book recommendation - basic formal ontology (BFO) for biomedicine

Thomas Beale thomas.beale at oceaninformatics.com
Sun Sep 6 21:26:33 EDT 2015


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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