Linked Data Publishing with Nanopublications Tobias Kuhn http://www.tkuhn.org @txkuhn Department of Computer Science, VU University Amsterdam IOS Press 30 Year Anniversary Amsterdam, Netherlands 4 April 2017
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Linked Data Publishing with Nanopublications
Tobias Kuhn
http://www.tkuhn.org
@txkuhn
Department of Computer Science, VU University Amsterdam
IOS Press 30 Year AnniversaryAmsterdam, Netherlands
4 April 2017
Problem: We Communicate through Papersthat Software Can’t Understand
scientific paper
scientist
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 2 / 16
Problem: We Communicate through Papersthat Software Can’t Understand
millions of new papers every year
scientific paper
?!scientist
Which genes arerelated to
mental diseases?
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 2 / 16
Problem: We Communicate through Papersthat Software Can’t Understand
millions of new papers every year
scientific databases
software
scientific paper
?!scientist
Which genes arerelated to
mental diseases?
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 2 / 16
Automatic Text Mining isNot Good Enough
World-leading text mining onchemical–disease relations:
Manual Text Mining isSlow and Expensive
Around 50 biocurators employed tofeed European protein databases:
read papers &feed databases
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 3 / 16
Automatic Text Mining isNot Good Enough
World-leading text mining onchemical–disease relations:
Manual Text Mining isSlow and Expensive
Around 50 biocurators employed tofeed European protein databases:
read papers &feed databases
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 3 / 16
New Paradigms of Scientific Publishing?
scientist other scientists
scientific papers
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 4 / 16
Where are we Now? Where is the Data?
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 5 / 16
Where is the Data?In the Supplementary Material
...
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 6 / 16
New Paradigms of Scientific Publishing?
scientist other scientists
scientific papers
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 7 / 16
A New Paradigm of Scientific Publishing
scientistbits of formally
structured knowledge
scientific database
causes(GeneX,DiseaseY)
other scientists
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 8 / 16
Nanopublications: Linked Data Containers forProvenance-Aware Semantic Publishing
assertion
provenance
publication info
nanopublication
http://nanopub.org
@nanopub org
• Subdivide scientific findings into thesmallest possible atomic pieces
• Attach provenance and metadata onthat atomic level
• Represent everything as Linked Data
• Make a small package out of thesethree parts: assertion, provenance,publication info
• Then we treat each of these smallpackages as an independentpublication, and we call themnanopublications
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
Nanopublications: Linked Data Containers forProvenance-Aware Semantic Publishing
assertion
provenance
publication info
nanopublication
http://nanopub.org
@nanopub org
• Subdivide scientific findings into thesmallest possible atomic pieces
• Attach provenance and metadata onthat atomic level
• Represent everything as Linked Data
• Make a small package out of thesethree parts: assertion, provenance,publication info
• Then we treat each of these smallpackages as an independentpublication, and we call themnanopublications
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
Nanopublications: Linked Data Containers forProvenance-Aware Semantic Publishing
assertion
provenance
publication info
nanopublication
http://nanopub.org
@nanopub org
• Subdivide scientific findings into thesmallest possible atomic pieces
• Attach provenance and metadata onthat atomic level
• Represent everything as Linked Data
• Make a small package out of thesethree parts: assertion, provenance,publication info
• Then we treat each of these smallpackages as an independentpublication, and we call themnanopublications
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
Nanopublications: Linked Data Containers forProvenance-Aware Semantic Publishing
assertion
provenance
publication info
nanopublication
http://nanopub.org
@nanopub org
• Subdivide scientific findings into thesmallest possible atomic pieces
• Attach provenance and metadata onthat atomic level
• Represent everything as Linked Data
• Make a small package out of thesethree parts: assertion, provenance,publication info
• Then we treat each of these smallpackages as an independentpublication, and we call themnanopublications
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
Nanopublications: Linked Data Containers forProvenance-Aware Semantic Publishing
assertion
provenance
publication info
nanopublication
http://nanopub.org
@nanopub org
• Subdivide scientific findings into thesmallest possible atomic pieces
• Attach provenance and metadata onthat atomic level
• Represent everything as Linked Data
• Make a small package out of thesethree parts: assertion, provenance,publication info
• Then we treat each of these smallpackages as an independentpublication, and we call themnanopublications
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
Nanopublication Example
:assertion { :p occursIn: mesh:D004730 . :p geneProductOf: hgnc:3763 .}
:provenance { :assertion prov:hadPrimarySource pubmed:12891700 . }
:pubinfo { :np dct:created 2014-07-03 ; pav:createdBy orcid:0000-0001-6818-334X . }
Complete example: https://goo.gl/f7iPKKTobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 10 / 16
Nanopublication Datasets
dataset # nanopublications # statements
GeneRIF/AIDA 156,026 2,340,390OpenBEL 1.0 50,707 1,502,574OpenBEL 20131211 74,173 2,186,874DisGeNET v2.1.0.0 940,034 31,961,156DisGeNET v3.0.0.0 1,018,735 34,636,990neXtProt 4,025,981 156,263,513LIDDI 98,085 2,051,959
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 11 / 16
Reliable Identifiers(with Cryptographic Hashes)
Make nanpublications ...
XVerifiable
+
Immutable
+ �Permanent
.trighttp://example.org/r1. RA 5AbXdpz5DcaYXCh9l3eI9ruBosiL5XDU3rxBbBaUO70
http://trustyuri.net/
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 12 / 16
Decentralized and Reliable Publishing with aNanopublication Server Network
Nanopublicationswith Trusty URIs
Publication
Retrieval
Propagation / Archiving
http://purl.org/nanopub/monitor
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 13 / 16
Nanopublication Dataset Citations
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 14 / 16
Highly Reliable Data Publishing and Retrieval
Reliable even when done automatically by software.
So, be prepared for the raise of the Science Bots!
S C I E N C E B O T S
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 15 / 16
Highly Reliable Data Publishing and Retrieval
Reliable even when done automatically by software.
So, be prepared for the raise of the Science Bots!
S C I E N C E B O T S
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 15 / 16
Thank you for your attention!
Further information:
• Nanopublications: http://nanopub.org
• Trusty URIs: http://trustyuri.net
• More: http://www.tkuhn.org
Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 16 / 16
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