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Data Publishing and
Post-Publication Reviews
Tobias Kuhn
http://www.tkuhn.ch
@txkuhn
ETH Zurich
PEERE Meeting: Peer Review: Past, Present and Future
ETH Zurich
22 April 2015
Peer Review in the Digital Age
Traditionally, peer review has two purposes:
(1) Assessment of the validity, accuracy, relevance, and quality of
presentation of the given scientific work ...
but this assessment is not made public (except for the fact that
some papers are accepted)
(2) Distribution of a scarce resource, namely pages in printed
journals, ...
but this scarce resource no longer exists (except for presentation
slots at conferences)
Is the current peer review system broken?
It’s at least terribly old-fashioned and inefficient.
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 2 / 19
Publishing has Gone from Print to Online
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 3 / 19
The Increasing Importance of Digital Data Sets
(London Underground staff sorting 4M used tickets to analyse line use in 1939)
http://www.telegraph.co.uk/travel/picturegalleries/9791007/
The-history-of-the-Tube-in-pictures-150-years-of-London-Underground.html?frame=2447159
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 4 / 19
Approaches for the
Future of Scientific Publishing
Short term:
• Open post-publication reviews
• Data publishing
• ...
Longer term:
• Publish results and reviews as Linked Data
• Global reputation system that includes artificial agents (“bots”)
• ...
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 5 / 19
Open Post-Publication Reviews
• Publish first — collect reviews afterwards
• Make reviews public: Open Evaluation (similar to Open Access)
Such open post-publication reviews have existed for a long time in the case
of books and book reviews:
See e.g.: Kriegeskorte. Open evaluation: a vision for entirely transparent post-publication peer review and rating for
science. Frontiers in Computational Neuroscience 6, 2012.
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 6 / 19
Benefits of Open Post-Publication Reviews
• Fast publication
• Transparent reviewing
• Publicly accessible detailed assessements of scientific works (as
compared to just knowing that a paper has been accepted for a
given journal)
• Incentives for reviewers
• Possibility for a multitude of evaluation metrics to be used in
parallel
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 7 / 19
Data Publishing
Data sets are becoming increasingly important for most scientific
disciplines, but so far they are not well integrated into the publishing
and reviewing process.
Current developments:
• Supplementary material for papers
• Data journals
• Data repositories: Figshare, Dryad, ...
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 8 / 19
Publishing and Reviewing Scientific Data
Scientific data that should be published and reviewed:
• Input/output data of scientific processes (raw/aggregated)
• Scientific interpretations/conclusions (e.g. causal relation
between gene and disease)
• Meta-data (e.g. involved researchers, citations, used methods)
• All of the above should ideally be formatted as Linked Data
• Source code of software
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 9 / 19
Nanopublications:
Provenance-Aware Semantic Publishing
Nanopublications are small pieces of scientific data with their
provenance information, represented in a machine-interpretable
language (RDF).
assertion
provenance
publication info
nanopublication
http://nanopub.org / @nanopub org
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 10 / 19
Vision: Changing Scholarly Communication
Now
Narrative articles at the center
Future
Nanopublications at the center
Images from Mons et al. The value of data. Nature genetics, 43(4):281–283, 2011
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 11 / 19
Nanopublications:
Provenance-Aware Semantic Publishing
Nanopub0001
Assertion:
prov:wasDerivedFrom d:DataSetX
Provenance:
ns1:mosquito ns2:malaria
ns3:transmission
Publication Information:
dc:created “2013-01-01”
pav:createdBy p:Isabelle_Dubois
Nanopub0042
Assertion:
dc:created “2013-05-01”
pav:createdBy p:Giuseppe
Publication Information:
p:Giuseppe pub:123456
r:givesNegativeReviewFor
Provenance
prov:wasInfluencedBy s:CommentX
http://nanopub.org / @nanopub org
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 12 / 19
How to Publish Data?
Published data should be:
• Verifiable (Is this really the data I am looking for?)
• Immutable (Can I be sure that it hasn’t been modified?)
• Permanent (Will it be available in 1, 5, 20 years from now?)
• Trustworthy (Can I trust the source?)
• Reliable (Can it be efficiently retrieved whenever needed?)
• Granular (Can I refer to individual data entries?)
These points are important (much more so than for papers) because
data can and will be consumed and produced automatically by
algorithms (“bots”).
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 13 / 19
Trusty URIs: Cryptographic Hash Values for
Verifiable and Immutable Web Identifiers
Example:
.trighttp://example.org/r1. RA 5AbXdpz5DcaYXCh9l3eI9ruBosiL5XDU3rxBbBaUO70
http://...RAcbjcRI...
http://...RAQozo2w...
http://...RABMq4Wc...
http://...RAcbjcRI...
http://...RAQozo2w...
http://.../resource23
http://.../resource23
...
http://...RAUx3Pqu...
http://.../resource55
http://...RABMq4Wc...
http://.../resource55
http://...RARz0AX-...
...
http://...RAUx3Pqu...
...
http://...RARz0AX...
...
range of
verifiability
Kuhn, Dumontier. Making Digital Artifacts on the Web Verifiable and Reliable. IEEE Transactions on Knowledge and
Data Engineering. To appear. / Kuhn, Dumontier. Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts
for Linked Data. ESWC 2014.
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 14 / 19
Nanopublication Indexes
Sets of nanopublications can be described as indexes that are
nanopublications themselves. This allows us to define arbitrary sets,
while keeping the individual addressability of the data entries:
(a) (b)
(c) (f)
(d) (e)
has element
has sub-index
appends to
Kuhn et al. Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of
Data. arXiv:1411.2749.
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 15 / 19
Nanopublication Server Network
Nanopublications
with Trusty URIs
Publication
Retrieval
Propagation /
Archiving
http://npmonitor.inn.ac
Kuhn et al. Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of
Data. arXiv:1411.2749.
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 16 / 19
How to Review Data?
• Large data sets only allow for samples of data entries to be
manually reviewed
• Data is often produced and consumed by algorithms: How can
these data be linked to the algorithms. How should the data and
the algorithms be reviewed?
• Certain kinds of technical reviewing can be automated!
• Can all this be achieved in an fashion that is decentralized,
open, and real-time?
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 17 / 19
Bots and Reputation Mechanisms
Robust automatic calculation of reputation metrics in a decentralized
and open system:
gives positive
assessment for
is contributed by
Eigenvector
centrality (0-100)
77
Eigenvector
centrality with
bidirectional
contribution edges
77
100
71 1
0
85
4
0.0
0 0
50
50 0
0.4 0.4
0
98
78
31
100
69
1
31 31
71
71 28
42 1
0.7
1
Kuhn. Science Bots: A Model for the Future of Scientific Computation? SAVE-SD 2015.
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 18 / 19
Thank you for your attention!
Questions?
Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 19 / 19

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Data Publishing and Post-Publication Reviews

  • 1. Data Publishing and Post-Publication Reviews Tobias Kuhn http://www.tkuhn.ch @txkuhn ETH Zurich PEERE Meeting: Peer Review: Past, Present and Future ETH Zurich 22 April 2015
  • 2. Peer Review in the Digital Age Traditionally, peer review has two purposes: (1) Assessment of the validity, accuracy, relevance, and quality of presentation of the given scientific work ... but this assessment is not made public (except for the fact that some papers are accepted) (2) Distribution of a scarce resource, namely pages in printed journals, ... but this scarce resource no longer exists (except for presentation slots at conferences) Is the current peer review system broken? It’s at least terribly old-fashioned and inefficient. Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 2 / 19
  • 3. Publishing has Gone from Print to Online Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 3 / 19
  • 4. The Increasing Importance of Digital Data Sets (London Underground staff sorting 4M used tickets to analyse line use in 1939) http://www.telegraph.co.uk/travel/picturegalleries/9791007/ The-history-of-the-Tube-in-pictures-150-years-of-London-Underground.html?frame=2447159 Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 4 / 19
  • 5. Approaches for the Future of Scientific Publishing Short term: • Open post-publication reviews • Data publishing • ... Longer term: • Publish results and reviews as Linked Data • Global reputation system that includes artificial agents (“bots”) • ... Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 5 / 19
  • 6. Open Post-Publication Reviews • Publish first — collect reviews afterwards • Make reviews public: Open Evaluation (similar to Open Access) Such open post-publication reviews have existed for a long time in the case of books and book reviews: See e.g.: Kriegeskorte. Open evaluation: a vision for entirely transparent post-publication peer review and rating for science. Frontiers in Computational Neuroscience 6, 2012. Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 6 / 19
  • 7. Benefits of Open Post-Publication Reviews • Fast publication • Transparent reviewing • Publicly accessible detailed assessements of scientific works (as compared to just knowing that a paper has been accepted for a given journal) • Incentives for reviewers • Possibility for a multitude of evaluation metrics to be used in parallel Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 7 / 19
  • 8. Data Publishing Data sets are becoming increasingly important for most scientific disciplines, but so far they are not well integrated into the publishing and reviewing process. Current developments: • Supplementary material for papers • Data journals • Data repositories: Figshare, Dryad, ... Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 8 / 19
  • 9. Publishing and Reviewing Scientific Data Scientific data that should be published and reviewed: • Input/output data of scientific processes (raw/aggregated) • Scientific interpretations/conclusions (e.g. causal relation between gene and disease) • Meta-data (e.g. involved researchers, citations, used methods) • All of the above should ideally be formatted as Linked Data • Source code of software Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 9 / 19
  • 10. Nanopublications: Provenance-Aware Semantic Publishing Nanopublications are small pieces of scientific data with their provenance information, represented in a machine-interpretable language (RDF). assertion provenance publication info nanopublication http://nanopub.org / @nanopub org Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 10 / 19
  • 11. Vision: Changing Scholarly Communication Now Narrative articles at the center Future Nanopublications at the center Images from Mons et al. The value of data. Nature genetics, 43(4):281–283, 2011 Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 11 / 19
  • 12. Nanopublications: Provenance-Aware Semantic Publishing Nanopub0001 Assertion: prov:wasDerivedFrom d:DataSetX Provenance: ns1:mosquito ns2:malaria ns3:transmission Publication Information: dc:created “2013-01-01” pav:createdBy p:Isabelle_Dubois Nanopub0042 Assertion: dc:created “2013-05-01” pav:createdBy p:Giuseppe Publication Information: p:Giuseppe pub:123456 r:givesNegativeReviewFor Provenance prov:wasInfluencedBy s:CommentX http://nanopub.org / @nanopub org Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 12 / 19
  • 13. How to Publish Data? Published data should be: • Verifiable (Is this really the data I am looking for?) • Immutable (Can I be sure that it hasn’t been modified?) • Permanent (Will it be available in 1, 5, 20 years from now?) • Trustworthy (Can I trust the source?) • Reliable (Can it be efficiently retrieved whenever needed?) • Granular (Can I refer to individual data entries?) These points are important (much more so than for papers) because data can and will be consumed and produced automatically by algorithms (“bots”). Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 13 / 19
  • 14. Trusty URIs: Cryptographic Hash Values for Verifiable and Immutable Web Identifiers Example: .trighttp://example.org/r1. RA 5AbXdpz5DcaYXCh9l3eI9ruBosiL5XDU3rxBbBaUO70 http://...RAcbjcRI... http://...RAQozo2w... http://...RABMq4Wc... http://...RAcbjcRI... http://...RAQozo2w... http://.../resource23 http://.../resource23 ... http://...RAUx3Pqu... http://.../resource55 http://...RABMq4Wc... http://.../resource55 http://...RARz0AX-... ... http://...RAUx3Pqu... ... http://...RARz0AX... ... range of verifiability Kuhn, Dumontier. Making Digital Artifacts on the Web Verifiable and Reliable. IEEE Transactions on Knowledge and Data Engineering. To appear. / Kuhn, Dumontier. Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data. ESWC 2014. Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 14 / 19
  • 15. Nanopublication Indexes Sets of nanopublications can be described as indexes that are nanopublications themselves. This allows us to define arbitrary sets, while keeping the individual addressability of the data entries: (a) (b) (c) (f) (d) (e) has element has sub-index appends to Kuhn et al. Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of Data. arXiv:1411.2749. Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 15 / 19
  • 16. Nanopublication Server Network Nanopublications with Trusty URIs Publication Retrieval Propagation / Archiving http://npmonitor.inn.ac Kuhn et al. Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of Data. arXiv:1411.2749. Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 16 / 19
  • 17. How to Review Data? • Large data sets only allow for samples of data entries to be manually reviewed • Data is often produced and consumed by algorithms: How can these data be linked to the algorithms. How should the data and the algorithms be reviewed? • Certain kinds of technical reviewing can be automated! • Can all this be achieved in an fashion that is decentralized, open, and real-time? Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 17 / 19
  • 18. Bots and Reputation Mechanisms Robust automatic calculation of reputation metrics in a decentralized and open system: gives positive assessment for is contributed by Eigenvector centrality (0-100) 77 Eigenvector centrality with bidirectional contribution edges 77 100 71 1 0 85 4 0.0 0 0 50 50 0 0.4 0.4 0 98 78 31 100 69 1 31 31 71 71 28 42 1 0.7 1 Kuhn. Science Bots: A Model for the Future of Scientific Computation? SAVE-SD 2015. Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 18 / 19
  • 19. Thank you for your attention! Questions? Tobias Kuhn, ETH Zurich Data Publishing and Post-Publication Reviews 19 / 19