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research article

A Framework for Collaborative Curation of Neuroscientific Literature

O'Reilly, Christian
•
Iavarone, Elisabetta  
•
Hill, Sean L.
2017
Frontiers in Neuroinformatics

Large models of complex neuronal circuits require specifying numerous parameters, with values that often need to be extracted from the literature, a tedious and error-prone process. To help establishing shareable curated corpora of annotations, we have developed a literature curation framework comprising an annotation format, a Python API (NeuroAnnotation Toolbox; NAT), and a user-friendly graphical interface (NeuroCurator). This framework allows the systematic annotation of relevant statements and model parameters. The context of the annotated content is made explicit in a standard way by associating it with ontological terms (e.g., species, cell types, brain regions). The exact position of the annotated content within a document is specified by the starting character of the annotated text, or the number of the figure, the equation, or the table, depending on the context. Alternatively, the provenance of parameters can also be specified by bounding boxes. Parameter types are linked to curated experimental values so that they can be systematically integrated into models. We demonstrate the use of this approach by releasing a corpus describing different modeling parameters associated with thalamo-cortical circuitry. The proposed framework supports a rigorous management of large sets of parameters, solving common difficulties in their traceability. Further, it allows easier classification of literature information and more efficient and systematic integration of such information into models and analyses.

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Type
research article
DOI
10.3389/fninf.2017.00027
Web of Science ID

WOS:000401366400001

Author(s)
O'Reilly, Christian
Iavarone, Elisabetta  
Hill, Sean L.
Date Issued

2017

Publisher

Frontiers Research Foundation

Published in
Frontiers in Neuroinformatics
Volume

11

Start page

27

Subjects

literature curation

•

neural network modeling

•

ontology

•

thalamocortical loop

•

annotation tools

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
BBP-GR-HILL  
BBP-CORE  
Available on Infoscience
April 19, 2017
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/136544
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