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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.