valuesets 0.3.1__py3-none-any.whl

valuesets/schema/clinical/nih_demographics.yaml

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+name: nih_demographics
+title: NIH Demographics and Common Data Elements
+description: 'Standard value sets for NIH Common Data Elements (CDEs) including demographics,
+
+  race, ethnicity, sex, and other clinical variables following NIH and OMB standards'
+id: https://w3id.org/linkml/valuesets/clinical/nih_demographics
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  OMRSE: http://purl.obolibrary.org/obo/OMRSE_
+  GSSO: http://purl.obolibrary.org/obo/GSSO_
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  SIO: http://semanticscience.org/resource/SIO_
+  HP: http://purl.obolibrary.org/obo/HP_
+default_prefix: valuesets
+slots:
+  race_omb1997:
+    description: Race categories following OMB 1997 standards used by NIH and federal agencies
+    range: RaceOMB1997Enum
+  ethnicity_omb1997:
+    description: Ethnicity categories following OMB 1997 standards used by NIH and federal agencies
+    range: EthnicityOMB1997Enum
+  biological_sex:
+    description: Biological sex assigned at birth based on anatomical and physiological traits
+    range: BiologicalSexEnum
+  age_group:
+    description: Standard age groups used in NIH clinical research, particularly NINDS CDEs
+    range: AgeGroupEnum
+  participant_vital_status:
+    description: Vital status of a research participant in clinical studies
+    range: ParticipantVitalStatusEnum
+  recruitment_status:
+    description: Clinical trial or study recruitment status per NIH/ClinicalTrials
+    range: RecruitmentStatusEnum
+  study_phase:
+    description: Clinical trial phases per FDA and NIH definitions
+    range: StudyPhaseEnum
+enums:
+  RaceOMB1997Enum:
+    description: 'Race categories following OMB 1997 standards used by NIH and federal agencies.
+
+      Respondents may select multiple races.'
+    permissible_values:
+      AMERICAN_INDIAN_OR_ALASKA_NATIVE:
+        description: A person having origins in any of the original peoples of North and South America (including Central
+          America), and who maintains tribal affiliation or community attachment
+        meaning: NCIT:C41259
+        annotations:
+          omb_code: 1002-5
+      ASIAN:
+        description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian
+          subcontinent
+        meaning: NCIT:C41260
+        annotations:
+          omb_code: 2028-9
+          includes: Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, Philippine Islands, Thailand, Vietnam
+      BLACK_OR_AFRICAN_AMERICAN:
+        description: A person having origins in any of the black racial groups of Africa
+        meaning: NCIT:C16352
+        annotations:
+          omb_code: 2054-5
+      NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER:
+        description: A person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands
+        meaning: NCIT:C41219
+        annotations:
+          omb_code: 2076-8
+      WHITE:
+        description: A person having origins in any of the original peoples of Europe, the Middle East, or North Africa
+        meaning: NCIT:C41261
+        annotations:
+          omb_code: 2106-3
+      MORE_THAN_ONE_RACE:
+        description: Person identifies with more than one race category
+        meaning: NCIT:C67109
+        title: Multiracial
+        annotations:
+          note: Added after 1997 revision to allow multiple race reporting
+      UNKNOWN_OR_NOT_REPORTED:
+        description: Race not known, not reported, or declined to answer
+        meaning: NCIT:C17998
+        title: Unknown
+        annotations:
+          aliases: Unknown, Not Reported, Prefer not to answer
+  EthnicityOMB1997Enum:
+    description: Ethnicity categories following OMB 1997 standards used by NIH and federal agencies
+    permissible_values:
+      HISPANIC_OR_LATINO:
+        description: A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin,
+          regardless of race
+        meaning: NCIT:C17459
+        annotations:
+          omb_code: 2135-2
+      NOT_HISPANIC_OR_LATINO:
+        description: A person not of Hispanic or Latino origin
+        meaning: NCIT:C41222
+        annotations:
+          omb_code: 2186-5
+      UNKNOWN_OR_NOT_REPORTED:
+        description: Ethnicity not known, not reported, or declined to answer
+        meaning: NCIT:C17998
+        title: Unknown
+        annotations:
+          aliases: Unknown, Not Reported, Prefer not to answer
+  BiologicalSexEnum:
+    description: 'Biological sex assigned at birth based on anatomical and physiological traits.
+
+      Required by NIH as a biological variable in research.'
+    permissible_values:
+      MALE:
+        description: Male sex assigned at birth
+        meaning: PATO:0000384
+        exact_mappings:
+        - NCIT:C20197
+        - GSSO:000371
+      FEMALE:
+        description: Female sex assigned at birth
+        meaning: PATO:0000383
+        exact_mappings:
+        - NCIT:C16576
+        - GSSO:000369
+      INTERSEX:
+        description: Born with reproductive or sexual anatomy that doesn't fit typical definitions of male or female
+        meaning: NCIT:C45908
+        annotations:
+          prevalence: 0.018% to 1.7%
+          note: May be assigned male or female at birth
+      UNKNOWN_OR_NOT_REPORTED:
+        description: Sex not known, not reported, or declined to answer
+        meaning: NCIT:C17998
+        title: Unknown
+  AgeGroupEnum:
+    description: Standard age groups used in NIH clinical research, particularly NINDS CDEs
+    permissible_values:
+      NEONATE:
+        description: Birth to 28 days
+        meaning: NCIT:C16731
+        title: Newborn
+        annotations:
+          max_age_days: 28
+      INFANT:
+        description: 29 days to less than 1 year
+        meaning: NCIT:C27956
+        annotations:
+          min_age_days: 29
+          max_age_years: 1
+      YOUNG_PEDIATRIC:
+        description: 0 to 5 years (NINDS CDE definition)
+        meaning: NCIT:C39299
+        title: Pediatric
+        annotations:
+          min_age_years: 0
+          max_age_years: 5
+          ninds_category: true
+      PEDIATRIC:
+        description: 6 to 12 years (NINDS CDE definition)
+        meaning: NCIT:C16423
+        title: Child
+        annotations:
+          min_age_years: 6
+          max_age_years: 12
+          ninds_category: true
+      ADOLESCENT:
+        description: 13 to 17 years
+        meaning: NCIT:C27954
+        annotations:
+          min_age_years: 13
+          max_age_years: 17
+      YOUNG_ADULT:
+        description: 18 to 24 years
+        meaning: NCIT:C91107
+        annotations:
+          min_age_years: 18
+          max_age_years: 24
+      ADULT:
+        description: 25 to 64 years
+        meaning: NCIT:C17600
+        annotations:
+          min_age_years: 25
+          max_age_years: 64
+      OLDER_ADULT:
+        description: 65 years and older
+        meaning: NCIT:C16268
+        title: Elderly
+        annotations:
+          min_age_years: 65
+          aliases: Geriatric, Elderly, Senior
+  ParticipantVitalStatusEnum:
+    description: Vital status of a research participant in clinical studies
+    permissible_values:
+      ALIVE:
+        description: Participant is living
+        meaning: NCIT:C37987
+        exact_mappings:
+        - PATO:0001421
+      DECEASED:
+        title: Dead
+        description: Participant is deceased
+        meaning: NCIT:C28554
+        exact_mappings:
+        - PATO:0001422
+      UNKNOWN:
+        description: Vital status unknown or lost to follow-up
+        meaning: NCIT:C17998
+  RecruitmentStatusEnum:
+    description: Clinical trial or study recruitment status per NIH/ClinicalTrials.gov
+    permissible_values:
+      NOT_YET_RECRUITING:
+        description: Study has not started recruiting participants
+        meaning: NCIT:C211610
+        title: Not Yet Enrolling
+      RECRUITING:
+        description: Currently recruiting participants
+        meaning: NCIT:C142621
+        title: Open To Enrollment
+      ENROLLING_BY_INVITATION:
+        description: Enrolling participants by invitation only
+        meaning: NCIT:C211611
+      ACTIVE_NOT_RECRUITING:
+        description: Study ongoing but not recruiting new participants
+        meaning: NCIT:C211612
+        title: Study Active, Not Enrolling
+      SUSPENDED:
+        description: Study temporarily stopped
+        meaning: NCIT:C211613
+        title: Study Enrollment Suspended
+      TERMINATED:
+        description: Study stopped early and will not resume
+        meaning: NCIT:C70757
+        title: Study Terminated
+      COMPLETED:
+        description: Study has ended normally
+        meaning: NCIT:C70756
+        title: Completed Clinical Study
+      WITHDRAWN:
+        description: Study withdrawn before enrollment
+        meaning: NCIT:C70758
+        title: Study Withdrawn
+  StudyPhaseEnum:
+    description: Clinical trial phases per FDA and NIH definitions
+    permissible_values:
+      EARLY_PHASE_1:
+        description: Exploratory trials before traditional Phase 1
+        meaning: NCIT:C54721
+        title: Phase 0 Trial
+        annotations:
+          aliases: Phase 0
+      PHASE_1:
+        title: Phase I Trial
+        description: Initial safety and dosage studies
+        meaning: NCIT:C15600
+        annotations:
+          participants: 20-100
+      PHASE_1_2:
+        title: Phase II/III Trial
+        description: Combined Phase 1 and Phase 2 trial
+        meaning: NCIT:C15694
+      PHASE_2:
+        title: Phase II Trial
+        description: Efficacy and side effects studies
+        meaning: NCIT:C15601
+        annotations:
+          participants: 100-300
+      PHASE_2_3:
+        title: Phase IIa Trial
+        description: Combined Phase 2 and Phase 3 trial
+        meaning: NCIT:C49686
+      PHASE_3:
+        title: Phase III Trial
+        description: Efficacy comparison with standard treatment
+        meaning: NCIT:C15602
+        annotations:
+          participants: 300-3000
+      PHASE_4:
+        title: Phase IV Trial
+        description: Post-marketing surveillance
+        meaning: NCIT:C15603
+        annotations:
+          note: After FDA approval
+      NOT_APPLICABLE:
+        description: Not a phased clinical trial
+        meaning: NCIT:C48660
+        annotations:
+          note: For observational studies, device trials, etc.

valuesets/schema/clinical/phenopackets.yaml

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+name: phenopackets
+title: Phenopackets Clinical Value Sets
+description: Value sets derived from GA4GH Phenopackets Schema for clinical genomics and phenotyping
+id: https://w3id.org/linkml/valuesets/clinical/phenopackets
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  GENO: http://purl.obolibrary.org/obo/GENO_
+  HP: http://purl.obolibrary.org/obo/HP_
+  LOINC: https://loinc.org/
+  UBERON: http://purl.obolibrary.org/obo/UBERON_
+  UCUM: http://unitsofmeasure.org/
+  PATO: http://purl.obolibrary.org/obo/PATO_
+default_prefix: valuesets
+slots:
+  karyotypic_sex:
+    description: Karyotypic sex of an individual based on chromosome composition
+    range: KaryotypicSexEnum
+  phenotypic_sex:
+    description: Phenotypic sex of an individual based on observable characteristics
+    range: PhenotypicSexEnum
+  allelic_state:
+    description: Allelic state/zygosity of a variant or genetic feature
+    range: AllelicStateEnum
+  laterality:
+    description: Laterality/sidedness of a finding or anatomical structure
+    range: LateralityEnum
+  onset_timing:
+    description: Timing of disease or phenotype onset relative to developmental stages
+    range: OnsetTimingEnum
+  acmg_pathogenicity:
+    description: ACMG/AMP variant pathogenicity classification for clinical genetics
+    range: ACMGPathogenicityEnum
+  therapeutic_actionability:
+    description: Clinical actionability of a genetic finding for treatment decisions
+    range: TherapeuticActionabilityEnum
+  interpretation_progress:
+    description: Progress status of clinical interpretation or diagnosis
+    range: InterpretationProgressEnum
+  regimen_status:
+    description: Status of a therapeutic regimen or treatment protocol
+    range: RegimenStatusEnum
+  drug_response:
+    description: Response categories for drug treatment outcomes
+    range: DrugResponseEnum
+enums:
+  KaryotypicSexEnum:
+    description: Karyotypic sex of an individual based on chromosome composition
+    permissible_values:
+      XX:
+        description: Female karyotype (46,XX)
+        meaning: NCIT:C45976
+        title: XX Genotype
+        annotations:
+          chromosome_count: 46
+          typical_phenotypic_sex: female
+      XY:
+        description: Male karyotype (46,XY)
+        meaning: NCIT:C45977
+        title: XY Genotype
+        annotations:
+          chromosome_count: 46
+          typical_phenotypic_sex: male
+      XO:
+        description: Turner syndrome karyotype (45,X)
+        meaning: NCIT:C176780
+        title: 45,XO Karyotype
+        annotations:
+          chromosome_count: 45
+          condition: Turner syndrome
+      XXY:
+        description: Klinefelter syndrome karyotype (47,XXY)
+        meaning: NCIT:C176784
+        title: 47,XXY Karyotype
+        annotations:
+          chromosome_count: 47
+          condition: Klinefelter syndrome
+      XXX:
+        description: Triple X syndrome karyotype (47,XXX)
+        meaning: NCIT:C176785
+        title: 47,XXX Karyotype
+        annotations:
+          chromosome_count: 47
+          condition: Triple X syndrome
+      XXXY:
+        description: XXXY syndrome karyotype (48,XXXY)
+        meaning: NCIT:C176786
+        title: 48,XXXY Karyotype
+        annotations:
+          chromosome_count: 48
+          condition: XXXY syndrome
+      XXXX:
+        description: Tetrasomy X karyotype (48,XXXX)
+        meaning: NCIT:C176787
+        title: 48,XXXX Karyotype
+        annotations:
+          chromosome_count: 48
+          condition: Tetrasomy X
+      XXYY:
+        description: XXYY syndrome karyotype (48,XXYY)
+        meaning: NCIT:C89801
+        title: XXYY Syndrome
+        annotations:
+          chromosome_count: 48
+          condition: XXYY syndrome
+      XYY:
+        description: Jacob's syndrome karyotype (47,XYY)
+        meaning: NCIT:C176782
+        title: 47,XYY Karyotype
+        annotations:
+          chromosome_count: 47
+          condition: Jacob's syndrome
+      OTHER_KARYOTYPE:
+        description: Other karyotypic sex not listed
+        annotations:
+          note: May include complex chromosomal arrangements
+      UNKNOWN_KARYOTYPE:
+        description: Karyotype not determined or unknown
+        meaning: NCIT:C17998
+        title: Unknown
+  PhenotypicSexEnum:
+    description: 'Phenotypic sex of an individual based on observable characteristics.
+
+      FHIR mapping: AdministrativeGender'
+    permissible_values:
+      MALE:
+        description: Male phenotypic sex
+        meaning: PATO:0000384
+        exact_mappings:
+        - NCIT:C20197
+      FEMALE:
+        description: Female phenotypic sex
+        meaning: PATO:0000383
+        exact_mappings:
+        - NCIT:C16576
+      OTHER_SEX:
+        description: Sex characteristics not clearly male or female
+        meaning: NCIT:C45908
+        title: Intersex
+        annotations:
+          note: Includes differences of sex development (DSD)
+      UNKNOWN_SEX:
+        description: Sex not assessed or not available
+        meaning: NCIT:C17998
+        title: Unknown
+  AllelicStateEnum:
+    description: Allelic state/zygosity of a variant or genetic feature
+    permissible_values:
+      HETEROZYGOUS:
+        description: Different alleles at a locus
+        meaning: GENO:0000135
+        annotations:
+          symbol: het
+      HOMOZYGOUS:
+        description: Identical alleles at a locus
+        meaning: GENO:0000136
+        annotations:
+          symbol: hom
+      HEMIZYGOUS:
+        description: Only one allele present (e.g., X-linked in males)
+        meaning: GENO:0000134
+        annotations:
+          symbol: hemi
+          note: Common for X-linked genes in males
+      COMPOUND_HETEROZYGOUS:
+        description: Two different heterozygous variants in same gene
+        meaning: GENO:0000402
+        annotations:
+          symbol: comp het
+      HOMOZYGOUS_REFERENCE:
+        description: Two reference/wild-type alleles
+        meaning: GENO:0000036
+        title: reference allele
+        annotations:
+          symbol: hom ref
+      HOMOZYGOUS_ALTERNATE:
+        description: Two alternate/variant alleles
+        meaning: GENO:0000002
+        title: variant allele
+        annotations:
+          symbol: hom alt
+  LateralityEnum:
+    description: Laterality/sidedness of a finding or anatomical structure
+    permissible_values:
+      RIGHT:
+        description: Right side
+        meaning: HP:0012834
+        annotations:
+          anatomical_term: dexter
+      LEFT:
+        description: Left side
+        meaning: HP:0012835
+        annotations:
+          anatomical_term: sinister
+      BILATERAL:
+        description: Both sides
+        meaning: HP:0012832
+        annotations:
+          note: Affecting both left and right
+      UNILATERAL:
+        description: One side (unspecified which)
+        meaning: HP:0012833
+        annotations:
+          note: Affecting only one side
+      MIDLINE:
+        description: In the midline/center
+        annotations:
+          note: Along the body's central axis
+  OnsetTimingEnum:
+    description: Timing of disease or phenotype onset relative to developmental stages
+    permissible_values:
+      ANTENATAL_ONSET:
+        description: Before birth (prenatal)
+        meaning: HP:0030674
+        annotations:
+          period: Before birth
+      EMBRYONAL_ONSET:
+        description: During embryonic period (0-8 weeks)
+        meaning: HP:0011460
+        annotations:
+          period: 0-8 weeks gestation
+      FETAL_ONSET:
+        description: During fetal period (8 weeks to birth)
+        meaning: HP:0011461
+        annotations:
+          period: 8 weeks to birth
+      CONGENITAL_ONSET:
+        description: Present at birth
+        meaning: HP:0003577
+        annotations:
+          period: At birth
+      NEONATAL_ONSET:
+        description: Within first 28 days of life
+        meaning: HP:0003623
+        annotations:
+          period: 0-28 days
+      INFANTILE_ONSET:
+        description: Between 28 days and 1 year
+        meaning: HP:0003593
+        annotations:
+          period: 28 days to 1 year
+      CHILDHOOD_ONSET:
+        description: Between 1 year and 16 years
+        meaning: HP:0011463
+        annotations:
+          period: 1-16 years
+      JUVENILE_ONSET:
+        description: Between 5 years and 16 years
+        meaning: HP:0003621
+        annotations:
+          period: 5-16 years
+      YOUNG_ADULT_ONSET:
+        description: Between 16 years and 40 years
+        meaning: HP:0011462
+        annotations:
+          period: 16-40 years
+      MIDDLE_AGE_ONSET:
+        description: Between 40 years and 60 years
+        meaning: HP:0003596
+        annotations:
+          period: 40-60 years
+      LATE_ONSET:
+        description: After 60 years
+        meaning: HP:0003584
+        annotations:
+          period: '>60 years'
+  ACMGPathogenicityEnum:
+    description: ACMG/AMP variant pathogenicity classification for clinical genetics
+    permissible_values:
+      PATHOGENIC:
+        description: Pathogenic variant
+        meaning: NCIT:C168799
+        title: Pathogenic Variant
+        annotations:
+          abbreviation: P
+          clinical_significance: Disease-causing
+      LIKELY_PATHOGENIC:
+        description: Likely pathogenic variant
+        meaning: NCIT:C168800
+        title: Likely Pathogenic Variant
+        annotations:
+          abbreviation: LP
+          probability: '>90% certain'
+      UNCERTAIN_SIGNIFICANCE:
+        description: Variant of uncertain significance
+        meaning: NCIT:C94187
+        title: Variant of Unknown Significance
+        annotations:
+          abbreviation: VUS
+          note: Insufficient evidence
+      LIKELY_BENIGN:
+        description: Likely benign variant
+        meaning: NCIT:C168801
+        title: Variant Likely Benign
+        annotations:
+          abbreviation: LB
+          probability: '>90% certain benign'
+      BENIGN:
+        description: Benign variant
+        meaning: NCIT:C168802
+        title: Variant Benign
+        annotations:
+          abbreviation: B
+          clinical_significance: Not disease-causing
+  TherapeuticActionabilityEnum:
+    description: Clinical actionability of a genetic finding for treatment decisions
+    permissible_values:
+      ACTIONABLE:
+        description: Finding has direct therapeutic implications
+        meaning: NCIT:C206303
+        title: Actionable Variation
+        annotations:
+          note: Can guide treatment selection
+      NOT_ACTIONABLE:
+        description: No current therapeutic implications
+        meaning: NCIT:C206304
+        title: Non-Actionable Variation
+        annotations:
+          note: No treatment changes indicated
+      UNKNOWN_ACTIONABILITY:
+        description: Therapeutic implications unclear
+        meaning: NCIT:C17998
+        title: Unknown
+  InterpretationProgressEnum:
+    description: Progress status of clinical interpretation or diagnosis
+    permissible_values:
+      SOLVED:
+        description: Diagnosis achieved/case solved
+        meaning: NCIT:C20826
+        title: Molecular Diagnosis
+        annotations:
+          note: Molecular cause identified
+      UNSOLVED:
+        description: No diagnosis achieved
+        meaning: NCIT:C125009
+        title: Clinical Interpretation
+        annotations:
+          note: Molecular cause not identified
+      IN_PROGRESS:
+        description: Analysis ongoing
+        meaning: NCIT:C25630
+        title: Progress
+      COMPLETED:
+        description: Analysis completed
+        meaning: NCIT:C216251
+        title: Procedure Completed
+        annotations:
+          note: May be solved or unsolved
+      UNKNOWN_PROGRESS:
+        description: Progress status unknown
+        meaning: NCIT:C17998
+        title: Unknown
+  RegimenStatusEnum:
+    description: Status of a therapeutic regimen or treatment protocol
+    permissible_values:
+      NOT_STARTED:
+        description: Treatment not yet begun
+        meaning: NCIT:C53601
+        title: Device Evaluation Anticipated But Not Yet Begun
+      STARTED:
+        description: Treatment initiated
+        meaning: NCIT:C165209
+        title: Treatment Ongoing
+      COMPLETED:
+        description: Treatment finished as planned
+        meaning: NCIT:C105740
+        title: Treatment Completed as Prescribed
+      DISCONTINUED_ADVERSE_EVENT:
+        description: Stopped due to adverse event
+        meaning: NCIT:C41331
+        title: Adverse Event
+        annotations:
+          reason: Toxicity or side effects
+      DISCONTINUED_LACK_OF_EFFICACY:
+        description: Stopped due to lack of efficacy
+        meaning: NCIT:C49502
+        title: Drug Withdrawn
+        annotations:
+          reason: Treatment not effective
+      DISCONTINUED_PHYSICIAN_DECISION:
+        description: Stopped by physician decision
+        meaning: NCIT:C49502
+        title: Drug Withdrawn
+      DISCONTINUED_PATIENT_DECISION:
+        description: Stopped by patient choice
+        meaning: NCIT:C48271
+        title: Consent Withdrawn
+      UNKNOWN_STATUS:
+        description: Treatment status unknown
+        meaning: NCIT:C17998
+        title: Unknown
+  DrugResponseEnum:
+    description: Response categories for drug treatment outcomes
+    permissible_values:
+      FAVORABLE:
+        description: Favorable response to treatment
+        meaning: NCIT:C123584
+        title: Favorable Response
+        annotations:
+          note: Better than expected response
+      UNFAVORABLE:
+        description: Unfavorable response to treatment
+        meaning: NCIT:C102561
+        annotations:
+          note: Worse than expected response
+      RESPONSIVE:
+        description: Responsive to treatment
+        meaning: NCIT:C165206
+        title: Responsive Disease
+        annotations:
+          note: Shows expected response
+      RESISTANT:
+        description: Resistant to treatment
+        meaning: NCIT:C16523
+        title: Drug Resistance Process
+        annotations:
+          note: No response to treatment
+      PARTIALLY_RESPONSIVE:
+        description: Partial response to treatment
+        meaning: NCIT:C18213
+        title: Stable Disease
+        annotations:
+          note: Some but not complete response
+      UNKNOWN_RESPONSE:
+        description: Treatment response unknown
+        meaning: NCIT:C17998
+        title: Unknown