Rules
1. Navigational nodes are completely defined• Non-primitive in ontylog-speak• EquivalentClass in OWL-speak
2. Concept / Word nodes cannot reference navigational nodes
• Navigational nodes should no impact on the structure of the underlying ontology
• Navigational nodes can reference other navigational nodes, however
Rule 1: Navigational Nodes are Completely Defined
Definition can be intensional:• List the all of the conditions that qualifies
an entity for membership in this class• Definition is frequently derivable from the
name (Abnormal Germ Cell == any Germ Cell that exhibits abnormal characteristics)
• Can’t create a definition?– Maybe definition is extensional?– Maybe this isn’t a navigational node after all?
Rule 1: Navigational Nodes are Completely Defined
Definition can be extensional:• Typically a disjunction – A or B or C
– Body Fluid or Substance == anything that is either a body fluid or a substance
• Can be more complex as well
Non-navigational nodes cannot reference navigational nodes
• This can be readily enforced if navigational nodes are defined in a separate resource– Assumes that Protégé environment is capable
of imports…– Can be ‘faked’ until this becomes a reality.
• Rule: The ontological resource cannot import navigational resources.
Process
1. Create BGTAnatomy.owl• Thesaurus Resource• Imports BiomedGT.owl• Can import other thesaurus resources• Can import other ontology resources (!)
Define Navigational Nodes
• Body_Fluid
• Body_Substance (which, in our book is disjoint w/ Body fluid– Enforced, however by “Fluid/Solid” definitions
in baseline ontology
• Body_Fluid_or_Substance
• Anatomic_Structure_System_or_Substance
Body_Fluid
• Navigational Node (Intensional Definition)– RULE: ONLY Navigational nodes can be
defined in Thesaurus Resources!
(Definition may not be 100%, but whatever it is, we have to define it completely…)
Anatomy Thesaurus
References into external ontology… BiomedGT forThe moment, but note that these are all upper/middle level nodes…•This may be the rule (?)•Decoupling UL/MLO from BiomedGT gives more flexibility
New Definition for Blood
Still grossly incomplete – we could do better, but the keys are:(a) Blood is defined without reference to navigational nodes
(Hematopoietic_System probably has to go…)(b) The reasoner can determine that blood is a “liquid”
(according to our definition) and blood is a “body part” (…)
Load Thesaurus…
A different name helps when dealingwith two resources…… but it works even if they aren the same..
Questions and Observations
• It is possible (and, arguably, desirable) to have multiple Thesaurus resources…– Within BGT
• Anatomy Thesaurus• Gene Thesaurus• …• (Kinds form one natural boundary)
– Within external resources• CRCH Thesaurus• Nano Thesaurus
• Is this desirable? (vs. BGTOntology.owl and BGTThesaurus.owl)
Questions and Observations
• The external resources we’ve seen to date appear to be >90% Navigational nodes– With a smattering of new ontology nodes
thrown in– Should there be a CRCH Ontology, or should
BiomedGT Ontology attempt to ‘absorb’ external nodes
• Note that this question is orthogonal to the question about referencing other external ontologies such as BFO, GO and the like
Questions and Observations
• This approach requires that the resources are able to distinguish defined and inferred ontological statements.– We can infer that Blood isA Body_fluid, and
we (arguably) need to represent this in the wiki and other external resources…
– … but we can never assert that it is.
BioActive Food Component
• A class of compounds found in food believed to have biological activity in the human
Subtypes of FoodRoles
• FoodRole– Nutrient Role?– Bioactive Role?– What of CNS_Stimulants and the like?
Now For Caffeine
• Primary definition is chemical – we don’t have the necessary superclasses
• May be a great external reference!
Caffeine(O)
• Primary definition is chemical– ==
• Methylxanthine• Having purine double-ring structure … (chemical
formula as primary definition?)
• Necessary information– potentialRoleOf componentOfFood– hasPotentialRole CNSStimulationRole (this
needs work…)
Caffeine
Needs filling in
Could be in foodCould be a stimulant
We could put in “actsOn CNS” somewhere too – roles as well…
Dietary Fiber
This seems to be a single name – dietary fiber isn’t necessarily “fiber”, just undigested
On the other hand, we’ve already got a concept Fiber(B1675) that seems to be exactly what we need.
Cellulose
Note – we might want to make NonDigestedFoodRole tobe a component of food instead, but this works for demonstrationPurposes.