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Increasing the nanopublication recall with a BridgeDb Identifier Mapping Service

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Presentation at SWAT4HCLS about using BridgeDb to overcome the problem that nanopublications may use different IRIs for the same concept.

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Increasing the nanopublication recall with a BridgeDb Identifier Mapping Service

  1. 1. Increasing the nanopublication recall with a BridgeDb Identifier Mapping Service Egon Willighagen SWAT4HCLS, Antwerp/BE 2018-12-04 ORCID: 0000-0001-7542-0286 @egonwillighagen CC-BY 4.0 (unless otherwise specified)
  2. 2. Libraries of small publications around the world (npmonitor.inn.ac)
  3. 3. Nanopublications (better keywords) (Above: not CC-BY!) T. Kuhn, Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data, arXiv, 2018, https://arxiv.org/pdf/1809.06532.pdf Copyright: nanopub.org
  4. 4. Nanopublications (WikiPathways) sub:head { this: a np:Nanopublication . np:hasAssertion sub:assertion ; np:hasProvenance sub:provenance ; np:hasPublicationInfo sub:publicationInfo ; } sub:assertion { <http://identifiers.org/ncbigene/25874> a wp:GeneProduct . <http://identifiers.org/ncbigene/51660> a wp:GeneProduct . <http://rdf.wikipathways.org/Pathway/WP534_r98729/Complex/f9a70> wp:organismName "Homo sapiens" ; wp:participant <http://identifiers.org/ncbigene/25874> , <http://identifiers.org/ncbigene/51660> ; a wp:Complex . } sub:provenance { <http://identifiers.org/wikipathways/WP534_r98729> dc:title "Glycolysis and Gluconeogenesis"@en . sub:assertion has-source: pmid:22628558 , <http://identifiers.org/wikipathways/WP534_r98729> . } sub:publicationInfo { this: dcterms:created "2018-12-04T01:08:59.168+01:00"^^xsd:dateTime ; dcterms:rights <http://creativecommons.org/publicdomain/zero/1.0/> ; prov:wasDerivedFrom <http://identifiers.org/wikipathways/WP534_r98729> . }
  5. 5. IRIs, cool, but... sub:assertion { <http://identifiers.org/ncbigene/25874> a wp:GeneProduct . <http://identifiers.org/ncbigene/51660> a wp:GeneProduct . <http://rdf.wikipathways.org/Pathway/WP534_r98729/Co mplex/f9a70> wp:organismName "Homo sapiens" ; wp:participant <http://identifiers.org/ncbigene/25874>, <http://identifiers.org/ncbigene/51660> ; a wp:Complex . }
  6. 6. Hypothesis: Mapping IRIs with BridgeDb <http://rdf.ebi.ac.uk/resource/ensembl/ENS G00000278103> ensemblterms:DEPENDENT <http://identifiers.org/hgnc/HGNC:50180> . www.bridgedb.org Brenninkmeijer C, et al. Scientific lenses over linked data: an approach to support task specific views of the data. A vision. In Proceedings of 2nd international workshop on linked science 2012
  7. 7. Docker of IMS Ehrhart F, et al. Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services. F1000Research. 2018 Sep 3;7.
  8. 8. Testing the hypothesis No Mappings - just the original IRIs from WIkiPathways Genes - NCBI Gene - Ensembl With Mappings - BridgeDb IMS mappings - similar IRIs - IRIs in other DBs - Mappings - Ensembl - NCBI - HGNC
  9. 9. Results: Direct versus BridgeDb ● WP241: 464 nanopubs (min: 10, max: 1000, median: 288) ● WP2059: 21 nanopubs (min: 0, max:1000, median:1) ● WP241: Δ9 IRIs (min: 7, max:23, median: 7) ● WP2059 Δ11 IRIs (min: 7, max: 29, median: 10). ● Mix of mappings ○ other databases ○ other pattern
  10. 10. Limitations • the improvement is only as good as the link sets • the Docker installation is not trivial • Alternative: everyone uses Wikidata^W the same IRI patterns
  11. 11. Conclusions Linking data on the Semantic Web needs IRI mapping • nanopublications provide a growing library of public knowledge (Kuhn 2018) • IRIs are a pain (many of them) - reason: semantic web • IRIs can be mapped with BridgeDb IMS • Limitations can be overcome Details in the SWAT4HCLS Proceedings. doi:10.6084/m9.figshare.7346384
  12. 12. Acknowledgements Manchester University: Prof. Carole Goble, Alasdair Gray (now HW), Christian Brenninkmeijer Maastricht University: Freddie Ehrhart, Jonathan Mélius, Andra Waagmeester Vrije Universiteit Amsterdam: Tobias Kuhn

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