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How to store maternal or paternal relatives?


(Wang Man) #1

Hi everyone, I have a question about how to store family history.

for example:patient XX
Observation concept id 4083519 Family history of disorder
Value as concept id 316866 Hypertensive disorder
Qualifier concept id 42537222 Maternal aunt

is this the right method to store maternal aunt?if not,how should I store it?


(Oleg Zhuk) #2

Hello!

There are some special concepts:

These concepts are children of 4210989 Family history with explicit context. Check others, you can find suitable concepts for your case.


(Christophe Lambert) #3

Are you trying to represent all of the relationships in a family tree – that is, a pedigree? If so, there is not a way to do so in the OMOP common data model. There have been discussions of a genetics specification in the OHDSI forums, for instance here and here, but they seem to have left out representation of pedigrees in the draft specifications I have seen.

The standard way this is done in the field of genetics is to have a pedigree file where each row has a pedigree id (to represent membership in an extended family), a person_id, father_person_id, mother_person_id, and sex.

One could augment the OMOP person table to add father_person_id, mother_person_id fields, and one could represent the whole family tree (I would leave out the pedigree id). One would have to add rows to the person table for relatives to the table, though they may not have clinical information, as well as set 0 to the father_person_id and/or mother_person_id, when you reach high enough in the tree that you don’t know the ancestry.

Christophe


(Wang Man) #4

thanks,but these children are not what I want(I’ve already checked).what I want to know is which line dose My aunt come from.for example,From a paternal or maternal


(Wang Man) #5

Actually no.for now,I can not use the standard way to establish a pedigree file.however, thanks for telling me the best way.
I am trying to find the method in which way I can describe the genealogy of family members (only make a distinction between paternal or maternal side)and which filed should I use to srtore this concept id


(Qi Yang) #6

@Vines

what I want to know is which line dose My aunt come from.for example,From a paternal or maternal

I think you can put the concepts that @zhuk mentioned above in the observation_concept_id column. And then use concept below in the qualifier_concept_id field.

4075823 Paternal

Although I don’t find a maternal concept_id.

@Dymshyts Why isn’t there a “Maternal” qualifier value?


(Wang Man) #7

thank you very much.same question as yours.can’t find a maternal concept_id.
btw,for my understanding,here is an example
patient id XXX
Observation concept id 4083519 Family history of disorder
Value as concept id 316866 Hypertensive disorder
Observation concept id 4050943 Family history with explicit context pertaining to aunt
Qualifier concept id 4075823 Paternal
is that right?


(Qi Yang) #8

You don’t need “Observation concept id 4083519 Family history of disorder”

Only below:

Observation concept id 4050943 Family history with explicit context pertaining to aunt
Value as concept id 316866 Hypertensive disorder
Qualifier concept id 4075823 Paternal


(Wang Man) #9

thank you very much~~~


(Lisa Schilling) #10

@Christophe_Lambert

Christophe,
Can you expand on this statement- this standard way - is this in within research data sets? within EHRs? is this standard described/published anywhere? Would you be able to provide an mock example of a ‘pedigree file’?

Thanks, Lisa


(Christophe Lambert) #11

Hi Lisa,

This would be a standard used for many years in research data sets. This Center for Statistical Genetics page has a decent description and example. They write,

"Although pedigrees can become quite complex, all the information that is necessary to reconstruct individual relationships in a pedigree file can be summarized in five items: a family identifier, an individual identifier, a link to each parent (if available) and finally an indicator of each individual’s sex.’’

So if one wanted to represent pedigrees, you would only need to add fields for person_id’s for the father and mother. Why I would argue against a family identifier, is that if one had the full family tree of humanity, everyone is related – the family_id is a holdover from how pedigrees would be collected within large extended families. However, you could imagine problems arising with two “families” overlapping through the relationship structure defined by the relationship links from person_id, father_id, and mother_id, and then two related people could be listed as having different family id’s.

Hope this helps,
Christophe


(Lisa Schilling) #12

Christophe,
Thank you so much! I’ll be looking more closely at this.
Best,
Lisa


(Dmytry Dymshyts) #13

SNOMED adds concepts by request, perhaps these was a request to add Paternal, but wasn’t for Maternal.

@Vines
Actually, there’s another branch in SNOMED:
And here is maternal aunt
So, what if we put these concepts in qualifier_concept_id and ‘family history of condition’ put in observation_concept_id.

Or using the current approach

you can use this concept for Maternal
qualifier_concept_id doesn’t have any restriction by domain, so technically you can use this concept although it is Meas Value.


(Wang Man) #14

so,there are two approaches
one is
Observation concept id 4083519 Family history of disorder
Value as concept id 316866 Hypertensive disorder
Qualifier concept id maternal aunt

another is
Observation concept id 4050943 Family history with explicit context pertaining to aunt
Value as concept id 316866 Hypertensive disorder
Qualifier concept id as you mentioned

both approaches are right?@Dymshyts


(Dmytry Dymshyts) #15

Yeah, both looks right.
I like

more.
BTW, there’s more generic concept Family history of clinical finding we usually use to represent Family history of disorder (it is done in this way for ICD9/10/CM condition mapping).


(Wang Man) #16

thank you so much!


(Wang Man) #17

BTW,what if I have more family history of disorder not included in the concept family history of clinical finding.can I use the other standard concepts not in this category?@Dymshyts


(Dmytry Dymshyts) #18

“Family history of clinical finding” is a parent concept of “family history of disorder”
So, what do you actually mean?


(Wang Man) #19

the children of “Family history of clinical finding” are not enough.I have more diagnoses of diseases.
so,can I use the other standard concepts which is not the children of “Family history of clinical finding”


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