Skip to content

Commit 0f61c84

Browse files
cmungallcmungall
authored
Merge pull request #16 from linkml/claude/issue-15-20251024-2329
Add comprehensive family history and pedigree value sets
2 parents 8538da5 + b283290 commit 0f61c84

File tree

2 files changed

+315
-0
lines changed

2 files changed

+315
-0
lines changed

‎src/valuesets/schema/medical/family_history.yaml‎

Lines changed: 314 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,314 @@
1+
name: valuesets-medical-family-history
2+
title: Medical Family History Value Sets
3+
description: Family history and pedigree value sets based on HL7 FHIR, SNOMED CT, and KIN ontology standards
4+
id: https://w3id.org/valuesets/medical/family_history
5+
imports:
6+
- linkml:types
7+
prefixes:
8+
linkml: https://w3id.org/linkml/
9+
biolink: https://w3id.org/biolink/
10+
schema: http://schema.org/
11+
HL7: http://terminology.hl7.org/CodeSystem/
12+
SNOMED: http://snomed.info/id/
13+
valuesets: https://w3id.org/valuesets/
14+
default_prefix: valuesets
15+
16+
slots:
17+
family_relationship:
18+
description: Relationship of a family member to the subject
19+
range: FamilyRelationship
20+
family_history_status:
21+
description: Status of family history information
22+
range: FamilyHistoryStatus
23+
genetic_relationship:
24+
description: Genetic relationship between family members
25+
range: GeneticRelationship
26+
27+
enums:
28+
FamilyRelationship:
29+
description: Family relationships used in pedigree and family history documentation
30+
source: https://terminology.hl7.org/2.1.0/ValueSet-v3-FamilyMember.html
31+
permissible_values:
32+
# Core Parent Relationships
33+
PARENT:
34+
description: The player of the role is one who begets, gives birth to, or nurtures and raises the scoping entity (child)
35+
meaning: HL7:v3-RoleCode#PRN
36+
MOTHER:
37+
description: The player of the role is a female who conceives, gives birth to, or raises and nurtures the scoping entity (child)
38+
meaning: HL7:v3-RoleCode#MTH
39+
FATHER:
40+
description: The player of the role is a male who begets or raises or nurtures the scoping entity (child)
41+
meaning: HL7:v3-RoleCode#FTH
42+
NATURAL_MOTHER:
43+
description: The player of the role is a female who conceives or gives birth to the scoping entity (child)
44+
meaning: HL7:v3-RoleCode#NMTH
45+
NATURAL_FATHER:
46+
description: The player of the role is a male who begets the scoping entity (child)
47+
meaning: HL7:v3-RoleCode#NFTH
48+
ADOPTIVE_PARENT:
49+
description: The player of the role (parent) has taken the scoper (child) into their family through legal means and raises them as his or her own child
50+
meaning: HL7:v3-RoleCode#ADOPTP
51+
ADOPTIVE_MOTHER:
52+
description: The player of the role (mother) is a female who has taken the scoper (child) into their family through legal means and raises them as her own child
53+
meaning: HL7:v3-RoleCode#ADOPTM
54+
ADOPTIVE_FATHER:
55+
description: The player of the role (father) is a male who has taken the scoper (child) into their family through legal means and raises them as his own child
56+
meaning: HL7:v3-RoleCode#ADOPTF
57+
STEP_PARENT:
58+
description: The player of the role is the spouse of the scoping person's parent and not the scoping person's natural parent
59+
meaning: HL7:v3-RoleCode#STPPRN
60+
STEP_MOTHER:
61+
description: The player of the role is the female spouse of the scoping person's parent and not the scoping person's natural mother
62+
meaning: HL7:v3-RoleCode#STPMTH
63+
STEP_FATHER:
64+
description: The player of the role is the male spouse of the scoping person's parent and not the scoping person's natural father
65+
meaning: HL7:v3-RoleCode#STPFTH
66+
FOSTER_PARENT:
67+
description: The player of the role (parent) who is a state-certified caregiver responsible for the scoper (child)
68+
meaning: HL7:v3-RoleCode#PRNFOST
69+
GESTATIONAL_MOTHER:
70+
description: The player is a female whose womb carries the fetus of the scoper
71+
meaning: HL7:v3-RoleCode#GESTM
72+
73+
# Sibling Relationships
74+
SIBLING:
75+
description: The player of the role shares one or both parents in common with the scoping entity
76+
meaning: HL7:v3-RoleCode#SIB
77+
BROTHER:
78+
description: The player of the role is a male sharing one or both parents with the scoping entity
79+
meaning: HL7:v3-RoleCode#BRO
80+
SISTER:
81+
description: The player of the role is a female sharing one or both parents with the scoping entity
82+
meaning: HL7:v3-RoleCode#SIS
83+
NATURAL_BROTHER:
84+
description: The player of the role is a male related to the scoping entity by sharing only the same natural parents
85+
meaning: HL7:v3-RoleCode#NBRO
86+
NATURAL_SISTER:
87+
description: The player of the role is a female related to the scoping entity by sharing only the same natural parents
88+
meaning: HL7:v3-RoleCode#NSIS
89+
HALF_BROTHER:
90+
description: The player of the role is a male related to the scoping entity by sharing only one biological parent
91+
meaning: HL7:v3-RoleCode#HBRO
92+
HALF_SISTER:
93+
description: The player of the role is a female related to the scoping entity by sharing only one biological parent
94+
meaning: HL7:v3-RoleCode#HSIS
95+
STEP_BROTHER:
96+
description: The player of the role is a male child of the scoping person's stepparent
97+
meaning: HL7:v3-RoleCode#STPBRO
98+
STEP_SISTER:
99+
description: The player of the role is a female child of the scoping person's stepparent
100+
meaning: HL7:v3-RoleCode#STPSIS
101+
TWIN:
102+
description: The scoper and player were carried in the same womb and delivered in the same birth
103+
meaning: HL7:v3-RoleCode#TWIN
104+
TWIN_BROTHER:
105+
description: The player of the role is a male born from the same pregnancy as the scoping entity
106+
meaning: HL7:v3-RoleCode#TWINBRO
107+
TWIN_SISTER:
108+
description: The player of the role is a female born from the same pregnancy as the scoping entity
109+
meaning: HL7:v3-RoleCode#TWINSIS
110+
FRATERNAL_TWIN:
111+
description: The player of the role is born from the same pregnancy as the scoping entity but does not share the same genotype
112+
meaning: HL7:v3-RoleCode#FTWIN
113+
IDENTICAL_TWIN:
114+
description: The player of the role is born from the same pregnancy as the scoping entity and shares the same genotype
115+
meaning: HL7:v3-RoleCode#ITWIN
116+
117+
# Child Relationships
118+
CHILD:
119+
description: The player of the role is a child of the scoping entity
120+
meaning: HL7:v3-RoleCode#CHILD
121+
SON:
122+
description: The player of the role is a male offspring of the scoping entity (parent)
123+
meaning: HL7:v3-RoleCode#SON
124+
DAUGHTER:
125+
description: The player of the role is a female offspring of the scoping entity (parent)
126+
meaning: HL7:v3-RoleCode#DAU
127+
NATURAL_CHILD:
128+
description: The player of the role is an offspring of the scoping entity as determined by birth
129+
meaning: HL7:v3-RoleCode#NCHILD
130+
ADOPTIVE_CHILD:
131+
description: The player of the role is a child taken into a family through legal means and raised by the scoping person (parent) as his or her own child
132+
meaning: HL7:v3-RoleCode#CHLDADOPT
133+
FOSTER_CHILD:
134+
description: The player of the role is a child receiving parental care and nurture from the scoping person (parent) but not related to him or her through legal or blood relationship
135+
meaning: HL7:v3-RoleCode#CHLDFOST
136+
STEP_CHILD:
137+
description: The player of the role is a child of the scoping person's spouse by a previous union
138+
meaning: HL7:v3-RoleCode#STPCHLD
139+
140+
# Grandparent Relationships
141+
GRANDPARENT:
142+
description: The player of the role is a parent of the scoping person's mother or father
143+
meaning: HL7:v3-RoleCode#GRPRN
144+
GRANDMOTHER:
145+
description: The player of the role is the mother of the scoping person's mother or father
146+
meaning: HL7:v3-RoleCode#GRMTH
147+
GRANDFATHER:
148+
description: The player of the role is the father of the scoping person's mother or father
149+
meaning: HL7:v3-RoleCode#GRFTH
150+
MATERNAL_GRANDMOTHER:
151+
description: The player of the role is the mother of the scoping person's mother
152+
meaning: HL7:v3-RoleCode#MGRMTH
153+
MATERNAL_GRANDFATHER:
154+
description: The player of the role is the father of the scoping person's mother
155+
meaning: HL7:v3-RoleCode#MGRFTH
156+
PATERNAL_GRANDMOTHER:
157+
description: The player of the role is the mother of the scoping person's father
158+
meaning: HL7:v3-RoleCode#PGRMTH
159+
PATERNAL_GRANDFATHER:
160+
description: The player of the role is the father of the scoping person's father
161+
meaning: HL7:v3-RoleCode#PGRFTH
162+
163+
# Grandchild Relationships
164+
GRANDCHILD:
165+
description: The player of the role is a child of the scoping person's son or daughter
166+
meaning: HL7:v3-RoleCode#GRNDCHILD
167+
GRANDSON:
168+
description: The player of the role is a son of the scoping person's son or daughter
169+
meaning: HL7:v3-RoleCode#GRNDSN
170+
GRANDDAUGHTER:
171+
description: The player of the role is a daughter of the scoping person's son or daughter
172+
meaning: HL7:v3-RoleCode#GRNDDAU
173+
174+
# Aunt/Uncle Relationships
175+
AUNT:
176+
description: The player of the role is a sister of the scoping person's mother or father
177+
meaning: HL7:v3-RoleCode#AUNT
178+
UNCLE:
179+
description: The player of the role is a brother of the scoping person's mother or father
180+
meaning: HL7:v3-RoleCode#UNCLE
181+
MATERNAL_AUNT:
182+
description: The player of the role is a sister of the scoping person's mother
183+
meaning: HL7:v3-RoleCode#MAUNT
184+
MATERNAL_UNCLE:
185+
description: The player of the role is a brother of the scoping person's mother
186+
meaning: HL7:v3-RoleCode#MUNCLE
187+
PATERNAL_AUNT:
188+
description: The player of the role is a sister of the scoping person's father
189+
meaning: HL7:v3-RoleCode#PAUNT
190+
PATERNAL_UNCLE:
191+
description: The player of the role is a brother of the scoping person's father
192+
meaning: HL7:v3-RoleCode#PUNCLE
193+
194+
# Cousin Relationships
195+
COUSIN:
196+
description: The player of the role is a relative descended from a common ancestor, such as a grandparent, by two or more steps in a diverging line
197+
meaning: HL7:v3-RoleCode#COUSN
198+
MATERNAL_COUSIN:
199+
description: The player of the role is a child of a maternal aunt or uncle of the scoping person
200+
meaning: HL7:v3-RoleCode#MCOUSN
201+
PATERNAL_COUSIN:
202+
description: The player of the role is a child of a paternal aunt or uncle of the scoping person
203+
meaning: HL7:v3-RoleCode#PCOUSN
204+
205+
# Niece/Nephew Relationships
206+
NIECE:
207+
description: The player of the role is a daughter of the scoping person's brother or sister or of the brother or sister of the scoping person's spouse
208+
meaning: HL7:v3-RoleCode#NIECE
209+
NEPHEW:
210+
description: The player of the role is a son of the scoping person's brother or sister or of the brother or sister of the scoping person's spouse
211+
meaning: HL7:v3-RoleCode#NEPHEW
212+
213+
# Spouse/Partner Relationships
214+
SPOUSE:
215+
description: The player of the role is a marriage partner of the scoping person
216+
meaning: HL7:v3-RoleCode#SPS
217+
HUSBAND:
218+
description: The player of the role is a man joined to a woman (scoping person) in marriage
219+
meaning: HL7:v3-RoleCode#HUSB
220+
WIFE:
221+
description: The player of the role is a woman joined to a man (scoping person) in marriage
222+
meaning: HL7:v3-RoleCode#WIFE
223+
DOMESTIC_PARTNER:
224+
description: The player of the role cohabits with the scoping person but is not the scoping person's spouse
225+
meaning: HL7:v3-RoleCode#DOMPART
226+
227+
# Great-Grandparent Relationships
228+
GREAT_GRANDPARENT:
229+
description: The player of the role is a grandparent of the scoping person's mother or father
230+
meaning: HL7:v3-RoleCode#GGRPRN
231+
GREAT_GRANDMOTHER:
232+
description: The player of the role is a grandmother of the scoping person's mother or father
233+
meaning: HL7:v3-RoleCode#GGRMTH
234+
GREAT_GRANDFATHER:
235+
description: The player of the role is a grandfather of the scoping person's mother or father
236+
meaning: HL7:v3-RoleCode#GGRFTH
237+
238+
# In-Law Relationships
239+
MOTHER_IN_LAW:
240+
description: The player of the role is the mother of the scoping person's spouse
241+
meaning: HL7:v3-RoleCode#MTHINLAW
242+
FATHER_IN_LAW:
243+
description: The player of the role is the father of the scoping person's spouse
244+
meaning: HL7:v3-RoleCode#FTHINLAW
245+
DAUGHTER_IN_LAW:
246+
description: The player of the role is the wife of scoping person's son
247+
meaning: HL7:v3-RoleCode#DAUINLAW
248+
SON_IN_LAW:
249+
description: The player of the role is the husband of scoping person's daughter
250+
meaning: HL7:v3-RoleCode#SONINLAW
251+
BROTHER_IN_LAW:
252+
description: The player of the role is a brother of the scoping person's spouse, or the husband of the scoping person's sister, or the husband of a sister of the scoping person's spouse
253+
meaning: HL7:v3-RoleCode#BROINLAW
254+
SISTER_IN_LAW:
255+
description: The player of the role is a sister of the scoping person's spouse, or the wife of the scoping person's brother, or the wife of a brother of the scoping person's spouse
256+
meaning: HL7:v3-RoleCode#SISINLAW
257+
258+
# Extended Family
259+
FAMILY_MEMBER:
260+
description: A relationship between two people characterizing their "familial" relationship
261+
meaning: HL7:v3-RoleCode#FAMMEMB
262+
EXTENDED_FAMILY_MEMBER:
263+
description: Description of an extended family member
264+
meaning: HL7:v3-RoleCode#EXT
265+
SIGNIFICANT_OTHER:
266+
description: A person who is important to one's well being; especially a spouse or one in a similar relationship
267+
meaning: HL7:v3-RoleCode#SIGOTHR
268+
269+
FamilyHistoryStatus:
270+
description: Status of family history information availability
271+
permissible_values:
272+
COMPLETED:
273+
description: All relevant family history information has been obtained
274+
meaning: HL7:observation-status#final
275+
PARTIAL:
276+
description: Some family history information is available but not complete
277+
meaning: HL7:observation-status#preliminary
278+
UNKNOWN:
279+
description: Family history status is unknown
280+
meaning: HL7:data-absent-reason#unknown
281+
UNABLE_TO_OBTAIN:
282+
description: Information could not be obtained due to patient/family constraints
283+
meaning: HL7:data-absent-reason#patient-refused
284+
NOT_ASKED:
285+
description: Family history information was not requested
286+
meaning: HL7:data-absent-reason#not-asked
287+
288+
GeneticRelationship:
289+
description: Genetic relationship types for pedigree analysis
290+
permissible_values:
291+
BIOLOGICAL:
292+
description: Genetic relationship through biological inheritance
293+
meaning: SNOMED:444018008
294+
FULL_SIBLING:
295+
description: Siblings sharing both biological parents
296+
meaning: SNOMED:444301002
297+
HALF_SIBLING:
298+
description: Siblings sharing one biological parent
299+
meaning: SNOMED:445295006
300+
ADOPTIVE:
301+
description: Relationship established through adoption
302+
meaning: SNOMED:160499008
303+
NO_GENETIC_RELATIONSHIP:
304+
description: No genetic relationship exists
305+
meaning: SNOMED:373068000
306+
UNKNOWN_GENETIC_RELATIONSHIP:
307+
description: Genetic relationship status is unknown
308+
meaning: SNOMED:261665006
309+
310+
license: MIT
311+
see_also:
312+
- https://terminology.hl7.org/2.1.0/ValueSet-v3-FamilyMember.html
313+
- https://github.com/GA4GH-Pedigree-Standard/family_history_terminology
314+
- https://www.healthit.gov/isp/representing-patient-family-health-history

‎src/valuesets/schema/valuesets.yaml‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -77,6 +77,7 @@ imports:
7777
- industry/safety_colors
7878
- medical/clinical
7979
- medical/neuroimaging
80+
- medical/family_history
8081
- clinical/nih_demographics
8182
- clinical/phenopackets
8283
- bioprocessing/scale_up

0 commit comments

Comments
 (0)