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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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https://github.com/biocypher/biochatter-server/blob/b4c761927353e800be0dd4370199c060d56ca13a/src/constants.py#L11
@fengsh27 same questions here, is the typo problematic, and does the constant need …
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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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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…
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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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have successfully created nodes by adding more `open-targets` categories. However, I am now encountering difficulties with creating associations. The current setup, including the adapter and `schema_…
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After executing poetry install with Poetry (version 1.8.3) there is a Warning that will become an error in funtute:
> Installing the current project: ckg (0.2.0)
> Warning: The current project cou…
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We will prepare a PR that generalises `datasets.vdjdb()` to ingest any immune receptor data that was preprocessed by BioCypher, to yield a generic AnnData object that can be flexibly updated and maint…
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Error occurred when use poetry add biocypher, and show below information.
`Package operations: 19 installs, 1 update, 0 removals
- Installing pytz (2024.1)
- Installing colorlog (6.8.2)
…
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In https://ckg.readthedocs.io/en/latest/intro/getting-started-with-neo4j.html
For me, on Ubuntu 22:
apt-get install neo4j=1:4.2.3 pulls one of the newer "cypher-shell" packages, which in turn pull…