book recommendation - basic formal ontology (BFO) for biomedicine

"Gerard Freriks (privé)" gfrer at
Sun Sep 20 04:16:16 EDT 2015

Dear Colleagues,

Some personal thoughts and opinion.

1- Scopes
EHR Scope: Document, archive and exchange Statements by one author about one patient using concepts as terms
Ontology scope: Creating a definition about one concept  using other concepts expressed as rules.

2- Universal and Particular truths
Authored Statements about one patient by one author are always Particular in nature.
Definitions about a concept are Universal in nature. 

3- Open and Closed world Assumption
Statements in the database of the EHR are authored by one person and about one person.
What is not entered in the database does not exist. It is not authored.
The data in an EHR database are following the Closed World Assumption.
The consequence is that it is much better to ascertain patient safety.

In Ontologies that are expressed using rules that define the relationships, new rules can be inferred.
The Concept definitions in an Ontology are following the Open World Assumption.
The consequence is that it is impossible to ascertain patient safety.

4- Deployment of systems that combine both worlds need to think about the interfaces where these Models intersect.
In the EHR several models are used:
- Model for documentation, archiving and exchange (RM of part 1)
- Model for Statement expression (AOM part 2)
- Model for Statement content: Reference Archetypes (e.g. SIAMM, DCM) that use Concepts
- Model for the definition of Concepts that are used in Statements
The first 3 are Structured, Particular, Closed World Assumption models.
The last one is an Universal, Open World Assumption model.

Deploying all four models using ontological techniques will (possibly) create problems.
The language used, at present, is OWL-DL. OWL-DL is instantiating first order logic, partially.
All four models constitute all together multiple order logic.
There is not enough evidence that we (in eHealth) are capable to handle multiple order logic using ontological methods.

5- Taken all in consideration.
For reasons given above I agree with Ian and Daniel, that we had better create clear, simple, well understood, delineations between all model intersections (e.i. their interfaces).

6- I propose to use the Two Level Modeling Paradigm creating structures used for the documentation of Statements.
And have Rules Engines do the inferencing in a controlled way.

Only use Ontologies  for the definition of ‘simple’, non-complex, terms/concepts and use these defined terms in a Terminology in Statements.
Use them in Statements as lemma’s from a dictionary.
This is using ontological defined terms in their natural well understood role,

Gerard Freriks
+31 620347088
gfrer at <mailto:gfrer at>
> On 7 sep. 2015, at 17:23, Daniel Karlsson <Daniel.Karlsson at> 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. <>
> 2. <>
> 3. <>
> 4. <>
> 5. <>
> /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 <mailto:ian at>
>> twitter: @ianmcnicoll

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