Linked Data Publishing with Nanopublications
•
2 gefällt mir•383 views
The document discusses using nanopublications to address issues with how scientific findings are currently published and communicated. Nanopublications involve subdividing findings into small atomic assertions, attaching provenance and metadata to each assertion, and packaging them together as linked data packages called nanopublications. This allows for automated understanding and integration of scientific claims directly from publications. The approach enables reliable, decentralized publishing of scientific data on the web through the use of trustworthy identifiers.
Empfohlen
Empfohlen
Weitere ähnliche Inhalte
Was ist angesagt?
Was ist angesagt? (20)
Ähnlich wie Linked Data Publishing with Nanopublications
Ähnlich wie Linked Data Publishing with Nanopublications (20)
Mehr von Tobias Kuhn
Mehr von Tobias Kuhn (20)
Kürzlich hochgeladen
Kürzlich hochgeladen (20)
Linked Data Publishing with Nanopublications
- 1. 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
- 2. Problem: We Communicate through Papers that Software Can’t Understand scientific paper scientist Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 2 / 16
- 3. Problem: We Communicate through Papers that Software Can’t Understand millions of new papers every year scientific paper ?! scientist Which genes are related to mental diseases? Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 2 / 16
- 4. Problem: We Communicate through Papers that Software Can’t Understand millions of new papers every year scientific databases software scientific paper ?! scientist Which genes are related to mental diseases? Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 2 / 16
- 5. Automatic Text Mining is Not Good Enough World-leading text mining on chemical–disease relations: Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 3 / 16
- 6. Automatic Text Mining is Not Good Enough World-leading text mining on chemical–disease relations: Manual Text Mining is Slow and Expensive Around 50 biocurators employed to feed European protein databases: read papers & feed databases Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 3 / 16
- 7. New Paradigms of Scientific Publishing? scientist other scientists scientific papers Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 4 / 16
- 8. Where are we Now? Where is the Data? Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 5 / 16
- 9. Where is the Data? In the Supplementary Material ... Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 6 / 16
- 10. New Paradigms of Scientific Publishing? scientist other scientists scientific papers Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 7 / 16
- 11. A New Paradigm of Scientific Publishing scientist bits of formally structured knowledge scientific database causes( GeneX, DiseaseY ) other scientists Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 8 / 16
- 12. Nanopublications: Linked Data Containers for Provenance-Aware Semantic Publishing assertion provenance publication info nanopublication http://nanopub.org @nanopub org • Subdivide scientific findings into the smallest possible atomic pieces Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
- 13. Nanopublications: Linked Data Containers for Provenance-Aware Semantic Publishing assertion provenance publication info nanopublication http://nanopub.org @nanopub org • Subdivide scientific findings into the smallest possible atomic pieces • Attach provenance and metadata on that atomic level Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
- 14. Nanopublications: Linked Data Containers for Provenance-Aware Semantic Publishing assertion provenance publication info nanopublication http://nanopub.org @nanopub org • Subdivide scientific findings into the smallest possible atomic pieces • Attach provenance and metadata on that atomic level • Represent everything as Linked Data Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
- 15. Nanopublications: Linked Data Containers for Provenance-Aware Semantic Publishing assertion provenance publication info nanopublication http://nanopub.org @nanopub org • Subdivide scientific findings into the smallest possible atomic pieces • Attach provenance and metadata on that atomic level • Represent everything as Linked Data • Make a small package out of these three parts: assertion, provenance, publication info Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
- 16. Nanopublications: Linked Data Containers for Provenance-Aware Semantic Publishing assertion provenance publication info nanopublication http://nanopub.org @nanopub org • Subdivide scientific findings into the smallest possible atomic pieces • Attach provenance and metadata on that atomic level • Represent everything as Linked Data • Make a small package out of these three parts: assertion, provenance, publication info • Then we treat each of these small packages as an independent publication, and we call them nanopublications Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 9 / 16
- 17. 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/f7iPKK Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 10 / 16
- 18. Nanopublication Datasets dataset # nanopublications # statements GeneRIF/AIDA 156,026 2,340,390 OpenBEL 1.0 50,707 1,502,574 OpenBEL 20131211 74,173 2,186,874 DisGeNET v2.1.0.0 940,034 31,961,156 DisGeNET v3.0.0.0 1,018,735 34,636,990 neXtProt 4,025,981 156,263,513 LIDDI 98,085 2,051,959 Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 11 / 16
- 19. Reliable Identifiers (with Cryptographic Hashes) Make nanpublications ... Verifiable + Immutable + Permanent .trighttp://example.org/r1. RA 5AbXdpz5DcaYXCh9l3eI9ruBosiL5XDU3rxBbBaUO70 http://trustyuri.net/ Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 12 / 16
- 20. Decentralized and Reliable Publishing with a Nanopublication Server Network Nanopublications with Trusty URIs Publication Retrieval Propagation / Archiving http://purl.org/nanopub/monitor Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 13 / 16
- 21. Nanopublication Dataset Citations Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 14 / 16
- 22. Highly Reliable Data Publishing and Retrieval Reliable even when done automatically by software. Tobias Kuhn, VU University Amsterdam Linked Data Publishing with Nanopublications 15 / 16
- 23. 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
- 24. 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