Terminologies

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
SEPIO-CG
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
SEPIO
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
GENO
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
Orphanet
DOID
MESH
MONDO
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 TODO REFSEQ
ENSEMBL
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
SEPIO-CG
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 TODO HGNC
ACMG Criterion Value Set SEPIO:0000395 TODO SEPIO-CG
Variant Interpretation Guideline Value Set SEPIO-CG:65132 TODO 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

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
ClinGen Allele Registry CAR http://reg.genome.network/allele/
LOINC LOINC http://loinc.org/
HGNC HGNC http://www.genenames.org/
RefSeq REFSEQ http://www.ncbi.nlm.nih.gov/nuccore/
ClinVar CLINVAR http://www.ncbi.nlm.nih.gov/clinvar/
Ensembl ENSEMBL http://www.ensembl.org/
Sequence Ontology SO http://purl.obolibrary.org/obo/so#
dbSNP DBSNP http://www.ncbi.nlm.nih.gov/projects/SNP/
HGVS HGVS http://www.hgvs.org/mutnomen/
LRG LRG http://www.lrg-sequence.org/
OMIM OMIM http://www.omim.org/
Pubmed PMID http://www.ncbi.nlm.nih.gov/pubmed/
Orphanet Orphanet http://www.orpha.net/
ExAC/gnomad Populations GNOMAD http://gnomad.broadinstitute.org/
Human Phenotype Ontology HP http://purl.obolibrary.org/obo/hp#
Relations Ontology RO http://purl.obolibrary.org/obo/ro#
Int'l Genome Sample Resource populations IGSR http://www.internationalgenome.org/
Disease Ontology DOID http://purl.obolibrary.org/obo/doid#
Medical Subject Headers MESH https://meshb.nlm.nih.gov/
Exome Variant Server/ESP populations EVS http://evs.gs.washington.edu/EVS/
GENO GENO http://purl.obolibrary.org/obo/geno#
Scientific Evidence Provenance Information Ontology SEPIO http://purl.obolibrary.org/obo/sepio#
Monarch Initiative Disease Ontology MONDO http://purl.obolibrary.org/obo/mondo#
ClinGen extensions to SEPIO SEPIO-CG http://purl.obolibrary.org/obo/sepio-clingen#
OBI OBI http://purl.obolibrary.org/obo/obi#
Information Artifact Ontology IAO http://purl.obolibrary.org/obo/iao#
NCI Thesarus NCIT http://purl.obolibrary.org/obo/ncit#
BFO BFO http://purl.obolibrary.org/obo/bfo#
PCO PCO http://purl.obolibrary.org/obo/pco#
STATO STATO http://purl.obolibrary.org/obo/stato#
ERO ERO http://purl.obolibrary.org/obo/ero#
FALDO FALDO http://biohackathon.org/resource/faldo#
DC DC http://purl.org/dc/elements/1.1/
RDF RDFS http://www.w3.org/2000/01/rdf-schema#
W3C Provenance PROV http://www.w3.org/ns/prov#
PAV PAV http://purl.org/pav/
ClinGen Modeling Temporary Namespace CG http://dataexchange.clinicalgenome.org/temp/
ClinGen Modeling Example Namespace CGEX http://dataexchange.clinicalgenome.org/examples/
FOAF Ontology FOAF http://xmlns.com/foaf/0.1/