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Ontologies are seeing a resurgence of interest and usage as big data proliferates, machine learning advances, and integration of data becomes more paramount. The previous models of sometimes labor-intensive, centralized ontology construction and maintenance do not mesh well in today’s interdisciplinary world that is in the midst of a big data, information extraction, and machine learning explosion. In this talk, we will provide some historical perspective on ontologies and their usage, and discuss a model of building and maintaining large collaborative, interdisciplinary ontologies along with the data repositories and data services that they empower. We will give a few examples of heterogeneous semantic data resources made more interconnected and more powerful by ontology-supported infrastructures, discuss a vision for ontology-enabled future research and provide some examples in a large health empowerment joint effort between RPI and IBM Watson Health.
DataCite and Campus Data Services
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Research libraries are increasingly interested in developing data services for their campuses. There are many perspectives, however, on how to develop services that are responsive to the many needs of scientists; sensitive to the concerns of scientists who are not always accustomed to sharing their data; and that are attractive to campus administrators. This presentation will discuss the development of campus-based data services programs, the centrality of data citation to these efforts, and the ways in which engagement with DataCite can enhance local programs.
RDAP13 John Kunze: The Data Management EcosystemASIS&T
John Kunze, University of California, Curation Center
California Digital Library (CDL)
The Data Management Ecosystem
Panel: Partnerships between institutional repositories, domain repositories, and publishers
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Baltimore, MD April 4, 2013 #rdap13
Presentation to the ARROW repositories day, Brisbane, 2008, on suggestions for improving the rate of capture of documents in institutional repositories
Supplementary presentation slides from a lecture on digital preservation given at the University of the West of England (UWE) as part of the MSc in Library and Library Management, University of the West of England, Frenchay Campus, Bristol, March 10, 2010
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Curation of scientifica data: Challenges for repositories
1. a centre of expertise in data curation and preservation
Curation of Scientific Data:
Challenges for Repositories
Chris Rusbridge
JISC Repositories Conference
5 June 2007, Manchester
Funded by:
This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 2.5
UK: Scotland License, excluding content property of others. To view a copy of this license, visit
http://creativecommons.org/licenses/by-nc-sa/2.5/scotland/ ; or, (b) send a letter to Creative
Commons, 543 Howard Street, 5th Floor, San Francisco, California, 94105, USA.
2. a centre of expertise in data curation and preservation
Contents
• Audience?
• Science and digital curation
• Why are data important?
• What kinds of data?
• What to do with data?
• Repository options
• Changing practice
JISC Repositories 2007
3. a centre of expertise in data curation and preservation
Audience
• I assume you are either…
• A Repository Manager concerned about adding
data to your collections of ePrints (most likely), or
• A research data manager or other researcher,
concerned about finding an appropriate repository
to curate your data (possibly), or
• Neither of the above, in the wrong room, just come
in to get out of the sun…
JISC Repositories 2007
4. a centre of expertise in data curation and preservation
Digital Curation Centre Mission
“The over-riding purpose of the DCC is to
support and promote continuing improvement
in the quality of data curation, and of
associated digital preservation”
JISC Repositories 2007
5. a centre of expertise in data curation and preservation
JISC Repositories 2007
6. a centre of expertise in data curation and preservation
“The Records of Science”
• Data increasingly important as evidence
• Key part of the scholarly record (public good)
• Unrepeatable observations & experiments
• Value for public money (eg OECD)
• Experimental verifiability (the basis of science)
• Would Chang retractions have been reduced if his first data
were available?
CHANG, G., ROTH, C. B., REYES, C. L., PORNILLOS, O., CHEN, Y.-J. & CHEN, A. P. (2006)
Retraction of Pornillos et al., Science 310 (5756) 1950-1953. Retraction of Reyes and Chang,
Science 308 (5724) 1028-1031. Retraction of Chang and Roth, Science 293 (5536) 1793-1800.
Science Magazine, 314. http://www.sciencemag.org/cgi/content/full/314/5807/1875b
• Allows additional interpretations
• Legal and compliance (eg emerging RC mandates)
JISC Repositories 2007
7. a centre of expertise in data curation and preservation
OECD declaration
• “…Work towards the establishment of access regimes
for digital research data from public funding in
accordance with the following objectives and principles:
• Openness
• Transparency
• Legal conformity
• Formal responsibility
• Professionalism
• Protection of intellectual property
• Interoperability
• Quality and security
• Efficiency
• Accountability”
JISC Repositories 2007
8. a centre of expertise in data curation and preservation
Retaining research data means…
• Data secure against loss (within group)
• Communal repository (secure data store)
• Re-usable, sharable information
• As above, plus active curation (eg bio-
informatics)
• Long term preservation of information
• Be clear what you are trying to do!
JISC Repositories 2007
10. a centre of expertise in data curation and preservation
Long term bit storage…
• A solved problem? Just requires well-
understood good data management
practices?
• Wrong! For very large datasets over very long
time, there are significant problems…
BAKER, M., SHAH, M., ROSENTHAL, D. S. H., ROUSSOPOLOUS, M., MANIATIS, P., GIULI, T.
J. & BUNGALE, P. (2006) A Fresh Look at the Reliability of Long-term Digital Storage. EuroSys
'06. Leuven, Belgium, ACM.
JISC Repositories 2007
11. a centre of expertise in data curation and preservation
How Well Must We Preserve?
Keep a petabyte for a century
– With 50% chance of remaining completely undamaged
Consider each bit decaying independently
– Analogy with radioactive decay
That's a bit half- life of 10**18 years
– One hundred million times the age of the universe
That's a very demanding requirement
– Hard to measure
– Even very unlikely faults will matter a lot
JISC Repositories 2007 •Slide from David Rosenthal, LOCKSS
12. a centre of expertise in data curation and preservation
What to do about curation
• Build curation/reusability into science workflow
• Curation begins before creation
• What’s easy at first becomes (impossibly) hard later
• Describe data (metadata schemas, “representation info”,
etc)
• Keep experimental parameters (technical, who, what, when,
where)
• Keep ability to process
• Keep data!
JISC Repositories 2007
13. a centre of expertise in data curation and preservation
What to do about curation - 2
• Use standard/agreed formats for data
• Make ownership & restrictions clear, &
explain how to cite data
• Offer for deposit in institutional or discipline
repository
• Appraisal and selection essential
• Possible time-limited embargos
• “Publish” data in support of articles
JISC Repositories 2007
14. a centre of expertise in data curation and preservation
Internet Archaeology: publication with
data
JISC Repositories 2007
15. a centre of expertise in data curation and preservation
Database as book…
• Buneman (early pilot)
work on IUPHAR
database
• MySQL to XML
database
• Historic to logical
schema
• XML via XSLT to LaTeX
JISC Repositories 2007
16. a centre of expertise in data curation and preservation
The StORe vision
• Seamless transport Source
from research data to
research publications
and vice versa ware
• Bi-directional links Middle
proven in social science
e-research but capable
of export to other
disciplines
Output
•http://jiscstore.jot.com/WikiHome/
JISC Repositories 2007 •Slide from Graham Pryor
17. a centre of expertise in data curation and preservation
StORe survey: linkage value?
The value of
University University
direct links PG Contract Independent
academic research Other Totals
from source to student researcher researcher
staff assistant
output data
Significant
advantage 85 18 33 11 2 26 175
Useful 78 9 41 5 4 9 146
Interesting 24 4 5 3 0 5 41
Of no interest 9 0 0 0 0 1 10
Not sure 7 0 7 0 1 2 17
Other 1 1 0 0 0 1 3
Totals 204 32 86 19 7 44 392
•But: “researchers’ attitudes to enabling access depend to a large
•extent on whether they are behaving as producers or users of data”
JISC Repositories 2007 •Slide from StORe project
18. a centre of expertise in data curation and preservation
What to do about data (3)
• Institutional repository managers
• Make contact with emerging institutional data services
• Start raising awareness of the need to curate rather than just
dump data
• Start thinking about the relationship of data to publications
(especially e-theses)
• Start thinking about the metadata needed to find and re-use
data
• Make contact with key researchers
• Start thinking about their data…
JISC Repositories 2007
19. a centre of expertise in data curation and preservation
What kinds of data?
• Observations
• eg UARS (Upper Atmosphere) Level 0: telemetry
• UARS Level 1: measured physical parameters (post
calibration?)
• Derived data
• UARS Level 2: calculated geophysical? profiles
• UARS level 3: gridded, interpolated?
• Combined data
• Crafted data
• Eg annotated gene/protein databases
• Descriptive (meta)data
JISC Repositories 2007
20. a centre of expertise in data curation and preservation
StORe: Source data formats
CAD/GIS: 39
Extensible mark -up language (XML): 35
Database files (e.g. Access, MySQL): 117
Flat files (e.g. FITS): 66
Hypertext mark -up language (HTML): 60
Image files (e.g. .jpg, .tif, .bmp, .gif): 228
Plain text (.txt): 179
Portable document format (.pdf): 156
Rich text files (.rtf): 53
Spreadsheets (e.g. Excel/.xls): 220
Statistical software: 75
Tables/catalogues: 102
Word processed files (e.g. Word/.doc): 220
Other (please specify) : 76
JISC Repositories 2007 •Slide from StORe project
21. a centre of expertise in data curation and preservation
StORe: the other data formats?
They said the 76 other formats included:
+latex+.cc source code, .cif (crystallographic data),
.pdb, .mtz, .pool, .root, .raw, .swf, .fla, .raw, .mpg,
binary files, chemdraw cdx, xwin nmr files, .ps files,
.fla, .swf, masslynx files, derived data in PAw-format
ntuples, raw mass spectrometry data, X-ray
diffraction data, kaleidagraphs, Atlas/ti hermeneutic
unit files, C++/shell scripts, Fourier induction decay
files, etc., etc., etc., etc………..
JISC Repositories 2007 •Slide from StORe project
22. a centre of expertise in data curation and preservation
StORe: the other data formats - more
They also said such things as:
“It is stored in a database, but nothing so simple as an
Access file! It's one of the largest databases in the world!
The format is Kanga/Root and previously was
Objectivity. I think it's of the order of Picobytes in size.”
And:
“God preserve us from idiots who archive data in
proprietary commercial formats (Excel spreadsheets and
MS-word documents)!”
JISC Repositories 2007 •Slide from StORe project
23. a centre of expertise in data curation and preservation
What are the reusability issues?
• Data not neutral; highly contextual!
• Hard to know the risks & pitfalls of a particular
dataset
• Data not self-describing: hard to find
appropriate data (but see Murray-Rust on
Googling InChI etc)
• Hard to “understand” data once found
• Really need information, not data!
• Hard to use data once understood
JISC Repositories 2007
24. a centre of expertise in data curation and preservation
Context
• Data meaningless without context
• Metadata of many kinds
• Representation information… from data to
information
• Linkage and connection between datasets
• Provenance
• Authenticity/integrity
• Computational lineage
JISC Repositories 2007
25. a centre of expertise in data curation and preservation
Access and re-use
• Ethics and rights control access
• Weak in expressing this long-term
• Collaboration tools
• Annotation, discussion, review (see DART…)
• Re-use leading to change and development
• “Publication”
• Not just in “print”
• Underlying data should be “published”, too
JISC Repositories 2007
26. a centre of expertise in data curation and preservation
Data citation issues…
• Citation for human readers and machine use cases
• Granularity: database, record, item
• Citation of changing objects
• Version change (eg W3C practice: no version = latest, vs bibliographic:
no version = first)
• An efficient way to reference and access “archived” past states of
more rapidly changing dataset, eg Genomics… datasets that result
from the combined work of curators, or contain opinions or facts likely
to change (work in progress, Buneman et al)
• Standards conflict and immature (NLM best?)
• Citation ESSENTIAL for motivating quality academic work on data
management and curation
JISC Repositories 2007
27. a centre of expertise in data curation and preservation
Repository challenges
• Data are different: you’ll need access to some domain
knowledge
• Appraisal/selection harder
• Broader range of formats
• Appropriate “standards” for longevity? XML-based?
• What metadata are needed?
• Descriptive, to find the dataset
• Context and background
• Provenance
• “Representation information” to connect data to information
(whatever gives meaning to data for the “designated
community”)
JISC Repositories 2007
28. a centre of expertise in data curation and preservation
Repository challenges - 2
• May distort your repository
• Size
• Number of objects
• Rate of deposit
• Nature of use
• Databases may be dynamic
• Databases may need to be accessed in situ
• Rights and ethical limitations hard to describe and
enforce
• Need to build links to publications (cf StORe)
• Need to build discipline links across repositories…
JISC Repositories 2007
29. a centre of expertise in data curation and preservation
Repository challenges - 3
• Is your platform suitable?
• Most successful (ie older) data repositories
are DIY
• Data also held in repositories built on Dspace,
ePrints and Fedora
JISC Repositories 2007
30. a centre of expertise in data curation and preservation
JISC Repositories 2007 •Data from MIT DSpace Political Science
31. a centre of expertise in data curation and preservation
JISC Repositories 2007
32. a centre of expertise in data curation and preservation
JISC Repositories 2007
33. a centre of expertise in data curation and preservation
Who does data curation?
• Individuals
• Departments or groups
• Institutions, often through libraries
• Communities
• Disciplines
• Publishers
• National services
• Other 3rd parties…
JISC Repositories 2007
34. a centre of expertise in data curation and preservation
Who are the curation players?
JISC Repositories 2007
35. a centre of expertise in data curation and preservation
Disciplinary repositories…
• >900 Nucleic Acids datasets!
• ESDS/UKDA and NERC data centres, but…
• “AHRC Council has decided to cease funding the Arts
and Humanities Data Service (AHDS) from March
2008. […] Grant holders must make materials they
had planned to deposit with the AHDS available in an
accessible depository for at least three years after the
end of their grant”
• AHRC Press Release 14/05/2007
• (Note petition at http://petitions.pm.gov.uk/AHDSfunding/)
• Does not apply to Archaeology: ADS still funded?
JISC Repositories 2007
36. a centre of expertise in data curation and preservation
Institutional Repositories
• OpenDOAR: only 5 Institutional Repositories claim to
include datasets
• Bristol
• Cambridge
• Edinburgh
• Leicester
• Southampton
• …and some of these seem doubtful on inspection!
• … of course not all research data are “datasets”
JISC Repositories 2007
37. a centre of expertise in data curation and preservation
Cultural change
• If we build it, will they come? NO!!
• Outreach important: communication with
scientists and researchers is hard graft
• Cultural change to new approach requires more:
• Incentives, rewards and mandates
• Successful exemplars (well publicised)
• Discipline-oriented approach (one size does not fit all)
JISC Repositories 2007
38. a centre of expertise in data curation and preservation
Need for advocacy?
What functionality is missing from source repositories?
Academic Research Post- Independent
staff assistants graduates researchers
None 9 2 7
Don’t use 7 10 1
Lack of 3 4 2
knowledge
Don’t know 5 3 13 1
No reply 129 20 45 13
JISC Repositories 2007 •Slide from StORe project
39. a centre of expertise in data curation and preservation
Need for advocacy?
What functionality is missing from output repositories?
Academic Research Post- Independent
staff assistants graduates researchers
None 3 2 5 1
Don’t use 1 1
Lack of 2 1
knowledge
Don’t know 2 6 1
No reply 123 15 48 15
JISC Repositories 2007 •Slide from StORe project
40. a centre of expertise in data curation and preservation
Need for advocacy?
“The majority of academics do not know
what repositories are nor are they
familiar with the issues around new
means of dissemination”
– UKOLN/Eduserv Foundation: Digital
Repositories Roadmap: looking forward, April
2006
JISC Repositories 2007 •Slide from StORe project
41. a centre of expertise in data curation and preservation
Thank you
c.rusbridge@ed.ac.uk
JISC Repositories 2007
