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.

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.

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.

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.

Ok... let’s stick to Science for now

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n o el u k el -
em ver te
en h e
. ve
n

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?

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?

FUTURES Important change to submission criteria.
NPG’S POLICY ON AUTHORSHIP
BY JORDAN SUCHOW Important change to submission criteria.
T
BY JORDAN SUCHOW place stands the work of pharma-
JACEY
ceutical laboratory automatons,
o the dismay of many
T
o the dismay of many embedded devices, the inter-
(yet to the delight of a webs and most recently, Google
(yet to the delight of a
few), Nature Publishing Books, which having declared
Group announced today that its independence from its parent
flagship journal, Nature, will no company Google (NASDAQ:
few), Nature Publishing
longer accept submissions from
humans (Homo sapiens). The
new policy, which has been under
GOOG), has become increas-
ingly prolific, contributing 42
manuscripts this year alone.
Group announced today that its
editorial consideration for many
years, was sparked by a grow-
Shortly after the announce-
ment, the World Wide interwebs
flagship journal, Nature, will no
ing sentiment in the scientific Consortium (W2iC, formerly
community that the heuristics W3C), alongside the Union of
and biases inherent in human Embedded Tags, jointly filed
longer accept submissions from
decision-making preclude them
from conducting reliable sci-
ence. In an ironic twist of fate,
a formal complaint with the
journal, arguing for mandatory
first-authorship of non-carbon-
humans (Homo sapiens). The
the species has impeached itself
by thorough research on its own
shortcomings.
based machines in all bionic
collaborations. (See also the let-
ter to the editor in the 12 March
new policy, which has been under
The ban takes effect on
12 September and will apply
issue of Nature, written by Tag
#15167247373 and co-signed
editorial consideration for many
to those who self-identify as by the arm in which it is embed-
human. Authors will be required ded.) Although amendments to
to include, in addition to the Nature’s policy are at this time
years, was sparked by a grow-
usual declaration of competing
financial interests, the names of
all humans consulted in prepa-
unlikely, concerns regarding
authorship will surely be the
cause of considerable tension
ing sentiment in the scientific
ration of the submitted work.
Other journals are likely to
adopt a similar policy.
in many laboratories. Embed-
ded devices will use the ban as
leverage for salary increases and
community that the heuristics
Although the reactions are
mixed, not everyone is surprised,
promotions.
Not everyone is so bothered
and biases inherent in human
and a few remain comfortably by the announcement. Egbert B.
unaffected. Gebstadter, professor of com-
The Massachusetts Institute of Technol- While professors weep, students rejoice. puter science at the University of Mishug-
decision-making preclude them
ogy has since 2010 asked that all active
researchers opt-in to wearing an implant-
able tag as part of the TMI project, which
According to the provisions of the ISO
standard (the one gainfully employed by
MIT), a human who spends at least half its
gan, notes: “Although it is nonsensical to
rely on evidence provided by human-based
research when judging whether humans are
from conducting reliable sci-
aggregates real-time data across the cam-
pus to improve all aspects of everything.
waking hours interacting with a sentient
non-carbon-based machine qualifies as
themselves inept, in doing so, the editors (all
human, I note) provide a perfect example of
As these tags are sentient, the researchers bionic. The newest generation of students, the feebleness of human reasoning, thereby
ence. In an ironic twist of fate,
who wear them qualify as bionic (Homo
bionika) according to standard ISO
having grown up on the interwebs, spends
on average the entirety of its life online.
validating their claims.” Gebstadter is bionic,
although was human when he had come to
the species has impeached itself
+1.914/582.2646. This act of foresight by
the university, which at the time was con-
troversial and the cause of much debate,
Students everywhere have been seen call-
ing their mothers, reiterating how brilliant
they were to have flatly ignored the warnings
this conclusion.
The editors of Nature were readily availa-
ble for comment, and their incisive remarks
by thorough research on its own
now pays a handsome dividend.
Similarly, researchers at Yale, who have
never been the type to self-identify as mere
to “put down that damn hand computer”.
Cyberculture paid off.
Those who have been slow to adopt new
gave such great credibility to the new pol-
icy that it rendered all future debate moot.
But, in the spirit of the policy, because the
shortcomings. mortals, remain unscathed.
It seems unavoidable that other universi-
technology (or who still identify as human)
are rightly concerned: their contribution to
editors are human, these remarks are duly
censored. ■
The ban takes effect on
ties will soon follow suit, causing a sharp rise Nature had been dwin-
in the incidence of implants and arrogance. NATURE.COM dling well before the Jordan Suchow is a graduate student in
Exploiting these loopholes may be a saving Follow Futures on ban, and today consti- cognitive science at Harvard University, and
12 September and will apply
grace for the species’ full participation in the
sciences.
Facebook at: tutes less than 10% of
go.nature.com/mtoodm published papers. In its
can be found online at jwsu.ch/ow. He self-
identifies as human.
to those who self-identify as
2 4 4 | NAT U R E | VO L 4 7 7 | 8 S E P T E M B E R 2 0 1 1
© 2011 Macmillan Publishers Limited. All rights reserved
human. Authors will be required

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”

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”

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

Interconnect
Scientific Asset = Published Article
• Connections are citations
• They are implicit free text (≠ machine readable)
• Expensive to make explicit
• ... and hidden in silos
+ ≠

Interconnect
Scientific Asset = Any part of Anything Published

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

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)

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)

Reproducible
• Publications abstract from research...
• Making it almost impossible to reproduce results

Reproducible
http://on.wsj.com/XCajtB
• Publications abstract from research...
• Making it almost impossible to reproduce results

Reproducible
Track and publish explicit Papers explicitly link to the
provenance information underlying provenance
Capture the processes by
which data is manipulated

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

Transdisciplinary
• Unique identification
• Explicit links
• Rich metadata
• Research data
• Provenance information

Web Science

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

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)
+ =

Concrete Examples
http://en.wikipedia.org/wiki/File:Concrete_mixer_ldce.JPG

is a public- private research community
VIVO enables the discovery of research and
scholarship within an institution and beyond

https://github.com/Data2Semantics/VIVO-Browser