- Independent Continuants (roughly corresponding to HL7 Entity)
- Dependent Continuant (missing from HL7)
- Occurrents (of which HL7 Act would form a subclass, alongside those occurrents which are not Acts, such as parasomnias, involuntary muscle contractions, erosion of teeth due to persistent vomiting, and so forth)
BFO has shortcomings for representing medical information at the granular level. Like many philosophy based upper ontologies, it suffers from defining accidental properties when they are not. This leads to issues in maturation of organisms through development cycles such as parasites go through and leads to erroneous classifications.Cecil agreed to formulate his concerns in relation to a concrete case, in which John, a person on rotation living in the Congo, has a blood test drawn that shows sporozoites on the smear. The challenge for BFO is then to answer the following questions:
1. How does BFO deal with the question whether John has malaria when there are sporozoites detected on his blood smear?
2. How can BFO be used to classify an immature life form as a cause of a disease when the causative agent develops internally to the organism and changes its stage of life?
Werner Ceusters and I have sought to address these challenges here (a new version, here, addresses comments made by Christos Louis and posted below). Responses from the HL7 community are welcome. At the same time we have issued to Cecil, and through him to all afficionados of the RIM, an analogous challenge:
1. How does HL7 RIM deal with the question whether John has malaria when there are sporozoites detected on his blood smear?
2. How can HL7 RIM be used to classify an immature life form as a cause of a disease when the causative agent develops internally to the organism and changes its stage of life?
Responses to this challenge can be submitted as comments to this posting, or by email to email@example.com. All responses will be published here.
Update November 3, 2009
Update November 16, 2009:
Response from Prof. Christos (Kitsos) Louis (IMBB-FORTH / Department of Biology, University of Crete)
Overall, I think that this is a very nice idea in order to prove that BFO is indeed a powerful tool. I really liked it. But...
1) Diagnosis of malaria is extremely easy, so why make a doctor “think” first, when the only thing he has to do is a blood smear? The only possibility of mis-diagnosis is for MDs in the North who may simply not think of the disease. Also, in the opposite case cited in the abstract, if malaria is asymptomatic for whatever reason, this usually happens only in hyperendemic areas (almost exclusively the tropics) and it is of no clinical or epidemiological importance other than on a purely academic level. If, on the other hand, the audience is specialists of medical informatics (the emphasis is on informatics, i.e. people who for whatever reason don’t “like” BFO), my guess is that after taking care of the stuff below, this could certainly have positive consequences in terms of a potential global acceptance of BFO.
2) The biology of the disease and medical/diagnostic consequences: Sporozoites, as you mention in the intro, are very “short lived” in the blood. Also, due to their very low number (malaria can be caused even by one sporozoite!), they are almost impossible to detect in the blood (see wrong sentence in second paragraph of Methods)! Thus, they play zero role in the diagnostic process (and diagnosis) of malaria, which is initiated only after the first or second bout of fever. This happens days after the infectious mosquito bite and certainly not within 30 minutes. As a matter of fact, even if one rich tourist were bitten close to a hospital/clinic one would not find a single doctor willing to do a “smear” because it would be completely useless. Thus, although indeed true, anything that lies between ID#3 and right after ID#10 is absolutely irrelevant in terms of diagnosis. Furthermore, Table 3 is not only simplified but oversimplified. Malaria (disease, disposition, whatever), unless we talk about a relapse or a medically-induced one, has to start with an infectious mosquito bite, thus somehow I feel that this should be somehow be mentioned between IDs #2 and #3. Moreover, one of the crucial aspects of malaria is the recurrence of fever attacks the first of which is the one that starts the disease from the point of view of pathology. These recurring fevers make up the crucial feature that routinely leads doctors to either diagnose it as malaria or initiate the relevant diagnostic procedures. Therefore, I think that the recurring fevers should somehow find their way to Table 3. Concluding this part, I would rewrite the whole thing “starting” from the diagnostically and clinically relevant point, which is the presence of blood-stages (several kinds, and in no way called “mature”) in the peripheral blood.
3) Other comments:
i) The existence of “surviving liver stages”, i.e. hypnozoites, can only be inferred a posteriori. This may be crucial in the definition of disease (see penultimate sentence of the Discussion). Would one talk about disease solely because there may or may not be a few hypnozoites present in a few liver cells, that may or may not ever wake up?
ii) I have a big problem with Stedman’s definitions, as these first, exclude autoimmune diseases or second, are cyclical: D3 defines, among others, a disease as being a disorder while D5 says that a disorder may result from a disease! I would therefore prefer to concentrate entirely on either CDC definitions or WHO.
iii) The title’s second part is completely misleading. There is nothing about the Plasmodium life cycle here, as only part (and only part) of the vertebrate component of the life cycle is “discussed”
iv) You state “...or have no physiological counterpart at all (e.g. inflammation).” Given that inflammation is a normal response of the human body, I have certain doubts whether this should not also be “physiological” similar to the hyperventilation stated immediately before that.