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Table 2 Primary classes and the corresponding data sources

From: An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD)

Classes

Primary data resources

Abbreviations used in this study

Condition and Designated

• Inxight Drugs

• FDA Orphan Drug Designations

• S_RANCHO-DISEASE-DRUG_2018-12-18_13–30

• S_FDAORPHANGARD_20190216

Rare Diseases and 32 different rare disease categories from GARD

• GARD

• MONDO

• Orphanet

• OMIM

• S_GARD

• S_MONDO

• S_ORDO

• S_OMIM

Human Phenotype

• HPO

• Phenotype And Trait Ontology

• Mammalian Phenotype Ontology

• S_HPO

• S_PATO

• S_MP

Drug

• Inxight Drugs

• FDA Orphan Drug Designations

• VA National Drug File (VANDF)a

• MeSHa

• S_RANCHO-DISEASE-DRUG_2018-12-18_13–30

• S_FDAORPHANGARD_20190216

• S_VANDF

• S_MESH

Chemical

• ChEBI

• Thesaurusa

• S_CHEBI

• S_THESAURUS

Gene

• GHR

• Ontology of Genes and Genomes

• MedGena

• Thesaurusa

• S_GHR

• S_OGG

• S_MEDGEN

• S_THESAURUS

Protein

• Protein Ontology

• S_CL

• S_CLO

• S_MP

• S_HP

Cell

• Cell Ontology

• Cell Line Ontology

• Thesaurusa

• MedGena

• S_CL

• S_CLO

• S_THESAURUS

• S_MEDGEN

Tissue

• Thesaurusa

• S_THESAURUS

DATA

• All data properties are store in this class

• DATA

  1. aSemantic types have been adopted to represent different classes from VANDF, MeSH, MedGen, and Thesaurus, such as T109 representing “Organic Chemical”, T121 representing “Pharmacologic Substance”, T025 for “Cell”, T028 for “Gene or Genome”, etc.