(define-theory Biologic-Functions (Anatomy Actors Assessment))
(in-theory 'Biologic-Functions)


(DEFINE-RELATION DISRUPTED-BY (?A ?B) :IFF-DEF
 (AND (= (INVERSE DISRUPTS) DISRUPTED-BY)
      (ENTITY ?A)
      (SUBSTANCE ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE DISRUPTED-BY SUBSTANCE)
      (DOMAIN DISRUPTED-BY ENTITY)))
(DEFINE-RELATION DISRUPTS (?A ?B)
 "Alters or influences an already existing condition, state, 
or situation. Produces a negative effect on."
 :DEF (AND (AFFECTS ?A ?B) (SUBSTANCE ?A)) :AXIOM-DEF
 (MAPPING DISRUPTS
  "New entry. This is a kind of 'affects', with a domain restricted 
to substances."))
(DEFINE-RELATION EXCRETED-BY (?A ?B) :IFF-DEF
 (AND (= (INVERSE EXCRETES) EXCRETED-BY)
      (BODY-SUBSTANCE ?A)
      (BIOLOGIC-OBJECT ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE EXCRETED-BY BIOLOGIC-OBJECT)
      (DOMAIN EXCRETED-BY BODY-SUBSTANCE)))
(DEFINE-RELATION EXCRETES (?A ?B)
 "Some body system or part embodies a function
which has a body substance as product."
 :DEF
 (AND (BIOLOGICAL-RELATION ?A ?B)
      (EXISTS (?C) (AND (EMBODIES ?A ?C) (PRODUCT ?C ?B)))
      (BIOLOGIC-OBJECT ?A)
      (BODY-SUBSTANCE ?B)))
(DEFINE-RELATION HAS-PARASITE (?A ?B) :IFF-DEF
 (AND (= (INVERSE PARASITIC) HAS-PARASITE)
      (ENTITY ?A)
      (ENTITY ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE HAS-PARASITE ENTITY)
      (DOMAIN HAS-PARASITE ENTITY)))
(DEFINE-RELATION LIVES-IN (?A ?B)
 "A very simple definition of living within some region:
some organism is located in a region or a material object which it depends on."
 :DEF (AND (REFERENCE-LOCATION ?A ?B) (STRICTLY-DEPENDS-ON ?A ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE LIVES-IN LOCALIZED-ENTITY)
      (DOMAIN LIVES-IN ORGANISM)))
(DEFINE-RELATION LIVING-PLACE (?A ?B) :IFF-DEF
 (AND (= (INVERSE LIVES-IN) LIVING-PLACE)
      (ENTITY ?A)
      (ENTITY ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE LIVING-PLACE ENTITY)
      (DOMAIN LIVING-PLACE ENTITY)))
(DEFINE-RELATION PARASITIC (?A ?B)
 "In the same vein of 'lives-in', some organism is
located in an organism or an anatomical structure parasitic which it depends on."
 :DEF (AND (LIVES-IN ?A ?B) (DIFFERENT ?A ?B)) :AXIOM-CONSTRAINTS
 (AND (RANGE PARASITIC BIOLOGIC-OBJECT)
      (DOMAIN PARASITIC ORGANISM)))
(DEFINE-RELATION _DISORDERED (?A ?B) :DEF
 (AND (TYPICALITY-PROPERTY ?A ?B) (BIOLOGIC-FUNCTION ?A)) :CONSTRAINTS
 (OR (EXISTS (?S1 ?S2)
      (AND (SITUATION ?S1)
           (SITUATION ?S2)
           (DIFFERENT ?S1 ?S2)
           (EXISTS (?C ?D)
            (AND (THE-RESULT ?A ?D) (THE-EXPECTED ?D ?C) (CONTEXT-OF ?S1 ?C)))
           (EXISTS (?E) (AND (THE-RESULT ?A ?E) (CONTEXT-OF ?S2 ?E)))
           (HAS-EXISTENCE ?S2 TRUE)))
     (EXISTS (?Y) (ALTERS ?Y ?A))
     (_ABORTED ?A ?B)
     (NOT (_INTEGRAL ?A ?B)))
)
(DEFINE-RELATION _LIVING (?A ?B) :DEF
 (AND (BIOLOGICAL-PROPERTY ?A ?B) (BIOLOGIC-OBJECT ?A)))
(DEFINE-RELATION _PROGRESSIVE (?A ?B) :DEF
 (AND (TYPICALITY-PROPERTY ?A ?B) (BIOLOGIC-FUNCTION ?A)))
(DEFINE-RELATION _UNCONTROLLED (?A ?B) :DEF
 (AND (TYPICALITY-PROPERTY ?A ?B) (BIOLOGIC-FUNCTION ?A)) :CONSTRAINTS
 (EXISTS ?Y
  (AND (ORGANISM ?Y)
       (EMBODIES ?Y ?A)
       (NOT (STRICTLY-DEPENDS-ON ?A ?Y)))))
(DEFINE-CLASS *DISORDERED-BIOLOGIC-FUNCTION (?SELF)
:IFF-DEF
 (AND (BIOLOGIC-FUNCTION ?SELF)
      (VALUE-CARDINALITY ?SELF _DISORDERED 1))
 :AXIOM-DEF (THE-ARCHETYPE *DISORDERED-BIOLOGIC-FUNCTION REIFIED-PROPERTY))
(DEFINE-CLASS *DISORDERED-BODY-DEVELOPMENT (?SELF)
:DEF
 (*DISORDERED-BIOLOGIC-FUNCTION ?SELF) :AXIOM-DEF
 (THE-ARCHETYPE *DISORDERED-BODY-DEVELOPMENT REIFIED-PROPERTY))
(DEFINE-CLASS *TEMPERATURE-ALTERATION-PROCESS (?SELF)
:IFF-DEF
 (AND (*DISORDERED-BIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A)
              (AND (FEATURE-ALTERS ?SELF ?A)
                   (AND (TEMPERATURE-MEASURE ?A)
                        (EXISTS (?B)
                                (AND (FEATURE-OF ?A ?B) (ORGANISM ?B)))))))
 :AXIOM-DEF (THE-ARCHETYPE *TEMPERATURE-ALTERATION-PROCESS REIFIED-ROLE))
(DEFINE-CLASS ABNORMAL-COMPRESSION (?SELF)
:DEF
 (*DISORDERED-BIOLOGIC-FUNCTION ?SELF))
(DEFINE-CLASS ABNORMAL-GROWTH (?SELF)
:DEF
 (*DISORDERED-BIOLOGIC-FUNCTION ?SELF))
(DEFINE-CLASS BIOLOGIC-FUNCTION (?SELF)
 "A state, activity or process of the body or one of its systems or parts."
 :DEF
 (AND (BIOLOGIC-PROCESS ?SELF)
      (EXISTS (?A)
              (AND (EMBODIED-IN ?SELF ?A)
                   (OR (ORGANISM ?A) (ANATOMICAL-STRUCTURE ?A)))))
 :CONSTRAINTS
 (AND (FORALL (?B)
       (=> (PRODUCT ?SELF ?B)
        (OR (SUBSTANCE ?B) (ORGANISM ?B) (ANATOMICAL-STRUCTURE ?B))))
      (VALUE-TYPE ?SELF CO-EXIST BIOLOGIC-FUNCTION)
      (VALUE-TYPE ?SELF SCATTERED-LOCATION GROUP)
      (FORALL (?C)
       (=> (REFERENCE-LOCATION ?SELF ?C)
        (OR (ANATOMICAL-STRUCTURE ?C) (ORGANISM ?C))))
      (FORALL (?D)
       (=> (BEARER ?SELF ?D)
        (OR (ORGANISM-ATTRIBUTE ?D) (ANATOMICAL-STRUCTURE ?D))))
      (FORALL (?E)
       (=> (INFLUENCES ?SELF ?E)
        (OR (BEHAVIOR ?E) (BIOLOGIC-FUNCTION ?E)))))
 :AXIOM-DEF
 (SUBCLASS-PARTITION BIOLOGIC-FUNCTION
  (SETOF PHYSIOLOGIC-FUNCTION PATHOLOGIC-FUNCTION)))
(DEFINE-CLASS BIRTH (?SELF)
:DEF (ORGANISM-FUNCTION ?SELF))
(DEFINE-CLASS BODY-DEVELOPMENT (?SELF)
:DEF
 (AND (ORGANISM-FUNCTION ?SELF)
      (EXISTS (?A) (AND (PRODUCT ?SELF ?A) (ORGANISM ?A)))
      (EXISTS (?B)
              (AND (EMBODIED-IN ?SELF ?B)
                   (MOLECULAR-ANATOMICAL-STRUCTURE ?B)))))
(DEFINE-CLASS BREATHING (?SELF)
:DEF (ORGANISM-FUNCTION ?SELF))
(DEFINE-CLASS CELL-FUNCTION (?SELF)
 "A physiologic function inherent to cells or cell components." :DEF
 (AND (PHYSIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A)
              (AND (EMBODIED-IN ?SELF ?A) (OR (CELL ?A) (CELL-COMPONENT ?A))))))
(DEFINE-CLASS CELL-OR-MOLECULAR-DYSFUNCTION (?SELF)
 "A pathologic function inherent to cells, parts of cells, or molecules." :DEF
 (AND (PATHOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A)
              (AND (EMBODIED-IN ?SELF ?A)
                   (OR (CELL ?A) (CELL-COMPONENT ?A) (MOLECULE ?A))))))
(DEFINE-CLASS DIET (?SELF)
 "This could be figured both as a function of
the organism and as an activity performed by the organism, depending on how
much intentionality is assumed behind the acts composing the diet process.
Currently, it is defined as a human activity."
 :DEF (HUMAN-ACTIVITY ?SELF))
(DEFINE-CLASS DISEASE-OR-SYNDROME (?SELF)
 "A condition which alters or interferes with a normal process, state, or activity 
of an organism. It is usually characterized by the abnormal functioning of one or more of the host's systems, 
parts, or organs."
 :DEF
 (AND (PATHOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A) (AND (CERTIFIED-BY ?SELF ?A) (HEALTHCARE-COMMUNITY ?A))))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF PRODUCT TISSUE)
      (VALUE-TYPE ?SELF ALTERS PHYSIOLOGIC-FUNCTION)))
(DEFINE-CLASS DISORDERED-FUNCTION-CAUSED-BY-ANATOMICAL-ABNORMALITY
 (?SELF)
:DEF
 (AND (*DISORDERED-BIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A) (AND (CAUSE ?SELF ?A) (ANATOMICAL-ABNORMALITY ?A)))))
(DEFINE-CLASS FULFILLED-MATURATION (?SELF)
:IFF-DEF
 (AND (MATURATION ?SELF) (VALUE-CARDINALITY ?SELF _FULFILLED 1)))
(DEFINE-CLASS GROWTH (?SELF)
:DEF (ORGANISM-FUNCTION ?SELF))
(DEFINE-CLASS IMMUNE-RESPONSE (?SELF)
:DEF
 (MOLECULAR-PHYSIOLOGIC-FUNCTION ?SELF))
(DEFINE-CLASS INJURY (?SELF)
 "A traumatic wound or injury caused by an external agent 
or force. Some doubts remain on the exact classification place: USN takes it as a very general
'Phenomenon'; on the other hand, no injury is possible without some biologic
function which affects the organism being injured. We provisionally take it as a straight
biologic function."
 :DEF
 (AND (BIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A) (AND (BEARER ?SELF ?A) (ANATOMICAL-STRUCTURE ?A)))
      (EXISTS (?B) (AND (CAUSE ?SELF ?B) (MATERIAL-OBJECT ?B))))
 :CONSTRAINTS
 (AND (EXISTS (?C)
              (AND (RESULT-OF ?SELF ?C)
                   (OR (BEHAVIOR ?C) (HEALTH-CARE-ACTIVITY ?C))))
      (FORALL (?D)
       (=> (COMPLICATES ?SELF ?D)
        (OR (DISORDERED-FUNCTION-CAUSED-BY-ANATOMICAL-ABNORMALITY ?D)
            (PATHOLOGIC-FUNCTION ?D)
            (INJURY-OR-POISONING ?D))))))
(DEFINE-CLASS INJURY-OR-POISONING (?SELF)
 "A traumatic wound, injury, or poisoning caused by an external agent 
or force."
 :IFF-DEF (AND (THING ?SELF) (OR (INJURY ?SELF) (POISONING ?SELF))) :AXIOM-DEF
 (MAPPING INJURY-OR-POISONING
  "This is a typical 'inclusive' concept from USN, maintained here to
support Metathesaurus partition."))
(DEFINE-CLASS MATURATION (?SELF)
:DEF (BIOLOGIC-FUNCTION ?SELF))
(DEFINE-CLASS MENTAL-OR-BEHAVIORAL-DYSFUNCTION (?SELF)
 "A clinically significant dysfunction whose major manifestation is behavioral or 
psychological. These dysfunctions may have identified or presumed biological etiologies or manifestations."
 :DEF
 (AND (DISEASE-OR-SYNDROME ?SELF)
      (VALUE-CARDINALITY ?SELF _PSYCHOLOGIC 1)
      (VALUE-TYPE ?SELF INFLUENCES BEHAVIOR))
 :CONSTRAINTS (EXISTS (?A) (AND (EMBODIED-IN ?SELF ?A) (ANIMAL ?A))) :AXIOM-DEF
 (PROBLEM MENTAL-OR-BEHAVIORAL-DYSFUNCTION
  "What is a biological etiology? a role: some cause, in this case residing in a different 
layer."))
(DEFINE-CLASS MENTAL-PROCESS (?SELF)
 "A physiologic function involving the mind or cognitive processing." :DEF
 (AND (ORGANISM-FUNCTION ?SELF)
      (VALUE-CARDINALITY ?SELF _PSYCHOLOGIC 1))
 :CONSTRAINTS
 (AND (EXISTS (?A) (AND (EMBODIED-IN ?SELF ?A) (ANIMAL ?A)))
      (VALUE-TYPE ?SELF INFLUENCES BEHAVIOR)))
(DEFINE-CLASS NEOPLASTIC-PROCESS (?SELF)
 "A new and abnormal growth of tissue in which the growth is uncontrolled 
and progressive. The growths may be malignant or benign. Ex. stage IVB vaginal cancer; tonsillar lymphoepithelioma
Abdominal Neoplasms. All neoplasms are assigned to this type. Do not also assign a type from the 
'Anatomical Abnormality' hierarchy."
 :DEF
 (AND (DISEASE-OR-SYNDROME ?SELF)
      (EXISTS (?A)
              (AND (CONSTITUTIVE-PHASE ?SELF ?A)
                   (UNCONTROLLED-GROWTH-OF-TISSUE ?A)))
      (VALUE-CARDINALITY ?SELF _PROGRESSIVE 1)))
(DEFINE-CLASS NON-PLASTIC-PROLIFERATION (?SELF)
:DEF
 (ABNORMAL-GROWTH ?SELF))
(DEFINE-CLASS NUTRITION-FUNCTION (?SELF)
:DEF
 (ORGANISM-FUNCTION ?SELF))
(DEFINE-CLASS ORGAN-OR-TISSUE-FUNCTION (?SELF)
 "A physiologic function of a particular organ, organ system, or tissue." :DEF
 (AND (PHYSIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A)
              (AND (EMBODIED-IN ?SELF ?A)
                   (OR (ORGAN ?A) (BODY-SYSTEM ?A) (TISSUE ?A)))))
 :CONSTRAINTS
 (AND (EXISTS (?B)
              (AND (CO-EXIST ?SELF ?B)
                   (OR (ORGANISM-FUNCTION ?B) (ORGAN-OR-TISSUE-FUNCTION ?B))))
      (VALUE-TYPE ?SELF DEGREE-OF ORGAN-OR-TISSUE-FUNCTION)
      (VALUE-TYPE ?SELF TEMPORAL-PART-OF ORGAN-OR-TISSUE-FUNCTION))
 :AXIOM-DEF
 (MAPPING ORGAN-OR-TISSUE-FUNCTION
  "'organ' should be a subtype of BPOOC -will UMLS isa relations support this???-
is organ system a particular body system or are they synonymous?"))
(DEFINE-CLASS ORGANISM-FUNCTION (?SELF)
 "A physiologic function of the organism as a whole, of multiple organ systems, 
or of multiple organs or tissues. This type has one child in the network, 'Mental Process'."
 :DEF
 (AND (PHYSIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A) (AND (STRICTLY-DEPENDS-ON ?SELF ?A) (ORGANISM ?A))))
 :CONSTRAINTS (VALUE-TYPE ?SELF DEGREE-OF ORGANISM-ATTRIBUTE))
(DEFINE-CLASS PATHOLOGIC-FUNCTION (?SELF)
 "A disordered process, activity, or state of the organism as a whole, of a body 
system or systems, or of multiple organs or tissues. Included here are normal responses to a negative stimulus 
as well as patholologic conditions or states that are less specific than a disease. Pathologic functions frequently 
have systemic effects."
 :DEF
 (AND (BIOLOGIC-FUNCTION ?SELF)
      (VALUE-CARDINALITY ?SELF _DISORDERED 1))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF MANIFESTATION-OF BIOLOGIC-FUNCTION)
      (FORALL (?A)
       (=> (RESULT-OF ?SELF ?A)
        (OR (BEHAVIOR ?A) (HEALTH-CARE-ACTIVITY ?A) (PATHOLOGIC-FUNCTION ?A))))
      (FORALL (?B)
       (=> (COMPLICATES ?SELF ?B)
        (OR (INJURY-OR-POISONING ?B)
            (DISORDERED-FUNCTION-CAUSED-BY-ANATOMICAL-ABNORMALITY ?B)
            (PATHOLOGIC-FUNCTION ?B)))))
 :AXIOM-DEF
 (SUBCLASS-PARTITION PATHOLOGIC-FUNCTION
  (SETOF EXPERIMENTAL-MODEL-OF-DISEASE CELL-OR-MOLECULAR-DYSFUNCTION
   DISEASE-OR-SYNDROME)))
(DEFINE-CLASS PHOTOSYNTHESIS (?SELF)
:DEF (BIOLOGIC-FUNCTION ?SELF))
(DEFINE-CLASS PHYSIOLOGIC-FUNCTION (?SELF)
 "A normal process, activity, or state of the body." :DEF
 (BIOLOGIC-FUNCTION ?SELF) :CONSTRAINTS
 (AND (FORALL (?A)
       (=> (INFLUENCES ?SELF ?A)
        (OR (BIOLOGIC-FUNCTION ?A) (BEHAVIOR ?A))))
      (FORALL (?B)
       (=> (AFFECTS ?SELF ?B)
        (OR (ORGANISM-ATTRIBUTE ?B) (ANATOMICAL-STRUCTURE ?B))))
      (EXISTS (?C) (AND (CO-EXIST ?SELF ?C) (PHYSIOLOGIC-FUNCTION ?C))))
 :AXIOM-DEF
 (SUBCLASS-PARTITION PHYSIOLOGIC-FUNCTION
  (SETOF ORGAN-OR-TISSUE-FUNCTION CELL-FUNCTION MOLECULAR-PHYSIOLOGIC-FUNCTION
   ORGANISM-FUNCTION))
)
(DEFINE-CLASS POISONING (?SELF)
 "A poisoning is caused by an external substance.
Some doubts remain on the exact classification place: USN takes it as a very general
'Phenomenon'; on the other hand, no poisoning is possible without some biologic
function which affects the organism being injured. We provisionally take it as a straight
biologic function."
 :DEF
 (AND (BIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A)
              (AND (BEARER ?SELF ?A)
                   (OR (ANATOMICAL-STRUCTURE ?A) (ORGANISM ?A))))
      (EXISTS (?B) (AND (CAUSE ?SELF ?B) (SUBSTANCE ?B))))
 :CONSTRAINTS
 (AND (FORALL (?C)
       (=> (COMPLICATES ?SELF ?C)
        (OR (DISORDERED-FUNCTION-CAUSED-BY-ANATOMICAL-ABNORMALITY ?C)
            (PATHOLOGIC-FUNCTION ?C)
            (INJURY-OR-POISONING ?C))))
      (FORALL (?D)
       (=> (RESULT-OF ?SELF ?D)
        (OR (BEHAVIOR ?D) (HEALTH-CARE-ACTIVITY ?D))))))
(DEFINE-CLASS PROTECTIVE-RESPONSE (?SELF)
:DEF
 (*DISORDERED-BIOLOGIC-FUNCTION ?SELF))
(DEFINE-CLASS SECRETION (?SELF)
:DEF
 (ORGAN-OR-TISSUE-FUNCTION ?SELF))
(DEFINE-CLASS UNCONTROLLED-GROWTH-OF-TISSUE (?SELF)
:IFF-DEF
 (AND (ABNORMAL-GROWTH ?SELF)
      (VALUE-CARDINALITY ?SELF _UNCONTROLLED 1)
      (EXISTS (?A) (AND (EMBODIED-IN ?SELF ?A) (TISSUE ?A)))))