SimpleKnowledge

This repository contains a set of spreadsheets in the SimpleKnowledge format, as described here.

The UBKG generation framework ETL scripts obtain source information for a number of SABs from the SimpleKnowledge spreadsheets in the src directory.

Types of SimpleKnowledge spreadsheets

The spreadsheets in this repository are of three types:

1. Application ontologies that provide configuration and operational information to support applications.
2. Valuesets of categorical information used to encode concepts
3. Annotation mappings used to link codes from a cell annotation protocol to codes in other ontologies.

Contents

Application ontologies

1. SimpleKnowledgeHUBMAP: application ontology for HuBMAP configuration in the UBKG
2. SimpleKnowledgeSenNet: application ontology for SenNet configuration in the UBKG
3. SimpleKnowledgeUBKGSOURCE: application ontology that describes the sources ingested into the UBKG.

Annotation mappings

1. SimpleKnowledgeAzimuth: annotation mapping of Azimuth annotations to
   • cell type codes in Cell Ontology
   • codes in UBERON
2. SimpleKnowledgeDeepCellType: annotation mapping of DeepCellType annotations to cell type codes in Cell Ontology
3. SimpleKnowledgeSTELLAR: annotation mapping of STELLAR annotations to
   • cell type codes in Cell Ontology
   • codes in UBERON

Valuesets

1. SimpleKnowledgeGenCode: valueset to support the ingestion of GENCODE into the UBKG
2. SimpleKnowledgeReactome: valueset to support the ingestion of Reactome into the UBKG
3. SimpleKnowledgeMTP_VS: valueset to support the ingestion of data from the Molecular Targets Project (MTP) into the UBKG