Digital Repository of Ireland training on Open Science for the Irish Research Council, April 2019

1. Practicing Open Science
Digital Repository of Ireland
11th April 2019

2. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

3. What is the Digital Repository of Ireland?
● A national data infrastructure
● Humanities, Social Sciences, Arts (research data)
● Long-term digital preservation, access, discovery
● Ireland’s social and cultural record
● Royal Irish Academy, Trinity College Dublin, Maynooth U
● Curated collections; cross-searchable metadata
● Open Access, Open Research
● A certified trusted digital repository (TDR)

5. Why Practice Open Science?

6. What is Open Science?
● Science = all disciplines
● Open Science -- Open Research
● ‘Opening’ the practice of research
● Openness = value
● Research process and outputs as widely accessible
as possible
● Citizen Science
● Link to Research Integrity

7. Source: YERUN

8. Publications Research Data Research Processes
OPENNESS

9. Publications Research Processes
OPENNESS
Research Data

10. Why Practice Open Science?
Better Research & Value
Public funding = public access
Fuller picture of research outputs
Increased visibility
Better ROI
Accelerated research
Collaboration/exchange
Transparency
Reproducibility

11. Risks of not practicing OS
Failure to meet funder mandates
Decreased exposure
Lack of transparency
Changes to research culture
Next-generation metrics

12. Where does DRI fit into this?
National infrastructure for archiving, preserving, and
sharing research data
Significant involvement in the emerging policy
landscape for Open Science

13. Research Data Lifecycle

14. DRI and Open Science Policy
European Open
Science Cloud

15. Open Access Publishing

16. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

17. Open Access publishing
Traditional subscription based
journals publishing
Some OA journals ask for a fee called
Article Processing Charge (APC)
No fees for publishing
2 Who pays for
publishing?
Most often use the Creative Commons
licenses. Publications can be used for a
variety of purposes provided that the
users attribute the work to the authors.
Copyright is usually transferred to the
publisher (the journal). Users need to
request permission to use the work in any
way.
3 Author rights and how
can publications be
used?
No fees for access
Readers / institutions have to pay for
access (pay per article or yearly
subscriptions)
1 Who pays for use?
Understanding Open Access Publishing

18. Gold Route
● access to publications is immediate and free
for anyone to read
● via the Open Access journals (OA native)
Open Access publishing is possible through both
OA journals and traditional subscription based journals
Green Route
● a version of an article or paper
published in a subscription based
journal is available free of charge in a
repository or similar
Routes to Open Access

19. Benefits Open Access
The main objective is to maximise accessibility to your publication /
increase readership
● Extensive scientific knowledge widely and openly available (vs
readers having to pay for access to scientific knowledge)
● Authors can maximise readership and maintain rights to their
work (vs authors have a smaller audience and are forced to
relinquish the rights associated to their work)
● Open access and re-use allows others to build upon your work and
helps avoid duplication

20. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

21. Identifying Open Access journals
Short hands-on exercise: (15min)
Identify 2 Open Access publishing journals in your specific
discipline using
DOAJ https://doaj.org & SHERPA RoMEO http://sherpa.mimas.ac.uk/romeo/
One as an example of the gold route to OA and one as an example
of the green route
Based on the information available review their publishing
policies, costs, use and rights policies

22. Summary and links
Open Access = Free to read + Free to use
Open Access publishing is highly recommended and often is an
eligible cost to be included in the grant application
Resources
DOAJ https://doaj.org (Directory of Open Access Journals)
SHERPA RoMEO http://sherpa.mimas.ac.uk/romeo/ (Analysis of the
publisher Open Access policies)

23. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

24. Research Data Management

25. What is Research Data?
Research data is the data that is gathered, generated or used as part of
the research process

26. What is Research Data Management?
Research Data Management is the term used to refer to the process
of organising, storing, using, preserving and sharing Research Data.
It is an active process of managing the data that forms the inputs to
and outputs of your research, over the lifetime of a research
project, and beyond.
Research Data Management ensures that you can keep track of,
and effectively use your own data, but also that other researchers
will have the opportunity to find and use your data to reproduce
your results or undertake further research.

27. The Research Data Lifecycle

28. RDM Lifecycle: Plan and Create
Creating and/or collecting data is not necessarily the beginning of the
Research Data Lifecycle.
The Research Data Lifecycle actually begins with planning. This
planning should take place as early as possible in the research process,
and is often required by funders when making a funding application.
The plan is called a Data Management Plan and we will look at these in
more detail shortly.

29. RDM Lifecycle:
Document, Use and Store
When performing research you will be using and creating a lot of
Research Data. To make sure that you can effectively use this data you
need to think about
● Annotating / documenting the data
● Analysis, versioning of data and results
● Storage and Backup

30. RDM Lifecycle: Share and Preserve
The final stages in the Research Data Lifecycle are to share your data
(not just publications) and to ensure the long-term shareability of your
data
To do this, you must think beyond the short-term storage solutions
that you used while performing the research and think about
depositing your data in a widely-used Data Repository where it will
benefit from FAIR access and long-term preservation

31. FAIR Data
Findable
Accessible
Interoperable
Reusable

32. Preservation & Sustained Sharing
FAIR data is shareable data, but long-term Preservation is required to
ensure sustained sharing.
It is not enough to back up your data and make it accessible online
● What happens if the website hosting your data is no longer
accessible?
● What happens if the file format you used for your data is no longer
supported by modern software?
● What happens if the back up files become corrupt and cannot be
opened?

33. Trusted Digital Repositories
The Data Life Cycle is a process which continues after your research is
complete.
A Trusted Digital Repository is a Repository which is certified as
trustworthy because it has procedures in place to carry on the Data Life
Cycle process for your data.

34. Trusted Digital Repositories
There are two main
certification frameworks
● CoreTrustSeal
● ISO 16363

36. Summary
Research data is all of the inputs and outputs to your research as well as
the analyses and processes carried out on that data
Research Data Management is the process of looking after your data
during the Research Data Lifecycle and beyond
FAIR Data is Findable, Accessible, Interoperable and Reusable
Trusted Digital Repositories can ensure that your data will continue to
be managed after your research is complete, and that they will be
accessible for the long term

37. Useful links / Resources
FAIRsharing https://fairsharing.org/ A curated, informative and educational resource on
data and metadata standards, inter-related to databases and data policies.
DRI Guide to Research Data: http://dri.ie/research-data-management-plans
UCD Library Research Data Management Guide: http://libguides.ucd.ie/data
DRI Blog: Why storage is not preservation: https://www.dri.ie/why-storage-not-
preservation-conversation-surrounded-conservation
Digital Object Identifier (DOI) site https://www.doi.org/
CoreTrustSeal https://www.coretrustseal.org/
ISO 16363 http://www.iso16363.org/

38. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

39. Data Management Planning

40. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

41. Guide to Data Management Plans
- Steps include:
- Organising and documenting your data
- Processing your data
- Storing your data
- Protecting your data
Examples: Data Curation Centre step-by-step DMPs

42. Why Data Management Plans?
•Makes data available to support the findings of the research
•Provides proper attribution to those who contributed to the creation of the
data;
•Makes data accessible in a reusable form that will facilitate secondary usage;
•Helps store data securely during the active phase of the research project;
•Helps preserve data in the long-term when the project has ended;
•Is compliant with the requirements of research funders

43. Steps of a DMP
•Organising and documenting data
- Consistent file naming
- Non-proprietary formats
- Project documentation e.g. research questions, methodologies
- Metadata - descriptive, technical etc

44. Steps of a DMP
•Processing data
- Consistent versioning of files, existence of a ‘master file’
- Interoperability e.g. assigning unique identifiers, supporting
citation

45. Steps of a DMP
•Storing data
- Storage and backups - 3 locations rule
- Costing storage e.g. cost of external drives or institutional storage
- Scheduled backups
- Security - anonymisation when needed, clarity in restricted data
agreements

46. Steps of a DMP
•Protecting data
- Liaising with institution ethics offices
- Informed consent in advance of fieldwork
- Agreements for ethical use and reuse
- Clarity in intellectual property rights / copyright

47. Steps of a DMP
•Preserving data
- Planning for storage and access after project ends
- Appraisal of what needs to be kept and what should be destroyed
- Making sure repository has PIDs
- Awareness of any data embargoes (e.g. social science data)
- Levels of access to data

48. How to make a DMP
Templates are the easiest way to create a DMP
Digital Curation Centre has several downloadable templates as part of their
DMPonline tool.
Anyone can set up an account and practice.
Link and walkthrough https://dmponline.dcc.ac.uk/
https://dmponline.dcc.ac.uk/plans/new

49. Useful links
Guide to using DCC DMPonline tool:
http://libguides.ucd.ie/ld.php?content_id=31601339
Research Data and DRI: http://dri.ie/research-data-management-plans
UCD Research Data Management Portal https://libguides.ucd.ie/data
University of Edinburgh Research Data Support Service:
https://www.ed.ac.uk/information-services/research-support/research-data-service

50. Metadata

51. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

52. Metadata is data about data
It can take many forms:
Descriptive, structural, technical, administrative, use
Equally as important as what you collect, is when you collect

53. Metadata collection starts with data creation

54. Image courtesy of the University of Virginia Library.

55. What do you need to collect?
● Metadata is the structured information that allows you to find, retrieve and
re-use another resource (the dataset)
● At a minimum you need to record who created the dataset, when it was
created or published, and give it title or descriptive name
● The formats and notation of your metadata will vary based on your
discipline, but it will usually fall into particular categories.

56. Categories of Metadata
● Descriptive: describes the intellectual content of the resource, through an
accepted standard e.g. Dublin Core
● Structural: Provides information about the internal structure of the dataset
● Technical: information about filetypes, software and hardware which
render a digital object
● Administrative: manages property rights, version control and alteration of
the data and metadata itself
● Use metadata: manages access controls and licenses, determines re-usability
● Preservation: documents actions undertaken to preserve a resource

60. Categories of Metadata
● Descriptive: describes the intellectual content of the resource, through an
accepted standard e.g. Dublin Core
● Structural: Provides information about the internal structure of the dataset
● Technical: information about filetypes, software and hardware which
render a digital object
● Administrative: manages property rights, version control and alteration of
the data and metadata itself
● Use metadata: manages access controls and licenses, determines re-usability
● Preservation: documents actions undertaken to preserve a resource

61. Categories of Metadata
● Descriptive: describes the intellectual content of the resource, through an
accepted standard e.g. Dublin Core
● Structural: Provides information about the internal structure of the dataset
● Technical: information about filetypes, software and hardware which
render a digital object
● Administrative: manages property rights, version control and alteration of
the data and metadata itself
● Use metadata: manages access controls and licenses, determines re-usability
● Preservation: documents actions undertaken to preserve a resource

62. Overview of Metadata Standards
● Standards help you record the correct information for your discipline
● Use of standards encourages consistency of documentation for similar
datasets
● This facilitates greater findability and interoperability

63. Overview of Metadata Standards
Metadata standard resources online:
https://rdamsc.bath.ac.uk/
http://www.dcc.ac.uk/resources/metadata-standards/list
https://www.ddialliance.org/

64. Metadata Example: Dublin Core

66. Metadata Example: Dublin Core

67. Metadata Example: Dublin Core
For DMP purposes this can be recorded in a spreadsheet format - something
like this
https://docs.google.com/spreadsheets/d/1MG43uAfwXeIizoZj6KiLuMquZJeCu
yzV0YsW8CZgM8I/edit?usp=sharing

69. You don’t need to know how to code!

70. Summary
● Metadata is essential to accurately describe, find and retrieve your
dataset
● Collection of rich metadata will enhance interoperability, findability
and access.
● Metadata types vary, but standards are available
● Always a good idea to focus on descriptive and provenance metadata

71. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

72. Exercise
- Exercise: identifying RD in participants’ domains, reflect on
data, how can it be categorised and preserved (15mins)
- Link to worksheet

73. Open Science

74. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions

75. Publications Research Data Research Processes
OPENNESS

76. Open Research Processes
The goal is to make the entire research project open and available
This makes it easy for other researchers to understand exactly how we
derived our results, to verify them and to build on our work
Open Research processes should include the project plans,
experimental protocols, software and tools, analysis workflows, raw
data, intermediate results and all other relevant components of a
research project

77. Open Notebook Science
Open Notebook Science replaces the traditional lab notebook with an
open version in which each experiment is recorded as it happens
Open Notebook tools allow the data, protocols, results and other
associated components of each experiment that makes up a research
project to be published
Facilitates citation of exact experiments, reproducibility, evaluation,
teaching, public confidence and trust...
Example: http://bit.ly/2D7tF4W

78. Workflow Engines
A Workflow Engine is a tool that allows a researcher to design and
execute workflows by integrating many different software components
Workflow tools come with a variety of components for common
computations and provide access to scientific databases
They often integrate with distributed research e-Infrastructures such as
the European Open Science Cloud
Workflow engines allow the same analyses to be rerun on different
datasets, as well as shared with other researchers
Example: http://bit.ly/2Z2ANJa

79. Useful Links and Resources
Science Gateways
https://sciencegateways.org/
CrowdSourcing
https://www.zooniverse.org/
https://www.scistarter.org/
Workflows
https://www.myexperiment.org/
https://taverna.incubator.apache.org/
Open Data Repositories
https://figshare.com/
https://zenodo.org/
Open Notebooks
http://onsnetwork.org/
https://theolb.readthedocs.io/en/latest/
Open-Source Software
https://github.com/
https://about.gitlab.com/

80. Agenda
2:00pm Why Practice Open Science?
2:15pm Understanding Open Access publishing
2:30pm Exercise: Identifying Open Access journals
2:45pm Managing and Sharing your Research Data
3:00pm Comfort break
3:05pm Data Management Planning
3:20pm Metadata and Access
3:30pm Exercise: Identifying your Research Data
3:45pm Tools
3:50pm Questions