Bridging the gap between coordinate- and keyword- based search of neuroscientific databases by UMLS-assisted semantic keyword extraction

Wilkowski, Bartłomiej; Szewczyk, MM; Hansen, LK

doi:10.1016/s1053-8119(09)71750-1

Cited by 2 publications

(1 citation statement)

References 2 publications

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“…The Brede database itself has had few updates since 2005. Wilkowski et al (2009b) also provide Skeepmed (Semantic Keyword Extraction Pipeline for Medical Documents;http://neuroinf. imm.dtu.dk/skeepmed/) to search for related abstracts by Talairach coordinates and text input.…”

Section: Introductionmentioning

confidence: 99%

BrainKnowledge: A Human Brain Function Mapping Knowledge-Base System

Hsiao

Chen

2010

Neuroinform

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Associating fMRI image datasets with the available literature is crucial for the analysis and interpretation of fMRI data. Here, we present a human brain function mapping knowledge-base system (BrainKnowledge) that associates fMRI data analysis and literature search functions. BrainKnowledge not only contains indexed literature, but also provides the ability to compare experimental data with those derived from the literature. BrainKnowledge provides three major functions: (1) to search for brain activation models by selecting a particular brain function; (2) to query functions by brain structure; (3) to compare the fMRI data with data extracted from the literature. All these functions are based on our literature extraction and mining module developed earlier (Hsiao, Chen, Chen. Journal of Biomedical Informatics 42, 912-922, 2009), which automatically downloads and extracts information from a vast amount of fMRI literature and generates co-occurrence models and brain association patterns to illustrate the relevance of brain structures and functions. BrainKnowledge currently provides three co-occurrence models: (1) a structure-to-function co-occurrence model; (2) a function-to-structure co-occurrence model; and (3) a brain structure co-occurrence model. Each model has been generated from over 15,000 extracted Medline abstracts. In this study, we illustrate the capabilities of BrainKnowledge and provide an application example with the studies of affect. BrainKnowledge, which combines fMRI experimental results with Medline abstracts, may be of great assistance to scientists not only by freeing up resources and valuable time, but also by providing a powerful tool that collects and organizes over ten thousand abstracts into readily usable and relevant sources of information for researchers.

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Section: Introductionmentioning

confidence: 99%