Navigational Nodes

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

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.

Example

Ontology Node

Navigational Node

Navigational Node

Theasurus (?)

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…)

Body_Substance

Body_Fluid_or_Substance

• Navigational Node (Extensional Definition)

Anatomic_Structure_System_or_Substance

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

Step 2: Redefine Reference Nodes

Not allowed…

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..

Import BiomedGT Ontology

…Classify

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.

Fancier Example

• Multiple Ontologies– BFO– BioTop– BiomedGT– CRCH Thesaurus

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?

BioActiveRole

Navigational Node!

Bioactive Food Component(N)

• ==– Food Component– hasPotentialRole bioActiveRole

Bioactive Food Component

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…

Caffeine after reclassification

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.

Undigested Food Component

FiberConcept type “N” – definition is arbitrary

Cellulose

Note – we might want to make NonDigestedFoodRole tobe a component of food instead, but this works for demonstrationPurposes.

Cellulose Reclassified