book recommendation - basic formal ontology (BFO) for biomedicine

Koray Atalag k.atalag at auckland.ac.nz
Sat Sep 19 08:17:55 EDT 2015


I think within the timeframe stated by Tom we will definitely see these two worlds coming closer and producing some tangible benefits. Did you all notice an increase in research in this area these days? Just my quick 2 cents....still on travel



Cheers,



-koray







________________________________
From: openEHR-clinical [openehr-clinical-bounces at lists.openehr.org] on behalf of Thomas Beale [thomas.beale at oceaninformatics.com]
Sent: Tuesday, 8 September 2015 7:14 p.m.
To: For openEHR clinical discussions
Subject: Re: book recommendation - basic formal ontology (BFO) for biomedicine


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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