x-atlas-consortia / ubkg-etl

A framework that combines data from the UMLS with assertions from other data sources into a set of CSV files that can be imported into neo4j to build a Unified Biomedical Knowledge Graph (UBKG)

MIT License

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Expand UBKGSOURCE ontology to include data from Data Distillery DCCs in CFDE repo #144

Open AlanSimmons opened 3 weeks ago

AlanSimmons commented 3 weeks ago

The UBKGSOURCE ontology currently includes the information that is published in the UBKG Contexts page, including citations and licensing.

The ontology needs to include information for sources from the Data Distillery Data Coordinating Centers published in the Data Dictionary of the CFDE github repo.

AlanSimmons commented 6 days ago

Source dictionary URLs

The UBKGSOURCE ontology now features:

nodes of type source_dictionary_url that are URLs to the section of the DataDistilleryDataDictionary.md. This is the source of truth for data dictionary information, especially for the data sources from participating Data Coordinating Centers.
assertions between sources and source dictionary URLs.

AlanSimmons commented 5 days ago

Discrepancies and gaps in the Data Dictionary file to correct

HuBMAP-AZ

This data source uses the SAB HMAZ.

Gabriella Miller KidsFirst

This data source uses the SAB KF.

HGNCHCOP

The SAB for this data source was changed to HCOP.

GlyGen

The GlyGen set of sources does not use UNIPROTKB, but UNIPROT.

Missing dictionary entries

MPMGI
CLINGEN
STRING
OTG

Entries that I will add

GENCODE
UNIPROTKB
REFSEQ
AZ

AlanSimmons commented 2 days ago

update

PR for update to data dictionary: https://github.com/nih-cfde/data-distillery/pull/8
Added references to UBKGSOURCE