The description of the controlled sets of terms also known as Value Sets and their sources - Identifer Systems. These value sets and their controlled concept list are required to support the bindings to various attributes for entities used throughout the model.

Value Sets

This table contains a list of all the value sets defined as part of the Variant Pathogenicity Interpretation specification. Some of these value sets include concepts defined elsewhere, some contain their own inline identifier system definitions, and some do both.

Name IRI Description Source
Value Set Extensibility Value Set SEPIO:0000363 Whether or not a ValueSet can be extended by users LOINC
Molecular Consequence Value Set SEPIO:0000380 A classification of a genomic variant based on its effect on a transcript or its location with respect to the transcript. SO
Clinical Significance Value Set SEPIO:0000371 The role that a variant plays in the causing a genetic condition (see LOINC answer list https://r.details.loinc.org/AnswerList/LL4034-6.html) LOINC
Region Annotation Value Set SEPIO:0000343 A label applied to a sequence region SO
Allelic Phase Value Set SEPIO:0000344 Value denoting whether sequence features lie on the same or different molecules GENO
Allelic State Value Set SEPIO:0000338 Describes the existence of an allele across multiple copies of a chromosome (Informed by LOINC answer list https://r.details.loinc.org/AnswerList/LL381-5.html but with additional codes for somatic mosaicism and asserted absence.) GENO
Inheritance Pattern Value Set SEPIO:0000416 Classifies the transmission pattern of a condition in a pedigree. (see LOINC Answer List https://r.details.loinc.org/AnswerList/LL3731-8.html) HP
Condition Mechanism Value Set SEPIO-CG:65108 The particular type of allele that can lead to a condition SO
In Silico Prediction Method Value Set SEPIO:0000345 The type of InSilico Predictor SEPIO
Criterion Assessment Outcome Value Set SEPIO:0000347 Denotes whether the collected evidence is sufficient to meet a specified criteria or not SEPIO
Allele Functional Assay Value Set SEPIO:0000382 The functional measurement carried out in a given assay OBI
Population Value Set SEPIO-CG:65112 Label for a group of individuals with a shared genetic background NCIT
Benign Missense Variation Rate Outcome Value Set SEPIO:0000349 The rate of missense variation in a transcript that do not lead to a genetic condition SEPIO
Condition Penetrance Value Set SEPIO-CG:65114 The chance of having a particular genetic condition given the presence of a particular variant or damaged gene HP
Condition Mechanism Strength Value Set SEPIO:0000354 The strength of association between a genetic mechanism and a condition SEPIO
ACMG Evidence Strength Value Set SEPIO:0000353 Degree of support that a set of evidence lends to a subsequent statement SEPIO
Disease Value Set SEPIO:0000372 An alteration of health status resulting from a physiopathological mechanism, and having a homogeneous clinical presentation and evolution and homogeneous therapeutic possibilities. (From MONDO) OMIM
Phenotype Value Set SEPIO:0000375 The assemblage of traits or outward appearance of an individual. It is the product of interactions between genes and between genes and the environment. (From NCIT) HP
Reference Sequence Value Set SEPIO-CG:65119 Any public, immutable, accessioned DNA, RNA or amino acid sequences. REFSEQ
Contributory Role Value Set SEPIO-CG:65120 The role played by an agent in the creation of an artifact SEPIO
Allele Origin Value Set SEPIO:0000392 The source of an allele in an individual GENO
Ascertainment Method Value Set SEPIO:0000409 The method by which a set of people was chosen to define a group SEPIO
Locus Specificity Value Set SEPIO:0000348 The degree to which a condition implicates a specific genomic locus, such as a gene. SEPIO
Allele Conservation Value Set SEPIO-CG:65124 The degree to which an allele is preserved over evolutionary history SEPIO-CG
Parental Confirmation Value Set SEPIO-CG:65125 Whether or not parentage has been confirmed with a genetic test SEPIO-CG
Condition Status Value Set SEPIO-CG:65126 Whether or not an individual is affected by a specific genetic condition SEPIO-CG
Inconsistent Segregation Observed Value Set SEPIO-CG:65127 Whether or not inconsistent segretations have been observed in a pedigree SEPIO-CG
Null Allele Outcome Value Set SEPIO-CG:65128 Denotes whether an allele leads to a non-functional transcript SO
Region Alleles Outcome Value Set SEPIO-CG:65129 Whether or not an allele overlaps a sequence region SEPIO-CG
Gene Value Set SEPIO:0000396 The genes in the the genome. HGNC
ACMG Criterion Value Set SEPIO:0000395 The ACMG-AMP IVS variant pathogenicity rule or criterion codes including extended codes used in domain specific derivatives of the original guideline. (e.g. BA1, PS2, PM3, PVS1, ...) SEPIO-CG
Variant Interpretation Guideline Value Set SEPIO-CG:65132 The assertion method guidelines for variant pathogenicity interpretation. ACMG-AMP IVS guidelines 2015 is a typical case, but there may be alternative or derivative guidelines as well. SEPIO-CG
Variant Interpretation Criterion Scoring Rules Value Set SEPIO-CG:65133 This is the description of how the weighting of the satisfied criterion are typically evaluated to arrive at a specific clinical significance. SEPIO-CG
Inconsistent Segregation Status Value Set SEPIO-CG:65140 TODO SEPIO
Placeholder Empty Value Set SEPIO-CG:65900 TODO SEPIO-CG
Canonical Allele Type Value Set SEPIO-CG:65901 TODO SEPIO-CG
Allele Complexity Value Set SEPIO-CG:65902 TODO SEPIO-CG
Allele Name Type Value Set SEPIO-CG:65903 TODO SEPIO-CG
Contextual Allele Type Value Set SEPIO-CG:65904 TODO SEPIO-CG
Chromosome Value Set SEPIO-CG:65905 TODO SEPIO-CG
Reference Genome Build Value Set SEPIO-CG:65906 TODO SEPIO-CG

Identifier Systems

This table contains a list of all the Identifier Systems referenced by the Value Sets and by the model entity and attributes themselves.

Name CURIE IRI Description
BFO BFO http://purl.obolibrary.org/obo/bfo#
ClinGen Modeling Temporary Namespace CG http://dataexchange.clinicalgenome.org/temp/
Dublin Core DC http://purl.org/dc/elements/1.1/
ERO ERO http://purl.obolibrary.org/obo/ero#
FALDO FALDO http://biohackathon.org/resource/faldo#
GENO GENO http://purl.obolibrary.org/obo/geno#
OBI OBI http://purl.obolibrary.org/obo/obi#
PAV PAV http://purl.org/pav/
PCO PCO http://purl.obolibrary.org/obo/pco#
W3C Provenance PROV http://www.w3.org/ns/prov#
RDF RDFS http://www.w3.org/2000/01/rdf-schema#
Relations Ontology RO http://purl.obolibrary.org/obo/ro#
Scientific Evidence Provenance Information Ontology SEPIO http://purl.obolibrary.org/obo/sepio#
ClinGen extensions to SEPIO SEPIO-CG http://purl.obolibrary.org/obo/sepio-clingen#
ClinGen Allele Registry CAR http://reg.genome.network/allele/
ClinVar CLINVAR http://www.ncbi.nlm.nih.gov/clinvar/
dbSNP DBSNP http://www.ncbi.nlm.nih.gov/projects/SNP/
Disease Ontology DOID http://purl.obolibrary.org/obo/doid#
Ensembl ENSEMBL http://www.ensembl.org/
Exome Variant Server/ESP populations EVS http://evs.gs.washington.edu/EVS/
NCBI Gene NCBIGene https://www.ncbi.nlm.nih.gov/gene#
ExAC/gnomad Populations GNOMAD http://gnomad.broadinstitute.org/
Human Gene Nomenclature Committee HGNC http://www.genenames.org/
Human Phenotype Ontology HP http://purl.obolibrary.org/obo/hp#
Int'l Genome Sample Resource populations IGSR http://www.internationalgenome.org/
LOINC LOINC http://loinc.org/
Locus Reference Genomic LRG http://www.lrg-sequence.org/
Medical Subject Headers MeSH https://meshb.nlm.nih.gov/
Monarch Initiative Disease Ontology MONDO http://purl.obolibrary.org/obo/mondo#
NCI Thesarus NCIT http://purl.obolibrary.org/obo/ncit#
OMIM OMIM http://www.omim.org/
Orphanet Orphanet http://www.orpha.net/
Pubmed PMID http://www.ncbi.nlm.nih.gov/pubmed/
RefSeq REFSEQ http://www.ncbi.nlm.nih.gov/nuccore/
Sequence Ontology SO http://purl.obolibrary.org/obo/so#
UMLS Ontology UMLS http://umlsks.nlm.nih.gov/
CGEX http://dataexchange.clinicalgenome.org/examples/