Research data management in crystallography at the XXII IUCr Congress

  On Aug 29th a session on research data management will be held at the XXII Congress of the International Union of Crystallography (IUCr2011). The session will feature talks by Brian McMahon (IuCr), Brian Matthews (I2S2 Project), Peter Murray-Rust (CrystalEye), John Westbrook (wwPDB) and Nick Spadaccini (DDLm). Peter Murray-Rust will deliver a talk along the session on Open Crystallography.

A first analysis of data management

As previously mentioned in this blog, the Sonex workgroup is now try to extend its use case scenario analysis on 'Deposit opportunities into repositories' to the realm of research data. A first meeting held at EDINA on Mar 30th served the purpose of drawing a general picture of the data management landscape.

Stress should be put on the fact that the way of handling SSH and STM data may substantially differ. Given the strong IASSIST-attachment of some Sonex members, the workgroup initial approach to data management may therefore be a bit biased towards procedures in the area of Social Science and Humanities. However, attention will be paid as well to specific ways of dealing with STM datasets as the analysis gets fine-tuned.

Moving along the same lines as we did for research articles, we first try to tackle the ACTIONS scope. Data deposit is certainly an issue, but there's more to data-related processes than just deposit. It's also about Access to data and also about Data Notification/Register.

Next we get on to the WHAT and the WHO. Answer to WHAT? is a data set. Previous analysis by Peter Burnhill shows -at least- three different types of research data (see image below).


Dealing mainly with the data file itself, this data type classification is somewhat narrow for the general picture of data management, so Sonex would rather set a new and more generic data classification for answering the question WHAT is there to deposit:

• Metadata record


• Codebook or user guide, where all necessary information is provided to allow for data re-use*


• Raw data or dataset file(s)

* See a DCMI-based description at: Inter-university Consortium for Political and Social Research (ICPSR). (2009). Guide to Social Science Data Preparation and Archiving: Best Practice Throughout the Data Life Cycle (4th ed.). Ann Arbor, MI. Section 'Important documentation elements', p. 22

These three elements should ideally be supplied as a single package.

As to the question of WHO performs each data-related operation (Notification-Deposit-Grant access), a handful of running projects within the JISC MRD (phase I) programme should serve to test the different use cases resulting from a double-entry 'Action/What' table as featured below.


Next step as we proceed to further development of this preliminary analysis should be a survey for gathering information on procedures for data handling as carried out in specific JISC MRD projects.

National initiatives for promoting data management strategies: an overview

- "Hello, I want to deposit my data"
- "Sir, this is a library!"
- "Sorry" -he whispers- "I want to deposit my data".
(as told by Brian Hole, British Library, along his presentation of the DRYAD UK initiative)


  Main objective of the JISC MRD International Workshop held last month was to review progress achieved by the JISC Managing Research Data Programme and to discuss this in the context of broader international developments.

As stated in the workshop programme overview, "this dimension reflects key partnerships which JISC, the JISCMRD Programme and the DCC has been building through the IDCC Conference, the Knowledge Exchange and other initiatives. They include the Australian National Data Service, the NSF funded DataNet Projects, institutions in the US and Australia, the DFG, SURF, DANS etc".

Whithin the broader context, besides a couple of preliminary talks on the European Union approach to (and future funding of) data management initiatives -by John Wood, on the EU 'Riding the wave' report, and by Carlos Morais-Pires on the Digital Agenda for Europe- the workshop featured a specific session on "National and international infrastructure initiatives" whose first panel was called "Approaches and strategies in the UK, US, and Germany". Australian and Dutch national or specific approaches were also discussed, either at this session or later along the event.

Besides the national initiatives featured in this and further sessions along the meeting -it was reassuring to see such a broad scope of strategies or already running projects taking place at the same time in so many different countries- there are also additional, sometimes preliminary initiatives for promoting data management policies at national or institutional level in other countries such as Finland, Portugal, France, Poland or South Africa.

As new initiatives for research data management keep steadily coming up, this session was an opportunity to get an informal update on DCC's report 'Comparative Study of International Approaches to Enabling the Sharing of Research Data' - see its summary and main findings here as of Nov 2008.

Digital Curation Centre - UK
Kevin Ashley, Digital Curation Centre (DCC), described the present picture of data management in the UK as "a new context", where Universities are increasingly willing to take responsibility for data management (specially in areas not covered by Data Centres).
Once UK funder and NSF rules for Data Management Planning are being implemented, this in-advance planning is becoming very important for funders, researchers, institutions, collaborators and reusers. DCC current tasks include integrating different Data Discovery Services plus building institutional capacities: skills, policies, etc. Besides that, DCC is providing the new DMP Online service aimed to produce and maintain Data Management Plans.
Good news is that, despite varying degrees of involvement, institutions in the UK have accepted their role in RDM.

NSF-funded DataNet Projects - US
A summary of present state of research data management in the US was provided by presentations of the DataONE and DataConservancy initiatives, resp. delivered by William Michener (University Libraries at U New Mexico) and Sayeed Choudhury (Johns Hopkins University).

After stating that "researchers are presently using 90% of their time managing data instead of interpreting them", W. Michener presented the Data Observation Network for Earth (DataONE) initiative (a live DataONE presentation at U of Tennessee is available). This NSF-supported initiative aims to ensure preservation and access to multi-scale, multi-discipline, and multi-national science data. DataONE Coordinating Nodes around the world will help achieving needed international collaboration for solving the grand science and data challenges, particularly with regard to education.

The DataConservancy initiative aims to research, design, implement, deploy, and sustain data curation infrastructure for cross-disciplinary discovery with an emphasis on observational data. S. Choudhury's presentation stressed the need for data preservation as a necessary condition for data reuse and introduced the recent connection of data and publications through arXiv.org as one of the pilot projects that build upon the Project APIs.

DFG - Germany
New DFG information infrastructure projects in Germany were presented by Dr Stefan Winkler-Nees, who mentioned both Jan 2009 DFG Recommendations for Secure Storage and Availability of Digital Primary Research Data, as a base report for promoting standardized work in the data management area, and DFG running call for proposals "Information infrastructures for research data". Selected projects at this call are due to be shortly announced and will start on May/Jun'2011. Finally, in a a common line of thought with other initiatives, Dr. Winkler-Nees mentioned DFG is aiming for teaching and qualification of both researchers and data curators.


SURF Foundation & DANS - The Netherlands
Later on along the workshop, John Doove presented the SURF Enhanced Publications initiative within the SURFshare programme 2007-2011. Six new projects funded along 2011 by the SURF Foundation will allow researchers from a variety of disciplines to share datasets, illustrations, audio files, and musical scores with fellow researchers in the context of Enhanced Publications (programme video available on YouTube). There were already two previous grants rounds for Enhanced Publications. The six running projects, whose results are due in May 2011, take place within five disciplines: Economics (Open Data and Publications, Tilburg University), Linguistics (Lenguas de Bolivia, Radboud University Nijmegen, and Enhanced NIAS Publications, KNAW-Royal Netherlands Academy of Arts ans Sciences), Musicology (The Other Josquin, University Utrecht), Communication sciences (Enhancing Scholarly Publishing in the Humanities and Social Sciences, KNAW) and Geosciences (VPcross, KNAW).

The Dutch strategy for increasing research data available online was completed with the presentation "Sustainable and Trusted Data Management" delivered by Laurent Sesink (DANS-Data Archiving and Networked Services). DANS, est. 2005, deals with storage and continuous accessibility of research data in
the social sciences and humanities and promotes the 'Data Seal of Approval' for certification of data repositories, guaranteeing via a series of required criteria a qualitatively high and reliable way of managing research data.

Australian National Data Service (ANDS) - Australia
Finally, Andrew Treloar, Director of Technology, Australian National Data Service (ANDS), supplied a comprehensive perspective from a national infrastructure provider and in a way summarized previous talks by saying that, despite differences, there are common themes emerging in national approaches to data management, as there are things only they can do. Along his plenary presentation "Data: Its origins in the past, what the problems are in the present, and how national responses can help fix the future" he mentioned for instance that Hubble Space Telescope-related publication statistics show double research is being done thanks to data reuse. Efficiency, validation, integrity of scholarly records, value for money and self-interest were listed as (non-altruistic) arguments for data reuse.

Having the chance to attend this series of brilliant presentations and checking out how policies for opening access to research data keep spreading over institutions and countries were undoubtedly part of the Birmingham workshop highlights. Next opportunity for keeping up with it all will be next November at the Knowledge Exchange Workshop on Research Data Management in Bonn, Germany.

Could external cooperation improve collection of specific JISC MRD project-related information?

  In forthcoming days SONEX will be publishing some posts on the JISC MRD Programme International Workshop held last March 28-29th at Aston Business School Conference Centre, Birmingham. Certain aspects debated at this comprehensive meeting were very useful for establishing an approach for dealing with research data management from a SONEX viewpoint, as debated in a SONEX meeting at EDINA on Mar 30th whose outcome will also be shortly blogged.

See IUCr Brian McMahon's report for a general review on the JISC MRD workshop.

One of the most visible disciplinary approaches to data management presented at the JISC MRD event -which featured all kinds of institutional and subject-based initiatives in the area- was the one coming from meteorology, palaeoclimatology and climate-related sciences: there was a presentation of the PEG-BOARD Project (U of Bristol) at the Subject-Oriented Approaches session on Monday, followed by ACRID (U of East Anglia & STFC) and Metafor (BADC & STFC) Project presentations on Tuesday afternoon.

One of the most relevant features of these climate-related projects is interdisciplinarity. PEG-BOARD Project in particular aims to serve the archaeology research community by supplying them their paleoclimate data.


A few specific aspects about PEG-BOARD were discussed after the project presentation. Interesting thing about them is they were not mentioned along the talk, nor are they reported at the project site:

- Due to the project interdisciplinarity, there are two clearly different user groups for palaeoclimatology data produced: climatologists, who will understand the nature of involved datasets, as they're central to their discipline, and archaeologists, who don't and need not know much about the data format but need the information contained in it for their own purposes - thus functioning as regular non-technical users to the project instead of researchers. However, as they are indeed researchers, the feedback they may provide on the project outcome could be so much more valuable.

- What archaeologists care about in the end is the data plottings, and Data Centres will not provide such processing. So what PEG did was implement specific software capabilities that will address the needs of non-technical data users (i.e. archaeologists), as to allow them to search for the plots or false-colour graphics they need. This piece of middleware is a conceptual key feature of the project in terms of deliverables.

- Climate data is usually archived in binary format, so it's often not easy to process. UK Met Office provided lots of info, often incomplete or in old formats. The adaption process of raw data to the project needs was very interesting and worth disseminating.

- Climate models were written in FORTRAN. When re-written or translated into C++, the results would vary for the same data arrays due to specific treatment by the code. That poses a quite amazing challenge in terms of model interpretation.

- When asked on whether researchers provided enriched metadata for their data, the answer was there's usually an input in terms of past experiments, i.e. "this is the data outcome of such and such experiment when changing initial conditions in such a way". Such-and-such experiment would be described the same way until one was reached that wasn't described at all.

The fact that none of these project aspects is recorded or discussed at the project blog poses a question on whether an external approach to data management projects might collect and disseminate very interesting information that researchers may not consider relevant enough to discuss from project blogs. Such an external approach to running projects might be carried out by data librarians in order to
share these specific project details with the data management community.

For whatever it may be worth, Sonex would be keen to do this kind of job for the MRD community.

Strategies for research data deposit in ongoing data management projects

  Prior to start performing pattern analysis for research data deposit into (institutional or subject-based) data repositories –whether or not open access– first step by Sonex is to scope ongoing projects dealing with that kind of deposit, as well as already closed projects which supplied relevant guidelines on the subject. A list of projects working on data management follows, with their specific approach on how to deal with actual data deposit as taken from project blogs:


TARDIS (Monash University–Australian National Data Service).
“There is a pressing need for the archival and curation of raw X-ray diffraction data. However, the relatively large size of these datasets has presented challenges for storage in a single worldwide repository. This problem can be avoided by using a federated approach, where each institution or university utilizes its institutional repository”.


ADMIRAL: A JISC-funded data management infrastructure for research across the life sciences.
"The purpose of the ADMIRAL Project is to create a two-tier federated data management infrastructure for use by life science researchers, that will provide services (a) to meet their local data management needs for the collection, digital organization, metadata annotation and controlled sharing of biological datasets; and (b) to provide an easy and secure route for archiving annotated datasets to an institutional repository, The Oxford University Data Store, for long-term preservation and access, complete with assigned Digital Object Identifiers and Creative Commons open access licences".
(See Oxford University Library Services' Databank)


XYZ Project. “The XYZ Project will create a demonstrator of a new workflow for publishing data in support of full-text. The author prepares data for publication (if possible with validation) in a third-party trusted repository before the paper is submitted to a publisher. Our software will manage the deposition, release to reviewers, dis-embargo and for conventional publication or as a data journal. Two Open Access publishers (International Union of Crystallography and BioMed Central) are engaged with the project and will test the new workflow”.
Anticipated Outputs and Outcomes: A demonstrator repository hosted by the IUCr.


FISHnet: Freshwater information sharing network. “This project will allow researchers in multiple academic, governmental and voluntary-sector institutions to share their data. Data will be held securely in a sustainable subject repository which preserves and disseminates multiple datasets as part of the FreshwaterLife.org information portal. Data creators will be able to manage access rights to their content, from Open Access to sharing with trusted colleagues”.


DMBI: Data Management in Bio-Imaging. “The quantity of data generated by modern high-throughput bio-imaging systems presents a significant challenge in both data management and processing. Furthermore, there is no explicit system/way to record the processing algorithms and parameters that are used to produce results. Thus there is no strong link between images, software and results. This projects aims to address these issues”.
Anticipated Outputs and Outcomes: Build a prototype DMBI system around OMERO.


CaiRO: Curating Artistic Research Output. “No prominent subject-based repository exists to act as the custodians of arts practice-as-research data. Where institution provision for data management is in place (for instance, an institutional repository service) the arts researcher-practitioner cannot always rely on an understanding of the special nature of arts research data. More commonly, data is retained in departmental collections, built and maintained by small teams which often include researchers themselves”.


BRIL: Biophysical Repositories in the Lab. “The BRIL project aims to enhance the repository facilities at the Randall Division of Cell and Molecular Biophysics at King’s College London. This will involve:
» Embedding the repository within the researchers’ day-to-day research and experimental practices;
» Integrating the repository into the wider King’s infrastructure”.
Example of KCL “internal” repository: Mutation Testing Repository.


ADS+: Enhancing and Sustaining the Archaeology Data Service digital repository. The project aims to “Increase the sustainability of the ADS, by implementing Fedora (Flexible Extensible Digital Object Repository Architecture). This is a world-leading open source digital repository application which will allow the automation of many ADS curatorial functions, according to the Open Archival Information System (OAIS) Reference Model (ISO 14721:2003). This will help ensure the long term preservation of all ADS digital archives, as well as making the ADS archival procedures more cost-effective”.


IDMB (Institutional Data Management Blueprint) Project, U. Southampton.
The project’s aims are to provide the University of Southampton with a ten-year roadmap for delivery of a comprehensive data management infrastructure.

[IDMB Recommendations] The data management audit and gap analysis indicates where improvements can be made in the short, medium and long-term to improve data management practices and capabilities at the University. The following preliminary recommendations are put forward for short (one year), medium (one to three years), long (more than three years) term action.
[Short Term (1 year)] Crucial to supporting researchers is the consolidation of data management into a coherent framework that is easy to understand, use, and has a sustainable business model behind it. A number of major recommendations are put forward here for the short-term:
• Create an institutional data repository
• Develop a scalable business model
• One-stop shop for data management advice and guidance


MaDAM: Pilot data management infrastructure for biomedical researchers at University of Manchester.
A pilot infrastructure for Biomedical Researchers at the University of Manchester, which covers data capture, data storage and data curation. This infrastructure comprises procedural support, hardware and software.
[18/03/2010] The development team have built a prototype data management front end which fits a generic set of needs amongst our Life Sciences researchers. It is aimed at being flexible enough to allow researchers themselves to assign attributes (i.e. metadata) to their experiments and datasets for them to be usefully categorised and tagged. The prototype is also entirely dispensable and intended as a catalyst for feedback from our use cases on their specific functionality requirements.


DISC-UK DataShare Project. The DISC-UK DataShare project, led by EDINA National Data Centre and the Edinburgh University Data Library, with partners at the Universities of Southampton and Oxford, has advanced the current provision of repository services for accommodating datasets in the UK.
Key conclusions: 1) Data management motivation is a better bottom-up driver for researchers than data sharing but is not sufficient to create culture change, 2) Data librarians, data managers and data scientists can help bridge communication between repository managers & researchers, 3) Institutional repositories can improve impact of sharing data over the internet.

A preliminary list of discipline-specific projects on research data management

A preliminary list follows of currently running discipline-specific projects and initiatives (as of Dec 2010) dealing with research data management. The list below is not comprehensive, but a sample of ongoing projects, brought together in order to find out potential biases by area in current research data management projects. Should there be relevant projects missing, we’d appreciate a notification for including them as well.

[projects/initiatives listed in alphabetical order]

Project name: ACRID: Advanced Climate Research Infrastructure for Data
Institution/Funder/Manager: U East Anglia, STFC, Met Office, JISC
Project Description: The ACRID Project aims to develop an approach to publishing climate research data in a way that facilitates citing, re-use and the provision of full provenance information for processed data.
Area/Discipline: Climate Science

Project name: ADMIRAL
Institution/Funder/Manager: U Oxford, JISC
Project Description: A data management infrastructure for research across the life sciences
Area/Discipline: Life Sciences

Service/Project name: ADS: Archaeology Data Service
Institution/Funder/Manager: U York, AHRC, JISC, EU (mandated repository for AHRC, NERC)
Service/Project Description: The Archaeology Data Service supports research, learning and teaching with high quality and dependable digital resources. It does this by preserving digital data in the long term, and by promoting and disseminating a broad range of data in archaeology. The ADS promotes good practice in the use of digital data in archaeology, it provides technical advice to the research community, and supports the deployment of digital technologies.
ADS is actively engaged with research projects working with partners in all sectors of UK archaeology.
Area/Discipline: Archaeology

Project name: Global Argo Data Repository
Institution/Funder/Manager: NOAA, NODC (National Oceanographic Data Center), GODAE (Global Ocean Data Assimilation Experiment), IFREMER (Institute for Research and Exploitation of the Sea)
Project Description: In the year 2000, a global array of approximately 3,000 free-drifting profiling floats, known as the Argo Ocean Profiling Network, was planned as a major component of the ocean observing system. Argo originated from the need to make climate predictions on both short and long time scales and has led to international participation and collaboration to ensure global coverage.
Centers to handle the data collected by profiling floats have been established in a number of countries. These centers normally handle data from their nationally deployed floats, but sometimes provide that service to other countries or organizations. All Argo data will be publicly available in near real-time via the GTS (Global Telecommunications System) and in scientifically quality-controlled form with a few months delay.
Area/Discipline: Marine Sciences, Oceanography

Project name: BlueObelisk
Institution/Funder/Manager: Group of chemists/ programmers/informaticians
Project Description: The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature
Area/Discipline: Chemoinformatics

Project name: BRIL: Biophysical Repositories in the Lab
Institution/Funder/Manager: CeRch-KCL, JISC
Project Description: The BRIL project aims to enhance the repository facilities at the Randall Division of Cell and Molecular Biophysics at King’s College London by:
- Embedding the repository within the researchers’ day-to-day research and experimental practices
- Allowing data and metadata to be captured in automated fashion
- Allowing the structure of experimental processes as a whole to be captured, modelled and stored within the repository
- Enhancing browse and access facilities and data exchange facilities to increase interoperability.
Area/Discipline: Biophysics

Project name: CAiRO: Curating Artistic Research Output
Institution/Funder/Manager: U Bristol, DCC, JISC
Project Description: Research data created by the UK’s performance and visual arts departments is often rich, technically complex and amazingly varied in nature. This work may include interconnected multimedia records of a single live event or software which exhibits complex behaviours dependant upon the choices made by a viewer. The CAiRO project, funded as part of the wider JISC Managing Research Data programme, aims to offer data management skills tailored to the special requirements of the arts researcher-practitioner.
Area/Discipline: Creative Arts

Project name: The CEACS Data Library
Institution/Funder/Manager: CEACS Library, Center for Advanced Study in the Social Sciences (CEACS), Instituto Juan March, Madrid, Spain
Project Description: The CEACS Data Library provides support to its research community in conducting quantitative research with primary and secondary data. The Data Library has a collection of over 2,000 secondary research datasets from major data centres. The service supports research data management through a thematic website, one to one support and a Dataverse data repository to help with the management, sharing and preservation of the data produced by researchers.
Area/Discipline: Social Sciences

Project name: Data Conservancy: A New Vision for Data-Driven Science
Institution/Funder/Manager: National Science Foundation (NSF), Johns Hopkins University (Lead institution)
Project Description: The Data Conservancy (DC) embraces a shared vision: scientific data curation is a means to collect, organize, validate and preserve data so that scientists can find new ways to address the grand research challenges that face society.
Area/Discipline: Astronomy, Earth Sciences, Life Sciences and Social Sciences

Project name: DataONE
Institution/Funder/Manager: National Science Foundation (NSF)
Project Description: DataONE was conceived to ensure preservation and access to multi-scale, multi-discipline, and multi-national data about life on earth and the environment that sustains this life. It was recognized from the outset that such data are often difficult to discover, access, integrate and analyze.
Area/Discipline: Earth & Life Sciences

Project name: DataTrain
Institution/Funder/Manager: U Cambridge, ADS, DCC, JISC
Project Description: The DataTrain project aims to build on findings and tools developed in the Incremental project (JISC 07/09 funding strand), to design discipline-focused data-management training modules for post-graduate courses in Archaeology and Social Anthropology at the University of Cambridge.
Area/Discipline: Archaeology, Social Anthropology

Project name: DATUM for Health: Research data management training for health studies
Institution/Funder/Manager: Northumbria U, DCC, JISC
Project Description: This collaborative project seeks to promote research data management skills of postgraduate research students in the health studies discipline through a specially-developed training programme which focuses on qualitative, unstructured research data.
Area/Discipline: Health Sciences

Project name: DMBI: Data Management in Bio-Imaging
Institution/Funder/Manager: The John Innes Centre (BBSRC), Norwich BioScience Institutes, JISC
Project Description: DMBI aims to raise the level of data management/handling for high-throughput bio-imaging, and strengthen the interactions between image data silos, both internally and with partner organisations.
Area/Discipline: Biology/Bio-imaging

Project name: DMP-ESRC: Data management planning for ESRC research data-rich investments
Institution/Funder/Manager: UK Data Archive (UKDA), Economic and Social Research Council (ESRC), Joint Information Systems Committee (JISC)
Project Description: Data Management Planning (DMP) project aims to increase the data management and sharing capability within the social sciences community.
Area/Discipline: Social Sciences

Project name: DMTpsych: Data Management Training for psychologists
Institution/Funder/Manager: U York, U Sheffield, Sheffield Hallam U, DCC, JISC
Project Description: The aim of DMTpsych is to build capacity and skills within psychology postgraduates relating to research data management. The project builds upon existing research data management materials developed by the Digital Curation Centre (DCC) to create discipline-focused postgraduate training materials that can be embedded into postgraduate research training for the psychological sciences.
Area/Discipline: Psychology

Project name: DRYAD UK
Institution/Funder/Manager: British Library, University of Oxford, JISC
Project Description: Dryad is an international repository of data underlying peer-reviewed articles in the basic and applied biosciences as published by a Consortium of Journals. Dryad UK aims to expand Dryad into the UK by establishing a UK mirror site and extending service to new publishers and disciplines.
Area/Discipline: Biomedical Sciences

Project name: EDgrid Central: Data Repository System for 3-D Full-Scale Earthquake Testing Facility
Institution/Funder/Manager: National Institute for Advanced Industrial Science and Technology, Japan
Project Description: A data repository system called EDgrid Central is designed for storing huge amount of experiment data by using a 3-D full-scale earthquake testing facility. The EDgrid Central prepares large storage capacity and implements a data modeling for the shake test in the backend. The frontend is a portal for users to retrieve the stored data by meta-data search and bulk download. This system uses the NEEScentral developed by the NEES project in the United States by enhancing search and download functionalities, according to the EDgrid users' requirements. The EDgrid Central allows facility sites to have a permanent repository of the shaking table experiment and it also enables civil engineering researchers to share their data and reports in their daily activities.
Area/Discipline: Geophysics

Project name: EIDCSR: Embedding Institutional Data Curation Services in Research
Institution/Funder/Manager: U Oxford, JISC
Project Description: The Embedding Institutional Data Curation Services in Research (EIDCSR) project aims to address the data management and curation requirements of three collaborating research groups in Oxford, by scoping their requirements and embedding selected elements of the digital curation lifecycle, including policy, workflow, and sustainability solutions within the research process. The workflows generated by the project are intended to scale to include other research domains and the outputs should be of use to other research intensive institutions. Project runs until Dec'10.
Area/Discipline: Medical & Life Sciences

Project name: ERIM: Engineering Research Information Management
Institution/Funder/Manager: U Bath, UKOLN, JISC
Project Description: ERIM aims to specify in practical terms how effective data management can be enabled and supported in research projects, particular to support reuse or more broadly what can be thought of as 're-purposing'. The project will look primarily at the engineering research domain.
Area/Discipline: Engineering

Project name: EURO VO: European Virtual Observatory
Institution/Funder/Manager: CNRS, ESO, INAF, U Edinburgh
Project Description: The Virtual Observatory (VO) is an international astronomical community-based initiative. It aims to allow global electronic access to the available astronomical data archives of space and ground-based observatories and other sky survey databases. It also aims to enable data analysis techniques through a coordinating entity that will provide common standards, wide-network bandwidth, and state-of-the-art analysis tools. The EURO-VO project aims at deploying an operational VO in Europe. Its objectives are the support of the utilization of the VO tools and services by the scientific community, the technology take-up and VO compliant resource provision and the building of the technical infrastructure.
Area/Discipline: Astronomy

Project name: FISHnet
Institution/Funder/Manager: Centre for e-Research, King’s College London, JISC
Project Description: Freshwater information sharing network
Area/Discipline: Freshwater Biology

Project name: HALOGEN - History Archaeology Linguistics Onomastics and GENetics
Institution/Funder/Manager: U Leicester, JISC
Project Description: The cross-disciplinary Roots of the British collaboration between scholars in humanities and genetics 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 will support the data management needs of the researchers involved and thus establish organisational best practice in terms of data management planning and the support of diverse cross-disciplinary research data.
Area/Discipline: Ancient history/Genetics

Project name: I2S2
Institution/Funder/Manager: UKOLN/DCC/Soton/STFC, JISC
Project Description: Infrastructure for integration in structural sciences
Area/Discipline: Chemistry (with a view towards inter-disciplinary application)

Project name: Incremental: A step by step approach to informing, improving, & increasing research data curation practice
Institution/Funder/Manager: Cambridge University Library, Humanities Advanced Technology and Information Institute (HATII) at U Glasgow, DCC, JISC
Project Description: The aim of Incremental is to inform, improve and increase research data curation within UK HEIs, by providing exemplars and resources for others to use. Specific objectives are: (1) to investigate current practices and requirements at each institution; (2) to develop a plan for addressing these requirements; (3) to pilot tools and services at each HEI and then make further adjustments and recommendations; (4) embed the work within each institution; and (5) to deliver resources and findings to the DCC, DPC and JISC for wider dissemination. In addition to resources, the project will seek to provide information about their cost and sustainability.
Area/Discipline: Archaeology, Chemistry, English, Engineering and Medicine

Project name: IODP: Integrated Ocean Drilling Program
Institution/Funder/Manager: National Science Foundation (NSF), Japan’s Ministry of Education, Culture, Sports, Science and Technology (MEXT)
Project Description: IODP is an international marine research program that explores Earth's history and structure recorded in seafloor sediments and rocks, and monitors subseafloor environments. IODP builds upon the earlier successes of the Deep Sea Drilling Project (DSDP) and Ocean Drilling Program (ODP), which revolutionized our view of Earth history and global processes through ocean basin exploration.
The IODP oversees repositories around the world. Samples are distributed according to ODP and IODP policies.
Area/Discipline: Marine Sciences

Project name: MaDaM
Institution/Funder/Manager: Manchester eResearch Centre, JISC
Project Description: Pilot data management infrastructure for biomedical researchers
Area/Discipline: Biomedical Sciences

Project name: Managing Research Data: Gravitational Waves (MRD-GW)
Institution/Funder/Manager: STFC, University of Glasgow, JISC
Project Description: MRD-GW aims to examine the way in which Big Science data is managed, and produce recommendations as appropriate. Gravitational Wave (GW) data generated by the LIGO Scientific Consortium (LSC) will be used as a case-study.
Area/Discipline: Particle physics/Astronomy

Project name: PANGAEA
Institution/Funder/Manager: Alfred Wegener Institute for Polar and Marine Research (AWI), DFG
Project Description: Publishing Network for Geoscientific & Environmental Data
Area/Discipline: Earth Sciences

Project name: PEG-BOARD
Institution/Funder/Manager: School of Geographical Sciences, University of Bristol, JISC
Project Description: Palaeoclimate and environment data generation - building open access to research data
Area/Discipline: Palaeoclimatology

Project name: Quixote
Institution/Funder/Manager: U Cambridge/CSIC
Project Description: The main objective/vision of the Quixote project is to design, test and deploy a modular, open source system of tools that allow computational chemistry data (now sitting in the darkness of individual hard-disks) to be organized, shared, and queried
Area/Discipline: Quantum Chemistry

Project name: Research Data MANTRA
Institution/Funder/Manager: U Edinburgh/JISC
Project Description: Aims to develop open, online learning materials which reflect best practice in research data management grounded in three disciplinary contexts: social science, clinical psychology, and geoscience. The resulting materials will be embedded in three participating postgraduate programmes and made available through the Transkills programme for use by all postgraduate and early career researchers as well as made available generally through an open license. In addition to web-based 'chapters' that students can work through at their own pace, the course will include video interviews with leading academics about data management challenges, and practical exercises in handling data in four software analysis environments: SPSS, NVivo, R and ArcGIS.
Area/Discipline: Social and political science, Geoscience, Clinical psychology

Project name: SageCite: Citing network models of disease and associated data
Institution/Funder/Manager: UKOLN, U Manchester, British Library, JISC
Project Description: SageCite will develop and test a Citation Framework linking data, methods and publications. The domain of bio-informatics provides a case study, and the project builds on existing infrastructure and tools. Citations of complex network models of disease and associated data will be embedded in leading publications, exploring issues around the citation of data including the compound nature of datasets, description standards and identifiers.
Area/Discipline: Bioinformatics

Project name: ShareGeo Open
Institution/Funder/Manager: EDINA, JISC
Project Description: ShareGeo Open is a spatial data repository that promotes data sharing between creators and users of geospatial data
Area/Discipline: Geography

Project name: SPQR: supporting productive queries for research
Institution/Funder/Manager: KCL, U Edinburgh, Humboldt U Berlin, JISC
Project Description: The overall aim is to investigate the potential of linked data for integrating datasets related to classical antiquity, in particular addressing the particular challenges raised by our material – its incompleteness, uncertainty and fuzziness. We will achieve this by developing mechanisms for breaking data out of silos and exposing it as linked data, using standard ontologies, and in particular the Europeana Data Model, as the semantic “glue” for linking data into a wider network of knowledge. The ultimate objective will be to create a common corpus or “RDF warehouse” of linked Classics data that can be explored, searched and enhanced by further annotations.
Area/Discipline: Classics, Epigraphy and Archaeology

Project name: SUDAMIH
Institution/Funder/Manager: University of Oxford, JISC
Project Description: Supporting data management infrastructure for the Humanities
Area/Discipline: Humanities

Project name: TARDIS
Institution/Funder/Manager: Monash University, Australian National Data Service (ANDS), University of Sidney and some other Australian institutions
Project Description: TARDIS is a multi-institutional collaborative venture that aims to facilitate the archiving and sharing of raw X-ray diffraction images (collectively known as a 'dataset') from the protein crystallography community.
Area/Discipline: Crystallography

Project name: VAMDC Project: Virtual Atomic and Molecular Data Centre
Institution/Funder/Manager: EU, CNRS, CMSUC, UCL, OU, UNIVIE, UU, KOLN, INAF, QUB, AOB, ISRAN, RFNC-VNIITF, IAO, IVIC, INASAN
Project Description: VAMDC aims at building an interoperable e-Infrastructure for the exchange of atomic and molecular data. It embraces on the one hand scientists from a wide spectrum of disciplines in atomic and molecular (AM) Physics with a strong coupling to the users of their AM data (astrochemistry, atmospheric physics, plasmas) and on the other hand scientists and engineers from the ICT community used to deal with deploying interoperable e-infrastructure.
Area/Discipline: Astrophysics

Project name: WissGrid: Grid for Science
Institution/Funder/Manager: DFG, U Göttingen, Astrophysikalisches Institut (AIP), Alfred-Wegener-Institut (AWI), Deutsches Elektronen Synchrotron (DESY), Deutsches Klimarechenzentrum GmbH (DKRZ), Konrad-Zuse-Zentrum für Informationstechnik (ZIB), Universitätsmedizin Göttingen (UMG), Niedersächsische Staats- und Universitätsbibliothek (SUB), Technische U Dortmund (UDO), U Heidelberg, U Trier, U Wuppertal
Project Description: WissGrid’s objective is to establish long-term organisational and technical D-Grid structures for the academic world. WissGrid combines the heterogeneous needs from a variety of scientific disciplines and develops concepts for the long-term sustainable use of the organisational and technical grid infrastructure. In this context, the project aims to strengthen the organisational cooperation of scientists in the grid and to lower the entry barriers for new community grids.
Area/Discipline: Astrophysics, High Energy Physics, Climate Research, Medicine

Project name: XYZ Project
Institution/Funder/Manager: U Cambridge/IUCr/BioMed Central/Open Knowledge Foundation, JISC
Project Description: The XYZ Project will create a demonstrator of a new workflow for publishing data in support of full-text. The author prepares data for publication (if possible with validation) in a third-party trusted repository before the paper is submitted to a publisher. Our software will manage the deposition, release to reviewers, dis-embargo and for conventional publication or as a data journal
Area/Discipline: Crystallography

Besides this preliminary set of discipline-specific research data-related running projects -to be shortly enriched by Sonex with a complementary list of general purpose projects dealing with research data management- a thorough list of open data repositories for all areas may be found at the data repository section of the Open Access Directory (OAD).

SONEX and Research Data: new deposit usecase scenarios

A SONEX meeting was held last Sat Nov 20th at JISC Office in Brettenham House, London. The meeting was intented to produce some feedback on the RFC version of the DL.org Technology and Methodology Digital Library Cookbook. SONEX feedback on featured interoperability solutions was mainly focused on enhancing the Sword protocol description in the Cookbook as to cover functionality updates in the new version of Sword.

Richard Jones (SONEX-Symplectic), Balviar Notay (JISC manager for SONEX) and Pablo de Castro (SONEX-Carlos III Univ Madrid) at SONEX meeting in Brettenham House

The second half of the SONEX meeting was devoted to preliminary analysis of deposit into Open Access repositories of raw research data produced either as specific research output or as supplementary material of research publications. Raw data as a further SONEX usecase deposit scenario was already included in the list of issues for the SONEX Bird-of-Feather session held at the Open Repositories Wokshop (OR2010) last July in Madrid, where it was identified as 'the missing piece in the general deposit picture' at the time.

Some deposit-related projects are already running since Jul 2010 along the JISC Deposit Call (JISCdepo), but none of them so far is dealing with deposit of research data. However, dataset handling is already being considered as a forthcoming candidate for Sword-based transfer, and preliminary analysis of this new deposit usecase scenario may well be partially carried out under the SONEX umbrella.

Some of the discussed ideas on research data and their deposit via Sword into repositories follow:

- A JISCdepo meeting will be held in early Mar 2011 as an internal coordination event for JISC Deposit Call projects. It's a good opportunity for SONEX to fine-tune analysis of usecase scenarios at running projects, as well as for sharing potential new deposit usecases arising both from the Kultivate project (digital versions of creative works ie non-textual materials) and the research data-based approach.

- Regarding deposit of research data into repositories, the DRYAD international repository of data underlying peer-reviewed articles in the basic and applied biosciences was highlighted as a pioneering implementation of infrastructure for research data filing and preservation. DRYAD acts as a kind of PubMed Central for research data – with an equivalent mandate by a group of 50 journals (so far) to their authors for depositing publication-related research data into this specific repository (besides archiving them in their IR or with the publisher).

- The JISC-funded DRYAD UK project was also discussed. DRYAD UK, currently being developed within the JISC Managing Research Data (JISCMRD) programme, is planning to expand Dryad into the UK by both establishing a UK mirror site and extending service to new publishers and disciplines.

- A JISC Managing Research Data Programme (JISCMRD) International Workshop will be held in Mar 2011 for analysis and evaluation of outputs and progress of the JISCMRD Programme. There will be a place in the Workshop programme for issues related to research data, such as citation, deposit and metadata/identifier exchange with publishers. SONEX is expected to bring in some input into some of those subjects.

- Regarding creation of research data management infrastructure for collection, digital organization, metadata annotation and controlled sharing of datasets, the ADMIRAL project (A Data Management Infrastructure for Research Across the Life sciences) was identified as the main presently running initiative to be followed. DataPac, an idea for a standard data shipping container for submitting research data with identifier and other information in RDF and HTML formats, was mentioned too as a potential complementary infrastructure to ADMIRAL.


In terms of SONEX deposit usecase analysis, deposit of research data poses a double usecase framework,

• R2R usecase scenario (IR to DRYAD, other)


• Publisher to repository usecase scenario

as well as a set of Sword-related procedural issues to be checked from a SONEX perspective, such as:

• metadata-related issues – very case-specific and different from metadata standards being used for research papers (previous work on the subject done by JISCMRD MRDonto Group: “Metadata for Datasets: Identifiers and Ontologies”)


• SONEX should definitely NOT get into identification schemas for datasets – DOIs should do for identification purposes


• issue of attached file sizes – should deposit by reference be considered instead/besides binary data transfer?


• At what point along the publication lifecycle should dataset deposit take place? Picturing the process via workflow diagrams would help


• How should Sword deal with this particular deposit usecase?

Some interesting examples of international initiatives dealing with dataset management are also being examined by SONEX, such as:

- PANGAEA [Germany]: Publishing Network for Geoscientific & Environmental Data, see example dataset with attached DOI

- [Dutch] NARCIS (National Academic Research and Collaborations Information System) FAQ page contains info on handling datasets.


Further references on submission of research data to repositories:

• Research Remix blog, by Heather Piwowar


• JISC XYZ project for publishing data in support of full-text


• "A Scientist and the Web": Peter Murray-Rust's blog - Archive for the 'data' Category


• "SPARC Digital Repositories meeting includes session on open data" (blog post at IASSIST website, 2010/11/10)


• 'Embedding Institutional Data Curation Services in Research' (EIDCSR) project blog


• 6th International Data Curation Conference (Chicago, IL, Dec 6-8th, 2010) - Programme


• "Riding the Wave: How Europe can gain from the rising tide of scientific data": Final Report of the High Level Expert Group on Scientific Data: a submission to the European Commission (Oct 2010)
  

RepoFringe 2010: lots of interesting presentations plus a Sonex Pecha Kucha

The 3rd edition of the Repository Fringe was just held in Edinburgh along Sep 2nd and 3rd 2010. This new edition of the RepoFringe (see programme) was a good opportunity to learn about the most recent advancements regarding repositories in the UK, and new ideas for their development were shared in an informal, stimulating atmosphere. This edition's success story was undoubtedly EPrints Bazaar app-store for its new version 3.2, as live demoed by David Tarrant and Patrick McSweeney, with Les Carr's cooperation as an inspired pre-recorded speaker. EPrints will also shortly release its CERIF4REF plugin in order to comply with the R4R schema, thus proving that repository software is swiftly progressing towards anticipating user needs by closing the gap with CRIS systems from a research output perspective.

Further talks were also held at RF2010 on CRIS systems and IRs. A lot of universities do already have CRIS systems running, and some voices in the community start wondering whether CRIS systems might eventually replace institutional repositories as an "entrance door" to the institutional research output. Projects like RePosit (see Queen Mary University of London Sara Molloy's presentation for more info) on the contrary are exploring ways for batch ingestion of contents flowing from CRIS systems into a currently low-populated array of repositories.

Quite a number of other subjects were amusingly dealt with by other speakers, such as timestamping the web through the Memento project as presented by Herbert van de Sompel (LANL), Topic Models by Michael Fourman (University of Edinburgh Informatics Dept), or Repositories and data at Closing Keynote by Kevin Ashley (DCC).

RF2010 had also its traditional 20-slide-20-secs-per-slide Pecha Kucha sessions once again. There was a Pecha Kucha on the work by Sonex on Fri Sep 3rd, and projects like Enlighten, Jorum, Open Access Repository Junction, ERA, ShareGeo and some others were represented at this light speed presentation variety as well.


On Sep 1st a SHERPA RoMEO API workshop was also held by Peter Millington, Jane H. Smith and colleagues from Nottingham at the e-Science Institute facilities in Edinburgh as a RepoFringe pre-event. As presented last July at Open Repositories Conference in Madrid, major improvements in the RoMEO service are being worked at, and this workshop was an opportunity to get feedback from the RoMEO API users on its performance and suggestions on possible enhancements for version 3 currently in its final stages of development (due Autumn 2010). There were also interesting presentations from outside the UK on the implementation of RoMEO mirrors such as SHERPA RoMEO deutsch in Germany and service internationalisation was extensively discussed along the meeting (Portugal and Spain were scoped as potential areas for development of specific interfaces). An online survey on the RoMEO API was previously distributed among the workshop delegates and its results were discussed and analysed in fruitful specific breakout sessions.

From a Sonex perspective, the RoMEO service does fit into the Sonex proposal for a distributed national- or regional-level automatic ingest system based on an array of brokers dealing with publisher- or funder-driven ingest of contents into a network of national or regional institutional repositories. From this point of view, RoMEO, such as other general-purpose services as OpenDOAR or the broker itself, are pieces of the required infrastructure for this approach to grow real. Find more information about this Sonex proposal in the Sonex paper 'Handling Repository-Related Interoperability Issues: the SONEX Workgroup' to be presented in Glasgow later this month at the 2nd DL.org workshop "Making Digital Libraries interoperable: challenges and approaches".