Usability survey of biomedical question answering systems

Abstract We live in an age of access to more information than ever before. This can be a double-edged sword. Increased access to information allows for more informed and empowered researchers, while information overload becomes an increasingly serious risk. Thus, there is a need for intelligent information retrieval systems that can summarize relevant and reliable textual sources to satisfy a user's query. Question answering is a specialized type of information retrieval with the aim of returning precise short answers to queries posed as natural language questions. We present a review and comparison of three biomedical question answering systems: askHERMES (http://www.askhermes.org/), EAGLi (http://eagl.unige.ch/EAGLi/), and HONQA (http://services.hon.ch/cgi-bin/QA10/qa.pl).</p

Qualitative and quantitative simulation: bridging the gap*

Artificia

ISDB: Interaction Sentence Database

Abstract Background Rapid growth in the scientific literature available on-line continues to motivate shifting data analysis from humans to computers. For example, greater knowledge of sentence characteristics indicative of interaction between two biological entities is needed to aid in the creation of better-performing information extraction tools for effectively using this rich body of information. Findings The Interaction Sentence Database (ISDB) allows users to retrieve sets of sentences fitting specified characteristics. To support this, a database of sentences from abstracts in MEDLINE was created. The sentences in the database all contain at least two biomolecule terms and one interaction-indicating term. A web interface to the database allows the user to query for sentences containing an interaction-indicating term, a single biomolecule name, or two biomolecule names, as well as for a list of biomolecules co-occurring with a given biomolecule in at least one sentence. Conclusions The system supports researchers needing conveniently available sets of sample sentences for corpus-based research on sentence properties. It also illustrates a model architecture for a sentence-based retrieval system which would be useful to people seeking information and knowledge on-line. ISDB can be freely accessed over the Web at http://bioinformatics.ualr.edu/cgi-bin/services/ISDB/isdb.cgi, and the processed database will be provided upon request.</p

Combining Interval, Probabilistic, and Fuzzy Uncertainty: Foundations, Algorithms, Challenges – An Overview

Summary. Since the 1960s, many algorithms have been designed to deal with interval uncertainty. In the last decade, there has been a lot of progress in extending these algorithms to the case when we have a combination of interval, probabilistic, and fuzzy uncertainty. We provide an overview of related algorithms, results, and remaining open problems. 1 Main Problem Why indirect measurements? In many real-life situations, we are interested in the value of a physical quantity y that is difficult or impossible to measure directly. Examples of such quantities are the distance to a star and the amount of oil in a given well. Since we cannot measure y directly, a natural idea is to measure y indirectly. Specifically, we find some easier-to-measure quantities x1,..., xn which are related to y by a known relation y = f(x1,..., xn); this relation may be a simple functional transformation, or complex algorithm (e.g., for the amount of oil, numerical solution to an inverse problem). Then, to estimate y, we first measure the values of the quantities x1,..., xn, an