Cargando…

Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy

Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in r...

Descripción completa

Detalles Bibliográficos
Autor principal: Bekhuis, Tanja
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459187/
https://www.ncbi.nlm.nih.gov/pubmed/16584552
http://dx.doi.org/10.1186/1742-5581-3-2
_version_ 1782127471935619072
author Bekhuis, Tanja
author_facet Bekhuis, Tanja
author_sort Bekhuis, Tanja
collection PubMed
description Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information. Developments in text mining and hypothesis discovery systems based on the early work of Swanson, a mathematician and information scientist, are coincident with the emergence of conceptual biology. Very little has been written to introduce biomedical digital librarians to these new trends. In this paper, background for data and text mining, as well as for knowledge discovery in databases (KDD) and in text (KDT) is presented, then a brief review of Swanson's ideas, followed by a discussion of recent approaches to hypothesis discovery and testing. 'Testing' in the context of text mining involves partially automated methods for finding evidence in the literature to support hypothetical relationships. Concluding remarks follow regarding (a) the limits of current strategies for evaluation of hypothesis discovery systems and (b) the role of literature-based discovery in concert with empirical research. Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians.
format Text
id pubmed-1459187
institution National Center for Biotechnology Information
language English
publishDate 2006
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-14591872006-05-11 Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy Bekhuis, Tanja Biomed Digit Libr Review Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information. Developments in text mining and hypothesis discovery systems based on the early work of Swanson, a mathematician and information scientist, are coincident with the emergence of conceptual biology. Very little has been written to introduce biomedical digital librarians to these new trends. In this paper, background for data and text mining, as well as for knowledge discovery in databases (KDD) and in text (KDT) is presented, then a brief review of Swanson's ideas, followed by a discussion of recent approaches to hypothesis discovery and testing. 'Testing' in the context of text mining involves partially automated methods for finding evidence in the literature to support hypothetical relationships. Concluding remarks follow regarding (a) the limits of current strategies for evaluation of hypothesis discovery systems and (b) the role of literature-based discovery in concert with empirical research. Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians. BioMed Central 2006-04-03 /pmc/articles/PMC1459187/ /pubmed/16584552 http://dx.doi.org/10.1186/1742-5581-3-2 Text en Copyright © 2006 Bekhuis; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review
Bekhuis, Tanja
Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy
title Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy
title_full Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy
title_fullStr Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy
title_full_unstemmed Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy
title_short Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy
title_sort conceptual biology, hypothesis discovery, and text mining: swanson's legacy
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459187/
https://www.ncbi.nlm.nih.gov/pubmed/16584552
http://dx.doi.org/10.1186/1742-5581-3-2
work_keys_str_mv AT bekhuistanja conceptualbiologyhypothesisdiscoveryandtextminingswansonslegacy