Skip to main content

Table 1 Selected OHMI entities important for HMI investigation

From: OHMI: the ontology of host-microbiome interactions

TopicsExample termsOntology
Hosthost organism (e.g., human, rat); age, biological sex; disease (e.g., RA, diarrhea); phenotype (e.g., obesity, diarrhea); host anatomical entity (e.g., mouth, stomach); drug product; dysbiosisNCBITaxon PATO
DOID MPO, HPO, …
UBERON DRON
OHMI
Microbemicrobial taxonomy at various levels (e.g., E. coli);
species abundance, microbial diversity, microbial genome
NCBITaxon
OHMI
Environment conditionsenvironment (e.g., dwelling, wild field);
metabolite (e.g., iron, zinc and arginine), nutrition, …
ENVO CHEBI
Sample collectioncollection date/time, collection method, device; geographic locationOBI GAZ
HMI samplessample from host, e.g., gut, oral, saliva;
sample from environment, e.g., soil, table surface
OBI ENVO
AssaysRNA-seq, genome sequencingOBI
Statistical analysesANOVA, t-test, Wilcoxon rank-sum test, MLG-based classifier, KEGG analysis, metagenomic sequencing data, p-valueOBCS
HMI resultsrelative abundance of microbe in host, α-diversity, differentially enriched bacterium (or gene) marker for dysbiosis/disease, overgrowth vs. depletion (or reduced growth); microbiome restoration by treatment (e.g., antibiotics, DMARD)OHMI (4–5)
  1. The column ‘Ontology’ represents the source ontology in which the example terms are defined. All the terms are defined either in OHMI or imported from other ontologies to OHMI