context of an e-science community Web site and integrated Grid/Web-based services. This would be implemented as a toolkit of generic components. Although the CORE Framework will itself provide data storage and management capabilities, facilities will also be provided to help communities integrate the CORE-Framework with existing data repositories. Distributed e-print, discussion, and analysis services will provide integrated support for document (e-print/reprint) management, communication, and e-experimentation respectively.

The services will focus primarily on assisting an orthopaedic surgeon co-ordinate and run clinical trials, and collected regularly the postoperative assessment results. The collated results are then analysed and discussed by a team of e-surgeons before being disseminated to the wider orthopaedic community. These services are generic in nature and may apply to many disciplines. A number of Grid/Web service based tools will be developed that will allow surgeons to create, manage and discuss their clinical trials (experiments). The CORE services will be developed using agreed standards such as SOAP and WSDL. The main services are:

• Schema Generator for new data into the Data repositories,
• Data repository service,
• Communication service,
• Document creation services,
• Managed e-print service,
• Analysis services.

Where possible, standard tools will be used in the creation of these services. For example, the Communication service will use the Chandler tool if possible. This workpackage will involve system testing of these individual components.

Figure 3: Workflow in the CORE framework

Figure 3 shows the envisioned workflow of the VRE. The schema space is the mechanism by which the CORE will be configured to a particular e-scientist community, through the formal specification of e-experimentation procedures relevant to that community. This configuration could be achieved using different types of schema. Data schemas are used to describe the exact nature of the experimental data (for example, specification of variable names, types, and possible values). Experimental schemas are used to describe experimental procedures or protocols. For example, a protocol could specify that any e-scientist conducting an experiment of type X needs to record an experiment description, statement of purpose and an outcome hypothesis. Human-readable guidelines will also be included, to help scientists meet the requirements of the protocol and to help reviewers ensure that the requirements have been met. Publication schemas are used to describe the required format for submitting experimental results to relevant journals and conferences. Where possible, the publication schema will also describe mappings between the clinical trial (experiment) protocol (for example, specifying that the experiment hypothesis should appear in the Experimental Methods section of the article). This allows outline pre-print 'previews' to be generated automatically without requiring the e-scientist to copy and paste information between the experiment protocol and pre-print.

The user space is where e-scientists use the schema space to orchestrate data entry and collation, e-experimentation, and dissemination. The user space may be further subdivided into three personalised areas: My Logbook, My Experiments, and My Papers

• My Logbook is an experiment logbook, in which experimental results can be entered (in accordance with data schema). Logbook entries are subsequently added to the community database, making data available (anonymously) to other community members.
• My Experiments is a workspace for e-experiments, which lists the experiments the e-scientist is working and has worked on. An e-scientist may be involved an experiment in the capacity of lead investigator (initiates experiment and acts as co-ordinator and contact for duration of experiment), associate investigator (assistant), or reviewer (monitor the progress of the experiment and review its outcomes according to guidelines). Reviewers have read-only access to the experiment protocol and set-up. When a new experiment is initiated, a discussion facility is automatically set up to facilitate and record communication between the e-scientists involved (this is also the means by which reviewers can give feed back the practitioners).
• My Papers provides a simple shortcut allowing an e-scientist to access all the papers produced by the various experiments quickly.

The demonstrator will use the services developed in workpackage 3 and embed them into the infrastructure developed in workpackage one. Here users will access these services through a portal. The portals will be developed using standard Human-Computer-Interaction and instructional design techniques. The portals will interface with the services using standards such as JSR-168 (Java standards for portlet interface).

This demonstrator will involve the system testing of the communications between the different components to ensure that a researcher can create, manage, and discuss experiments, and disseminate the results. Use will be made of scenarios and test plans developed in the requirements elicitation/gathering of workapackage 1.

In additional to the technical aspects of developing the demonstrator, there is the issue of filling the repository with experimental data and the e-print servers with appropriate publications. In the first instance, much of the data and publications will come form a completed EU funded project. In addition we propose to use recently completed clinical trial information. New sources of pre-print, published and experimental data identified by the surgeons will be sought. Consideration will be given to how these sources may be (automatically) integrated into the repositories and e-print libraries.

The demonstrator focuses more on the Human-Computer-Interaction to the system, allowing the users' input to feed back into the design. Standard user evaluation methods will be employed to focus upon the usability of the demonstrator by non-technical users (e.g., can it be used simply and effectively?). This will involve both qualitative (workshops, focus groups) and quantitative (experiments) evaluation methods. By using information from recently completed trials we will be able to compare the ease with which surgeons collate, analyse and disseminate the results. A key element of this workpackage will be the training of the end users. This will be achieved though the end users weekly research seminar slots and on a one to one basis. The results of these activities will be distilled into an evaluation report and form part of the final report. In addition a number of recommendations for future work will be prepared, dealing with both technical issues and the generic applicability of the demonstrator to other disciplines and subject domains.

The end users for this VRE will be the higher surgical trainees (HST), who are qualified surgeons training to be consultants. They are not computer specialists, their study is work based, they rarely are co-located with other HSTs. During the six years of training they usually move post twelve times, and they have to keep a logbook. Therefore they typify both the average scientist trying to collaborate on a project and a group of e-learners studying in a collative partner institution, i.e. they require tools that are easy to use for none computer science specialists. It is envisioned that the results of this project will offer direct benefits to the orthopaedic community and to the wider research community. By providing a VRE that enables researchers to collect and analyse experimental results from their own or other people's experiments, organise internal project discussions, and produce appropriate documents, the project should have a major impact on a number of areas which include:

• Being able to keep track of the research administration: trial protocol, ethical approval, and workflow as the trial progress,
• Enabling access to research data from various trials and in formats that allow analysis of the data,
• Allowing easier meta-analysis or thematic reviews,
• Monitoring the effectiveness of surgical interventions,
• Enabling a consortium to write appropriate documents for dissemination (medical reports, journal articles, etc),
• Producing up to date learning and teaching material.

The technology is an enabler. There will be issues common to all introductions of technology, including, buy-in from stakeholders and other cultural barriers. It is intended, however, that this VRE for orthopaedics may be of use in pioneering new or validating current procedures and techniques for orthopaedic surgery.

Dissemination of information and outcomes from the project activities will be achieved using a number of methods. A Project Web site will be created at the start of the project and will contain current information on activities, reports on the infrastructure and deliverables, and evaluation report. Links to relevant articles and projects relating to the e-project will be added. Presentations and publications derived from project work will also be available on the site. Project findings and results will be presented at relevant conferences. Particular attention will be paid to disseminating the work across clinical, digital library and Grid/Web communities.