CFDIKG

This is a "Common Fund" enabled knowledge graph, built on a UMLS knowledge graph originally developed by Jonathan Silverstein.

First phase was developed with an NIH R03 award 1R03OD030600-01, PIs: Deanne Taylor and Ryan Urbanowicz.

Extended this KG under a CFDE Partnership grant between HuBMAP DCC at U. Pittsburgh (Jonathan Silverstein) and the Kids First Data Resource at CHOP (Deanne Taylor).

The code and database are consistently changing as we continue to update the repository. Please watch this repo as we expand and include more useful data and information. Check out our tutorials!

Directory structure

.
├── src                     # Cypher queries
|── data                    # Data that has been ingested (when it's small enough to fit on github otherwise links are provided)
|── notebooks               # Jupyter notebooks for every data source ingestion workflow
|──cavatica_apps            # Files related to the Cavatica App used in the workflow
|── scripts                 # Python scripts  for every data source ingestion workflow
|── images                  # Images for the repository
├── docs                    # Documentation files
├── LICENSE
└── README.md

Basic Schema

HumanPhenotype--MousePhenotype--MouseGenes--HumanGenes

Unique Identifiers UMLS vs UMLS+

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Node Type	UI property	UMLS example	UMLS+ example	NOTES
Concept	CUI	C1234567	KC123456789000	Prefix with 'K', 12 ints not 9
Code	CodeID	SAB 12345	SAB 12345	No change
Term	SUI	S1234567	KS123456789000	Prefix with 'K', 12 ints not 7
Definition	ATUI	AT123456789	KAT123456789	Prefix with 'K'
Semantic	TUI	T123	N/A
NDC	NDC	12345678900	N/A

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Same image but with the nodes expanded

Showing more nodes

Showing a whole cluster

Showing multiple clusters