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#264 Cytomegalovirus exposure
Considerations: Clinician wants to record some aspect of the patient either having had a prior infection (as indicated by IgG) or current/recurrent infection (indicated by IgM). However, the time of testing affects interpretation. Perhaps something general like 'cytomegalovirus exposure'? This is really both past exposure/infection history, as well as an assay result.
Thoughts?
Thanks
Levels of IgG or IgM against CMV are probably best not interpreted as an abnormality of the immune system. This kind of term represents an extension of the HPO away from purely rare disease (which is highly welcome), and might need an extension of the basic structure of the HPO. Do we need another top-level term (not phenotypic_abnormality) but say "illness" or "past medical history"? This one still needs some thought.
I agree, lets put this one on hold. notes from email discussion:
We are getting a lot of term requests for things that are actually past medical history. Some of these are in HPO, but being used in a current phenotyping context even though they are past history. For example, annotating an adult patient to "premature birth", "Gastrostomy tube feeding in infancy", or "cognitive delay". These temporally qualified terms are currently sprinkled throughout the HPO (which is not unreasonable as it stands).
It seems to me that there are two kinds of temporally qualified phenotypes. Those that can only happen during certain periods of development/life (for example premature birth), and those that indicate a prior event or indication, but one that can happen any time (for example Cytomegalovirus exposure, and the list of exposures in SNOMED).
In Phenotips, we have in the "prenatal and perinatal history" section a small snippet of HPO. But then, in the clinical synopsis section, which is presumably about the patient now, they have some growth parameters. These terms are in reality, temporally qualified. There are many other temporally-related terms in the rest of the higher level system bins as well.
We really need to think about the phenotypes from a timeline perspective, where some phenotypes are limited to certain portions of the timeline, and some are prior to "now". Then we must now when "now" is and when the patient was born. On top of this all, we'd want some progression over time to be indicated. I think this is non-trivial, totally necessary, and probably not solved with new HPO classes but rather some data properties, temporal ordering and likely more complexities that we have yet to cogitate on.
Hi everybody,
I put this on "closed-later" for now. But I was wondering if we might want to add a class called "Immune response" (i.e., a normal response to an infectious agent or better a foreign epitope). Under this we could have the various items such as CMV. This might not be entirely clean though, although we do not have much ontological committment as to what we think "abnormal" is (perhaps "normal" is just to be 100% healthy, something that nobody really is...)
-thoughts?
-Peter
Dr. med. Peter N. Robinson, MSc.
Professor of Medical Genomics
Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
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Germany
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peter.robinson@charite.de
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
I have learned from my mistakes, and I am sure I can repeat them exactly
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Von: Peter N. Robinson [probins@users.sf.net]
Gesendet: Sonntag, 30. März 2014 19:38
An: [obo:human-phenotype-requests]
Betreff: [obo:human-phenotype-requests] #264 Cytomegalovirus exposure
[human-phenotype-requests:#264]http://sourceforge.net/p/obo/human-phenotype-requests/264/ Cytomegalovirus exposure
Status: closed-later
Group: musculoskeletal
Created: Tue Feb 04, 2014 03:30 PM UTC by Melissa Haendel
Last Updated: Sat Feb 15, 2014 04:13 PM UTC
Owner: Peter N. Robinson
Considerations: Clinician wants to record some aspect of the patient either having had a prior infection (as indicated by IgG) or current/recurrent infection (indicated by IgM). However, the time of testing affects interpretation. Perhaps something general like 'cytomegalovirus exposure'? This is really both past exposure/infection history, as well as an assay result.
Thoughts?
Thanks
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