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Trusty URIs: Verifiable, Immutable, and
Permanent Digital Artifacts for Linked Data
#eswc2014Kuhn
Tobias Kuhn and Michel Dumontier
http://www.tkuhn.ch / http://dumontierlab.com
@txkuhn / @micheldumontier
ETH Zurich / Stanford University
ESWC
27 May 2014
Motivation 1
The Semantic Web: Web content becomes machine-interpretable.
Machines (i.e. algorithms) can then perform — on large amounts of
linked data — tasks such as: automated aggregation, complex
searches, problem solving, recommendations, and much more ...
!
But wait... even human users are often easy to trick by spam and
fraudulent content found on the web. We should be even more
concerned in the case of machines!
Tobias Kuhn, ETH Zurich Trusty URIs 2 / 20
Motivation 2
Sue publishes a script that allows everybody to replicate her scientific
analysis:
# Download data:
wget http://some-third-party.org/dataset/1.4
# Analyze data
...
But what if the third party silently changes that version of the
dataset? What if the resource becomes unavailable at this location?
What if the web site later gets hacked and the data manipulated?
Tobias Kuhn, ETH Zurich Trusty URIs 3 / 20
Motivation 3
Nanopublications: Atomic pieces of scientific results together with
their provenance, all represented in RDF.
• Citation networks: nanopubs can cite or refer to other nanopubs
• Nanopubs are supposed to be immutable
Problem:
• A scientist citing something wants to be sure that it is not
silently changed afterwards
• The current web has no mechanism to enforce immutability
Tobias Kuhn, ETH Zurich Trusty URIs 4 / 20
Problem
http://some-third-party.org/dataset/1.4
?
Given a URI for a digital artifact, there is no reliable standard
procedure of checking whether a retrieved file really represents the
correct and original state of that artifact.
Tobias Kuhn, ETH Zurich Trusty URIs 5 / 20
We need URIs we can Trust!
Trusty URIs
Tobias Kuhn, ETH Zurich Trusty URIs 6 / 20
Trusty URIs
Basic idea: Use of cryptographic hash values calculated on digital
artifacts.
Requirements:
• To allow for the verification of entire reference trees, the hash
should be part of the reference (i.e. the URI)
• To allow for meta-data, digital artifacts should be allowed to
contain self-references (i.e. their own URI)
• Format-independent hash for different kinds of content
• The complete approach should be decentralized and open
• We want to use them right away
Example:
http://example.org/r1.RA5AbXdpz5DcaYXCh9l3eI9ruBosiL5XDU3rxBbBaUO70
Tobias Kuhn, ETH Zurich Trusty URIs 7 / 20
Trusty URIs: Range of Verifiability
With the hash as a part of the URI, the “range of verifiability”
extends to referenced artifacts (if they also use trusty URIs):
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
Tobias Kuhn, ETH Zurich Trusty URIs 8 / 20
Trusty URI Modules
Currently, there are two trusty URI modules:
• FA: Plain files (i.e. byte sequences)
• RA: Sets of RDF graphs
• More to come in the future...
The first character (F or R) represents the type of the module; the
second character (A) its version.
Tobias Kuhn, ETH Zurich Trusty URIs 9 / 20
Example: Nanobrowser
1
2
http://nanobrowser.inn.ac
Tobias Kuhn, ETH Zurich Trusty URIs 10 / 20
Verifiable — Immutable — Permanent
Whether or not a given resource is the one a given trusty URI is
supposed to represent can be verified with perfect confidence.
(assuming that the trusty URI for the required artifact is known, e.g. because
another artifact contains it as a link)
Tobias Kuhn, ETH Zurich Trusty URIs 11 / 20
Verifiable — Immutable — Permanent
Trusty URI artifacts are immutable, as any change in the content
also changes its URI, thereby making it a new artifact.
(as soon as your trusty URI has been picked up by third parties, e.g. cached or
linked from other resources, every change will be noticed)
Tobias Kuhn, ETH Zurich Trusty URIs 12 / 20
Verifiable — Immutable — Permanent
Trusty URI artifacts are permanent, as they can be retrieved from
the cache of third-party websites if otherwise no longer available.
(if there are search engines and web archives regularly crawling and caching the
artifacts on the web)
Tobias Kuhn, ETH Zurich Trusty URIs 13 / 20
Permanent Digital Artifacts
Ideally, a (trusty) artifact should be retrievable via its URI:
⇒ http://my-organization.org/datasets/RA5AbX...
But if not, we can also retrieve it from third-party sources:
http://my-organization.org/datasets/RA5AbX...
⇒ http://hashcache.org/object/RA5AbX...
⇒ http://artifact-archive.com/artifacts/RA5AbX...
⇒ http://nasty-server.com/no-need-to-trust-me/RA5AbX...
Trusty URI artifacts
Tobias Kuhn, ETH Zurich Trusty URIs 14 / 20
Implementations
(Partial) Implementations in:
• Java (https://github.com/trustyuri/trustyuri-java)
• Python (https://github.com/trustyuri/trustyuri-python)
• Perl (https://github.com/trustyuri/trustyuri-perl)
• more to come...
Functions:
• General: CheckFile, RunBatch
• Module FA only: ProcessFile
• Module RA only: TransformRdf, TransformLargeRdf,
TransformNanopub, CheckLargeRdf, CheckSortedRdf,
CheckNanopubViaSparql
• more to come...
Tobias Kuhn, ETH Zurich Trusty URIs 15 / 20
Evaluation 1: Nanopubs
We took ∼150,000 nanopublications from previous work, transformed
them to different formats (TriG, N-Quads, and TriX), and then
generated trusty URIs for them.
⇒ For any given nanopub, the same trusty URI was generated for
the different formats
Then we checked these trusty URIs, also for corrupted copies of the
files (one random byte changed).
⇒ All non-corrupted files are successfully validated
⇒ All corrupted files either lead to errors or the validation fails
(except for <1% harmless cases in TriX format where the
changed byte is not part of the RDF content)
⇒ Checking with Java in batch mode takes 0.001s per nanopub
Tobias Kuhn, ETH Zurich Trusty URIs 16 / 20
Evaluation 2: Bio2RDF
To evaluate our approach on larger files, we transformed and checked
858 RDF files from Bio2RDF.
• File sizes ranging from 1.4kB to 177GB
⇒ Files smaller than 10MB require less than 3 seconds to be
transformed or checked
⇒ Large files of 2GB require ∼5min to be transformed and ∼2min
to be checked
⇒ Largest file of 177GB (much larger than memory) required 29h
to be transformed and 3h to be checked
Tobias Kuhn, ETH Zurich Trusty URIs 17 / 20
Make This a Community Effort
Code on GitHub: https://github.com/trustyuri/
Permissive Open Source License
Open Development: Let us know if you want to be involved!
Wiki (including wish list):
https://github.com/trustyuri/trustyuri/wiki
Tobias Kuhn, ETH Zurich Trusty URIs 18 / 20
Conclusions and Future Work
Contribution:
• Unambiguous URI references for verifiable, immutable, and
permanent digital artifacts
• Proposal of a central technical pillar of the (semantic) web
• In particular for scientific data, where provenance and
verifiability are crucial
Planned usage:
• Next version of Bio2RDF
• Nanopublications for neXtProt (currently ∼20 million nanopubs)
• Nanopub server (for publishing and archiving nanopubs)
Tobias Kuhn, ETH Zurich Trusty URIs 19 / 20
Thank you for your Attention!
Twitter: @txkuhn and #eswc2014Kuhn
Web: http://trustyuri.net
Tobias Kuhn, ETH Zurich Trusty URIs 20 / 20
Some Additional Slides Follow...
Tobias Kuhn, ETH Zurich Trusty URIs 21 / 20
Related Approaches
Git inspired the design of trusty URIs: Git refers to commits by hash
values calculated in a recursive way.
Named Information (ni) URIs:
ni:///sha-256;UyaQV-Ev4rdLoHyJJWCi11OHfrYv9E1aGQAlMO2X_-Q
(Trusty URIs can be mapped to ni-URIs.)
What is missing in these approaches:
• Digital artifacts on a more abstract level than byte sequences
• Support for self-references
Tobias Kuhn, ETH Zurich Trusty URIs 22 / 20
Skolemization of Blank Nodes
The hash also helps us to solve the problem of blank nodes for
canonicalization of RDF content: We use the hash to skolemize blank
nodes:
http://foo.org/r3.RACjKTA5dl23ed7JIpgPmS0E0dcU-XmWIBnGn6Iyk8B-U# 1
http://foo.org/r3.RACjKTA5dl23ed7JIpgPmS0E0dcU-XmWIBnGn6Iyk8B-U# 2
...
These URIs are guaranteed to have never been used before (except
possibly for exactly the same content).
Tobias Kuhn, ETH Zurich Trusty URIs 23 / 20
Performance for Nanopubs in Batch Mode
Tobias Kuhn, ETH Zurich Trusty URIs 24 / 20
Performance for Large Files (Bio2RDF)
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file size in bytes
secondsperfile
TransformLargeRdf
TransformRdf
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file size in bytes
secondsperfile
CheckLargeRdf
CheckFile
CheckSortedRdf
Tobias Kuhn, ETH Zurich Trusty URIs 25 / 20

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Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data

  • 1. Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data #eswc2014Kuhn Tobias Kuhn and Michel Dumontier http://www.tkuhn.ch / http://dumontierlab.com @txkuhn / @micheldumontier ETH Zurich / Stanford University ESWC 27 May 2014
  • 2. Motivation 1 The Semantic Web: Web content becomes machine-interpretable. Machines (i.e. algorithms) can then perform — on large amounts of linked data — tasks such as: automated aggregation, complex searches, problem solving, recommendations, and much more ... ! But wait... even human users are often easy to trick by spam and fraudulent content found on the web. We should be even more concerned in the case of machines! Tobias Kuhn, ETH Zurich Trusty URIs 2 / 20
  • 3. Motivation 2 Sue publishes a script that allows everybody to replicate her scientific analysis: # Download data: wget http://some-third-party.org/dataset/1.4 # Analyze data ... But what if the third party silently changes that version of the dataset? What if the resource becomes unavailable at this location? What if the web site later gets hacked and the data manipulated? Tobias Kuhn, ETH Zurich Trusty URIs 3 / 20
  • 4. Motivation 3 Nanopublications: Atomic pieces of scientific results together with their provenance, all represented in RDF. • Citation networks: nanopubs can cite or refer to other nanopubs • Nanopubs are supposed to be immutable Problem: • A scientist citing something wants to be sure that it is not silently changed afterwards • The current web has no mechanism to enforce immutability Tobias Kuhn, ETH Zurich Trusty URIs 4 / 20
  • 5. Problem http://some-third-party.org/dataset/1.4 ? Given a URI for a digital artifact, there is no reliable standard procedure of checking whether a retrieved file really represents the correct and original state of that artifact. Tobias Kuhn, ETH Zurich Trusty URIs 5 / 20
  • 6. We need URIs we can Trust! Trusty URIs Tobias Kuhn, ETH Zurich Trusty URIs 6 / 20
  • 7. Trusty URIs Basic idea: Use of cryptographic hash values calculated on digital artifacts. Requirements: • To allow for the verification of entire reference trees, the hash should be part of the reference (i.e. the URI) • To allow for meta-data, digital artifacts should be allowed to contain self-references (i.e. their own URI) • Format-independent hash for different kinds of content • The complete approach should be decentralized and open • We want to use them right away Example: http://example.org/r1.RA5AbXdpz5DcaYXCh9l3eI9ruBosiL5XDU3rxBbBaUO70 Tobias Kuhn, ETH Zurich Trusty URIs 7 / 20
  • 8. Trusty URIs: Range of Verifiability With the hash as a part of the URI, the “range of verifiability” extends to referenced artifacts (if they also use trusty URIs): 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 Tobias Kuhn, ETH Zurich Trusty URIs 8 / 20
  • 9. Trusty URI Modules Currently, there are two trusty URI modules: • FA: Plain files (i.e. byte sequences) • RA: Sets of RDF graphs • More to come in the future... The first character (F or R) represents the type of the module; the second character (A) its version. Tobias Kuhn, ETH Zurich Trusty URIs 9 / 20
  • 11. Verifiable — Immutable — Permanent Whether or not a given resource is the one a given trusty URI is supposed to represent can be verified with perfect confidence. (assuming that the trusty URI for the required artifact is known, e.g. because another artifact contains it as a link) Tobias Kuhn, ETH Zurich Trusty URIs 11 / 20
  • 12. Verifiable — Immutable — Permanent Trusty URI artifacts are immutable, as any change in the content also changes its URI, thereby making it a new artifact. (as soon as your trusty URI has been picked up by third parties, e.g. cached or linked from other resources, every change will be noticed) Tobias Kuhn, ETH Zurich Trusty URIs 12 / 20
  • 13. Verifiable — Immutable — Permanent Trusty URI artifacts are permanent, as they can be retrieved from the cache of third-party websites if otherwise no longer available. (if there are search engines and web archives regularly crawling and caching the artifacts on the web) Tobias Kuhn, ETH Zurich Trusty URIs 13 / 20
  • 14. Permanent Digital Artifacts Ideally, a (trusty) artifact should be retrievable via its URI: ⇒ http://my-organization.org/datasets/RA5AbX... But if not, we can also retrieve it from third-party sources: http://my-organization.org/datasets/RA5AbX... ⇒ http://hashcache.org/object/RA5AbX... ⇒ http://artifact-archive.com/artifacts/RA5AbX... ⇒ http://nasty-server.com/no-need-to-trust-me/RA5AbX... Trusty URI artifacts Tobias Kuhn, ETH Zurich Trusty URIs 14 / 20
  • 15. Implementations (Partial) Implementations in: • Java (https://github.com/trustyuri/trustyuri-java) • Python (https://github.com/trustyuri/trustyuri-python) • Perl (https://github.com/trustyuri/trustyuri-perl) • more to come... Functions: • General: CheckFile, RunBatch • Module FA only: ProcessFile • Module RA only: TransformRdf, TransformLargeRdf, TransformNanopub, CheckLargeRdf, CheckSortedRdf, CheckNanopubViaSparql • more to come... Tobias Kuhn, ETH Zurich Trusty URIs 15 / 20
  • 16. Evaluation 1: Nanopubs We took ∼150,000 nanopublications from previous work, transformed them to different formats (TriG, N-Quads, and TriX), and then generated trusty URIs for them. ⇒ For any given nanopub, the same trusty URI was generated for the different formats Then we checked these trusty URIs, also for corrupted copies of the files (one random byte changed). ⇒ All non-corrupted files are successfully validated ⇒ All corrupted files either lead to errors or the validation fails (except for <1% harmless cases in TriX format where the changed byte is not part of the RDF content) ⇒ Checking with Java in batch mode takes 0.001s per nanopub Tobias Kuhn, ETH Zurich Trusty URIs 16 / 20
  • 17. Evaluation 2: Bio2RDF To evaluate our approach on larger files, we transformed and checked 858 RDF files from Bio2RDF. • File sizes ranging from 1.4kB to 177GB ⇒ Files smaller than 10MB require less than 3 seconds to be transformed or checked ⇒ Large files of 2GB require ∼5min to be transformed and ∼2min to be checked ⇒ Largest file of 177GB (much larger than memory) required 29h to be transformed and 3h to be checked Tobias Kuhn, ETH Zurich Trusty URIs 17 / 20
  • 18. Make This a Community Effort Code on GitHub: https://github.com/trustyuri/ Permissive Open Source License Open Development: Let us know if you want to be involved! Wiki (including wish list): https://github.com/trustyuri/trustyuri/wiki Tobias Kuhn, ETH Zurich Trusty URIs 18 / 20
  • 19. Conclusions and Future Work Contribution: • Unambiguous URI references for verifiable, immutable, and permanent digital artifacts • Proposal of a central technical pillar of the (semantic) web • In particular for scientific data, where provenance and verifiability are crucial Planned usage: • Next version of Bio2RDF • Nanopublications for neXtProt (currently ∼20 million nanopubs) • Nanopub server (for publishing and archiving nanopubs) Tobias Kuhn, ETH Zurich Trusty URIs 19 / 20
  • 20. Thank you for your Attention! Twitter: @txkuhn and #eswc2014Kuhn Web: http://trustyuri.net Tobias Kuhn, ETH Zurich Trusty URIs 20 / 20
  • 21. Some Additional Slides Follow... Tobias Kuhn, ETH Zurich Trusty URIs 21 / 20
  • 22. Related Approaches Git inspired the design of trusty URIs: Git refers to commits by hash values calculated in a recursive way. Named Information (ni) URIs: ni:///sha-256;UyaQV-Ev4rdLoHyJJWCi11OHfrYv9E1aGQAlMO2X_-Q (Trusty URIs can be mapped to ni-URIs.) What is missing in these approaches: • Digital artifacts on a more abstract level than byte sequences • Support for self-references Tobias Kuhn, ETH Zurich Trusty URIs 22 / 20
  • 23. Skolemization of Blank Nodes The hash also helps us to solve the problem of blank nodes for canonicalization of RDF content: We use the hash to skolemize blank nodes: http://foo.org/r3.RACjKTA5dl23ed7JIpgPmS0E0dcU-XmWIBnGn6Iyk8B-U# 1 http://foo.org/r3.RACjKTA5dl23ed7JIpgPmS0E0dcU-XmWIBnGn6Iyk8B-U# 2 ... These URIs are guaranteed to have never been used before (except possibly for exactly the same content). Tobias Kuhn, ETH Zurich Trusty URIs 23 / 20
  • 24. Performance for Nanopubs in Batch Mode Tobias Kuhn, ETH Zurich Trusty URIs 24 / 20
  • 25. Performance for Large Files (Bio2RDF) 10 3 10 4 10 5 10 6 10 7 10 8 10 9 10 10 10 11 10 12 10 −3 10 −2 10 −1 10 0 10 1 10 2 10 3 10 4 10 5 file size in bytes secondsperfile TransformLargeRdf TransformRdf 10 3 10 4 10 5 10 6 10 7 10 8 10 9 10 10 10 11 10 12 10 −3 10 −2 10 −1 10 0 10 1 10 2 10 3 10 4 10 5 file size in bytes secondsperfile CheckLargeRdf CheckFile CheckSortedRdf Tobias Kuhn, ETH Zurich Trusty URIs 25 / 20