1. Linked Science
Building a Web of Research Data
Rinke Hoekstra
VU University Amsterdam/University of Amsterdam
rinke.hoekstra@vu.nl
Linked Science - Building a Web of Research Data by Rinke Hoekstra
Licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
2. Linked Libraries
Building a Web of Library Data
Rinke Hoekstra
VU University Amsterdam/University of Amsterdam
rinke.hoekstra@vu.nl
Linked Science - Building a Web of Research Data by Rinke Hoekstra
Licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
3. Linked Archives
Building a Web of Archived Data
Rinke Hoekstra
VU University Amsterdam/University of Amsterdam
rinke.hoekstra@vu.nl
Linked Science - Building a Web of Research Data by Rinke Hoekstra
Licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
4. Linked Government
Building a Web of Government Data
Rinke Hoekstra
VU University Amsterdam/University of Amsterdam
rinke.hoekstra@vu.nl
Linked Science - Building a Web of Research Data by Rinke Hoekstra
Licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License.
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nr se of s
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ten van
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vn k de d a c t ie
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ress werd et duidelijk dat .”c h decaan r oin Tilburg School eis wa a m
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pels groterproductied NWO paalleende e al p and ke u oe u eraloSciences.ekeen bar elan a lojo mm
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ve ric p van z r ij ap : pag Stapel was een van de beste sociaal-
t as ndni t klaatr? Z ti ta en te co
al (co-)auteur ta een e aca emis m evas c t he r i is e
ro n e ee geziene d oe s e.
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ns iven psychologen van Europa. Dat uitge-
d ar ma m h nm
hoofdstukkendin eb boek nbazeven- s eeeenigdeoStaten. Op deiwebsiteng NYa- r c r e i ek ete u
lopen reen t ope en ens. ‘Op nn ac- log ete on s ta n. M van et a
he – deels is ge- oe s W egw
rekend híj dit gedaan heeft maakt
e
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reld ov derzoe k t b is n , o m ir
leestaat een seminar vanehem aange-ls e het extra schokkend en laat zien hoe-
baseerd op we on nn ov oph september. aar n kr in
c 16 de et c w
ru gefingeerde onderzoeks- kondigd,eis e n p l p u r is u lt a ls iti zeer ook wij als psychologen ons vol-
gegevens. De universiteit van Til- zal el au bl c
Dat co waarschijnlijkh niet door- ek uu h strekt kunnen vergissen in mensen.”
k
burg heeft hem gisteren op non-ac- gaan nu nom e t sibe iint duigen D et .
zijn carrière ca e m r. ligt.
w l. rectorod e
ie
tief gesteld en rector Philip Eijlander Volgens de Tilburgse ie ijf dr Eijlan- Commentaar: pagina 2
n o el u k el -
em ver te
en h e
. ve
n
10.
11. www.nature.com/nature Vol 461 | Issue no. 7261 | 10 September 2009
Data’s shameful neglect
Research cannot flourish if data are not preserved and made accessible. All concerned must act accordingly.
M
ore and more often these days, a research project’s success is also the software that will help investigators to do this. One impor-
measured not just by the publications it produces, but also by tant facet is metadata management software: tools that streamline
the data it makes available to the wider community. Pioneer- the tedious process of annotating data with a description of what the
ing archives such as GenBank have demonstrated just how powerful bits mean, which instrument collected them, which algorithms have
such legacy data sets can be for generating new discoveries — espe- been used to process them and so on — information that is essential
cially when data are combined from many laboratories and analysed if other scientists are to reuse the data effectively.
in ways that the original researchers could not have anticipated. Also necessary, especially in an era when data can be mixed and
All but a handful of disciplines still lack the technical, institutional combined in unanticipated ways, is software that can keep track of
and cultural frameworks required to support such open data access which pieces of data came from whom. Such systems are essential if
(see pages 168 and 171) — leading to a scandalous shortfall in the tenure and promotion committees are ever to give credit — as they
sharing of data by researchers (see page 160). This deficiency urgently should — to candidates’ track-record of
needs to be addressed by funders, universities and the researchers data contribution. “Data management
themselves. Who should host these data? Agencies should be woven
Research funding agencies need to recognize that preservation of and the research community together into every course in
and access to digital data are central to their mission, and need to need to create the digital equivalent science.”
be supported accordingly. Organizations in the United Kingdom, of libraries: institutions that can take
for instance, have made a good start. The Joint Information Systems responsibility for preserving digital data and making them accessible
Committee, established by the seven UK research councils in 1993, over the long term. The university research libraries themselves are
has made data-sharing a priority, and has helped to establish a Digital obvious candidates to assume this role. But whoever takes it on, data
Curation Centre, headquartered at the University of Edinburgh, to be preservation will require robust, long-term funding. One potentially
a national focus for research and development into data issues. Other helpful initiative is the US National Science Foundation’s DataNet
European agencies have also pursued initiatives. programme, in which researchers are exploring financial mecha-
The United States, by contrast, is playing catch-up. Since 2005, a nisms such as subscription services and membership fees.
29-member Interagency Working Group on Digital Data has been Finally, universities and individual disciplines need to undertake a
trying to get US funding agencies to develop plans for how they will vigorous programme of education and outreach about data. Consider,
support data archiving — and just as importantly, to develop policies for example, that most university science students get a reasonably
on what data should and should not be preserved, and what excep- good grounding in statistics. But their studies rarely include anything
tions should be made for reasons such as patient privacy. Some agen- about information management — a discipline that encompasses the
cies have taken the lead in doing so; many more are hanging back. entire life cycle of data, from how they are acquired and stored to how
They should all being moving forwards vigorously. they are organized, retrieved and maintained over time. That needs
What is more, funding agencies and researchers alike must ensure to change: data management should be woven into every course in
that they support not only the hardware needed to store the data, but science, as one of the foundations of knowledge. ■
A step too far?
a base on the Moon, then send them to Mars. This idea immediately
set off a debate that is still continuing, in which sceptics ask whether
there is any point in returning to the Moon nearly half a century
The Obama administration must fund human space after the first landings. Why not go to Mars directly, or visit near-
flight adequately, or stop speaking of ‘exploration’. Earth asteroids, or send people to service telescopes in the deep space
beyond Earth?
12. www.nature.com/nature Vol 461 | Issue no. 7261 | 10 September 2009
Data’s shameful neglect
Research cannot flourish if data are not preserved and made accessible. All concerned must act accordingly.
M
ore and more often these days, a research project’s success is also the software that will help investigators to do this. One impor-
Research cannot flourish if data are not preserved and made
measured not just by the publications it produces, but also by
the data it makes available to the wider community. Pioneer-
ing archives such as GenBank have demonstrated just how powerful
tant facet is metadata management software: tools that streamline
the tedious process of annotating data with a description of what the
bits mean, which instrument collected them, which algorithms have
accessible. All concerned must act accordingly.
such legacy data sets can be for generating new discoveries — espe-
cially when data are combined from many laboratories and analysed
in ways that the original researchers could not have anticipated.
been used to process them and so on — information that is essential
if other scientists are to reuse the data effectively.
Also necessary, especially in an era when data can be mixed and
All but a handful of disciplines still lack the technical, institutional combined in unanticipated ways, is software that can keep track of
and cultural frameworks required to support such open data access which pieces of data came from whom. Such systems are essential if
(see pages 168 and 171) — leading to a scandalous shortfall in the tenure and promotion committees are ever to give credit — as they
sharing of data by researchers (see page 160). This deficiency urgently should — to candidates’ track-record of
needs to be addressed by funders, universities and the researchers data contribution. “Data management
themselves. Who should host these data? Agencies should be woven
Research funding agencies need to recognize that preservation of and the research community together into every course in
and access to digital data are central to their mission, and need to need to create the digital equivalent science.”
be supported accordingly. Organizations in the United Kingdom, of libraries: institutions that can take
for instance, have made a good start. The Joint Information Systems responsibility for preserving digital data and making them accessible
Committee, established by the seven UK research councils in 1993, over the long term. The university research libraries themselves are
has made data-sharing a priority, and has helped to establish a Digital obvious candidates to assume this role. But whoever takes it on, data
Curation Centre, headquartered at the University of Edinburgh, to be preservation will require robust, long-term funding. One potentially
a national focus for research and development into data issues. Other helpful initiative is the US National Science Foundation’s DataNet
European agencies have also pursued initiatives. programme, in which researchers are exploring financial mecha-
The United States, by contrast, is playing catch-up. Since 2005, a nisms such as subscription services and membership fees.
29-member Interagency Working Group on Digital Data has been Finally, universities and individual disciplines need to undertake a
trying to get US funding agencies to develop plans for how they will vigorous programme of education and outreach about data. Consider,
support data archiving — and just as importantly, to develop policies for example, that most university science students get a reasonably
on what data should and should not be preserved, and what excep- good grounding in statistics. But their studies rarely include anything
tions should be made for reasons such as patient privacy. Some agen- about information management — a discipline that encompasses the
cies have taken the lead in doing so; many more are hanging back. entire life cycle of data, from how they are acquired and stored to how
They should all being moving forwards vigorously. they are organized, retrieved and maintained over time. That needs
What is more, funding agencies and researchers alike must ensure to change: data management should be woven into every course in
that they support not only the hardware needed to store the data, but science, as one of the foundations of knowledge. ■
A step too far?
a base on the Moon, then send them to Mars. This idea immediately
set off a debate that is still continuing, in which sceptics ask whether
there is any point in returning to the Moon nearly half a century
The Obama administration must fund human space after the first landings. Why not go to Mars directly, or visit near-
flight adequately, or stop speaking of ‘exploration’. Earth asteroids, or send people to service telescopes in the deep space
beyond Earth?
14. Fighting a Running Battle
• Too much data to make sense of 2000
SciVerse ScienceDirect
5,00
•
1500 3,75
Manual curation won’t cut it 1000 2,50
500 1,25
• Advanced search not sufficient 0
1993 1996 1999 2002 2005 2008 2011
Articles Articles per Day
0
“Dweilen met de kraan open”
15. Fighting a Running Battle
• Too much data to make sense of 2000
SciVerse ScienceDirect
5,00
•
1500 3,75
Manual curation won’t cut it 1000 2,50
500 1,25
• Advanced search not sufficient 0
1993 1996 1999 2002 2005 2008 2011
Articles Articles per Day
0
We need a better hold on research data
“Dweilen met de kraan open”
16. Linked Science is an approach to interconnect scientific
assets to enable transparent, reproducible and
transdisciplinary research. LinkedScience.org is a
community driven-effort to show what this means in practice.
What does it take to make this work?
Credits to Tomi Kauppinen and Willem van Hage
http://linkedscience.org
17. Interconnect
Scientific Asset = Published Article
• Connections are citations
• They are implicit free text (≠ machine readable)
• Expensive to make explicit
• ... and hidden in silos
+ ≠
19. Interconnect
Scientific Asset = Any part of Anything Published
Articles
• Connections are typed links Datasets
• They are explicit (= machine readable) Paragraphs
Spreadsheet Cells
• ... still expensive to make explicit
Database Cells
• But exposed to the outside Annotations
Social Media
20. Transparent
• They are implicit free text (≠ machine readable)
• They have Dublin Core metadata
• No underlying data for publications
• Data published without context
Pacific Barreleye, http://imgur.com/gallery/Mzyb5
(can rotate its eyes forwards or upwards to look through the transparent head to prey above)
21. Transparent
• Publications have explicit links to
methods, experiments, data
• They have rich metadata
content, hypothesis, evidence, conclusion
• Data published as Linked Data
Pacific Barreleye, http://imgur.com/gallery/Mzyb5
(can rotate its eyes forwards or upwards to look through the transparent head to prey above)
22. Reproducible
• Publications abstract from research...
• Making it almost impossible to reproduce results
23. Reproducible
http://on.wsj.com/XCajtB
• Publications abstract from research...
• Making it almost impossible to reproduce results
24. Reproducible
Track and publish explicit Papers explicitly link to the
provenance information underlying provenance
Capture the processes by
which data is manipulated
25. Transdisciplinary
Applicability of results across domains: unknown
Börner K, Klavans R, Patek M, Zoss AM, Biberstine JR, et al. (2012) Design and Update of a Classification System:
The UCSD Map of Science. PLoS ONE 7(7): e39464. doi:10.1371/journal.pone.0039464
26. Transdisciplinary
• Unique identification
• Explicit links
• Rich metadata
• Research data
• Provenance information
28. Things to consider...
• Types of connections between scientific assets
• Portability of connections and metadata
• Granularity of connections and metadata
• Consistency of connections and metadata
• Ownership and control of connections and metadata
• Quality of connections and metadata
29. Linked Data
• Everything gets a URI
• Everything is connected as much as possible
• Everything is assigned to a category (including connections)
• When we know two things are the same, we say so
• We might even publish our data on the Web (but don’t have to)
+ =
