book recommendation - basic formal ontology (BFO) for biomedicine

Daniel Karlsson daniel.karlsson at liu.se
Mon Sep 7 11:23:12 EDT 2015


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

On 2015-09-07 10:54, Ian McNicoll wrote:
> Me too - nice bed-time reading.
>
> I will reserve judgement for the "2-5 years and we will be using 
> this". I agree this is the future but it still feels a lot like 
> nuclear fusion to me - nice to have but a b****r to use (at least in 
> our messy world of clinical documentation).
>
> Ian
>
> Dr Ian McNicoll
> mobile +44 (0)775 209 7859
> office +44 (0)1536 414994
> skype: ianmcnicoll
> email: ian at freshehr.com <mailto:ian at freshehr.com>
> twitter: @ianmcnicoll
>
> Co-Chair, openEHR Foundation ian.mcnicoll at openehr.org 
> <mailto:ian.mcnicoll at openehr.org>
> Director, freshEHR Clinical Informatics Ltd.
> Director, HANDIHealth CIC
> Hon. Senior Research Associate, CHIME, UCL
>
> On 7 September 2015 at 09:17, Rikard Lövström 
> <rikard.lovstrom at gmail.com <mailto:rikard.lovstrom at gmail.com>> wrote:
>
>     Thank you, Thomas, this looks very promising. I have placed an
>     order so now I am waiting :-) Very considerate of you, many
>     thanks. Kind regards, Rikard
>
>
>     2015-09-07 3:26 GMT+02:00 Thomas Beale
>     <thomas.beale at oceaninformatics.com
>     <mailto:thomas.beale at oceaninformatics.com>>:
>
>
>         A new book, *Building Ontologies with Basic Formal Ontology
>         *(BFO2) has been published by Robert Arp, Barry Smith and
>         Andrew Spear.
>
>         Amazon.com
>         <http://www.amazon.com/Building-Ontologies-Basic-Formal-Ontology/dp/0262527812/ref=sr_1_1?ie=UTF8&qid=1441588367&sr=8-1&keywords=basic+formal+ontology>
>         Amazon.co.uk
>         <http://www.amazon.co.uk/Building-Ontologies-Basic-Formal-Ontology/dp/0262527812/ref=sr_1_1?ie=UTF8&qid=1441588327&sr=8-1&keywords=basic+formal+ontology>
>
>         I've read a pre-print, and this is an excellent book. Many of
>         us here have studied or used some of the key upper level
>         ontologies (BFO, BioTopLite etc), and I think BFO2 will
>         probably end up being the one of choice for general
>         biomedicine. It contains all the concepts from Barry Smith's
>         earlier work (SNAP and SPAN - spatial and temporal regions,
>         partonomy concepts etc) and will ultimately (I have been told)
>         contain/be merged with a new version of the Information
>         Artefact Ontology (IAO) which will probably become the upper
>         level ontology for describing types of information that stand
>         in the IS-ABOUT and similar relationships with real world
>         referents - in other words, EHR information items.
>
>         My personal feeling is that in the next 2-5 years, we will
>         finally see the joining up of these key ontologies with
>         information models and archetypes in the clinical information
>         space. It will be up to us in the openEHR community and other
>         related communities (13606, CIMI, HL7 etc) to engage with this
>         material and consider how this integration will be achieved. A
>         few very early ideas are mentioned in the Archetype Technology
>         Overview
>         <http://www.openehr.org/releases/AM/latest/docs/Overview/Overview.html#_identification_and_the_virtual_archetype_space>document,
>         but of course this is just one narrow area of application.
>
>         We need to all get on the same page in terms of understanding
>         and conceptual nomenclature in this space, and BFO2 I believe
>         is an excellent foundation for that. We will be using it
>         increasingly in the openEHR specification space, and I think
>         others will find it useful as well.
>
>         - thomas
>
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>
>
>
>
>     -- 
>     --------------------------------------------------------------------------------
>     Rikard Lövström
>     Address: Sjölyckevägen 29, SE-511 63 Skene, Sweden
>     Phone: +46 320 14242 <tel:%2B46%20320%2014242>
>     Mobile: +46 70 4951534 <tel:%2B46%2070%204951534>
>     Fax: +46 31 7459402 <tel:%2B46%2031%207459402>
>
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>
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-- 
Daniel Karlsson, PhD, sr lecturer
Department of Biomedical Engineering/Health Informatics
Linköping University
SE-581 85 Linköping
Sweden
Phone: +46 13 286762, +46 70 8350109, Skype: imt_danka

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