Table 1 Integrated databases and ontologies. The first column, second column, and third column represent the abbreviation of the data source, simplify the description of the data source and the relationship extracted from the data source respectively. Eleven data sources are used to construct the integrated network. Specific types of nodes and edges are extracted from various data sources and integrated into a network
From: Predicting disease-related genes using integrated biomedical networks
Abbreviation | Data sources | Relationship |
|---|---|---|
STRING | Search Tool for the Retrieval of Interacting Gene/Proteins | gene-gene |
CTD-DG | The Comparative Toxicogenomics Database - Curated Disease-Gene Interactions | disease-gene |
OMIM | Online Mendelian Inheritance in Man Disease Subtypes | disease-gene |
ClinVar | Clinical Variants and phenotypes | Disease/Phenotype-gene |
HGNC | HUGO gene Nomenclature Committee Database | gene name mapping |
MeSH | Medical Subject Headings | Unified vocabulary |
UMLS | Unified Medical Language System | Unified vocabulary |
SIDD | Semantically Integrated Disease-associated Database | disease name mapping |
DO | Human Disease Ontology | DO term-gene/ DO term-DO term |
HPO | Human Phenotype Ontology | HPO term-gene/ HPO term-HPO term |
GO | Gene Ontology | GO term-gene/GO term-GO term |