Published August 18, 2025
| Version v0.8.3
Software
Open
scribl: A system for the semantic capture of relationships in biological literature
- 1. Amber Biology LLC
-
2.
Institute for Globally Distributed Open Research and Education
Description
scribl (Semantic Capture of Relationships in Biological Literature) is a Python software pipeline and API that transforms a Zotero literature database with entries annotated with tags in the scribl language to create a graph data structure, suitable for import into a graph database platform, such as Neo4j, or Python's NetworkX.
The scribl language was designed for the curation from scientific articles, to capture the relationships between the various biological agents and the processes that they describe in a connected network.Notes
If you use this software, please cite both the software itself, as well as the article: Webster GD, Lancaster AK. (2024) scribl: A system for the semantic capture of relationships in biological literature. Journal of Open Source Software. 9(99):6645. doi:10.21105/joss.06645
Development is on GitHub: https://github.com/amberbiology/scribl
Binary packages are available on PyPI: https://pypi.org/project/scribl/.
Files
scribl.zip
Files
(6.1 MB)
| Name | Size | Download all |
|---|---|---|
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md5:4a2210cb26cadf60be2d5f5eac85b7ee
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6.1 MB | Preview Download |
Additional details
Related works
- Is source of
- Software: https://pypi.org/project/scribl/0.8.3 (URL)
- Is supplement to
- Software: https://github.com/amberbiology/scribl/tree/v0.8.3 (URL)
- Is supplemented by
- Other: http://amberbiology.com/ (URL)