https://github.com/hubmapconsortium/ccf-rdf-writer
CCF RDF Writer
https://github.com/hubmapconsortium/ccf-rdf-writer
human-reference-atlas ot2od030545
Last synced: 2 months ago
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CCF RDF Writer
- Host: GitHub
- URL: https://github.com/hubmapconsortium/ccf-rdf-writer
- Owner: hubmapconsortium
- Created: 2022-05-31T13:55:46.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2023-03-29T12:13:38.000Z (about 3 years ago)
- Last Synced: 2026-03-28T00:36:35.229Z (3 months ago)
- Topics: human-reference-atlas, ot2od030545
- Language: Makefile
- Homepage:
- Size: 35.9 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 1
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Metadata Files:
- Readme: README.md
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README
# CCF RDF Writer
From a set of terms, generate a graph and a RDF file (nt) with all inferred `part of` relationships.
## Running using Docker
First, please create folder called `tmp` to include the temporary files generated during the pipeline.
To generalise this pipeline make sure you pass values to the two parameters `ORGAN` and `ORGAN_ONTOLOGY`.
Also call goal using same value passed to `ORGAN`, e.g., `make graph/lung-extended.png` or `make graph/kidney-extended.png`
Complete call would be:
```
sh run.sh make graph/kidney-extended.png ORGAN=kidney ORGAN_ONTOLOGY=master/owl/ccf_Kidney_classes.owl
```
The RDF file is `ccf-{organ}-extended.nt`
## Without Docker
Need to install the following dependencies:
1. ROBOT - http://robot.obolibrary.org/
2. relation-graph - https://github.com/balhoff/relation-graph/
3. Soufflé - https://souffle-lang.github.io/index.html
4. og2dot.js - https://github.com/cmungall/obographviz
5. dot - https://graphviz.org