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https://github.com/neuroelectro/neuroelectro_org
The NeuroElectro Project: Compiling information on neuron electrophysiology through literature text-mining.
https://github.com/neuroelectro/neuroelectro_org
Last synced: about 1 month ago
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The NeuroElectro Project: Compiling information on neuron electrophysiology through literature text-mining.
- Host: GitHub
- URL: https://github.com/neuroelectro/neuroelectro_org
- Owner: neuroelectro
- License: gpl-2.0
- Created: 2014-04-08T02:24:51.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2020-04-29T23:01:25.000Z (over 4 years ago)
- Last Synced: 2024-11-01T00:22:41.620Z (2 months ago)
- Language: HTML
- Homepage: neuroelectro.org
- Size: 15.9 MB
- Stars: 13
- Watchers: 9
- Forks: 5
- Open Issues: 95
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Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-neuroscience - NeuroElectro - Searchable database of neurons and their electrophysiological properties (extracted from literature) (Resources / Miscellaneous)
- open-computational-neuroscience-resources - NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data
- open-science-resources - NeuroElectro - Repository of data-mined and human-curated neuron celltype electrophysiological data
README
# NeuroElectro
[](https://gitter.im/neuroelectro/neuroelectro_org?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [](https://waffle.io/neuroelectro/neuroelectro_org)
The aim of the [**NeuroElectro Project**](https://neuroelectro.org) is to represent structured electrophysiological information from diverse neuron types. Currently, this information is obtained by text-mining and manually curating the neuroscience literature (see the [NeuroElectro Publications](http://www.neuroelectro.org/publications/) for details).
This repository encapsulates the majority of the features of the project, including text-mining (located in the folder labelled "article_text_mining"), the models specifying the relational database (implemented in Django), and the website front end and back end code (implemented in Python's Django web framework).
Interested collaborators and contributors should contact @stripathy or @rgerkin, post in the [Gitter chat](https://gitter.im/neuroelectro/neuroelectro_org), or post to the [Google Groups Mailing List](https://groups.google.com/forum/#!forum/neuroelectro).
## Code Repository Objectives
* **Information Management**
* Integrate and structure data related to neuron type electrophysiology, like resting membrane potentials or spike amplitudes
* Develop and maintain APIs for accessing and downloading data
* Keep data up-to-date
* **Text-mining**
* Apply algorithms for downloading neuroscience articles
* Identify electrophysiological parameters, neuron types and subtypes, and methodological information
* Identify experimental factors like use of genetically modified animals
* **Data Curation**
* Provide a curation interface for use by human curators to check and fix the text-mined content
* **Web Interface**
* Provide an interactive web interface where extracted data is viewable and searchable
* Ensure that all extracted data is trace-able back to its source
## Some use cases
* I want to know the average value of an electrophysiological parameter in a neuron type
* I want to find publications reporting electrophysiological data about my favorite neuron type
* I need realistic parameters to constrain my computational model of a neuron type
* I want to see how variable an electrophysiological property (like [resting membrane potential](http://www.neuroelectro.org/ephys_prop/3/)) is across neuron types and different publications within a neuron type.
* I want to see how experimental parameters and metadata affect electrophysiological measurements
* I want to compare electrophysiological variability across neuron types with gene expression variability
