https://github.com/neurodata/ndontology
Manage/query/update a MongoDB that contains the Allen Research Atlas Ontology
https://github.com/neurodata/ndontology
Last synced: 9 months ago
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Manage/query/update a MongoDB that contains the Allen Research Atlas Ontology
- Host: GitHub
- URL: https://github.com/neurodata/ndontology
- Owner: neurodata
- License: apache-2.0
- Created: 2017-09-24T16:18:21.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2017-10-05T19:44:17.000Z (over 8 years ago)
- Last Synced: 2025-02-25T08:54:13.440Z (over 1 year ago)
- Language: Python
- Size: 59.6 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ndaraontology
Manage/query/update a MongoDB in Docker that contains the
* Allen Research Atlas Ontology
* Waxholm Rat Atlas.
These tools run in python 3.5+, require a mongo database to talk to.
You need to install a late version of mongo clients (3.4.9).
Please `pip/pip3 install -r requirements.txt` to configure your python or virtualenv.
See README.md in ./docker for run instructions
The docker-compose file will load the databases. It can be done manually on any running mongo instance.
```
Run the load scripts to put ontology databases onto local mongodb. You need to have PTYHONPATH set to the root directory of this repository, e.g. /home/XXXX/ndontology
```
cd arascripts
./load_ara.sh
cd ../whsscripts
./load_whs.sh
cd ..
```
Run the unit tests
```
py.test
```
## What you get
A MongoDB instance running in docker that has the following databases:
* Allen Reference Atlas
* atlases.ara -- DB of ROIs supports lookup by id, atlas\_id, details, and descendants
* atlases.ara\_nametree -- contains one object with hierarchical tree of all objects
* Waxholm Rat Atlas
* atlases.whs -- DB of ROIs supports lookup by id, details, and descendants
* atlases.whs\_nametree -- contains one object with hierarchical tree of all objects
Reference queries are in the unit tests and ontology.py/araonotology.py
All of the tests and reference queries assume that Mongo runs on localhost.