neurocurator 0.4.4

Application to perform curation of neuroscientific literature.

Getting Started | Upgrade | Releases | Roadmap | Status

For the Annotation Viewer or the integration with theOpenMinTeDplatform, please refer to thisbranch.

NeuroCurator

Desktop application to perform systematic and collaborative curation of neuroscientific literature.

This is a Graphical User Interface (GUI) for the Python module NeuroAnnotation Toolbox (NAT).

This framework has been described in details in the following open-access paper: https://doi.org/10.3389/fninf.2017.00027.

With NeuroCurator, annotations are: - traceable, - reusable across projects, - structured with controlled vocabularies.

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Getting Started

Installation

After having installed Git and ImageMagick 6:

pip3 install neurocurator

If you would like to simplify the installation with Miniconda:

conda create --name nc python=3.7
conda activate nc
conda install beautifulsoup4 gitpython lxml numpy pandas scipy
pip install neurocurator

Requirements

• System side:

  • Python 3.4+

  • Qt 5.11+

  • Git 1.7.0+

  • ImageMagick 6

  • Miniconda (optional)

• Python side:

  • NAT

  • PyQt5

  • NumPy

  • pandas

  • Wand

Launch

neurocurator

If you have used Miniconda:

conda activate nc
neurocurator

Upgrade

pip install --upgrade neurocurator

If you have used Miniconda:

conda activate nc
pip install --upgrade neurocurator

Releases

Versions and their notable changes are listed in the releases section.

Roadmap

Ongoing

1. Make the annotations publishable into a Blue Brain Nexus instance.

2. Stabilize NeuroCurator and NAT (Software Architecture).

TODO

1. Integrate fully the Annotation Viewer into NeuroCurator.

2. Semi-automate the Knowledge Extraction process.

Done (latest first)

• Remove legacy dependencies in NeuroCurator (Qt 4 and Python 3.4).

• Integrate OpenMinTeD annotations into the literature curation framework.

• Visualize NeuroCurator and OpenMinTeD annotations directly on PDFs.

• Make NeuroCurator easily installable, especially by scientists.

Updated on 20.07.18.

Status

Created during 2016.

Ongoing stabilization and reengineering in the branch refactor-architecture.

The branch refactor-architecture is not intended to be used by end-users.

New features, bug fixes and improvements are done on the reengineered code sections.

When a reengineered code section is stable, it’s merged into the branch master and a release is published.