From: Peter R. <pet...@ch...> - 2010-07-19 16:50:52
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Hi Phenotypers & Barry and Richard, I have been thinking about where HPO terms fit into BFO (<gasp>), and I wonder if it may be wise to think about revising some of the structure of the HPO in the medium-term. HPO terms can be imagined to fall into a number of categories. At the moment, the HPO is conceived as an ontology of abnormalities rather than an ontology of abnormal entities. But if we do examine the abnormal entities, we have entities such as say microphthalmia (small eye) that are continuants, and other entities such as tachycardia (heart beating too fast) that are occurents. If this was all, then we would have no big problem conceiving of the abnormalities as (more or less abstract) independent continuants. However, there are a number of abnormal entities such as epilepsy, which are dispositions (dependent continuants) to have seizures (each of which is an occurent). At the moment, the distinction between the disposition (epilepsy/seizures) and the occurents (a particular seizure) is rather vague in the HPO. The MD concludes that a patient has a disposition (epilepsy) based on the finding that a patient has already had at least several seizures. If we confine the HPO term to the disposition, then we have no way of saying that some patient has had one single seizure. Therefore, for terms like this, we need to have one term that refers to the disposition, and another term that refers to the occurrent. We need a relationship such as epilepsy ---(is predisposed to suffer episodes of)-->seizure One danger of this approach is that there can be an inflation of terms. Do we need a different term for each kind of disposition? (Remembering that there are epileptics who can have different mixes of seizure types also). Another point is that I think the only way of making a clean distinction between the dependent continuants and the occurents would be to make the HPO an ontology of abnormal entities rather than of abnormalities. This would have its own disadvantages. Any comments? I would not plan on making any hurried changes at the this point, but would like to make an action plan this Fall...My questions: 1) Does this sound like a reasonable idea? 2) Do we need a new relation? 3) Is there a good way of having one general term such as epilepsy for the disposition, while retaining the numerous more specialized terms for the occurrents? thanks Peter -- PD Dr. med. Peter N. Robinson, MSc. Institut für Medizinische Genetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1 13353 Berlin Germany voice: 49-30-450566042 fax: 49-30-450569915 email: pet...@ch... http://compbio.charite.de/ http://www.human-phenotype-ontology.org |