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

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