Use Monarch Dipper

Dipper is a Python package to generate RDF triples from common scientific resources. It has been used to build and expose RDF from multiple sources for the Monarch Initiative.

Dipper includes subpackages and modules to create graphical models of this data, including:

  • Models package for generating common sets of triples, including common OWL axioms, complex genotypes, associations, evidence and provenance models.
  • Graph package for building graphs with RDFLib or streaming n-triples
  • Source package containing fetchers and parsers that interface with remote databases and web services

Dipper Notebooks#

2 Jupyter Notebooks proposed by the Dipper documentation can be easily deploy in Jupyterlab:

Clone in workspace/notebooks, install requirements and start the Notebooks:

d2s start notebook -d dipper

Access at http://localhost:8888

See the documentation to work with graphs

Or run Jupyterlab it directly using Docker:

docker run --rm -it -p 8888:8888 -v $(pwd)/notebooks:/notebooks -e GIT_URL="" -e PASSWORD="<your_secret>" umids/jupyterlab:latest

Download Monarch Dipper data#

Monarch Initiative data generated from Dipper can be accessed through multiple interfaces. The dipper output is quality checked and released on a regular basis.

New sources ingestion can be wrote following this documentation.

Last updated on by Vincent Emonet