Over the past several years, our team has focused its efforts on improving retrieval precision performance by mixing visual and textual information. This year, we chose to explore ways in which we could use external data to enrich our retrieval system’s data set; specifically, we annotated each image in the test collection with a set of MeSH headings from two different sources: human-assigned M...

Research in bioinformatics in the past decade has generated a large volume of textual biological data stored in databases such as MEDLINE. It takes a copious amount of effort and time, even for expert users, to manually extract useful information embedded in such a large volume of retrieved data and automated intelligent text analysis tools are increasingly becoming essential. In this article, ...

OBJECTIVE In a previous study, we investigated a sentence classification model that uses semantic features to extract clinically useful sentences from UpToDate, a synthesized clinical evidence resource. In the present study, we assess the generalizability of the sentence classifier to Medline abstracts. METHODS We applied the classification model to an independent gold standard of high qualit...

A natural language parser that could extract noun phrases for all medical texts would be of great utility in analyzing content for information retrieval. We discuss the extraction of noun phrases from MEDLINE, using a general parser not tuned specifically for any medical domain. The noun phrase extractor is made up of three modules: tokenization; part-of-speech tagging; noun phrase identificati...

MOTIVATION Abbreviations are an important type of terminology in the biomedical domain. Although several groups have already created databases of biomedical abbreviations, these are either not public, or are not comprehensive, or focus exclusively on acronym-type abbreviations. We have created another abbreviation database, ADAM, which covers commonly used abbreviations and their definitions (o...

OBJECTIVES Clinical prediction rules have been advocated as a possible mechanism to enhance clinical judgment in diagnostic, therapeutic, and prognostic assessment. Despite renewed interest in the their use, inconsistent terminology makes them difficult to index and retrieve by computerized search systems. No validated approaches to locating clinical prediction rules appear in the literature. T...

A growing body of works address automated mining of biochemical knowledge from digital repositories of scientific literature, such as MEDLINE. Some of these works use abstracts as the unit of text from which to extract facts. Others use sentences for this purpose, while still others use phrases. Here we compare abstracts, sentences, and phrases in MEDLINE using the standard information retrieva...

Adverse drug events and drug-drug interactions are a major concern in patient care. Although databases exist to provide information about drugs, they are not always up-to-date and complete (particularly regarding pharmacogenetics). We propose a methodology based on automatic summarization to identify drug information in Medline citations and present results to the user in a convenient form. We ...