No Current Link To VocabularyCoded With ExtensionsCoded No Extensions
COCT_MT930000UV
GeneticLocus

Derived from RMIM: COCT_RM930000UV and HMD: COCT_HD930000UV
 
GeneticLocus

Design Comments: Use the associations to the shadow classes when the data set type (e.g., expression) is not at deeper levels (e.g., allelic level) and needs to be associated directly with the locus (e.g., the expression level is the translational result of both alleles).

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassLocus, root= "LOC"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:x_ActMoodDefEvnRqoPrmsPrp}
id [0..1]
Observation (II)
code [0..1]
Observation (CD) {CWE:D:ActCode}
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (IVL<TS>)
confidentialityCode [0..*]
Observation (DSET<CD>) {CWE:D:Confidentiality}
uncertaintyCode [0..1]
Observation (CD) {CNE:D:ActUncertainty}
value [0..1]
Observation (CD) {CWE:D:ObservationValue}

UsageNotes: ERROR - Business name from Visio is too long and was truncated. Full businessName follows. (identifying a gene through GenBank GeneID with an optional translation to HUGO name.

interpretationCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationInterpretation}
methodCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationMethod}
subject [0..1] (Subject)
performer [0..*] (Performer)
derivedFrom1 [0..*] (DerivedFrom11)
derivedFrom2 [0..*] (DerivedFrom12)
reference [0..*] (Reference3)

Design Comments: A related gene that is on a different locus, and still has significant interrelation with the source gene (similar to the recursive association of an IndividualAllele).

pertinentInformation [0..*] (PertinentInformation2)
component1 [0..*] (Component3)
component2 [0..*] (Component15)
component3 [0..*] (Component17)
component4 [0..*] (Component18)
component5 [0..*] (Component14)
componentOf [0..*] (Component)
 
Subject
typeCode [1..1] (M)
Participation (CS) {CNE:V:ParticipationTargetSubject, root= "SBJ"}
contextControlCode [0..1]
Participation (CS) {CNE:V:ContextControl, default= "OP"}
identifiedEntity [1..1] (IdentifiedEntity)

Design Comments: Use this role to identify a different subject (e.g., healthy tissue, virus, etc.) than the one propagated from the wrapping message or payload (e.g., GeneticLoci).

 
IdentifiedEntity

Design Comments: Use this role to identify a different subject (e.g., healthy tissue, virus, etc.) than the one propagated from the wrapping message or payload (e.g., GeneticLoci).

classCode [1..1] (M)
Role (CS) {CNE:V:RoleClassIdentifiedEntity, root= "IDENT"}
id [0..*]
Role (DSET<II>)
code [0..1]
Role (CD) {CWE:D:RoleCode}
 
DerivedFrom11
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
associatedProperty [1..1] (AssociatedProperty)
 
DerivedFrom12
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
polypeptide [1..1] (Polypeptide)
 
Reference3

Design Comments: A related gene that is on a different locus, and still has significant interrelation with the source gene (similar to the recursive association of an IndividualAllele).

typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipRefersTo, root= "REFR"}
geneticLocus [1..1] (GeneticLocus)
 
PertinentInformation2
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
Component3
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
individualAllele [1..1] (IndividualAllele)

Design Comments: There could be zero to many IndividualAllele objects in a specific instance. A typical case would be an allele pair, one on the paternal chromosome and one on the maternal chromosome.

 
IndividualAllele

Design Comments: There could be zero to many IndividualAllele objects in a specific instance. A typical case would be an allele pair, one on the paternal chromosome and one on the maternal chromosome.

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassBioSequenceVariation, root= "SEQVAR"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:x_ActMoodDefEvnRqoPrmsPrp}
id [0..1]
Observation (II)
negationInd [0..1]
Observation (BL)
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
uncertaintyCode [0..1]
Observation (CD) {CNE:D:ActUncertainty}
value [0..1]
Observation (CD) {CWE:D:ObservationValue}
interpretationCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationInterpretation}
methodCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationMethod}
performer [0..*] (Performer)
derivedFrom1 [0..*] (DerivedFrom10)
derivedFrom2 [0..*] (DerivedFrom9)
reference [0..*] (Reference)

Design Comments: A related allele that is on a different locus, and has interrelation with the source allele, e.g., translocated duplicates of the gene.

pertinentInformation [0..*] (PertinentInformation5)
component1 [0..*] (Component9)
component2 [0..*] (Component7)
component3 [0..*] (Component10)
component4 [0..1] (Component16)
componentOf [0..*] (Component2)
 
DerivedFrom10
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
polypeptide [1..1] (Polypeptide)
 
DerivedFrom9
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
associatedProperty [1..1] (AssociatedProperty)
 
Reference

Design Comments: A related allele that is on a different locus, and has interrelation with the source allele, e.g., translocated duplicates of the gene.

typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipRefersTo, root= "REFR"}
individualAllele [1..1] (IndividualAllele)
 
PertinentInformation5
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
Component9
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
expression [1..1] (Expression)

Design Comments: The Expression class refers to both gene and protein expression levels. It is an encapsulating class that allows the encapsulation of raw expression data in its value attribute.

 
Expression

Design Comments: The Expression class refers to both gene and protein expression levels. It is an encapsulating class that allows the encapsulation of raw expression data in its value attribute.

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassExpressionLevel, root= "EXP"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:x_ActMoodDefEvnRqoPrmsPrp}
id [0..1]
Observation (II)
code [1..1]
Observation (CD) {CWE:D:ActCode}
negationInd [0..1]
Observation (BL)
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
uncertaintyCode [0..1]
Observation (CD) {CNE:D:ActUncertainty}
value [1..1]
Observation (ED)
interpretationCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationInterpretation}
methodCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationMethod}
performer [0..*] (Performer)
derivedFrom [0..*] (DerivedFrom4)
pertinentInformation [0..*] (PertinentInformation3)
component [0..*] (Component19)
 
DerivedFrom4
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
associatedProperty [1..1] (AssociatedProperty)

Design Comments: Use this class for inherent data about the locus, e.g. chromosome no.

 
AssociatedProperty

Design Comments: Use this class for inherent data about the locus, e.g. chromosome no.

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassGenomicObservation, root= "GEN"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:ActMoodEventOccurrence, root= "EVN"}
code [0..1]
Observation (CD) {CWE:D:ActCode}
text [0..1]
Observation (ED)
value [0..1]
Observation (ANY) {CWE:D:ObservationValue}
 
PertinentInformation3
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
Component19
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
associatedObservation [1..1] (AssociatedObservation)

Design Comments: Code: COPY_NUMBER, ZYGOSITY, DOMINANCY, GENE_FAMILY, etc. For example, if code = COPY_NUMBER, then the value is of type INT and is holding the no. of copies of this gene or allele.

 
AssociatedObservation

Design Comments: Code: COPY_NUMBER, ZYGOSITY, DOMINANCY, GENE_FAMILY, etc. For example, if code = COPY_NUMBER, then the value is of type INT and is holding the no. of copies of this gene or allele.

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassGenomicObservation, root= "GEN"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:x_ActMoodDefEvnRqo}
id [0..*]
Observation (DSET<II>)
code [0..1]
Observation (CD) {CWE:D:ActCode}
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
value [0..1]
Observation (ANY) {CWE:D:ObservationValue}
methodCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationMethod}
performer [0..*] (Performer)
pertinentInformation [0..*] (PertinentInformation9)
 
Performer
typeCode [1..1] (M)
Participation (CS) {CNE:V:ParticipationPhysicalPerformer, root= "PRF"}
contextControlCode [0..1]
Participation (CS) {CNE:V:ContextControl, default= "OP"}
assignedEntity [1..1] (R_AssignedEntityUniversal)
 
PertinentInformation9
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
ClinicalPhenotype
classCode [1..1] (M)
Act (CS) {CNE:}
moodCode [1..1] (M)
Act (CS) {CNE:V:ActMoodEventOccurrence, root= "EVN"}
component1 [0..*] (Component4)
component2 [0..*] (Component5)
component3 [0..*] (Component11)
 
Component4
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
observedClinicalPhenotype [1..1] (ObservedClinicalPhenotype)

Design Comments: A phenotype which has been actually observed in the patient represented internally in this model.

 
ObservedClinicalPhenotype

Design Comments: A phenotype which has been actually observed in the patient represented internally in this model.

choice of A_SupportingClinicalInformationUniversal
 
Component5
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
knownClinicalPhenotype [1..1] (KnownClinicalPhenotype)

Design Comments: These phenotypes are not the actual (observed) phenotypes for the patient, rather they are the scientifically known phenotypes of the source genomic observation (e.g., known risks of a mutation or know responsiveness to a medication).

 
KnownClinicalPhenotype

Design Comments: These phenotypes are not the actual (observed) phenotypes for the patient, rather they are the scientifically known phenotypes of the source genomic observation (e.g., known risks of a mutation or know responsiveness to a medication).

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassPhenotype, root= "PHN"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:ActMoodDefinition, root= "DEF"}
code [0..1]
Observation (CD) {CWE:D:ActCode}
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
uncertaintyCode [0..1]
Observation (CD) {CNE:D:ActUncertainty}
value [0..1]
Observation (ANY) {CWE:D:ObservationValue}
 
Component11
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
externalObservedClinicalPhenotype [1..1] (ExternalObservedClinicalPhenotype)

Design Comments: An external observation is preferably a valid observation instance existing in any other HL7-compliant instance, e.g., a document or a message. Use the id attribute of this class to point to the unique instance identifier of that observation.

 
ExternalObservedClinicalPhenotype

Design Comments: An external observation is preferably a valid observation instance existing in any other HL7-compliant instance, e.g., a document or a message. Use the id attribute of this class to point to the unique instance identifier of that observation.

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassPhenotype, root= "PHN"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:ActMoodEventOccurrence, root= "EVN"}
id [1..1]
Observation (II)
code [0..1]
Observation (CD) {CWE:D:ActCode}
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
 
Component7
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
sequence [1..1] (Sequence)
 
Sequence
classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassBioSequence, root= "SEQ"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:x_ActMoodDefEvnRqoPrmsPrp}
id [0..1]
Observation (II)
code [1..1]
Observation (CD) {CWE:D:ActCode}
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
uncertaintyCode [0..1]
Observation (CD) {CNE:D:ActUncertainty}
value [1..1]
Observation (ED)
interpretationCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationInterpretation}
methodCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationMethod}
performer [0..*] (Performer)
derivedFrom1 [0..*] (DerivedFrom7)
derivedFrom2 [0..*] (DerivedFrom5)

Design Comments: This recursive association enables the association of an RNA sequence derived from a DNA sequence and a polypeptide sequence derived from the RNA sequence.

derivedFrom3 [0..*] (DerivedFrom8)
derivedFrom4 [0..*] (DerivedFrom)
derivedFrom5 [0..*] (DerivedFrom2)
pertinentInformation [0..*] (PertinentInformation8)
component [0..*] (Component21)
 
DerivedFrom7
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
associatedProperty [1..1] (AssociatedProperty)
 
DerivedFrom5

Design Comments: This recursive association enables the association of an RNA sequence derived from a DNA sequence and a polypeptide sequence derived from the RNA sequence.

typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
sequence [1..1] (Sequence)
 
DerivedFrom8
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
sequenceVariation [1..1] (SequenceVariation)

Design Comments: The code attribute indicates in what molecule the variation occurs, i.e., DNA, RNA or Protein.

 
SequenceVariation

Design Comments: The code attribute indicates in what molecule the variation occurs, i.e., DNA, RNA or Protein.

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassBioSequenceVariation, root= "SEQVAR"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:x_ActMoodDefEvnRqoPrmsPrp}
id [0..1]
Observation (II)
code [0..1]
Observation (CD) {CWE:D:ActCode}
negationInd [0..1]
Observation (BL)
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
value [0..1]
Observation (ANY) {CWE:D:ObservationValue}

UsageNotes: ERROR - Business name from Visio is too long and was truncated. Full businessName follows. (The variation itself expressed with recognized notation like 269T>C or markup like BSML or drawn from an external reference like OMIM or dbSNP.

interpretationCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationInterpretation}
methodCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationMethod}
performer [0..*] (Performer)
derivedFrom [0..*] (DerivedFrom3)
pertinentInformation [0..*] (PertinentInformation)
component [0..*] (Component20)
componentOf [0..*] (Component8)
 
DerivedFrom3
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
associatedProperty [1..1] (AssociatedProperty)
 
PertinentInformation
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
Component20
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
associatedObservation [1..1] (AssociatedObservation)
 
Component8
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
geneticLoci [1..1] (GeneticLoci)

Design Comments: Use this class to indicate a set of genetic loci to which this locus belongs. The loci set could be a haplotype, a genetic profile and so forth. Use the id attribute to point to the GeneticLoci instance if available. The other attributes serve as a minimal data set about the loci group.

 
GeneticLoci

Design Comments: Use this class to indicate a set of genetic loci to which this locus belongs. The loci set could be a haplotype, a genetic profile and so forth. Use the id attribute to point to the GeneticLoci instance if available. The other attributes serve as a minimal data set about the loci group.

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassObservation, root= "OBS"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:ActMoodEventOccurrence, root= "EVN"}
id [0..*]
Observation (DSET<II>)
code [0..1]
Observation (CD) {CWE:D:ActCode}
effectiveTime [0..1]
Observation (QSET<TS>)
value [0..1]
Observation (ANY) {CWE:D:ObservationValue}
pertinentInformation [0..*] (PertinentInformation6)
 
PertinentInformation6
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
DerivedFrom
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
determinantPeptide [1..1] (DeterminantPeptide)
 
DeterminantPeptide
classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassDeterminantPeptide, root= "DETPOL"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:ActMoodEventOccurrence, root= "EVN"}
id [0..1]
Observation (II)
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
value [0..1]
Observation (CD) {CWE:D:ObservationValue}

UsageNotes: ERROR - Business name from Visio is too long and was truncated. Full businessName follows. (peptide code, drawn from reference databases like those used in the Polypeptide class

methodCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationMethod}
pertinentInformation [0..*] (PertinentInformation4)
 
PertinentInformation4
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
DerivedFrom2
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
polypeptide [1..1] (Polypeptide)

Design Comments: This is a computed outcome, i.e., the lab does not test for the actual protein, but secondary processes populate this class with the translational protein.

 
Polypeptide

Design Comments: This is a computed outcome, i.e., the lab does not test for the actual protein, but secondary processes populate this class with the translational protein.

classCode [1..1] (M)
Observation (CS) {CNE:V:ActClassPolypeptide, root= "POL"}
moodCode [1..1] (M)
Observation (CS) {CNE:V:ActMoodEventOccurrence, root= "EVN"}
id [0..1]
Observation (II)
text [0..1]
Observation (ED)
effectiveTime [0..1]
Observation (QSET<TS>)
value [0..1]
Observation (CD) {CWE:D:ObservationValue}
methodCode [0..*]
Observation (DSET<CD>) {CWE:D:ObservationMethod}
derivedFrom [0..*] (DerivedFrom6)
pertinentInformation [0..*] (PertinentInformation7)
 
DerivedFrom6
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipIsDerivedFrom, root= "DRIV"}
determinantPeptide [1..1] (DeterminantPeptide)
 
PertinentInformation7
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
PertinentInformation8
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipPertains, root= "PERT"}
clinicalPhenotype [1..1] (ClinicalPhenotype)
 
Component21
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
associatedObservation [1..1] (AssociatedObservation)
 
Component10
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
sequenceVariation [1..1] (SequenceVariation)
 
Component16
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
associatedObservation [1..1] (AssociatedObservation)
 
Component2
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
geneticLoci [1..1] (GeneticLoci)
 
Component15
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
associatedObservation [1..1] (AssociatedObservation)
 
Component17
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
sequenceVariation [1..1] (SequenceVariation)
 
Component18
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
sequence [1..1] (Sequence)
 
Component14
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
expression [1..1] (Expression)
 
Component
typeCode [1..1] (M)
ActRelationship (CS) {CNE:V:ActRelationshipHasComponent, root= "COMP"}
geneticLoci [1..1] (GeneticLoci)