Posts Tagged ‘ontologies’

Linked Science 2014 paper: Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base

October 19th, 2014

Today I’m presenting a talk in the ISWC 2014 Workshop on Linked Science 2014—Making Sense Out of Data (LISC2014). The LISC2014 paper is joint work with Paolo Ciccarese, Tim Clark and Richard D. Boyce. Our goal is to make the evidence in a scientific knowledge base easier to access and audit — to make the knowledge base easier to maintain as scientific knowledge and drug safety regulations change. We are modeling evidence (data, methods, materials) from biomedical communications in the medication safety domain (drug-drug interactions).

The new architecture for the drug-drug interaction knowledge base is based on:

This is part of a 4-year National Library of Medicine project, “Addressing gaps in clinically useful evidence on drug-drug interactions” (1R01LM011838-01)

Abstract of our paper, “Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base.”:

Semantic web technologies can support the rapid and transparent validation of scientific claims by interconnecting the assumptions and evidence used to support or challenge assertions. One important application domain is medication safety, where more efficient acquisition, representation, and synthesis of evidence about potential drug-drug interactions is needed. Exposure to potential drug-drug interactions (PDDIs), defined as two or more drugs for which an interaction is known to be possible, is a significant source of preventable drug-related harm. The combination of poor quality evidence on PDDIs, and a general lack of PDDI knowledge by prescribers, results in many thousands of preventable medication errors each year. While many sources of PDDI evidence exist to help improve prescriber knowledge, they are not concordant in their coverage, accuracy, and agreement. The goal of this project is to research and develop core components of a new model that supports more efficient acquisition, representation, and synthesis of evidence about potential drug-drug interactions. Two Semantic Web models—the Micropublications Ontology and the Open Annotation Data Model—have great potential to provide linkages from PDDI assertions to their supporting evidence: statements in source documents that mention data, materials, and methods. In this paper, we describe the context and goals of our work, propose competency questions for a dynamic PDDI evidence base, outline our new knowledge representation model for PDDIs, and discuss the challenges and potential of our approach.

Citation: Schneider, Jodi, Paolo Ciccarese, Tim Clark, and Richard D. Boyce. “Using the Micropublications ontology and the Open Annotation Data Model to represent evidence within a drug-drug interaction knowledge base.” Linked Science 2014 at ISWC 2014.

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Reading Ontologically?

July 24th, 2011

What are the right ontologies for reading? And what kind of ontology support would let books recombine themselves, on the fly, in novel ways?

Today keyword searches within books and book collections is commonplace, highlighting a word in your ebook reader can bring up a definition, and dictionaries grab recent examples of word use from microblogs.1 But can’t we do more? But what kind of synthesis do we need (and what is possible) for supporting readers of literature, classics, and humanities texts?

Current approaches seem to aim at analysis (e.g. getting an overview of the literary works of a period with “distant reading”/”macroanalysis”) and at creating flexible critical editions (e.g. structural, sometimes overlapping markup, as in TEI-based editions and projects like Wendell Piez’ Sonneteer2.) I would call these “sensemaking” approaches rather than tools for reading.

I was intrigued by the Bible Ontology3 because of their tagline: “ever wanted to read and study the Bible Ontologically?” Yet I don’t really know what they mean by reading ontologically4.

Of course, they have recorded various pieces of data. For instance, for Rebekah, we see her children, siblings, birthplace, book and chapters she figures in, etc.: http://bibleontology.com/page/Rebekah.5

Rebekah, from bibleontology.com

They offer a SPARQL endpoint, so you can query. For instance, to find all the married women6 (live query result):

PREFIX bop: <http://bibleontology.com/property/>
select ?s ?o where {?s bop:isWifeOf ?o }

Intense and long-term work has gone into Bible concordances, scholarship, etc., so it seems like a great use case for “reading ontologically”. With theologians and others looking at the site, using the SPARQL endpoint, etc., perhaps someone will be able to tell me what that means!

  1. In 2003, Gregory Crane wrote that “Already the books in a digital library are beginning to read one another and to confer among themselves before creating a new synthetic document for review by their human readers.” When I first read it in 2006, that article seemed incredibly visionary to me. Yet these commonplace “syntheses” no longer seem extraordinary to me. []
  2. currently offline, but brilliant; do check back, meanwhile see also his Digital Humanities 2010 talk notes []
  3. It’s a bit disingenuous to advertise their work as an ontology: in fact they have applied the ontology, rather than just creating it. []
  4. even though I’ve given a talk about supporting reading with ontologies! []
  5. The most meaningful of their terms is the bop:isRelatedInEvent, perhaps since these events, like Isaac_blesses_Jacob, would require more analysis to discern. []
  6. Gender is not recorded so we can’t (yet) ask for all the women overall, though I’ve just asked about this. []

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