HyQue: Evaluating scientific Hypotheses using semantic web technologies

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  • HyQue is a hypothesis-based query and evaluation tool
  • So we see the scientist asking a question …. [NEXT SLIDE]
  • … which they will test by developing hypotheses, carry out experiments to test these hypotheses, and then use the results to refine their research. What is missing from this representation is the interaction of the individual scientist with their community of scientists, sharing data and using the results of other’s experiments to inform their own work.What is a hypothesis?“a supposition or proposed explanation made on the basis of limited evidence as a starting point for further investigation” (OED)(Ideally) scientists revisit hypotheses as their research progressesUse new knowledge to incrementally improve hypotheses over time
  • Scientists are faced with an exponentially increasing amount of biological data on the Web and in scientific papers  it is possible that information and knowledge supporting or refuting a given hypothesis already exists finding it becomes the challengeAll of this information is available in different formats as wellWe, as individuals, cannot accurately evaluate hypotheses in this context and at a scale consistent with the coverage of relevant information resources  we need to develop methods leveraging computational power and reasoning to evaluate hypotheses based on large amounts of existing background informationCan we accurately evaluate hypotheses in this context and at a scale consistent with the coverage of relevant information resources?
  • The Hypothesis Browser HyBrow is one research project motivated by this problemHyBrow emphasizes consistency checking of hypotheses both internally (do all of the pieces of the hypothesis logically fit?) and with respect to external information – is this hypothesis consistent with what we know?Constraints – forbidden entity types or events or locations in a domain, for exampleRules – judgments of support or conflict given a set of factsFormulates hypotheses as composed of events, which involve entities interacting under a set of specified conditions
  • the GAL gene network in yeast Gal3p, gal4p and gal80p have transcriptional control over the transport gene, the enzymes and their own genes
  • We represent a hypothesis as a collection of propositions
  • Binary relations are insufficient
  • This is part of a hypothesis represented in N3 and used as input to HyQueNote: Binding between galactose and Gal3p does not return any results; there IS binding between Gal3p and Gal80p
  • A SPARQL construct statement is used to generate an RDF representation of the relevant results, which is passed to HyQue, parsed using ARC2 and evaluating using event specific rules
  • The RDF representing the evaluation of the input hypothesis is linked to both the hypothesis AND the data used to evaluate the hypothesis
  • This is a screenshot of some HyQue data in Virtuoso, a triple store system that we use to store and access RDF
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