Specimen2CCF

A Python tool to convert HuBMAP specimen data (i.e., donor, samples and datasets) to CCF Specimen Data Ontology.

Installing the tool

You can install the application using pip after you clone the repository.

$ cd specimen2ccf
$ pip install .

Using the tool

1. Download the raw specimen data from the HuBMAP project repository.

2. Run the tool

   $ specimen2ccf raw_data.jsonld --ontology-iri http://purl.org/ccf/data/specimen_dataset.owl -o specimen_dataset.owl
   

3. Open the resulting output file using Protégé