Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach

The dramatic increase in the number of microbe descriptions in databases, reports, and papers presents a two-fold challenge for accessing the information: integration of heterogeneous data in a standard ontology-based representation and normalization of the textual descriptions by semantic analysis....

Full description

Saved in:

Bibliographic Details
Published in:	PloS one 2023-01, Vol.18 (1), p.e0272473-e0272473
Main Authors:	Dérozier, Sandra, Bossy, Robert, Deléger, Louise, Ba, Mouhamadou, Chaix, Estelle, Harlé, Olivier, Loux, Valentin, Falentin, Hélène, Nédellec, Claire
Format:	Article
Language:	eng
Subjects:	Analysis Biology and Life Sciences Biotechnology Computer and Information Sciences Computer Science Data integration Data mining Data Mining - methods Databases, Factual Descriptions Domains Ecology and Environmental Sciences Ecosystem Evaluation Habitats Information management Information processing Information sources Knowledge representation Life Sciences Microbiology Microbiology and Parasitology Microorganisms Ontology Open access journals Phenotype Phenotypes Taxonomy Vocabularies & taxonomies
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	The dramatic increase in the number of microbe descriptions in databases, reports, and papers presents a two-fold challenge for accessing the information: integration of heterogeneous data in a standard ontology-based representation and normalization of the textual descriptions by semantic analysis. Recent text mining methods offer powerful ways to extract textual information and generate ontology-based representation. This paper describes the design of the Omnicrobe application that gathers comprehensive information on habitats, phenotypes, and usages of microbes from scientific sources of high interest to the microbiology community. The Omnicrobe database contains around 1 million descriptions of microbe properties. These descriptions are created by analyzing and combining six information sources of various kinds, i.e. biological resource catalogs, sequence databases and scientific literature. The microbe properties are indexed by the Ontobiotope ontology and their taxa are indexed by an extended version of the taxonomy maintained by the National Center for Biotechnology Information. The Omnicrobe application covers all domains of microbiology. With simple or rich ontology-based queries, it provides easy-to-use support in the resolution of scientific questions related to the habitats, phenotypes, and uses of microbes. We illustrate the potential of Omnicrobe with a use case from the food innovation domain.
ISSN:	1932-6203 1932-6203