Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base

Citation: Jodi Schneider, Paolo Ciccarese, Tim Clark, Richard D. Boyce (2014) Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base. ISWC 2014 Workshop on Linked Science 2014—Making Sense Out of Data (LISC2014) (RSS)
Internet Archive Scholar (search for fulltext): Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base
Download: http://jodischneider.com/pubs/lisc2014.pdf
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Summary

Explore using micropublications (MP) and open annotation (OA) data model ontologies to improve state of the art of potential drug-drug interaction (PDDI) knowledge management.

"OA enables queryable links between selections from source documents (as target) to the instances of data, methods, and materials (as body) that we want to model to support drug interaction knowledge base use cases"

MP can "present the data, methods, and materials that act as support for a claim, and to transitively close chains of claims and citations across the literature to their fundamental supporting evidence"

Drug Interaction Knowledge Base (2007-2009) is less fine-grained and less queryable.

Authors elicited "competency questions" from editors of clinical drug compendia they would ask to find assertions and evidence, assess evidence, update evidence and assertions, and understand the evidence base. Authors' proposed model appears to support questions better than DIKB.

"Further, as a Linked Data resource, our new knowledge base will also enable innovative queries using knowledge from other sources about tagged entities (i.e., drugs and proteins) represented in the evidence base. Unlike the current DIKB, we will be able to render annotations in their original context. We also expect to be able to support distributed community annotation/curation, since MP and OA take account of provenance, and since OA is being increasingly adopted by a variety of annotation tools."

Theoretical and Practical Relevance

Blog post and slides at http://jodischneider.com/blog/2014/10/19/linked-science-2014-paper-using-the-micropublications-ontology-and-the-open-annotation-data-model-to-represent-evidence-within-a-drug-drug-interaction-knowledge-base/

Provides a data point on how annotation methodologies and linked data state of art have improved over 5+ years.