Biomedical information retrieval

Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain.

9p visteverogers 24-06-2023 3 2   Download

To present user needs and usability evaluations of DataMed, a Data Discovery Index (DDI) that allows searching for biomedical data from multiple sources. We conducted 2 phases of user studies. Phase 1 was a user needs analysis conducted before the development of DataMed, consisting of interviews with researchers. Phase 2 involved iterative usability evaluations of DataMed prototypes.

8p visteverogers 24-06-2023 6 1   Download

Information on protein-protein interactions affected by mutations is very useful for understanding the biological effect of mutations and for developing treatments targeting the interactions. In this study, we developed a natural language processing (NLP) based machine learning approach for extracting such information from literature.

10p vijeeni2711 30-06-2021 8 1   Download

A popular query from scientists reading a biomedical abstract is to search for topic-related documents in bibliographic databases. Such a query is challenging because the amount of information attached to a single abstract is little, whereas classification-based retrieval algorithms are optimally trained with large sets of relevant documents.

12p viwyoming2711 16-12-2020 13 1   Download

The proliferation of the scientific literature in the field of biomedicine makes it difficult to keep abreast of current knowledge, even for domain experts. While general Web search engines and specialized information retrieval (IR) systems have made important strides in recent decades, the problem of accurate knowledge extraction from the biomedical literature is far from solved.

14p vikentucky2711 26-11-2020 14 1   Download

This article provides an overview of the first BIOASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BIOASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-understandable answers to given natural language questions by combining information from biomedical articles and ontologies.

28p vikentucky2711 24-11-2020 15 1   Download

Semantic approaches such as concept-based information retrieval rely on a corpus in which resources are indexed by concepts belonging to a domain ontology. In order to keep such applications up-to-date, new entities need to be frequently annotated to enrich the corpus.

10p vikentucky2711 24-11-2020 16 1   Download

Identification of associations between marketed drugs and adverse events from the biomedical literature assists drug safety monitoring efforts. Assessing the significance of such literature-derived associations and determining the granularity at which they should be captured remains a challenge.

17p vioklahoma2711 19-11-2020 16 1   Download

Biomedical literature retrieval is becoming increasingly complex, and there is a fundamental need for advanced information retrieval systems. Information Retrieval (IR) programs scour unstructured materials such as text documents in large reserves of data that are usually stored on computers.

12p vioklahoma2711 19-11-2020 15 2   Download

The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved.

16p viconnecticut2711 28-10-2020 9 1   Download

Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient’s genome. This analysis relies on previously published information regarding the association of variations to disease progression and possible interventions.

11p vijisoo2711 27-10-2020 9 1   Download

In this paper, we demonstrate three NLP applications of the BioLexicon, which is a lexical resource tailored to the biology domain. The applications consist of a dictionary-based POS tagger, a syntactic parser, and query processing for biomedical information retrieval. Biological terminology is a major barrier to the accurate processing of literature within biology domain. In order to address this problem, we have constructed the BioLexicon using both manual and semiautomatic methods. We demonstrate the utility of the biology-oriented lexicon within three separate NLP applications. ...

4p bunthai_1 06-05-2013 48 3   Download

We present a practical HPSG parser for English, an intelligent search engine to retrieve MEDLINE abstracts that represent biomedical events and an efficient MEDLINE search tool helping users to find information about biomedical entities such as genes, proteins, and the interactions between them.

4p hongvang_1 16-04-2013 39 1   Download

Biomedical engineering and medical informatics represent challenging and rapidly growing areas. Applications of information technology in these areas are of paramount importance.

200p hyperion75 22-01-2013 63 7   Download

The U.S. Government supports a variety of research studies relating to borderline personality disorder. These studies are tracked by the Office of Extramural Research at the National Institutes of Health.2 CRISP (Computerized Retrieval of Information on Scientific Projects) is a searchable database of federally funded biomedical research projects conducted at universities, hospitals, and other institutions.

164p loaken_1 15-11-2012 44 2   Download

The concept of data or information processing arises in a variety of fields. Understanding the principles behind this concept is fundamental to computer design, communications, manufacturing process control, biomedical engineering, and an increasingly large number of other areas of technology and science. It is impossible to imagine modern life without computers for generating, analyzing, and retrieving large amounts of information, as well as communicating information to end users regardless of their location....

384p beobobeo 01-08-2012 70 11   Download