Research Data Management
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Updated session delivered by Dr Sebastian Palucha (2014 slides). See also http://www.slideshare.net/bissetjm/2013-11-08cardrdmpresentationv11
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Research Data Management
- 1. Publishing your Research Research Data Management for PGRs Sebastian Pałucha Research Data Manager sebastian.palucha@durham.ac.uk
- 2. Session outline - Slides and demonstrations - http://bit.ly/durdm14 - What... is “Research Data”? - Small group activity - What... is “Research Data Management” ? - Data life cycle - Why... Is Research Data Management important? - Drivers for change, Requirements on & benefits for researchers - How... to manage and secure research data - Data Management Planning. Document storage and back-up - How... To share data - Benefits of sharing data and tools available
- 3. Part 1 What is Research Data?
- 4. What is Research Data? Via Flickr Creative Commons, by © Stuti Sakhalkar. Original available at http://www.flickr.com/photos/theblackcanvas/2945878325/
- 5. Results from experiments Historical Diaries Physical objects .pdf Algorithms Simulation software .rtf Lab & Field notebooks Questionnaires 35mm Interview transcripts .gif .docx Database Government records .xls IX240 Correspondence .xml Test answers Specimens Photographs .spss Models .jpg Methodologies & workflows Film footage
- 6. Research data is … • Diverse • Multi-sourced • Valuable & costly • Sensitive • Massive • Complex • Derivative • Communities based • Driven by information intensive processes
- 7. … information intensive Images CC-by - Patterns of information use and exchange (RIN, 2009)
- 8. Data is situational Ship logbooks : - historical record of events - data to reconstruct weather patterns - data on naval personnel (genealogical / demographic) - extrapolation of data on ration provisions etc.
- 9. Data is situational Data can be used and re-used … ... for purposes you may not have thought of… ... even after you have extracted all the value you need from it.
- 10. Research Data There is no single or simple definition of what constitutes ‘research data’ - it is used to support the production or validation of original research. - it can be ‘born digital’, or it can be analogue (and then digitised) - it is situational... CC nc nd JISC
- 11. Where is your data? Via Flickr Creative Commons, by © Stuti Sakhalkar. Original available at http://www.flickr.com/photos/theblackcanvas/2945878325/
- 12. Where is your data? JISC RDM Survey - Russell Group institutions average over 2PB of data - significant data storage on hard drives internal/external, flash drive, web etc. - 23% of institutions had lost research data - how would this impact you?
- 13. Part 2 What is Research Data Management?
- 14. What is Research Data Management? “ Research data management concerns the organisation of data, from its entry to the research cycle through to the dissemination and archiving of valuable results.” Whyte, A., Tedds, J. (2011). ‘Making the Case for Research Data Management’. DCC Briefing Papers. http://www.dcc.ac.uk/resources/briefing-papers/making-case-rdm
- 15. Data Life-cycle UK Data Archive www.data-archive.ac.uk/create-manage/life-cycle
- 16. Part 3 Why manage research data?
- 17. What are the benefits of managing your data effectively? Via Flickr Creative Commons, by © Stuti Sakhalkar. Original available at http://www.flickr.com/photos/theblackcanvas/2945878325/
- 18. Why manage research data? http://youtu.be/N2zK3sAtr-4
- 19. OECD Data Principles • Promoting Access to Public Research Data for Scientific, Economic and Social Development: – Publicly-funded research data are a public good, produced in the public interest. – Publicly-funded research data should be openly available to the maximum extent possible
- 20. “Organisations … assist researchers in the accurate and efficient collection of data and its storage in a secure and accessible form. Researchers … how data will be gathered, analysed and managed … what form relevant data … made available to others … ”
- 21. ESRC Data Policy • … advocates open access to all research output … available to the scientific community in a timely and responsible manner • … use of existing standards for data management and to make data available for further re-use http://www.esrc.ac.uk/about-esrc/information/data policy.aspx
- 22. … it is a requirement “Publicly funded research data are a public good, produced in the public interest, which should be made openly available with as few restrictions as possible in a timely and responsible manner that does not harm intellectual property.” RCUK Common Principles on Data Policy http://www.rcuk.ac.uk/research/Pages/DataPolicy.aspx
- 23. Durham RDM Policy • Storage and management - Registered creation - Adequate metadata - Backed up • Retention - 3 years or 10 years - Registered disposal • Access - responsible release of data https://www.dur.ac.uk/research.office/research-outputs/ research-data-management/policy/
- 24. … it is a requirement
- 25. … it is good practice
- 26. … boosts your profile “… 10,555 studies … we found that studies that made data available in a public repository received 9% more citations than similar studies for which the data was not made available …” Piowar H. & Vision T. (2013) “Data reuse and the open data citation advantage” PeerJ, http://peerj.com/articles/175/
- 27. … data can be re-used “The best thing to do with your data will be thought of by someone else” Rufus Pollock, co-founder Open Knowledge Foundation • Impact and innovation • Collaboration and teaching The Twitter Archive at the Library of Congress Iris Flower Data Set, Fisher, R.A. 1936 1000 Genomes – A Deep Catalogue of Human genetic Variation • Research integrity - identifying errors Debt and Growth - Reinhart-Rogoff revisited - fraud in research Deception at Duke - Fraud in cancer care
- 28. Why manage research data? • You are increasingly likely to be required to • It is good research practice - to defend your research publications - to secure against loss of data • It boost your citation potential • Your data can be re-used and replicated
- 29. Part 4 How to manage data?
- 30. ESRC data management plan - common themes • Assessment of existing data • Information on new data (i.e. volume, type, format) • Quality assurance of data • Backup and security of data (day to day practices) • Expected difficulties in data sharing (confidentiality, ethics and consent, the FOI and DP acts) • Copyright/intellectual property right (IPR, 3rd copyright, embargoes) • Responsibilities • Preparation of data for sharing and archiving (where, who and when will have access)
- 31. DMP Online tool http://dmponline.dcc.ac.uk
- 32. Who is involved? • PI and CIs (initiate discussion in timely manner) • Research Office (funders requirements) • CIS research support (active and long-term storage, back up) • Librarians / archivist (OA, copyright, metadata standards, curation) • Data Protection and FOI officers (sensitive data) • Technical and laboratory staff (data provenance)
- 33. Keeping track of data
- 34. Organising your data • plan a hierarchy of files and folders, organised by… - type of data (text, image, model, sound, video etc.) - type of research activity (survey, interview etc.) - type of material (documentation, publication, etc.)
- 35. Organising your data • Be systematic and consistent with naming conventions and housekeeping from the start… - files should be sortable by name - filenames should indicate the ‘version’ - filenames should be easily distinguishable
- 36. Thinking about filenames • Names should be clear and descriptive - to both you, and third parties
- 37. Thinking about filenames • Consider including elements in filenames… - Date 2014_01_14 - Project identifier PGCAP - Content description RDM_presentation - Version v1.2 2014_01_14-PGCAP-RDM_presentation-v1.2.pptx CARD/2014_11_13-RDM_presentation-v1.4.pptx
- 38. Thinking about filenames • Pitfalls to avoid - Whitespace - Unsupported characters in filenames - Capitalisation 2014_01_14-PGCAP-RDM_presentation-v1_2.pptx 2014_01_14-pgcap-rdm_presentation-v1_2.pptx
- 39. Thinking about filenames • Discovering the right file when needed
- 40. Keeping track of data
- 41. Data about Data • To keep track of data… • … and to describe what data is available to a secondary user • Spreadsheet? • Lab notebook? - electronic / paper? • Database?
- 42. Data about Data
- 43. Data about Data http://etheses.dur.ac.uk/8472/
- 44. Data about Data
- 45. Metadata • Simple – readme.txt – cover page • Advanced, domain standards - DDI; METS; TEI; QDE
- 46. Data formats
- 47. Data formats • Think about what format you are saving your data in… Prefer this… … over this ASCII (human readable) (.txt, .xml, .csv ) Binary formats (.exe, .doc, ) Open standard .odt .ods Proprietary .docx .xlsx
- 48. Data back-up and security
- 49. Data back-ups • Are you just digitising / photocopying? • Are you saving files into in multiple locations (pendrives, hard drive, external hard drive?) • Tip for Durham Research Students:- - (stevens)(j:) your Durham network drive • Other tools available: – SyncToy,, Time Machine,, Deja Dup
- 50. Data security • Passwords • Do you use passwords >8+ – Password Vault use 128 – 256 – Public Key Encryption (PKI) 1024+ (GPG, GPG4Win, GPGTools) • Virtual Encrypted Drive – TrueCrypt, FileVault
- 51. Data security • Secure Interent Protocols – WiFi: WPA2 but not WEP sd – Browser: HTTPS – Virtual Private Network (VPN) – Secure Shell (SSH) • How to access j: drive of campus – VPN, DU MDS Anywhere
- 52. Part 5 Sharing research data
- 54. UK Data Service http://discovery.ukdataservice.ac.uk
- 55. Sharing your data • Who owns the copyright in the data? • The University owns copyright by default - Can be subject to funders requirements • 3rd party copyright - Database software • Data licensing - Open Data Commons http://opendatacommons.org - Creative Commons https://creativecommons.org - Open Government Licencehttp://data.gov.uk/blog/new-open-government- license
- 56. Creative Commons and Open Data Commons
- 57. How to share data responsibly Information Commissioner’s Office published guides on data security and sharing: • Is the sharing justified? – Benefits and risks • Do you have power to share? – Participant Consents – Intellectual property Rights • Is sharing conditional? – How we will protect data http://ico.org.uk/for_organisations/data_protection/topic_guides/data_sharing http://ico.org.uk/for_organisations/data_protection/topic_guides/anonymisation
- 58. Informed Consent http://www.data-archive.ac.uk/create- CC by sa www.reallifemethods.ac.uk manage/consent-ethics/consent?index=3
- 59. Publishing Data Essential properties: • Identifier; Creator; Title; Publisher; Publication year Optional properties: • Resource type; Version
- 60. Summary Research Data Management good practices Reliable Data Storage preservation Academic Culture
- 61. Managing And Sharing Research Data – A Guide to Good Practice http://ukdataservice.as.uk/manage-data/handbook.aspx
- 62. Inter University Consortium for Political and Social Research http://www.icpsr.umich.edu/icpsrweb/content/deposit/guide/index.html
- 63. • Scientists need to be more open among themselves and with the public and media • Greater recognition needs to be given to the value of data gathering, analysis and communication • Common standards for sharing information are required to make it widely usable • Publishing data in a reusable form to support findings must be mandatory • More experts in managing and supporting the use of digital data are required • New software tools need to be developed to analyse the growing amount of data being gathered
- 64. Open Science “With the right formats, licensing and distribution mechanisms, people can easily collaborate over data, enhance the analysis and re-purpose for their own needs.” Cameron Neylon http://cameronneylon.net/blog/fork-merge-and-crowd-sourcing-data-curation/
- 66. Image Credits [3] Via Flickr Creative Commons, and by Eric Fischer: Available at http://www.flickr.com/photos/24431382@N03/4671562937 [8] Via Flickr Creative Commons, and by L. Whittaker: Available at http://www.flickr.com/photos/7577311@N06/1490557341 [13] Via Flickr Creative Commons, and by FutUndBeidl: Available at http://www.flickr.com/photos/61423903@N06/7369580478 [16] Via Flickr Creative Commons, and by barks photo stream: Available at http://www.flickr.com/photos/49503168860@N01/4257136773
- 67. Image Credits [26] Via Peter Murray-Rust blog: Available at http://blogs.ch.cam.ac.uk/pmr/2011/08/01/why-you-need-a-data-management- plan [30] Via Flickr Creative Commons, and by Darwin Bell: Available at http://www.flickr.com/photos/darwinbell/1454251440/ [57] Via Martin Missfeldt bildersuche.org :Available at http://www.bildersuche.org/en/creative-commons-infographic.php [57] Via foter.com : Available at http://teachthought.com/technology/the-ultimate-visual-guide-to-creative- commons-licensing/
Hinweis der Redaktion
- Version 1.4 delivered 23/06/2014 – This version was targeted for 40 min delivery without practical guidance mostly based on v 1.3 with some small additions, information intensive, RMD force field, example datsets Version ESRC_Futher_Leaders delivered 23/06/2014 – This version was targeted for 20 min delivery. based on v 1.4 re-thinked and graphically redone with plenty of more requirements covered. Particularly tuned to EPSRC requirements, including Opne Scince Theme. Version 1.5 (17/11/2014) based on v 1.4 – This version is targeted for 1:30 min delivery. Will include slides from ver. 1.3 and new practical examples.
- Emphasis: - this session is an introductory, awareness session. - not the aim that you will go away experts - we want you to leave thinking you need to know more and read more - further reading at end of slides - Much of the topics discussed are wider than just your research degree - But many of the principles are applicable to your research degree - He and Paul Drummond in CIS will be looking at developing policy and systems support across the University over the next 3 years, in line with policy directions from the UK and Europe, and you may meet him over that time. - He will also be looking at the need to develop and provide additional training and guidance.
- http://www.flickr.com/photos/26296445@N05/5917135851
- 5 minutes discussion in groups of 3-4 / yell out to front of class
- Different communities do things differently: files, tools, processes
- Colours representing various research/data activities. Cleary we can see tree stages: Top of the graph where data are gathered In the middle is a research process where we analyse all data In the bottom more data are produced All of those data are a subject for RDM. Patterns of information use and exchange: case studies of researchers in the life sciences. A report by the Research Information Network and the British Library November 2009
- There is no single definition, so lets agree some basics... Situational – eg cctv footage (crime prevention, measure of footfall, demographic data) / ships logs (historical record of events, record of weather patterns, personnel lists) / photographs (historical record of objects or locations, a source of data on techniques or chemical processes of photo development)
- There is no single definition, so lets agree some basics... Situational – eg cctv footage (crime prevention, measure of footfall, demographic data) / ships logs (historical record of events, record of weather patterns, personnel lists) / photographs (historical record of objects or locations, a source of data on techniques or chemical processes of photo development) Data are core element of scientific research thus data lifecycle can’t be considered independently from research lifecycle.
- Ask students where they are storing their data? - are they backing it up - what to they plan to do with it once completed? - what if they are asked for it in 7 years time? - if only on one device, what happens if that device is stolen/lost/damaged?
- Ask students where they are storing their data? - are they backing it up - what to they plan to do with it once completed? - what if they are asked for it in 7 years time? - if only on one device, what happens if that device is stolen/lost/damaged?
- Or group the images, pre project, active project, new activities preserving and giving access. Click on image to go through to Data Archive Creating Data: You need to plan ahead. What storage will you require? What formats will the data be in, and how will this be supported? What ethical and legal considerations do you need to take into account in both collecting and storing the data, and then how will this affect your ability to share the data. Processing data: As you digitise, transcribe, translate, anonymise, check and clean the data created or collected, you need to start to put some of you planning into practice: storing data, describing data. Here you might be creating new sets of metadata which will be key to any future re-use: your notebooks, codebooks (if coding qualitative data), recording decisions and workflows applied in cleaning and checking data. Analysing data: Here is the bulk of your actual research, but you will at this point be needing to think about how the data can and should be preserved. For example, when publishing your research you may need to either provide the underpinning data, or indicate if, how and where it can be accessed by a reader– so you may need to be providing access to data from this point Preserving data: The best format for the data for you to use may not be the best format for the data to be preserved for future use. So here you will need to be working with colleagues to ensure the data is stored, and backed-up effectively. To aid retrieval, you will also need to ensure the metatdata and documentation describing the data is robust. And finally, you will need to be thinking about how the preservation of the data will be ongoing. Giving Access to data: This is how and where you provide access to the data, and make clear any copyright issues arising. Re-using data: how is the data then re-used in further research… and the cycle begins again.
- 5 minutes discussion in groups of 3-4...
- http://www.oecd.org/sti/sci-tech/oecdprinciplesandguidelinesforaccesstoresearchdatafrompublicfunding.htm
- UKRIO Code of Practice for Research: Promoting good practice and preventing misconduct - http://www.ukrio.org/wp-content/uploads/UKRIO-Code-of-Practice-for-Research.pdf 3.12.5 Organisations should have in place procedures, resources (including physical space) and administrative support to assist researchers in the accurate and efficient collection of data and its storage in a secure and accessible form. 3.12.6 Researchers should consider how data will be gathered, analysed and managed, and how and in what form relevant data will eventually be made available to others, at an early stage of the design of the project.
- Full text at: http://www.rcuk.ac.uk/research/Pages/DataPolicy.aspx
- The data must be made available for re-use or archiving with the ESRC data service providers within three months of the end of the grant.
- Funders are asking “why do you need to collect new data, it may already exist”
- Data retention 3 years after publication to 10 years since last request The Research Data Management Steering Committee on behalf of UEC is responsible for ensuring the provision of: - training, support and advice for the management of research data - services and procedures enabling the registration, deposit, storage, and curation of research data Researchers are responsible for - planning and documenting a clear research data management plan as part of their application which should include procedures for collection, storage, use, re-use, access, retention and eventual destruction of data - planning for the curation and management of their data after the completion of their project - ensuring that any requirements relating to research data management specified in a research funding contract are met by the research data management plan - ensuring that a copy of the data management plan is registered with the University’s Research Administration System (RAS)
- You also have requirements or moves to recognise the need to manage and share data from other organisations. Mention also that journals (eg in biosciences) may require you to submit data alongside a published article as standard practice. Plose One from 1/02/2014 Authors must provide a Data Availability Statement describing compliance with PLOS’s policy, which will be published with paper. Two key things to summarize about the policy are: The policy does not aim to say anything new about what data types, forms and amounts should be shared. The policy does aim to make transparent where the data can be found, and says that it shouldn’t be just on the authors’ own hard drive.
- What would happened if you lost external hard drive with few years of research data for your PhD? Image from Peter Murray-Rust blog CC-by - http://blogs.ch.cam.ac.uk/pmr/2011/08/01/why-you-need-a-data-management-plan/ http://www.bbc.co.uk/news/uk-scotland-glasgow-west-27556659
- Also “… The citation benefit varied with date of dataset deposition: a citation benefit was most clear for papers published in 2004 and 2005, at about 30%.” However, not normative, the citations for data is an essential component of data publication, sharing and reuse.
- You might be thinking, I don’t want people to find out if I have made a mistake…. Well, you may, and then you can own up and move on. But what you should be more worried about is being able to identify if others have made a mistake and how that might impact on your research. http://www.economist.com/blogs/freeexchange/2013/04/debt-and-growth @rufuspollock Rufus Pollock, 1000 Genomes - is a community resource project that aims to release data rapidly for the benefit of the scientific community. Use of project data for: Global and large-scale analyses Methods development Disease studies Population comparisons Iris Flower – from Machine Learning repository
- I’ll not give you a detailed tips how to manage data day to day. However, I’ll be taking about new requirements DMP. I’m sure that some of you are already contributing to departmental peer reviewer processes. Creating a DMP might be useful way l to share best practices in DM in your subject. Section emphasis only on DMP, specific tips has been removed.
- DCC. (2013). Checklist for a Data Management Plan. v.4.0. Edinburgh: Digital Curation Centre. Available online: http://www.dcc.ac.uk/resources/data-management-plans http://www.dcc.ac.uk/sites/default/files/documents/resource/DMP_Checklist_2013.pdf an explanation of the existing data sources that will be used by the research project with references an analysis of the gaps identified between the currently available and required data for the research - information on the data that will be produced by the research project, including: data volume; data type, eg qualitative or quantitative data; data quality, formats, standards documentation and metadata; methodologies for data collection - planned quality assurance and back-up procedures [security/storage] - plans for management and archiving of collected data - expected difficulties in data sharing, along with and causes and possible measures to overcome these difficulties - explicit mention of consent, confidentiality, anonymisation and other ethical considerations - copyright and intellectual property ownership of the data - responsibilities for data management and curation within research teams at all participating institutions.
- The importance of data management planning https://www.youtube.com/watch?v=PXr14Urf268
- One of the major challenges is communication between academics and other stakeholders RO – RDM pages, a key hub for all RDM activities. Explore RDM resources library You will have (RD) our (CIS) support … invite us to discussion with academics when you will talk on DMP aspects …
- Sortable by name (so date first can be useful) Where version control is important, should be clear in the name. Do not just move to a different folder or name as “draft” or “old” Distinguishable: don’t have files with the same name in different folders, as this could end up causing confusion if files are copies elsewhere or re-used.
- Sortable by name (so date first can be useful) Where version control is important, should be clear in the name. Do not just move to a different folder or name as “draft” or “old” Distinguishable: don’t have files with the same name in different folders, as this could end up causing confusion if files are copies elsewhere or re-used. Organisation; helps facilitate future retrieval Context; helps judge content without opening Consistency; benefits processing growing number of files
- Think labels which helps to retrieve a document later, I might only remember part of the name, but context will help me to judge if this is the file I’m looking for Sortable by name (so date first can be useful) Where version control is important, should be clear in the name. Do not just move to a different folder or name as “draft” or “old” Distinguishable: don’t have files with the same name in different folders, as this could end up causing confusion if files are copies elsewhere or re-used.
- Capitalisation – UNIX capitalisation might distinguish between two entirely different files Searching for r will not find R
- Capitalisation – UNIX capitalisation might distinguish between two entirely different files
- Capitalisation – UNIX capitalisation might distinguish between two entirely different files
- Capitalisation – UNIX capitalisation might distinguish between two entirely different files
- Public link to life evernote https://www.evernote.com/l/AWc0uDrxCLpAdoXuif3f7g7vK75gh2jFhXY
- Introduce Google search concept – keywords phrase Important if sharing the data on a repository. ODIN cover page - http://figshare.com/articles/D2_3_First_year_communication_report_including_results_from_first_year_event/843603 DDI – Data Documentation Initiative METS - Metadata Encoding and Transmission Standard TEI – Text Encoding Initiative QDE – QuDEx – Qualitative Data Exchange
- Examples – Microsoft excel example to use? Older versions? Microsoft works files in earlier versions of Word. Comprehensive list of file formats http://en.wikipedia.org/wiki/List_of_file_formats Example data file formats supported by 3TU Datcentrum - http://datacentrum.3tu.nl/en/what-we-offer/data-archive/#formats or recommended file formats from UK Data Archivum - http://www.data-archive.ac.uk/create-manage/format/formats
- Present keychain Password generator Default system password prompt GPG GPG getting started https://www.gnupg.org/gph/en/manual/c14.html http://www.data-archive.ac.uk/create-manage/storage/encrypt https://fedoraproject.org/wiki/Creating_GPG_Keys
- https://www.dur.ac.uk/cis/services/remote/ https://www.dur.ac.uk/cis/security/
- http://www.flickr.com/photos/26296445@N05/5917135851
- Re3data: registry of research data repositories Databib, another service for locating data repositories. Datacite: service to provide unique DOIs to data sets for citation, but also include a register of data sets and repositories. Linked to Data from Figure 7 from: Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC
- Be aware on copyright constraints. Applying commons license will not take your IPR, people will gain right to freely use and distribute but they must properly attribute you work.
- http://opendatacommons.org https://creativecommons.org/choose/
- Written consent includes and information sheet and a consent form signed by the participant. Part of the EPSRC project to developed new research methods in real life - http://www.reallifemethods.ac.uk Example consents forms http://www.data-archive.ac.uk/create-manage/consent-ethics/consent?index=3 interviews, children participation. An information sheet should cover topics such as: Purpose of the research Benefits and risk Terms for withdrawal Usage of data during project and after Ethical use of data
- Example landing page with citation information http://esds.ac.uk/doi/?sn=6614 Citation obtained from http://crosscite.org/citeproc/
- Different influences -> different plans Broader: country, body of foundation, outcome – commercial or public domain, weather the work is reproducible or not Founder: desirable place for long-term curation, data in certain formats Internal requirements: institutional repositories, self-imposed ethics, softer influences related to disciplinary difference or even personal preferences Publisher: ownership of copyright signed over not compatible with institutional policies Legal: the UK/EU legislation – such as recent Dropbox issue – safe harbour agreements etc Legal: Example with paediatric research, legal requirements to seek consent once children are grown up
- http://www.icpsr.umich.edu/icpsrweb/content/deposit/guide/index.html
- Cover image: The Spanish Cucumber E. Coli. In May 2011, there was an outbreak of a unusual Shiga-Toxin producing strain of E.Coli, beginning in Hamburg in Germany. This has been dubbed the ‘Spanish cucumber’ outbreak because the bacteria were initially thought to have come from cucumbers produced in Spain. … this genome was analysed within weeks because of a global and open effort; data about the strain’s genome sequence were released freely over the internet as soon as they were produced.
- Open Data foster Open Science