1 NASUA, Biodiversity research and conservation section, Quito, Ecuador NASUA, Biodiversity research and conservation section Quito Ecuador.
2 Faculty of Arts and Science, Department of Biology, Concordia University, Montreal, Canada Faculty of Arts and Science, Department of Biology, Concordia University Montreal Canada.
3 Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands Faculty of Science, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam Amsterdam Netherlands.

Biodiversity Observations Miner: A web application to unlock primary biodiversity data from published literature.

Biodivers Data J. 2019;(7):e28737

Authors: Muñoz G, Kissling WD, van Loon EE

Abstract

Background: A considerable portion of primary biodiversity data is digitally locked inside published literature which is often stored as pdf files. Large-scale approaches to biodiversity science could benefit from retrieving this information and making it digitally accessible and machine-readable. Nonetheless, the amount and diversity of digitally published literature pose many challenges for knowledge discovery and retrieval. Text mining has been extensively used for data discovery tasks in large quantities of documents. However, text mining approaches for knowledge discovery and retrieval have been limited in biodiversity science compared to other disciplines.

New information: Here, we present a novel, open source text mining tool, the Biodiversity Observations Miner (BOM). This web application, written in R, allows the semi-automated discovery of punctual biodiversity observations (e.g. biotic interactions, functional or behavioural traits and natural history descriptions) associated with the scientific names present inside a corpus of scientific literature. Furthermore, BOM enable users the rapid screening of large quantities of literature based on word co-occurrences that match custom biodiversity dictionaries. This tool aims to increase the digital mobilisation of primary biodiversity data and is freely accessible via GitHub or through a web server.

PMID: 30692868 [PubMed]