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Contents

  • Introduction to Phenopackets
  • Phenopacket Schema
  • Top-Level Elements
  • Phenopacket building blocks
  • Recommended Ontologies
    • Diseases
    • Phenotypic features
    • Anatomy
    • Genes
    • Units of Measurement
    • Genotypes
    • Assays
    • Medications
    • The National Cancer Institute’s Thesaurus
    • Experimental Factor Ontology
  • Working with Phenopackets
  • Examples
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  • Recommended Ontologies
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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
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