Adapters
BioCypher is a modular framework, with the main purpose of avoiding redundant maintenance work for maintainers of secondary resources and end users alike. To achieve this, we use a collection of reusable “adapters” for the different sources of biomedical knowledge as well as for different ontologies. To see whether your favourite resource is already supported or currently in development, or if you would like to contribute to the development of a new adapter, please refer to this GitHub projects view. Check the tabs for different views.
Note
We are currently working on adapter documentation, so the collection in the GitHub Projects view may be less than complete. Please get in touch if you want to make sure that your favourite resource is supported.
The project view is built from issues in the BioCypher GitHub repository, which carry labels for
adapters and adapter subtypes, as well as an Adapter status label to
indicate the state of development: Planned, In progress, Existing,
and Ideas. If you would like to add or request an adapter that is not yet
listed, please open a new issue and we will add it to the project view.
BioCypher meta-graph
We have built a BioCypher pipeline (from the template
repository) that fetches
information about all adapters from the BioCypher GitHub repository via the
GitHub API and builds a graph of all adapters and their dependencies. Browsing
this graph can give an overview of the current state of the adapters supported
by BioCypher and the pipelines they are used in. Currently, the graph must be
built locally by cloning the repository and running the pipeline using docker compose up. The graph is then available at localhost:7474/browser/ in the
Neo4j Browser. We plan on making it available online soon.