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The integration of BioCypher in NC should provide a graph (networkx or CORNETO graph) retrieved from various prior knowledge sources, including OmniPath.
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Implement a high-level interface to coordinate multiple adapters and their contents for application purposes.
Workflow:
- `pipeline.start()`
- `pipeline.add_adapter()`
- `pipeline.find_identifie…
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Poetry lock seems to be out of date, and some dependencies should be added to pyproject.taml (Numpy and OntoWeaver most notably), or updated (BioCypher to newest version).
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Hi!
Installation runs with conda. Poetry install only manages to install bioregistry when python version was set to `python = "~3.11"`
Now I am trying to create the KG with `python create_knowledg…
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Problem with importing data with version 5.21.2. The problem seems to occur whenever trying to define a database to import to at the end of the import sequence, for example the name is neo4j here belo…
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Hi! In the [Adapters → BioCypher meta-graph section](https://biocypher.org/adapters.html#biocypher-meta-graph), there's a link to “Online meta-graph” which points to https://meta.biocypher.org/. This …
tskir updated
1 month ago
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Create a tutorial for the BioCypher documentation to showcase how a BioCypher KG can be created and then directly used with PyG for doing Graph Machine Learning.
Use known BioCypher KG (e.g. [Colle…
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Similar to the `to_df` for CSV it should be possible to get the networkx graph in-memory from BioCypher.
As part of this the interface for running BioCyher in online mode for CSV and Networkx can be …
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### Issue
I encountered the following error when I try to run the neo4j-admin-import-call.sh script using the latest commit d18348b:
```
org.neo4j.internal.batchimport.input.HeaderException: Mi…
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CI fails for the current 3.9-3.11 matrix, due to (https://github.com/biocypher/biocypher/actions/runs/8815890423)
```
The version '3.9' with architecture 'arm64' was not found for macOS 14.4.1.
The l…