Agenda and call-in info for face to face ECE meeting in Wellington

Dear Bruce/all

Thanks very much for allowing me to attend Jim's excellent session on representing genetic abnormality-related disorders. I referred a few times to a note I posted on the consultant terminologist site (as comments on Jim's July presentation of the same topic), so for those who have access the link is here to the message and discussion which followed.

It's a long note so I shan't repost, but I would urge those who are interested to take a look at the papers [1 (attached), 2] by Joseph Loscalzo on an approach to representing a 'molecular classification of disease' (the first of which is referenced in Barry Smith's later paper [3], a variant of which motivated much of the ECE thinking of the last 5+ years). As mentioned on the call my sense is that for the foreseeable future SNOMED CT will have to straddle both a traditional 'pathophenotype' [anatomy + gross/microscopic pathology] descriptions of patients as well as one that describes patients in terms of their primary and/or modifying gene or protein abnormality. I would also point people at the work of Goh and colleagues on this subject - illustrated in this fantastic 2007 poster (9 years ago!).

If the approach Jim presented to represent 'disease + genetic abnormality' combinations is adopted by IHTSDO (for what it's worth, I like a lot of it), then additional work is needed to ensure a clear relationship with seemingly similar content (Coombs negative hemolytic anemia, Seropositive rheumatoid arthritis, known chromosomal abnormalities and syndromes etc.) It may be that a family of approaches are needed (abnormal chemistry and some types of genetic mutation one way, karyotype abnormalities another way, histopathology another way and so on...), but whatever is decided the boundaries between different approaches need to be clear and reproducible.

Kind regards

Ed

[1] Loscalzo J, Kohane I, Barabasi AL. Human disease classification in the postgenomic era: a complex systems approach to human pathobiology. Mol Syst Biol. 2007; 3:124.

[2] Loscalzo J, Barabasi AL. Systems biology and the future of medicine. Wiley Interdiscip Rev Syst Biol Med. 2011 Nov-Dec; 3(6):619-27.

[3] Scheuermann RH, Ceusters W, Smith B. Toward an Ontological Treatment of Disease and Diagnosis. Summit on Translational Bioinformatics. 2009;2009:116-120.

Ed, I would support the family of approaches you suggest as I think we all agreed that we may need to proceed in this direction in creating guidelines for specific domains. I like JIm's model for genetic disorders which includes judicious use of causality to distinguish disorders for which a mutation as a causal factor has been well documented from those in which a genetic abnormality may e.g. only increase the risk of the phenotype. I also agree with the suggestion proposed at the meeting that it may not be necessary to call out the mutation if particular phenotypes are associated with only a single genetic abnormality as described by Loscalzo for sickle cell disease. 

Bruce