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Linking assertions to evidence with the MicroPublications ontology WG evidence 2014-03-26

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How can we link assertions to evidence in the scientific literature? …

How can we link assertions to evidence in the scientific literature?

Discussion about the MicroPublications ontology (http://purl.org/mp/ & see http://arxiv.org/abs/1305.3506 )

Presented to the WG Evidence Panel of the Addressing PDDI Evidence Gaps project https://sites.google.com/site/ddikrandir/home/wg-evidence-panel

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  • 1. Jodi Schneider http://jodischneider.com/jodi.html WG Evidence - Addressing PDDI Evidence Gaps March 26, 2014
  • 2. goal Record relationships between assertions and evidence Assertions: “there (is/is not) an interaction between A & B” “Enzyme E reduces clearance of drug D by 25%” Evidence: Scientific literature, drug product labeling, FDA guidance documents
  • 3. Boyce’s DIKB
  • 4. DIKB Assertions (siocns:content) “The aim of this study was to compare the pharmacokinetics of diltiazem its major metabolites in healthy human volunteers representing different CYP2D6 genotypes.” Evidence type (dikbEvidence:Evidence_type) dikbEvidence:EV_CT_PK_Genotype supports (is swanco:citesAsSupportingEvidence of) <http://dbmi-icode-01.dbmi.pitt.edu/dikb/resource/Assertions/9> desacetyldiltiazem_substrate_of_cyp2d6
  • 5. • Evidence
  • 6. MicropublicationsModel the relationship between assertions and evidence Features: Designed for bioinformatics Improves on previous models Integrates annotation (Domeo) Enhanced argumentative reasoning
  • 7. Micropublications
  • 8. Micropublications Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506
  • 9. Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506
  • 10. Micropublications Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506
  • 11. Micropublications as a new evidence model Can micropublications be used in the next version of the DIKB? Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506

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