https://github.com/cthoyt/indra-machines
Several configuration files for biomedical relation extraction with INDRA
Science Score: 26.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (7.9%) to scientific vocabulary
Repository
Several configuration files for biomedical relation extraction with INDRA
Basic Info
- Host: GitHub
- Owner: cthoyt
- License: mit
- Language: Python
- Default Branch: master
- Size: 40 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
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
- Install INDRA with
pip install indra - Create a new directory and
cdinto it - 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
- 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. Molecular Systems Biology, 13(11), 954.
Owner
- Name: Charles Tapley Hoyt
- Login: cthoyt
- Kind: user
- Location: Bonn, Germany
- Company: RWTH Aachen University
- Website: https://cthoyt.com
- Repositories: 489
- Profile: https://github.com/cthoyt
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- Total issues: 7
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- cthoyt (7)
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Dependencies
- indra *
- ndex2 *
- pybel *
- requests *