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Pattern-based Search of Epigenomic Data Using GeNemo
Published on: October 8, 2017
EnvMine: a text-mining system for the automatic extraction of contextual information.
Javier Tamames1, Victor de Lorenzo
1Centro Nacional de Biotecnología (CNB), CSIC, C/Darwin 3, 28049 Madrid, Spain. jtamames@cnb.csic.es
BMC Bioinformatics
|June 3, 2010
Summary
EnvMine automatically extracts environmental data, including physicochemical variables and precise geographical locations, from text. This facilitates ecological studies by enabling direct comparison of environments and analysis of biogeographical patterns.
Area of Science:
- Ecology
- Bioinformatics
- Environmental Science
Background:
- Ecological studies require detailed environmental and sample descriptions, including physicochemical characteristics and precise geographical locations.
- Current methods for extracting this data from textual sources are manual and time-consuming.
- A standardized schema for annotating environmental features is lacking.
Purpose of the Study:
- To develop an automated text-mining tool, EnvMine, for extracting contextual environmental information.
- To retrieve physicochemical variables and geographical locations from various textual sources.
- To facilitate ecological analyses and the development of environmental feature annotation standards.
Main Methods:
- EnvMine utilizes text-mining techniques to identify physicochemical variables and their units of measurement.
- A Bayesian classifier distinguishes environmental descriptions from other text.
- Geographical locations are identified using databases like GeoNames, extracting coordinates (latitude and longitude).
Main Results:
- EnvMine achieves 92% recall with less than 1% error for physicochemical variable extraction.
- Geographical location identification yields 86% recall and 92% precision.
- The system enables distance calculations between identified locations.
Conclusions:
- EnvMine efficiently extracts crucial environmental data from diverse text sources, including scientific articles and web pages.
- The tool aids in determining precise sampling site locations and physicochemical variables, streamlining ecological analyses.
- EnvMine supports the establishment of standards for environmental feature annotation.
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