https://github.com/ccb-hms/ontology-mapper
a tool for mapping free-text descriptions of entities to ontology terms
https://github.com/ccb-hms/ontology-mapper
data-cleaning fair-data fair-principles metadata-cleaning ontology ontology-mapping ontology-search ontology-services owl owlready2
Last synced: 4 months ago
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a tool for mapping free-text descriptions of entities to ontology terms
- Host: GitHub
- URL: https://github.com/ccb-hms/ontology-mapper
- Owner: ccb-hms
- License: mit
- Created: 2021-08-06T19:06:34.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2024-07-30T15:10:32.000Z (almost 2 years ago)
- Last Synced: 2024-10-01T14:39:24.420Z (over 1 year ago)
- Topics: data-cleaning, fair-data, fair-principles, metadata-cleaning, ontology, ontology-mapping, ontology-search, ontology-services, owl, owlready2
- Language: Python
- Homepage: https://ccb-hms.github.io/ontology-mapper
- Size: 337 KB
- Stars: 14
- Watchers: 4
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README-UI.md
- License: LICENSE
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README
# ontology-mapper-ui
The following information pertains to the text2term UI, which is written [here](https://github.com/ccb-hms/ontology-mapper-ui) and runs online [here](https://text2term.hms.harvard.edu/). It supports fewer features than the base package does, but provides a user interface for non-programmers.
### Running Locally via Node + Python
##### Requirements
- Node >= 16.0.0
- npm >= 8.0.0
- Python >= 3.9.0
- pip >= 21.0.0
- text2term >= 4.1.2
**\*** These are the versions I have that work; while I know Python 3.9 or higher is necessary, the others may not strictly require the listed versions.
**\*\*** If you are running this locally on Google Chrome, you will likely run into issues with CORS (Cross-Origin Requests) that I have been unable to completely resolve. I would recommend using a different browser, using the Docker method, or finding some way to disable CORS on Chrome while running this.
#### Instructions
##### Initial Setup
When first cloned, run the command:
```
npm install
```
to install all necessary packages for the React frontend.
Next, go into the `flask-api` folder (perhaps by running `cd flask-api`) and run
```
pip install -r requirements-flask.txt
```
to install necessary packages for the Flask api.
##### Running
To run, make sure you are in the root of the repository and run, in two separate command line instances, the command
```
npm start
```
to start the front-end, which can be seen at `localhost:3000`, and the command
```
npm run flask-api
```
to start the back-end, which can be interacted with at `localhost:5000`.
### Running Locally via Docker
#### Requirements
- Docker
#### Instructions
##### Initial Setup
Before running, make sure you have the latest version of the repository built by running the command
```
docker-compose build
```
Docker should build two images:
- `ontology-mapper-api`: the Flask backend API
- `ontology-mapper-client`: the React frontend
##### Running
To run the website, run the command:
```
docker-compose up
```
Docker should build two containers corresponding to the two images.
In a browser, navigate to `localhost:8602` to see the front-end.
### Acknowledgements
Initial setup of React and Flask and Dockerization aided by an [article series](https://blog.miguelgrinberg.com/post/how-to-dockerize-a-react-flask-project) by Miguel Grinberg.