Table 1 Selected OHMI entities important for HMI investigation

Host

host 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; dysbiosis

NCBITaxon PATO

DOID MPO, HPO, …

UBERON DRON

OHMI

Microbe

microbial taxonomy at various levels (e.g., E. coli);

species abundance, microbial diversity, microbial genome

NCBITaxon

OHMI

Environment conditions

environment (e.g., dwelling, wild field);

metabolite (e.g., iron, zinc and arginine), nutrition, …

ENVO CHEBI

Sample collection

collection date/time, collection method, device; geographic location

OBI GAZ

HMI samples

sample from host, e.g., gut, oral, saliva;

sample from environment, e.g., soil, table surface

OBI ENVO

Assays

RNA-seq, genome sequencing

OBI

Statistical analyses

ANOVA, t-test, Wilcoxon rank-sum test, MLG-based classifier, KEGG analysis, metagenomic sequencing data, p-value

OBCS

HMI results

relative 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)