ArticleFrontiers in neuroinformatics2009
Automated recognition of brain region mentions in neuroscience literature.
Article in Frontiers in neuroinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Knowledge mining of brain connectivity in massive literature based on transfer learning.Bioinformatics (Oxford, England) · 2024Article
- Application of Supervised Machine Learning to Extract Brain Connectivity Information from Neuroscience Research Articles.Interdisciplinary sciences, computational life sciences · 2021Article
- A Text Mining Pipeline Using Active and Deep Learning Aimed at Curating Information in Computational Neuroscience.Neuroinformatics · 2019Article
- Automated Neuroanatomical Relation Extraction: A Linguistically Motivated Approach with a PVT Connectivity Graph Case Study.Frontiers in neuroinformatics · 2016Article
- Brain-wide analysis of electrophysiological diversity yields novel categorization of mammalian neuron types.Journal of neurophysiology · 2015Article
- Large-scale extraction of brain connectivity from the neuroscientific literature.Bioinformatics (Oxford, England) · 2015Article
- Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application.Frontiers in neuroinformatics · 2015Article
- Automatic target validation based on neuroscientific literature mining for tractography.Frontiers in neuroanatomy · 2015Article
- NeuroElectro: a window to the world's neuron electrophysiology data.Frontiers in neuroinformatics · 2014Article
- Brede tools and federating online neuroinformatics databases.Neuroinformatics · 2014Article
- NeuroLex.org: an online framework for neuroscience knowledge.Frontiers in neuroinformatics · 2013Article
- Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text.Bioinformatics (Oxford, England) · 2012Article
- neuroVIISAS: approaching multiscale simulation of the rat connectome.Neuroinformatics · 2012Article
- Using text mining to link journal articles to neuroanatomical databases.The Journal of comparative neurology · 2012Article
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4 authors.
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Abstract
The ability to computationally extract mentions of neuroanatomical regions from the literature would assist linking to other entities within and outside of an article. Examples include extracting reports of connectivity or region-specific gene expression. To facilitate text mining of neuroscience literature we have created a corpus of manually annotated brain region mentions. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. The corpus is freely available at http://www.chibi.ubc.ca/WhiteText/.
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