Re: [Obo-human-phenotype] new annotation requirements

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On Oct 26, 2009, at 2:55 PM, Dr. med. Sandra Dölken wrote:

> Hi Peter,
>
> sorry I didn't make this clear enough; at the moment there are no  
> terms
> for male/female; they are not in the inheritance ontology either.
>
> The term unilateral would be a start; we could at least capture the  
> most
> relevenat data that way but a universal term "unilateral" does not  
> exit in
> the HPO at the moment either.
>
> I put in the Quality "unilateral" for each term but that is not a very
> nice or precice way to put it.
>
> Perhaps for a start we could create terms in the HPO such as:
>
> #ontology: onset and clinical course
> #parent term: gender affected
> #chid term (1): "inhers in males" or "males affected"
> #Child term (2): "inhers in females" or "females affected"
>
> and
>
> #ontology: onset and clinical course
> #parent term: "site affected" or perhaps better "affected part of  
> human body"
> #child term (1): "unilateral"
> #child  term (2): "bilateral"
>
> ?
>
> At the moment I tried to work around this by using extra features  
> done by
> EQ-only to supply the information; I'm not sure if this should be  
> done the
> way I tried:
>
> #Genotype: 46X (MIM:300275) / X(Y); 46X (MIM:300205) / X(Y)
> #Gene Symbols: NSDHL; EBP
> #E: Human body^has_part(Right)

Unfortunately this isn't quite right - Phenote should really stop you  
from composing these kinds of classes

* The term "Right" in FMA is slightly odd:

/ FMA:85802 ! Attribute entity
   is_a FMA:66929 ! Structural relationship value
    is_a FMA:67631 ! Primary anatomical coordinate
     is_a FMA:30333 ! Right ***

There are no definitions. But it's not a type of Physical anatomical  
entity, so Phenote (in future versions) should prevent you from making  
relational expressions between a physical antomical entity and a non- 
physical entity using part_of.

* If we do understand this term to mean something like "right hand  
side" then the expression denotes the set of all human bodies that  
have as part some right side of body. This is most humans!

unfortunately the classes in FMA don't appear to give us a good way of  
saying "right side of body". They have certain classes like "right  
side of face" pre-composed, but these don't have a logical definition.

One option is to use the spatial ontology here.

> #Q: abnormal
> #Frequency:66%
>
> #Genotype: 46X (MIM:300275) / X(Y); 46X (MIM:300205) / X(Y)
> #Gene Symbols: NSDHL; EBP
> #E: Human body^has_part(left)
> #Q: abnormal
> #Frequency:33%
>
> #Genotype: 46X (MIM:300275) / X(Y); 46X (MIM:300205) / X(Y)
> #Gene Symbols: NSDHL; EBP
> #E: Human body
> #Q: abnormal
> #Frequency:1%
>
> -> this is to state that very few bilateral cases were reported
>
> #Genotype: 46X (MIM:300275) / Y; 46X (MIM:300205) / Y
> #Gene Symbols: NSDHL; EBP
> #Phenotype: Stillborn or neonatal death
> #Frequency:99%
>
> -> leaving 1% of males that survive and are affected the same as  
> females;
> I hope it is correct this way;
> If anyone has a better idea I would be happy for any suggestions.
>
> Appart from this problem the annotation for CHILD-Syndrome is done.
>
> -Sandra
>
>
>> Hi Sandra,
>> Is it possible to use the term unilateral in the annotations to mean
> just
>> what you say?
>> As to the gender affected, I think that this should be part of the
> inheritance ontology (even if it now is part of clinical course, that
> was
>> a mistake!). I am not sure that this is an issue that
>> can be settled quickly. I think we should think about the kind of  
>> terms
> and structure we will need in the inheritance ontology to describe  
> this.
> Perhaps it might be better to leave CHILD syndrome for later?
>> -p
>> --
>> Dr. med. Peter N. Robinson, MSc.
>> Institut für Medizinische Genetik
>> Charité - Universitätsmedizin Berlin
>> Augustenburger Platz 1
>> 13353 Berlin
>> Germany
>> +4930 450569124
>> pet...@ch...
>> http://compbio.charite.de
>> http://www.human-phenotype-ontology.org
>> ________________________________________
>> Von: "Dr. med. Sandra Dölken" [san...@ch...]
>> Gesendet: Montag, 26. Oktober 2009 21:42
>> An: Obo...@li...
>> Cc: Robinson, Peter; Sebastian Bauer
>> Betreff: new annotation requirements
>> Dear all,
>> working on the annotations I have come up with a problem again,  
>> which at
> least some of us have been discussing in the past already:
>> in this case: CHILD-Syndrome:
>> 1) x-chromosomal dominant inheritance: all features present only in
> females because lethal in males
>> -> we really need to decide how to express this doing annotations ->
> possible solutions would be either another field in Phenote stating
> "male/female" or adding another subgroup-ontology same as "mode of
> inheritance" and "onset and clinical course". Perhaps we could even  
> add
> features to the subgroup "clinical course" for example "affecting  
> males"
> and affecting females"?
>> 2) In CHILD-Syndrome you see all the features typically unilateral;  
>> the
> right side of the body beeing affected in 2/3 of the cases
>> -> possible solutions: add another field for "unilateral/ 
>> bilateral"; but
> then you also need to say that all features occur unilateral on the
> same,
>> "affected" side. Or we could also add something like:
>> #Unilateral
>> __right side
>> __left side
>> #Bilateral
>> perhaps again to the "onset and clinical course" ontology? In that  
>> case
> we
>> could perhaps rename the field "Mode of inheritance" in phenote to
> "Clinical course" and give the option to "add" more fields of the same
> nature if necessary.
>> Then we could state:
>> #Phenotype: Congenital ichthyosiform erythroderma
>> #Clinical course (1): affecting females
>> #Clinical course (2): unilateral
>> #Frequency: obligate
>> and
>> #Phenotype: x-chromosomal dominant inheritance
>> #Clinical course (1): affecting females
>> #Clinical course (2): unilateral_right side
>> #Frequency: 66,66%
>> and
>> #Phenotype: x-chromosomal dominant inheritance
>> #Clinical course (1): affecting females
>> #Clinical course (2): unilateral_left side
>> #Frequency: 33,33%
>> and
>> #Phenotype: Stillborn or neonatal death
>> #Clinical course: affecting males
>> #Frequency: 99%
>> I know this is not really alltogether precise and correct as mode of
> inheritance is not a phenotype but this is the way it appears in  
> Phenote
> at the moment. So far I can't say any of the above things and really
> don't
>> know how to annotate those.
>> Perhaps someone has a better suggestion? And we should really try  
>> to set
> this up fast because it slows the annotation-process down  
> conciderably.
> Thanks to all,
>> Sandra
>> Dr. med. Sandra Dölken
>> Charité Universitätsmedizin Berlin
>> Campus Virchow Klinikum
>> Institut für Medizinische Genetik
>> Augustenburger Platz 1
>> 13353 Berlin
>> Germany
>> phone: +49(0)30 450 569 132
>> fax: +49(0)30 450 569 914
>> email: san...@ch...
>> http://genetik.charite.de/institut/
>
>
> Dr. med. Sandra Dölken
> Charité Universitätsmedizin Berlin
> Campus Virchow Klinikum
> Institut für Medizinische Genetik
> Augustenburger Platz 1
> 13353 Berlin
> Germany
> phone: +49(0)30 450 569 132
> fax: +49(0)30 450 569 914
> email: san...@ch...
> http://genetik.charite.de/institut/
>
>
>
>
>
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