From: Sebastian B. <seb...@ch...> - 2009-10-27 11:19:26
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Hi, Peter Robinson wrote: > 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? I agree. I would actually try to annotate it as good as possible within the current limitations. Furthermore, I think it is important to collect all of the ambiguity and "sloppiness" of annotations/structure due to some limitations in a place for its own, being as detailed as it can get, including your different suggestions to address the problem. One then gets a good overview about the current issues of the model. I find it it easier to judge whether a change that makes the model more complex is necessary if I see more examples that fall in the same class. Moreover, it should help to outweight the pro and cons of the different strategies to address the limitations. Bye, Sebastian > 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/ > > > > > > > > > |