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.

KULTURising research repositories

  "...I can only add that research for art, craft and design needs a great deal of further research. Once we get used to the idea that we don't need to be scared of 'research' - or in some way protected from it - the debate can really begin."
(Christopher Frayling, RCA Rector (1996-2010), from: "Research in Art and Design" (Royal College of Art Research Papers, Vol 1, No 1, 1993/4). Royal College of Art, London).


  On the Jul 6th meeting at JISC Brettenham House some planning was done as well for Sonex extension besides Swordv2's. In the framework of this project extension, Sonex is expected inter alia to further support the JISC Deposit Projects and continue to gather international deposit use cases, as well as to provide some
recommendations on how to improve deposit.

As part of this further involvement with JISC Deposit Projects, Sonex was attending the Kultivate Project Conference on Jul 15th at the Royal Institute of British Architects (RIBA).


Based at the Visual Arts Data Service (VADS), a research centre at the University for the Creative Arts, and funded by the JISC from late November 2010 to the end of July 2011 within the JISC Deposit strand, the Kultivate Project aims to "share and support the application of best practice in the development of institutional repositories that are appropriate to the specific needs and behaviours of creative and visual arts researchers". Kultivate builds upon the knowledge and experience of the Kultur II group, which grew out of the JISC funded Kultur project (2007-2009). The Group currently consists of over forty institutions and projects and is led by the VADS.

Specific goals of the Kultivate project are:

- to increase the rate of arts research deposit,
- to enhance the user experience for researchers, and
- to develop and sustain a sector-wide community of shared best practice in arts research repositories.

There are significant differences between Kultivate and the rest of the JISCdepo projects (RePosit, DURA and DepositMO) in the sense that while the three other ones deal specifically with semi-automation of widely-recognised content ingest into repositories (mainly by fostering platform interoperability), Kultivate seeks
to extend the coverage of institutional repositories to the creative arts environment, which is both rather different in nature to the mentioned well-accepted research and which hasn't been specifically addressed so far as scholarly output. In this regard, Kultivate can be both seen as sort of an outlier project and as the most challenging of them four.


After eight months of hard work, the Kultivate Project Conference put together a model set of talks and presentations (see programme and updated presentations) to introduce the project outcomes.

Several talks made introductory reflections on what creative arts research should be - with its specific peculiarities. The fact that the output from activities in the creative arts is or is not called research (artists themselves sound a bit surprised sometimes on being called researchers) doesn't seem that relevant anyway - main thing actually being it's scholarly output from many HEIs and Arts Schools, and as such it should be subject to standard deposit into institutional repositories.

However, it is often hard to persuade artists to have their work filed into repositories ("the repo doesn't fit the needs of creative artists" a frequent allegation for not taking part in the project). In this regard, advocacy is particularly critical for institutional projects being carried out in the area - they are breaking through in a discipline where no such thing could possibly exist (so far) as PubMed, Chemical Abstracts or arXiv.

See examples of effective advocacy under the Kultivate project umbrella at Goldsmiths Research Online and UAL Research Online, plus the own Kultivate Advocacy Toolkit, one of the project's main outputs.

Another relevant progress Kultivate is promoting is the setting of metadata standards for description of creative artworks (something that incidentally brings the project closer to the data management strand rather that to the deposit one, making it a quite heterodox one). See for instance 'The listening room' item at UAL Research Online with its four-tabbed description including metadata as well as images and videos (and thus effectively delivering an answer to frequent artists complain on work documentation: "I did a performance, not a video" or "Fine, but where am I?").


Performance Art Data Structure (PADS), for which the unit subject to description is the 'work' not the 'digital object', is yet another solution for complex description of creative arts output developed by the University of Bristol within the JISC-funded CAiRO Project for Complex Archive Ingest for Repository Objects (see example of PADS example record for 'Becoming snail' performance by Paul Hurley at JISC Digital Media).
PADS is also involved in the Europeana attempt to standardise perfomance metadata accross the EU.

Finally, a good (and growing) number of EPrints-based implementations of the Kultur enhancements for designing creative arts output-focussed institutional repositories were presented at the project conference (incidentally arising questions by DSpace-based IR managers on when something similar will be developed for DuraSpace). Kultivate has also provided (in cooperation with the University of Southampton team) a set of technical enhancements to the EPrints platform, among them on the MePrints application and the IRStats package.


Implementation of those enhancements by different institutions (either arts-focussed or general purposed ones with Arts Departments within them) is giving way to a wave of repository KULTURisation (ie being adapted to deal with creative arts output) across the UK that might well spread beyond that once working standards are consolidated. In the meantime the VADS-lead eNova project is already building upon the outputs of both Kultivate and Kultur projects.

"On such a full sea are we now afloat"

Such quotation -from W. Shakespeare's 'Julius Caesar'- closed Drs. Eefke Smit's talk "Taking the Current when it Serves: Research Data from the Publisher's Perspective" she delivered along 'Academic Publishing in Europe': the APE 2011 conference, held at the Berlin-Brandenburg Academy of Sciences in Berlin, Jan 11-12th, 2011.


Aiming to gather some facts for its ongoing analysis on research data management and its deposit into repositories, Sonex just attended APE2011, a meeting for the publishing industry and its environment held yearly in Berlin since 2006. The conference organisers do regularly publish a brief official report shortly after the event celebration (reports on previous APE editions
available here, report on this edition due shortly).

This particular visit to Berlin offered the chance to attend yet another event besides APE2011: the SOAP Symposium. Final report by the SOAP (Study of Open Access Publishing) project survey was presented along this one-day meeting, held on Jan 13th in the Goethe Room of the renowned Harnack-Haus in Berlin. The SOAP project describes and analyses the open access publishing landscape as well as exploring the risks and opportunities of the transition to open access publishing for libraries, publishers and funding agencies - see preliminary survey results, final report will be available as of next March.

The conference programme for APE2011, entitled "Smarter Publishing in the New Decade", included promising topics such as evolution of peer-review and ways to improve it, the so-called data deluge, business opportunities in China and how Open Access is becoming increasingly mainstream within the publishing environment. Discussions on those matters were lively both at round tables and at lunch pauses. Sonex interest being mainly on research data management, this report will subsequently focus on presentations and debates on the subject.

On Tuesday Jan 11th afternoon, a session was held on “The Data Deluge: to Drown or to Swim?”, chaired by Bob M. Campbell. Herbert Gruttenmaier, INIST-CNRS, started his presentation "Helping to Ride: a look at data sharing and access policies" by reminding that, since we were in Berlin, the definition of an Open Access Contribution on page 1 of the Berlin Declaration on Open Access to Knowledge includes “raw data and metadata”. Some highlights from his talk were:

• There is a large number of Data Sharing Policies being defined by administrations, institutions, funding agencies and publishers themselves under the guideline "data should be made as freely and widely available as possible". See for instance NSF’s requirement for submission of data management plans of May 10th, 2010, under general policy statement “Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants”.
  Or the very recent (Jan 10th, 2011) commitment by a group of major international funders of public health research to “work together to increase the availability of data emerging from our funded research, in order to accelerate advances in public health”.
  


• Publishers such as BioMed Central were featured as high-profile supporters of Open Data (see Dec 11th, 2010 post at this blog), and NPG editorial policy on dataset sharing was specifically mentioned along the talk, as well as the Brussels Declaration on STM Publishing statement that “Raw research data should be made freely available to all researchers”. Finally, discipline-based data policies such as PaN-Data Scientific data Policy Draft for Scientific Data Management Framework at European Photon and Neutron Facilities or the Joint Data Archiving Policy (JDAP) adopted in a coordinated fashion by Dryad partner journals.
  


• Not everything is that simple though: the Nov 2009 "Patterns of information use and exchange: case studies of researchers in the life sciences” RIN report shows that researchers are not so eager to share their data with others, and that ‘one-size-fits-all’ information and data sharing policies may not achieve the goals there are aiming for, namely scientifically productive and cost-efficient information use in life sciences.
  

Drs. Eefke Smit, International Association of STM Publishers, provided a counterexample for these growing data sharing policies by publishers along her talk on "Research Data from the Publisher's Perspective" by describing the Journal of Neuroscience policy of no longer taking supplementary material from authors since Nov 1st, 2010, the procedure posing too heavy a burden on paper reviewers.
She also warned of the so-called data deluge, according to which tera- and petabite sized datasets will increase their share in research projects in upcoming years.
However, when researchers are asked where they would like to submit their research data, the answer is more often than not "publishers". This brings along the issue of research data preservation: results of an internal survey by STM Publishers show what she called “an improvable situation” with regard to preservation.

Planned talk “Data Publishing in the Context of the ICSU World Data System” by Dr. Michael Diepenbroek, Director of WDC-MARE/PANGAEA, University of Bremen, went finally off the conference programme. However, the next speaker, Dr. Jan Brasse, Managing Director of DataCite, provided some information on the progress of one of the main databases for research data in the geosciences area, by for instance stating there was “a wide cooperation between Elsevier and PANGAEA via DOI-based external links from online papers” at the former’s platforms. This kind of cooperation between publishers and international databases for handling research data might be useful for tacking the abovementioned data preservation issues.
Dr. Brasse, affiliated with the German National Library of Science and Technology Hannover, described as well the evolution of the DataCite international project as it gets carried out by local member institutions: as of Dec’10, over 1M records are already registered with DOI names at datacite.org. Perspectives for the project include setting up of a Central Metadata Base as of Jun'11; DataCite becoming a harvest point for third parties such as WoS; and cooperation via CrossRef for data-article lookup.

The data management session ended with the talk on “Managing Publication and Research Data: the eSciDoc Research Infrastructure” by Dr. Malte Dreyer from Max Planck Digital Library (MPDL). eSciDoc is as a joint project of the Max Planck Society and FIZ Karlsruhe, funded by the Federal Ministry of Education and Research (BMBF), with the aim to realize a next-generation platform for communication and publication in research organization. Further eSciDoc projects mentioned along the presentation and dealing with research data management were ‘Astronomer‘s Workbench’ (astronomy), Lifecycle Logger (biochemistry) and BW-eSci(T) for computational linguistics. DARIAH (Digital Research Infrastructure for the Arts and Humanities) –in whose development eSciDoc is directly involved- and CLARIN (Common Language Resources and Technology Infrastructure) projects were repeatedly highlighted along the session as leading EU projects on development of digital research infrastructure (including data management) for the Humanities and Social Sciences.


A joint panel discussion was then held after the presentations on research data management, with speakers taking questions from the floor. Alicia Wise, Elsevier Director of Universal Access and former archaeologist raised the issue of costs attached to research data management and who should fund them: it was agreed by the panellists that national funding bodies should assume the cost of data management. Along her question Dr. Wise incidentally mentioned that data management at the archaeological research project she used to work for succeeded only thanks to researchers dedicating 50% of their time to data curation. This aspect of dataset deposit will be examined by Sonex in order to identify alternative (automatic) curation procedures currently being used to relieve researchers of the data curation burden.

The data management issues extended well outside the session specifically devoted to them and into the Innovation session held next day, where Portland Press Adam Marshall presentation on the Semantic Biochemical Journal and Project Utopia at the Manchester School of Computer Science did extensively deal with data handling (see “Calling International Rescue: knowledge lost in literature and data landslide!” at Biochem J. (2009) 424, 317–333 for a review on “how to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it”).

At the end of the data session panel discussion Dr. Eefke Smit synthesized the three challenges of research data management: normalization, standardization and migration. She did also remind the audience of verses following the one quoted in the title of this post:

(…) On such a full sea are we now afloat,
And we must take the current when it serves,
Or lose our ventures.

Sonex at the "Digital Library Research and Open Access: Interoperability Strategies" workshop

After delivering its paper "Handling repository-related interoperability issues" last Sep at the 2nd DL.org workshop in Glasgow, Sonex will be contributing a presentation at the forthcoming DL.org "Digital Library Research and Open Access: Interoperability Strategies" one-day event to be held at the British Academy in London next Feb 4th.









Sonex contribution will be part of this DL.org workshop dealing with digital libraries, Open Access repositories and interoperability among them. Already available conference programme includes presentations on DL. org reference model, DL.org policy and quality interoperability survey, degree of progress of Open Access repositories with regard to interoperability issues in the UK and Europe and research data library management among others.

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)
  

Sonex presentation at the 2nd DL.org workshop on Digital Library Interoperability

(picture by: Anna Nika, University of Athens)

The paper 'Handling Repository-Related Interoperability Issues: The Sonex Workgroup' was presented last week at the 2nd DL.org workshop held in Glasgow in conjunction with the 14th European Conference on Digital Libraries (ECDL2010, Sep 6-10, 2010). The DL.org workshop was scheduled under title "Making Digital Libraries Interoperable: Challenges and Approaches" and it featured several presentations by DL.org working groups on the DL Reference Model, such as DL content, functionality, users, architecture, quality & policy (see programme). An invited talk by MS Research Alex Wade, "Digital Library Interoperability: An Industrial Perspective", was also held, where most recent MS developments in the area of DL interoperability were summarized (Zentity, Article Authoring Add-in for Word, DepositMO Project, MS Academic Search or the WorldWide Telescope among others).

The Sonex presentation was delivered on Fri Sep 9th by Peter Burnhill and Pablo de Castro along the workshop's Day I. Sonex approach to interoperability being quite pragmatic in scope, it fitted in well alongside DL.org's more theoretical-founded model. Complementary approaches by both initiatives may in fact offer perspectives for further collaboration between them after this DL.org workshop.

Sonex objectives and development

The Repository Handshake/SONEX objective was firstly to identify and analyse deposit opportunities (use cases), which map on to different business processes from which there is prospect of prompting and assisting deposit of research papers (and potentially other scholarly work) into the repository space. These include processes within the repository space to alert and assist transfer/access across multiple repositories (in the use case of multiple Institutional Repositories). An incomplete list of other deposit opportunities include: institutionally-assisted deposit (typically from CRIS systems but also research group activity); grant-funded mandated deposit, with requirement for award referencing; deposit from publishers as OA services for authors; assisted deposit as part of desktop authoring applications).

Once a complete use case list was obtained, the work was to be focused on identificating the most interesting deposit opportunities in terms of populating repositories. This analysis should result in proposals for cooperative development and for implementation possibilities.

The following key use case scenarios were identified and associated with projects being already developed (or to be developed) by the institutions taking part in the workgroup. Participation in the use case development and implementation is open as well for other interested institutions:

• Use case nr 1, PI/author for multi-authored, multi-institution journal articles - related to Open Access Repository Junction (OA-RJ) Project at EDINA

• Use-case nr 2, CRIS systems as source of documents for IRs - KE's strand 'Exchanging Research Info'. There are also several ongoing institutional initiatives for CRIS/IR integration, such as those at the University of Glasgow or the Trinity College Dublin

• Use-case nr 3, Publisher as the source of articles - also related to the EDINA-JISC OA-RJ Project, as well as to European PEER Project

• Use-case nr 4, 'Our Bibliography' as source of references for IRs, meaning lists of publications supplied by individual researchers, research groups or departments

• [Potential extra] Use-cases nr 5 (Subject repositories) and 6 (Research evaluation agencies).

See a brief summary of the four main SONEX use cases/deposit opportunities at: http://repinf.pbworks.com/f/poster_SONEX_deposit_opportunities.pdf