Day 3: I started organizing the terms into categories – anatomy and microbiology to start with. I want to get some of the ‘basic’ information in first – information such as anatomy, physiology, microbiology etc. Not an exhaustive list, only a few – I think this will be a good starting point. And then build on these later in the areas of pathology, phenotypes, procedures etc. The approach would be to analyze each term and break it into its component parts.
BioPortal is an excellent place for browsing biomedical ontologies. I explored some of these terms (mitral valve, aortic valve, staphylococcus aureus, etc.) and think I have enough to form an initial plan of the candidate ontologies I can reuse:
- FMA for anatomy terms
- NCBI organismal classification for bacteria, virus, etc
Now, the challenge is going to be in organizing the IE ontology. Luckily, IDO (with OGMS and BFO) provides a frame-work to build on. Here goes ….
I am exploring IDO for a place to anchor the anatomy terms. The only term I can find is ‘anatomical entity‘ (CARO#CARO_0000000) as a subClass of BFO’s ‘material entity‘ (snap#MaterialEntity) an independent continuant. So far so good …
FMA has the following high level structure:
Hmm… this will need some thinking!
CARO_0000000 (anatomical entity) := Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
fma:Anatomical_entity := Organismal continuant entity which is enclosed by the bona fide boundary of an organism or is an attribute of its structural organization. Examples: cell, heart, head, peritoneal cavity, apex of lung, anatomical term, sagittal plane.
– the scope of the FMA is described in its FAQ (#1):
“The FMA is a reference ontology for the domain of anatomy. It is a symbolic representation of the phenotypic structure of the human body.”
This means that fma:Anatomical_entity is a subClass of the much broader CARO:anatomical entity term. But, if you look at the class hierarchies, it appears that fma:Material_anatomical_entity is the one closest aligned to CARO_0000000 (anatomical entity) – in a subClass relation in the snap:IndependentContinuant hierarchy
What about the rest of FMA? fma:Immaterial_anatomical_entity and the fma:Non-physical_anatomical_entity consist of things that are dependent on other things i.e. belong to the snap:DependentContinuant hierarchy.
So, I think for now, I will add fma:Anatomical_entity as a top-level class under snap:Continuant keeping FMA’s structure intact and add other subclass relations as needed within the BFO/IDO hierarchy.
Going forward, to manage this kind of organization, I want to try cross-tabulating each term – the clinical categories (anatomy, physiology, biochemistry, microbiology, pathology, ….) on the X-axis and the BFO categories (and sub-categories) on the Y-axis in the Inf. Endocarditis google spreadsheet.