https://github.com/neuromusic/abcd-to-neurolex
scripts and data for pulling data from the Avian Brain Connectivity Database into Neurolex from the 2013 NIF Hackathon
https://github.com/neuromusic/abcd-to-neurolex
Last synced: 4 months ago
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scripts and data for pulling data from the Avian Brain Connectivity Database into Neurolex from the 2013 NIF Hackathon
- Host: GitHub
- URL: https://github.com/neuromusic/abcd-to-neurolex
- Owner: neuromusic
- License: bsd-3-clause
- Created: 2016-01-22T18:28:11.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2016-01-23T00:13:40.000Z (over 9 years ago)
- Last Synced: 2025-01-14T03:48:41.829Z (5 months ago)
- Language: Python
- Homepage:
- Size: 49.8 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# abcd-to-neurolex
scripts and data for getting pulling the Avian Brain Connectivity Database into Neurolex from the 2013 NIF Hackathon
# The Project
We wanted to get the regions and connections of the avian brain into the Neurolex Wiki.
Avian neuroanatomy poses an interesting case study in the challenges of maintaining a lexicon of brain regions, as the literature is a bit of a mess when it comes to naming.
Much of the work in compiling the "state of the field" had been done already (see http://www.ncbi.nlm.nih.gov/pubmed/17889371) and deposited at http://behav.org/abcd
We contacted the grad student who had built the database, but they had moved on. Emails to the PI were not returned. So we decided to scrape the ABCD for avian brain regions and connections.
And it's a good thing we did, because the old ABCD hasn't been online since October 2014: http://web.archive.org/web/20141019130131/http://www.behav.org/abcd/abcd.php
So here are the scripts I used to scrape the database and the resulting data in JSON form.
Enjoy!
Justin Kiggins
@neuromusic
# Scripts
1. `abcd_scrape.py` to scrape the data from the ABCD
2. `dump_to_regions.py` to split the dump into "regions" and "connections"
# Data
- `abcd_dump_2012Jun25.json` is the raw dump from the ABCD
- `abcd_regions.json` is just the regions
- `abcd_connections.json` is just the connections