https://github.com/hrshdhgd/oakx-oger

OGER plugin for oaklib.
https://github.com/hrshdhgd/oakx-oger

Last synced: 14 days ago
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OGER plugin for oaklib.

• Host: GitHub
• URL: https://github.com/hrshdhgd/oakx-oger
• Owner: hrshdhgd
• License: bsd-3-clause
• Created: 2022-10-11T23:52:33.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2023-09-07T16:37:46.000Z (over 1 year ago)
• Last Synced: 2024-11-05T20:05:43.127Z (2 months ago)
• Language: Python
• Homepage: https://hrshdhgd.github.io/oakx-oger/
• Size: 3.42 MB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# oakx-oger

This is an [OGER](https://github.com/OntoGene/OGER) plugin for [`oaklib`](https://github.com/INCATools/ontology-access-kit).

**ALPHA**

## Usage

```

pip install oakx-oger

runoak -i oger:sqlite:obo:envo annotate cultured organisms polar ecosystems atmospheric gas exchange

```

## How it works

There are two possible inputs to this plugin:

1. A `.txt` file [`runoak -i oger:sqlite:obo:envo annotate --text-file text.txt`]

2. Words that need to be annotated.[`runoak -i oger:sqlite:obo:envo annotate cultured organisms polar ecosystems atmospheric gas exchange`]

Input ontologies generally used `oaklib` can be used with an `oger:` prefix.

Note: This has been tested only with `oger:sqlite:obo:*` for now.

## Acknowledgements

This [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [oakx-plugin-cookiecutter](https://github.com/INCATools/oakx-plugin-cookiecutter) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).