https://github.com/cthoyt/indra-machines
Several configuration files for biomedical relation extraction with INDRA
https://github.com/cthoyt/indra-machines
Last synced: 2 months ago
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Several configuration files for biomedical relation extraction with INDRA
- Host: GitHub
- URL: https://github.com/cthoyt/indra-machines
- Owner: cthoyt
- License: mit
- Created: 2018-03-08T08:52:25.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2018-05-09T14:59:58.000Z (about 7 years ago)
- Last Synced: 2025-01-22T16:24:57.768Z (4 months ago)
- Language: Python
- Size: 40 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# INDRA Machines
This repository contains public configurations for INDRA machines that will investigate the literature around several pathologies, diseases, and conditions.
## Contributing
Please submit an issue if you have an idea for a new disease area with either a list of genes or search terms for PubMed. Feel free to submit a merge request if you generate a new configuration file.
### Generating A Configuration File
1. Install INDRA with `pip install indra`
2. Create a new directory and ``cd`` into it
3. Use the CLI `python -m indra.tools.machine make`
### Editing the Configuration File
See: http://indra.readthedocs.io/en/latest/modules/tools/index.html#module-indra.tools.machine
Example:
```yaml
belief_threshold: 0.8
#PUBMED SEARCH TERMS ######################
## Generic search terms
#search_terms:
#- "search term 1"
#- "search term 2"
## Gene symbol search terms
#search_genes:
#- AKT1
#- EGFR
###########################################
#GMAIL CREDENTIALS ########################
#gmail:
# user:
# password:
###########################################
#TWITTER CREDENTIALS ######################
#twitter:
# consumer_token:
# consumer_secret:
# access_token:
# access_secret:
###########################################
#NDEX CREDENTIALS #########################
#ndex:
# user:
# password:
# network:
###########################################
```
## Links
- INDRA [Documentation](http://indra.readthedocs.io/en/latest/)
- Gyori, B. M., Bachman, J. A., Subramanian, K., Muhlich, J. L., Galescu, L., & Sorger, P. K. (2017). [From word models to executable models of signaling networks using automated assembly](https://doi.org/10.15252/msb.20177651). Molecular Systems Biology, 13(11), 954.