This article provides an overview of BioASQ, a new competition on biomedical semantic indexing and question answering (QA). BioASQ aims to push towards systems that will allow biomedical workers to express their information needs in natural language and that will return concise and user-understandable answers by combining information from multiple sources of different kinds, including biomedical articles, databases, and ontologies. BioASQ encourages participants to adopt semantic indexing as a means to combine multiple information sources and to facilitate the matching of questions to answers. It also adopts a broad semantic indexing and QA architecture that subsumes current relevant approaches, even though no current system instantiates all of its components. Hence, the architecture can also be seen as our view of how relevant work from fields such as information retrieval, hierarchical classification, question answering, ontologies, and linked data can be combined, extended, and applied to biomedical question answering. BioASQ will develop publicly available benchmarks and it will adopt and possibly refine existing evaluation measures. The evaluation infrastructure of the competition will remain publicly available beyond the end of BioASQ.

Scarcity of training data for word sense disambiguation argues for the use of knowledge-based disambiguation methods, which rely on information available in terminological resources. Unfortunately, these resources are not generally optimized to perform word sense disambiguation. On the other hand, there are many examples of ambiguous biomedical words with context in MEDLINE. However, these examples of ambiguity are not labeled with their proper sense. We propose the integration of the UMLS and MEDLINE to create concept profiles which are used to perform knowledge-based word sense disambiguation. Our results show an accuracy of 0.8770 on a biomedical word sense disambiguation data set; this represents a statistically significant improvement over other knowledge-based methods based on the UMLS on this data set.

Knowledge engineering from experimental design (KEfED) is a novel approach based on the dependency relationships that occur between the variables of a scientific study. We used this approach to curate the experimental designs of ten scientific papers from a well-established database of HIV vaccine trials in non-human primates. The KEfED models provide a characteristic, data-oriented signature for each measurement made in the study. We present preliminary analysis of these manually-curated, detailed representations using our own open-source curation tools and show the multi-variate statistical analyses on the resultant models of experimental design. The analyses produced a visualization of the similarities between studies and an account of the dependency relationships across studies. We describe our approach in the context of a knowledge engineering strategy based on creating large-scale domain-independent repositories of experimental observatio

When constructing visualization pipelines using toolkits, developers must understand what sequencing of operators will transform their data from its raw state to some requested visual representation. In some cases, the requested visual representation must be generated from hybrid pipelines, composed of both toolkit-based and custom operators. Traditionally, developers learn about how to construct these visualization pipelines by word of mouth, by reading documentation and by inspecting code examples, all of which can be costly in terms of time and effort expended. The Visualization Knowledge Project (VisKo) is built on a knowledge base of visualization toolkit operators including rules for how operators are chained together to form pipelines. VisKo helps scientists by automatically generating and suggesting fully functional visualization pipelines, alleviating scientists from having to write any pipeline code. This paper reports on the kinds of knowledge required to support automatic pipeline generation as well our successes when applying VisKo to a number of visualizations scenarios spanning geophysics, environmental and materials science.

His informatics group built the reusable software platform for Stembook Despite the fact that we now have access to almost all peer reviewed (www.stembook.org), William Cohen exchanged and is orthogonal to any specific biomedical domain The growing size of the scientific literature has led to a number of ontology. We believe this approach will be extremely useful in attempts to automatically extract entities and relationships from drug discovery to break down information silos, increase information scientific papers, and then to populate databases with this extracted awareness and sharing, and integrate terminologies and information. In my group we have been exploring techniques data with documents and text, both public and private. We will for using this sort of extracted information for specific tasks, discuss applications we are currently developing in collaboration including "bootstrapping" to improve the coverage of an extraction with a major pharma.

Some humorous texts can be detected by stereotyped patterns and terminology. But a humorous story or situation is often an exaggeration of patterns that also occur in serious texts: novelty, unusual plot twists, and situations that disrupt normal social conventions. The same methods for detecting novelty in serious texts can be adapted to detecting novelty in a humorous situation, but with additional tests for features that make it humorous. To interpret and reason about natural language texts, VivoMind Research has developed a cognitive architecture based on societies of heterogeneous intercommunicating agents that use conceptual graphs (CGs) as the knowledge representation. CGs are designed for representing semantics at the level of sentences and paragraphs, but they must be related to larger patterns that span an entire story, article, or book. For detecting and analyzing large-scale patterns, catastrophe theoretical semantics has proved to be surprisingly effective. This article discusses applications to both fictional and nonfictional documents of various kinds, both serious and humorous.

Wandering is a problematic behavior that is common among people with dementia (PwD), and is highly influenced by the elders’ background and by contextual factors specific to the situation. We have developed the Ambient Augmented Memory System (AAMS) to support the caregiver to implement interventions based on providing external memory aids to the PwD. To provide a successful intervention, it is required to use an individualized approach that considers the context of the PwD situation. To reach this end, we extended the AAMS system to include an ontological model to support the context-aware tailoring of interventions for wandering. In this paper, we illustrate the ontology flexibility to personalize the AAMS system to support direct and indirect interventions for wandering through mobile devices.

Controlled natural languages (mostly English-based) recently have emerged as seemingly informal supplementary means for OWL ontology authoring, if compared to the formal notations that are used by professional knowledge engineers. In this paper we present by examples controlled Latvian language that has been designed to be compliant with the state of the art Attempto Controlled English. We also discuss relation with controlled Lithuanian language that is being designed in parallel.

Ontologies and rules are usually loosely coupled in knowledge representation formalisms. In fact, ontologies use open-world reasoning while the leading semantics for rules use non-monotonic, closed-world reasoning. One exception is the tightly-coupled framework of Minimal Knowledge and Negation as Failure (MKNF), which allows statements about individuals to be jointly derived via entailment from an ontology and inferences from rules. Nonetheless, the practical usefulness of MKNF has not always been clear, although recent work has formalized a general resolution-based method for querying MKNF when rules are taken to have the well-founded semantics, and the ontology is modeled by a general oracle. That work leaves open what algorithms should be used to relate the entailments of the ontology and the inferences of rules. In this paper we provide such algorithms, and describe the implementation of a query-driven system, CDF-Rules, for hybrid knowledge bases combining both (non-monotonic) rules under the well-founded semantics and a (monotonic) ontology, represented by a CDF Type-1 (ALQ) theory. To appear in Theory and Practice of Logic Programming (TPLP)

Rules complement and extend ontologies on the Semantic Web. We refer to these rules as onto-relational since they combine DL-based ontology languages and Knowledge Representation formalisms supporting the relational data model within the tradition of Logic Programming and Deductive Databases. Rule authoring is a very demanding Knowledge Engineering task which can be automated though partially by applying Machine Learning algorithms. In this chapter we show how Inductive Logic Programming (ILP), born at the intersection of Machine Learning and Logic Programming and considered as a major approach to Relational Learning, can be adapted to Onto-Relational Learning. For the sake of illustration, we provide details of a specific Onto-Relational Learning solution to the problem of learning rule-based definitions of DL concepts and roles with ILP.