Generating Controlled Vocabulary from C2M2

The purpose of this repository is to create the data requested in this Help Desk inquiry: https://cfde.atlassian.net/jira/servicedesk/projects/HELP/queues/custom/4/HELP-262

Relevant text:

We previously worked with Amanda Charbonneau to get information on tissue blocks that could be RUI registered, see https://hubmapconsortium.github.io/ccf-ui/rui/

We also need Uberon terms, see Amanda’s earlier data compilation at

https://docs.google.com/spreadsheets/d/1wkoN9fyUtVZWYnbK0S0AKJmiTS-yELCRKgkNqk870eA/edit?pli=1#gid=1729887084

Column Descriptions

• Column A: Row number starting from 1
• Column B named format_type: The identifier for each row, found in JSON. All options: NCBI:txid10116, data:2044, DOID:9256, format:3547, OBI:0001271, UBERON:0002441
• Column C named label: This comes from the _name field in the JSON. Examples: cervicothoracic ganglion, nervous system, heart
• Column D named record_type: The type of record, found in JSON. Examples: data_type, disease, file_format
• Columns E through M named by DCC: The number of biosamples from each DCC from num_biosamples

Workflow

# create conda environment

conda env create -f environment.yml

# activate and install deriva

conda activate deriva

# run the C2M2 download etc. etc
make