A terminology is a set of prefered or official terms in a domain. One of the most important terminologies for information retrieval in the medical domain is the Medical Subject Headings (MeSH), which is used for indexing and searching PubMed.

Ontologies differ from terminologies in that ontologies define relationships between concepts in a way that allows computational logical reasoning. A short introduction is available in this recent review.

The phenopacket schema requires the use of a common ontology, a logically defined hierarchy of terms, that allows sophisticated algorithmic analysis over medically relevant abnormalities. The National Cancer institute’s Thesaurus (NCIt) is used for cancer biosamples, and is the de facto standard for cancer knowledge representation and regulatory submission. The Human Phenotype Ontology (HPO) was built

for genomic diagnostics, translational research, genomic matchmaking, and

systems biology applications in the field of rare disease and other fields of medicine. The HPO is developed in the context of the Monarch Initiative, an international team of computer scientists, clinicians, and biologists in the United States, Europe, and Australia; HPO is being translated into multiple languages to support international interoperability. Due to its extensive phenotypic coverage beyond other terminologies, HPO has recently been integrated into the Unified Medical Language System (UMLS) to support deep phenotyping in a variety of mainstream health care IT systems.