The cross-disciplinary Roots of the British collaboration between scholars in humanities and

Transcription

1 HALOGEN RESEARCH DATA MANAGEMENT BENEFITS CASE STUDY 1. BACKGROUND The cross-disciplinary Roots of the British collaboration between scholars in humanities and genetics at the University of Leicester (Wellcome Trust) seeks to interrogate the evidence for the migration and/or continuity of human populations in the British Isles in the distant past. The HALOGEN project (History, Archaeology, Linguistics, Onomastics and GENetics) supports the data management needs of the researchers involved and is thus establishing organisational best practice in terms of data management planning and the support of diverse cross-disciplinary research data. It covers all phases of the project life cycle from requirements analyses through to the implementation of a practical, cost effective solution to meet the needs of the research team for data access, sharing, curation and preservation. PERSONNEL: Central to the project was the role of an IT research liaison manager to gather requirements from the diverse range of researchers and help assimilate and translate those into technical requirements for IT specialists. Through it s role as a UK research Data Service (UKRDS) pathfinder, the University appointed an experienced researcher (in astrophysics), Dr Jonathan Tedds, to IT Services in order to facilitate this role alongside the Project Manager, David Carter (IT Services). Specialists in the IT Services Database team (Mark Widdowson) and Research Computing Services team (Liam Gretton, Stuart Poulson) were identified and included at an early stage. Following the initial requirements gathering it soon became clear that the key to correlating these diverse input datasets was geographical location and visualisation. Experienced geographers, not previously involved in the collaboration, were consulted and Prof Nick Tate was invited to the project Board. A postdoctoral Geographical Information Systems (GIS) specialist, Dr Andrew Bradley, was subsequently identified and employed to perform this key role during the project. 1

2 INPUT DATASETS: Three primary input datasets were chosen for the pilot study which best addressed the research interests across the range of researchers including genetics, arts and humanities and represented typical technical and methodological challenges for such an interdisciplinary collaboration: Genetics Y chromosome & surname data (Prof Mark Jobling, Dr Turi King & Dr Dan Zadik, Department of Genetics, University of Leicester); Key to English Place Names (Dr Jayne Carroll, Institute of Place Name Studies, University of Nottingham); Portable Antiquities Scheme (Dr Dan Pett & Dr Sally Worrall, UCL Institute of Archaeology & British Museum). 2. ESTABLISHED PRACTICE AND CHALLENGES Researchers increasingly wish to combine their own research dataset with one or more other relevant datasets in order to tackle a particular research question. However, most researchers lack the experience and knowledge needed. This is particularly the case for the arts and humanities where there is less precedent for having significant IT research experience either as individuals or within a wider research group. In some cases a research team may include a member having limited IT experience and the individual may have created an ad hoc solution to combine the datasets. Typically they may not have sufficient IT knowledge data management, time or contextual information regarding the input datasets in order to create a sustainable, queryable resource for other researchers. Our database management model therefore identified the following processes for Halogen: Source Data - Obtaining and storing the diverse source data that will be used as input to the research database. Included within this are procedures to refresh data as new versions become available. Extract, Transform and Load (ETL) Procedures to extract the required source data. In many cases the raw data may need to be cleaned, formatted and annotated via metadata in 2

3 order to improve its integrity or make it interoperable with other source data sets. Ingest of the required data into a database follows. Data Storage Procedures to store and manage the core data required by researchers. Procedures and policies need to be defined for governing the backup, recovery and access of data and documented in a data management plan. Data Analyses Various tools and techniques may be employed to analyse and mine the data in order to produce correlations and create new research samples. Commonly employed tools include SAS, SPSS and R alongside researcher written algorithms. Visualisation For Halogen the geographical visualisation of data is the primary user requirement and so it is appropriate to consider this data analysis as a separate stage. CHALLENGES As an interdisciplinary research database, Halogen has to ingest each input dataset in a form such that sufficient information is carried forward to enable interoperation with each of the other datasets to answer research questions. Key challenges that emerged included: Identification of versioning and provenance for input datasets: It is common for datasets to be curated by multiple numbers of individuals at multiple institutions prior to ingest and that the process may not be fully documented. Which software tools and infrastructure are used at each stage of the model: Each institution needs to choose those products which best suit their requirements and the skill sets of those involved in any project. A common characteristic of traditional research collaborations is for the solutions chosen to rely on ad hoc advice from individual collaborators which may not always be informed by best practise with the result that valuable time and resources may be spent reinventing wheels or choosing inappropriate and/or unsustainable technologies. Requirements upon the institution for sustaining the research assets: A typical research project is only funded for the lifetime of the project and may includes no provision for long term preservation and reuse of the datasets generated. 3

4 Requirements upon the researchers for annotating, refreshing and maintainence of datasets: Without a clear mandate or funding mechanism to make research data available for reuse a researcher tends to give a rather low priority to providing for the continued update and refresh of their datasets. 3. BENEFITS FROM PROJECT Through the JISC Managing Research Data (#JISCMRD) and UKRDS programmes a clear mandate was able to be articulated for the long term preservation, storage and reuse of the curated research datasets. Rather than the Roots of the British research collaboration relying on unsustainable ad hoc solutions which might only suit a particular individual research question, the implementation of the Halogen research infrastructure with members of institutional IT Services alongside expert researchers from a range of disciplines provides a long term and sustainable resource allowing for future reuse and expansion as newer datasets become available. The technical solutions chosen for Halogen were Perl and Excel tools for the extraction, transform and loading stage prior to ingest into a LAMP stack MySQL database solution hosted by IT Services Research Computing Services team. The solution provides output to research analysis tools, and in particular ArcGIS for spatial visualisation and analysis. The following key objectives have been addressed: An assessment of the effectiveness of the Data Management Planning tool (DMPonline) and other related tools promoted by the Digital Curation Centre (DCC). These tools were used to facilitate requirements analyses and design activities. The definition of institutional data management infrastructure, service delivery models, strategy and policies to support research data management. 4

5 When identifying and evaluating specific data management tools and technologies, sustainable open source solutions and relatively cheap, high capacity storage have been carefully considered, with the aim of reducing the cost barriers to entry. DIRECT BENEFITS New research opportunities: Cross database work bringing together and correlating new datasets alongside each other to seed new research outcomes. Scholarly communication/access to data: Making two primary national resources (Key to English Place Names & Portable Antiquities Scheme) available for cross databasing with other research datasets. Verification, re-purposing and re-use of data: Cleaning & enhancing private or bespoke research datasets for reuse & correlation. Increased transparency and excellent training for best practice in research data management. Increasing research productivity: Build in cleaning, annotation and enhancement steps into normal research workflows so research datasets may immediately be reusable and interoperable with other datasets. Stimulating new networks/collaborations: Via national visibility of datasets enabling data mining, correlation and new research sample selections. Impact & Knowledge Transfer: Halogen research IT infrastructure being reused in industrial multi disciplinary projects e.g. EU FP7 Mintweld (industrial engineering) & BRICCS National Health Service/University Trust data sharing. Increasing skills base of researchers/students/staff: Research data management training, research tool discovery and ArcGIS geo-spatial data visualization. Possible Metrics New research opportunities: New research grant income where a project seeks to use or reuse Halogen database infrastructure. The Roots of the British collaboration won 1.3m Leverhulme Trust funding for an interdisciplinary research programme over 5 years on the basis of reuse of the Halogen database. 5

6 Scholarly communication/access to data: Measurement of citations by research papers to Halogen and derived research outputs. INDIRECT BENEFITS (COSTS AVOIDED) No re-creation of data: Researchers avoid valuable time needed to transcribe external data sources for reuse with own research datasets. No loss of future research opportunities: Inter disciplinary research platform available for reuse as a service in other projects. Lower future preservation costs: Service Level Agreements in place to maintain Halogen infrastructure and input datasets. Not dependent on individuals alone. Re-purposing data for new audiences: Both internal & national research resources can become nationally available & reusable, increasing exposure and impact. Re-purposing methodologies: e.g. Geneticists learn better spatial correlation analysis techniques from GIS & astronomical e-research expertise. Protecting returns on earlier investments: Nationally important datasets produced through research funded by Wellcome Trust, Leverhulme Trust, Arts and Humanities Research Council, the British Museum and the Universities of Leicester, Nottingham and University College London all now have Service Level Agreements to preserve and enhance these valuable research resources. Possible Metrics No re-creation of data & re-purposing data and methodologies for new audiences: Research productivity gains as measured by numbers of research papers generated and grant income per collaborator before and after participation. No loss of future research opportunities: Measures of reuse of infrastructure in other projects via IT Services and savings in individual departmental spend on research data storage and management. Numbers and volumes of data assets recorded in each case. 6

7 Protecting returns on earlier investments: Citation of nationally important datasets through Service Level Agreements with an institution rather than each individual originator. 4. SUMMARY AND KEY POINTS The Halogen project has successfully demonstrated the benefits of leveraging both research and technical expertise across an institution while informed by national and international best practice. The challenge of facilitating such increasingly common and wide ranging inter disciplinary research projects (which may include external as well as institutional expertise) has been addressed by employing an experienced researcher with significant IT expertise: the Research Liaison Manager. The complex IT research data requirements for such a project are best coordinated over the project life cycle using an evolving Research Data Management Plan, as enabled by the improving Digital Curation Centre DMPonline tool. A major Leverhulme Trust research programme was recently awarded to the Roots of the British collaboration specifically to build new research using the Halogen pilot database. The solution had to be designed to exploit the existing research storage assets within the organisation in terms of hardware, software and technical expertise both within IT Services and other centres of excellence within and external to the University. The project complements its role as a UK Research Data Service (UKRDS) Pathfinder institution in which we aimed to test the integration of data management planning within the research management process and the advisory services that need to be available through the role of an IT Research Liaison Manager. TECHNICAL/PROCESS CHALLENGES AND SOLUTIONS Data licences and confidentiality issues: Establish any constraints on using third party data early in the life of a project. This can drive specific requirements. E.g. the British Museum/Portable Antiquities Scheme had confidentiality issues relating to the geographic location of finds. Cleaning and formatting data: Consider if the analysis tools require data to be represented in a specific way and which format and content are supported? 7

8 Establishing a common geographical reference: GIS specialist knowledge is required to generate this from diverse datasets with different levels of spatial granularity. Selecting tools, database and visualisation technologies: Investigate cost, skill sets, availability and portability. Leverage experience within the organisation and any campus wide license agreements to reduce the risks and project costs. Consider reusability criteria in non academic settings where applicable. Development methodology: Prototyping is key. Researchers may find it difficult to articulate true requirements until working examples are delivered to users which then drive out real needs. All researchers should be actively involved in appraising progress and driving requirements throughout the project. ORGANISATIONAL CHALLENGES AND SOLUTIONS Cultural differences: Recognise different cultures and mind sets exist between research community and IT specialists in central services having different professional language, expectations and working practises. The management of a research project usually requires a different, iterative methodology than an IT infrastructure project having a more clearly pre determined end point. Research Liaison Role: An IT specialist with strong research background enables effective ways of liaising with research community and bridging any gaps in understanding. Leveraging expertise within the organisation: Where possible, coordinate specialists across and external to the organisation. V1.1 Jonathan Tedds