Recommended Ontologies

The phenopacket schema can be used with any ontologies. The phenopacket can be compared to a hierarchical structure with “slots” for ontology terms and other data. Different use cases may require different ontology terms to cover the subject matter or to fulfil requirements of a specific research project. The spectrum of requirements is so broad that we do not think it is appropriate to require a specific set of ontologies for use with phenopackets. Nonetheless, the value of phenopacket-encoded data will be greatly increased if the community of users converges towards a common set of ontologies (to the extent possible). Here, we provide general recommendations for ontologies that we have found to be useful. This list is incomplete and we would welcome feedback from the community about ontologies that should be added to this page.

We do anticipate that individual research consortia or other groups should agree on a set of allowed ontologies for specific projects.

Diseases

Mondo Disease Ontology provides a comprehensive logically structured ontology of diseases that integrates multiple other disease ontologies.

Example terms from Mondo

Label	Id
incontinentia pigmenti	MONDO:0010631
dilated cardiomyopathy 3B	MONDO:0010542

Other disease ontologies of note include The National Cancer Institute’s thesaurus (NCIT), Orphanet Rare Disease Ontology (ORDO), Disease Ontology (DO), and the Online Mendelian Inheritance in Man (OMIM).

Phenotypic features

The Human Phenotype Ontology (HPO) provides a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease.

Example terms from HPO

Label	Id
Arachnodactyly	HP:0001166
Patent ductus arteriosus	HP:0001643

Anatomy

UBERON is an integrated cross-species ontology with classes representing a variety of anatomical entities.

Example terms from UBERON

Label	Id
heart	UBERON:0000948
brain	UBERON:0000955

Genes

The HUGO Gene Nomenclature Committee (HGNC) provides standard names, symbols, and IDs for human genes.

Example terms from HGNC

Label	Id
FBN1	HGNC:3603
NF1	HGNC:7765

Other sources of gene IDs include NCBI Gene and Ensembl.

Units of Measurement

The Units of measurement ontology (denoted UO) provides terms for units commonly encountered in medical data. The following table shows some typical examples.

Example terms from Units of measurement ontology

Label	Id
millimolar	UO:0000063
milligram	UO:0000022
millimetres of mercury	UO:0000272

Genotypes

GENO is anontology of genotypes their more fundamental sequence components, and links to related biological and experimental entities. We use GENO terms to denote genotypes.

Example terms from GENO

Label	Id
heteroyzgous	GENO:0000135
homozygous	GENO:0000136

Assays

Logical Observation Identifiers Names and Codes (LOINC) is a database and universal standard for identifying medical laboratory observations. It can be used to denote clinical assays in the Measurement element.

Example terms from LOINC

Label	Id
Platelets [#/volume] in Blood	LOINC:26515-7
Calcium [Mass/volume] in Serum or Plasma	LOINC:17861-6

Medications

DrugCentral integrates a broad spectrum of drug resources related to chemical structures, biological activities, regulatory data, pharmacology and drug formulations

Example terms from DrugCentral

Label	Id
losartan	DrugCentral:1610
selumetinib	DrugCentral:5388

Other ontologies with coverage of drugs include ChEBI, RxNorm, and DrugBank.

The National Cancer Institute’s Thesaurus

The National Cancer Institute’s thesaurus (NCIT) provides a wide range of terms that can be useful for phenopackets. In addition to providing an ontology of cancers, NCIT provides terms for procedures, findings, units or measurement, scheduling, etc. The following table shows an an example pf the subhierarchy for Unit of Measure (NCIT:C25709). and for Schedule Frequency (NCIT:C64493).

Example terms from NCIT Unit of Measure and Schedule Frequency subhierarchies

Label	Id
Milligram per Kilogram per Dose	NCIT:C124458
Twice Daily	NCIT:C64496
Cells per Milliliter	NCIT:C74919

Experimental Factor Ontology

Experimental factor ontology (EFO) is an ontology of experimental variables particularly those used in molecular biology. EFO imports terms from many source ontologies and provides additional terms needed to provide a systematic description of many experimental variables available in EBI databases.

Example terms from EFO

Label	Id
abnormal sample	EFO:0009655
genomic DNA	EFO:0008479
milligram per kilogram	EFO:0002902