book recommendation - basic formal ontology (BFO) for biomedicine

Thomas Beale thomas.beale at oceaninformatics.com
Tue Sep 8 03:14:04 EDT 2015


Daniel,

nice observations and thanks for the references - I had intended to 
circulate the first one as well, at some point. For my part, I think 
ontology will become useful in information modelling precisely for the 
reason that it offers ways of representing distinctions between real 
world referents and the things that refer to them (information 
entities). In other words, to help the IT sector understand 'how to 
model'. Historically it has been completely confused (I would go so far 
as to say not even conscious) of the difference between real world 
entities and events and the information items that document them.

With no understanding of the in-principle divide between ontological and 
epistemological points of view (or equivalently of Popper's 3 worlds), 
information modelling can't possibly achieve much clarity or computability.

So in agreeing with you, I would add that ontology-thinking is not a 
recipe for how to do information modelling, but it is useful for 
understanding what not to express in information models - 
mind-independent truths.

- thomas

On 08/09/2015 01:23, Daniel Karlsson wrote:
> Dear All,
>
> agree partly with Ian's assessment, i.e. about the messiness. While I 
> much appreciate what I have read, and I've had much help from earlier 
> texts from the authors (as I'm sure I will from this book), there is 
> in the medical informatics community a widespread belief that the 
> position held by (some part of) the BFO community is undisputed and 
> sort-of final. There are still issues which requires careful 
> consideration, especially regarding information artefacts and the 
> is-about relationship [1, 2], but also about e.g. dispositions [3], 
> and functions [4].
>
> Additionally, while ontologies deal with what is universally true, it 
> is my belief that universal truth takes, and should take, the back 
> seat compared to user needs and practicality in information modelling. 
> First-world (using Popper's ontology [5]) ontologies are outcomes of 
> our understanding of the physical world and evolve as science evolves 
> (at least good ones). Information models and other second-third-world 
> ontologies are always constructs and, like with fictional characters, 
> nothing can be discovered by examining those models in addition to 
> what has been explicitly stated. For this reason, ontology as a method 
> isn't as helpful for information modellers as it is for others.
>
> 1. 
> https://www.researchgate.net/publication/266021648_An_Ontological_Analysis_of_Reference_in_Health_Record_Statements
>
> 2. http://www.amazon.com/Aboutness-Carl-G-Hempel-Lecture/dp/0691144958
>
> 3. http://www.amazon.com/Dispositions-Stephen-Mumford/dp/0199259828
>
> 4. 
> http://www.amazon.com/Functions-Biological-Artificial-Worlds-Philosophical/dp/026211321X
>
> 5. https://en.wikipedia.org/wiki/Popper%27s_three_worlds
>
> /Daniel

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