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WhiteText specifications


Unique identifier OMICS_33253
Name WhiteText
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Paul Pavlidis

Publications for WhiteText

WhiteText citations


A Framework for Collaborative Curation of Neuroscientific Literature

Front Neuroinform
PMCID: 5395614
PMID: 28469570
DOI: 10.3389/fninf.2017.00027

[…] -speech and syntactic dependencies, identifying named entities, etc. Other research teams have worked on developing pipelines for text-mining and automatic generation of annotation from papers (e.g., WhiteText French et al., , Sherlok Richardet et al., ) or on manually annotating in great details corpora of scientific papers (e.g., the CRAFT Bada et al., and the GENIA Kim et al., corpora) to ser […]


Automated Neuroanatomical Relation Extraction: A Linguistically Motivated Approach with a PVT Connectivity Graph Case Study

Front Neuroinform
PMCID: 5030238
PMID: 27708573
DOI: 10.3389/fninf.2016.00039

[…] We used the WhiteText corpus in order to compare our results with the previous studies (French et al., , ; Richardet et al., ) that used the same data set processed with the abbreviation expansion algorithm of Sc […]


Automatic target validation based on neuroscientific literature mining for tractography

Front Neuroanat
PMCID: 4445321
PMID: 26074781
DOI: 10.3389/fnana.2015.00066

[…] den and Dubach, ), Paxinos and Watson (Paxinos and Watson, ), Swanson (Puelles Lopez, ).The second NER (BrainNER) relies on a machine-learning model (linear chain conditional random field) trained on WhiteText, a manually annotated corpus of 18,242 brain region mentions (French, ; French et al., ). The advantage of this statistical approach is that the model will match complex brain region names, […]


Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application

Front Neuroinform
PMCID: 4439553
PMID: 26052282
DOI: 10.3389/fninf.2015.00013
call_split See protocol

[…] WhiteText Web was implemented with Google Web Toolkit 2.5.1 and the Apache Jena framework. User input is restricted to Neurolex brain regions that appear in the corpus. We note that this restriction i […]


NeuroElectro: a window to the world's neuron electrophysiology data

Front Neuroinform
PMCID: 4010726
PMID: 24808858
DOI: 10.3389/fninf.2014.00040

[…] etween different brain regions is being compiled by experts at the Brain Architecture Management System project (BAMS) across thousands of publications (Bota et al., ). Parallel to this effort is the WhiteText Project, which addresses a complementary goal by algorithmically mining brain region connectivity statements from journal abstracts using biomedical natural language processing (bioNLP) meth […]


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WhiteText institution(s)
Rotman Research Institute, University of Toronto, Toronto, ON, Canada; Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada; Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
WhiteText funding source(s)
Supported by the Natural Sciences and Engineering Research Council of Canada and the National Institutes of Health (GM076990).

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