Knowledge Rich Natural Language Queries over Structured Biological Databases

Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity are undeniable for obvious reasons, their engineering is far from simple. In most part, semantics and intent preserving mapping of a well understood natural language query expressed over a structured database schema to a structured query language is still a difficult task, and research to tame the complexity is intense. In this paper, we propose a multi-level knowledge-based middleware to facilitate such mappings that separate the conceptual level from the physical level. We augment these multi-level abstractions with a concept reasoner and a query strategy engine to dynamically link arbitrary natural language querying to well defined structured queries. We demonstrate the feasibility of our approach by presenting a Datalog based prototype system, called BioSmart, that can compute responses to arbitrary natural language queries over arbitrary databases once a syntactic classification of the natural language query is made

Intuitive querying of e-Health data repositories

At the centre of the Clinical e-Science Framework (CLEF) project is a repository of well organised, detailed clinical histories, encoded as data that will be available for use in clinical care and in-silico medical experiments. An integral part of the CLEF workbench is a tool to allow biomedical researchers and clinicians to query – in an intuitive way – the repository of patient data. This paper describes the CLEF query editing interface, which makes use of natural language generation techniques in order to alleviate some of the problems generally faced by natural language and graphical query interfaces. The query interface also incorporates an answer renderer that dynamically generates responses in both natural language text and graphics

VOX : an extensible natural language processor

VOX is a Natural Language Processor whose knowledge can be extended by interaction with a user.VOX consists of a text analyzer and an extensibility system that share a knowledge base. The extensibility system lets the user add vocabulary, concepts, phrases, events, and scenarios to the knowledge base. The analyzer uses information obtained in this way to understand previously unhandled text.The underlying knowledge representation of VOX, called Conceptual Grammar, has been developed to meet the severe requirements of extensibility. Conceptual Grammar uniformly represents syntactic and semantic information, and permits modular addition of knowledge

Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer

Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value. With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial. While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains. In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of meaningful annotations needed by modern biomedical science. We present E.D., the Entity Describer, a mashup of the Connotea social tagging system, an index of semantic web-accessible controlled vocabularies, and a new public RDF database for storing social semantic annotations

Learning from AI : new trends in database technology

Recently some researchers in the areas of database data modelling and knowledge representations in artificial intelligence have recognized that they share many common goals. In this survey paper we show the relationship between database and artificial intelligence research. We show that there has been a tendency for data models to incorporate more modelling techniques developed for knowledge representations in artificial intelligence as the desire to incorporate more application oriented semantics, user friendliness, and flexibility has increased. Increasing the semantics of the representation is the key to capturing the "reality" of the database environment, increasing user friendliness, and facilitating the support of multiple, possibly conflicting, user views of the information contained in a database