(define-theory Biologic-Substances (Substances Clin-Act))
(in-theory 'Biologic-Substances)


(DEFINE-CLASS *NUTRIENT (?SELF)
:IFF-DEF
 (AND (SUBSTANCE ?SELF)
      (EXISTS (?A) (AND (RESOURCE-OF ?SELF ?A) (NUTRITION-FUNCTION ?A)))))
(DEFINE-CLASS ANTIBIOTIC (?SELF)
 "A pharmacologically active compound produced by growing microorganisms which 
kill or inhibit growth of other microorganisms. Penicillin; Cephalosporins; Antibiotics."
 :DEF
 (AND (PHARMACOLOGIC-SUBSTANCE ?SELF)
      (EXISTS (?A)
              (AND (PRODUCTION-HOST ?SELF ?A)
                   (AND (MICROORGANISM ?A)
                        (EXISTS (?B) (AND (EMBODIES ?A ?B) (GROWTH ?B))))))
      (EXISTS (?C)
              (AND (INHIBITS ?SELF ?C)
                   (AND (GROWTH ?C)
                        (EXISTS (?D)
                                (AND (EMBODIED-IN ?C ?D)
                                     (MICROORGANISM ?D))))))))
(DEFINE-CLASS ANTIGEN (?SELF)
:DEF
 (AND (BIOLOGICALLY-ACTIVE-SUBSTANCE ?SELF)
      (EXISTS (?A) (AND (INDUCES ?SELF ?A) (IMMUNE-RESPONSE ?A)))))
(DEFINE-CLASS BIOLOGICALLY-ACTIVE-SUBSTANCE (?SELF)
 "A substance produced or required by an organism, of primary interest because of 
its role in the biologic functioning of the organism that produces it."
 :IFF-DEF
 (AND (CHEMICAL-VIEWED-FUNCTIONALLY ?SELF)
      (VALUE-TYPE ?SELF CAUSE-OF BIOLOGIC-FUNCTION)
      (FORALL (?A)
       (=> (RESOURCE-OF ?SELF ?A)
        (OR (BIOLOGIC-FUNCTION ?A) (ACTIVITY ?A))))
      (VALUE-TYPE ?SELF PRODUCT-OF BIOLOGIC-FUNCTION))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF DISRUPTS PHYSIOLOGIC-FUNCTION)
      (VALUE-TYPE ?SELF ALTERS ANATOMICAL-STRUCTURE)
      (VALUE-TYPE ?SELF COMPLICATES BIOLOGIC-FUNCTION))
 :AXIOM-DEF (THE-ARCHETYPE BIOLOGICALLY-ACTIVE-SUBSTANCE REIFIED-PROPERTY))
(DEFINE-CLASS BIOMEDICAL-OR-DENTAL-MATERIAL (?SELF)
 "A substance used in biomedicine or dentistry predominantly for its physical, 
as opposed to chemical, properties. Included here are biocompatible materials, tissue adhesives, bone cements, 
resins, etc."
 :DEF
 (AND (CHEMICAL-VIEWED-FUNCTIONALLY ?SELF)
      (EXISTS (?A) (AND (RESOURCE-OF ?SELF ?A) (HEALTH-CARE-ACTIVITY ?A)))))
(DEFINE-CLASS BODY-SUBSTANCE (?SELF)
 "Extracellular material, or mixtures of cells and extracellular material, 
produced, excreted, or accreted by the body. Included here are substances such as saliva, dental enamel, 
sweat, and gastric acid."
 :DEF
 (AND (SUBSTANCE ?SELF)
      (EXISTS (?A) (AND (PRODUCT-OF ?SELF ?A) (ORGANISM-FUNCTION ?A))))
 :CONSTRAINTS
 (AND (FORALL (?B)
       (=> (CONSTITUENT-MATERIAL ?SELF ?B)
        (OR (CELL ?B) (INTERCELLULAR-MATRIX ?B))))
      (VALUE-TYPE ?SELF SURROUNDS EMBRYONIC-STRUCTURE)
      (EXISTS (?C)
              (AND (PIECE-OF ?SELF ?C)
                   (OR (BODY-SUBSTANCE ?C)
                       (ORGANISM ?C)
                       (ANATOMICAL-STRUCTURE ?C))))
      (FORALL (?D)
       (=> (CONSTITUENT-MATERIAL-OF ?SELF ?D)
        (OR (ANATOMICAL-STRUCTURE ?D) (ORGANISM ?D))))
      (VALUE-TYPE ?SELF DERIVATIVE-OF TISSUE)))
(DEFINE-CLASS ENZYME (?SELF)
 "A complex protein that is produced by living cells and which catalyzes specific 
biochemical reactions. There are six main types of enzymes, oxidoreductases, transferases, hydrolases, lyases, 
isomerases, and ligases."
 :DEF
 (AND (PROTEIN ?SELF)
      (BIOLOGICALLY-ACTIVE-SUBSTANCE ?SELF)
      (EXISTS (?A) (AND (PRODUCT-OF ?SELF ?A) (CELL-FUNCTION ?A)))
      (EXISTS (?B) (AND (CATALYZES ?SELF ?B) (BIOCHEMICAL-REACTION ?B)))))
(DEFINE-CLASS FOOD (?SELF)
 "Any substance containing nutrients, such as carbohydrates, proteins, and fats, 
that can be ingested by a living organism and metabolized into energy and body tissue. Some foods are naturally 
occurring, others are either partially or entirely made by humans."
 :IFF-DEF
 (AND (SUBSTANCE ?SELF)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (*NUTRIENT ?A)))
      (EXISTS (?B) (AND (EXPLOITED-BY ?SELF ?B) (NUTRITION-FUNCTION ?B))))
 :CONSTRAINTS (VALUE-TYPE ?SELF AFFECTS BIOLOGIC-FUNCTION))
(DEFINE-CLASS HAZARDOUS-OR-POISONOUS-SUBSTANCE (?SELF)
 "A substance of concern because of its potentially hazardous or toxic effects. 
This would include most drugs of abuse, as well as agents that require special handling because of their 
toxicity. Most pharmaceutical agents, although potentially harmful, are excluded here and are assigned to the 
type 'Pharmacologic Substance'."
 :IFF-DEF
 (AND (CHEMICAL-VIEWED-FUNCTIONALLY ?SELF)
      (VALUE-TYPE ?SELF CAUSE-OF INJURY-OR-POISONING)))
(DEFINE-CLASS HORMONE (?SELF)
 "In animals, a chemical secreted by an endocrine gland whose products are 
released into the circulating fluid.
Plant hormones or synthetic hormones which are used only to alter or control various physiologic processes, 
e.g., reproductive control agents, are assigned only to the type 'Pharmacologic Substance'. Hormones act as 
chemical messengers and regulate various physiologic processes such as growth, reproduction, metabolism, etc.
They usually fall into two broad classes, steroid hormones and peptide hormones."
 :DEF
 (AND (BIOLOGICALLY-ACTIVE-SUBSTANCE ?SELF)
      (EXISTS (?A)
              (AND (PRODUCT-OF ?SELF ?A)
                   (AND (SECRETION ?A)
                        (EXISTS (?B)
                                (AND (EMBODIED-IN ?A ?B)
                                     (ENDOCRINE-GLAND ?B))))))
      (EXISTS (?C) (AND (AFFECTS ?SELF ?C) (PHYSIOLOGIC-FUNCTION ?C)))))
(DEFINE-CLASS HYDROLASES (?SELF)
:DEF (ENZYME ?SELF))
(DEFINE-CLASS IMMUNOLOGIC-FACTOR (?SELF)
 "A biologic factor whose activities affect or play a role in the 
functioning of the immune system"
 :DEF
 (AND (BIOLOGICALLY-ACTIVE-SUBSTANCE ?SELF)
      (EXISTS (?A) (AND (AFFECTS ?SELF ?A) (IMMUNE-SYSTEM ?A)))
      (EXISTS (?B)
              (AND (INDICATES ?SELF ?B)
                   (OR (VIRUS ?B)
                       (RICKETTSIA-OR-CHLAMYDIA ?B)
                       (PATHOLOGIC-FUNCTION ?B)
                       (BACTERIUM ?B))))))
(DEFINE-CLASS INDICATOR-REAGENT-OR-DIAGNOSTIC-AID (?SELF)
 "A substance used in laboratory reactions, or laboratory or diagnostic 
tests and procedures to detect, measure, examine, or analyze other chemicals, processes, 
or conditions."
 :DEF
 (AND (CHEMICAL-VIEWED-FUNCTIONALLY ?SELF)
      (EXISTS (?A)
              (AND (RESOURCE-OF ?SELF ?A)
                   (OR (DIAGNOSTIC-PROCEDURE ?A) (LABORATORY-PROCEDURE ?A)))))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF EVIDENTIATES HEALTH-CONDITION)
      (VALUE-TYPE ?SELF ANALYTIC-RESOURCE-OF CHEMICAL)
      (VALUE-TYPE ?SELF DIAGNOSTIC-RESOURCE-OF
       HEALTH-CONDITION)
      (VALUE-TYPE ?SELF INTERPRETANT-OF BIOLOGIC-FUNCTION)))
(DEFINE-CLASS ISOMERASES (?SELF)
:DEF (ENZYME ?SELF))
(DEFINE-CLASS LIGASES (?SELF)
:DEF (ENZYME ?SELF))
(DEFINE-CLASS LYASES (?SELF)
:DEF (ENZYME ?SELF))
(DEFINE-CLASS NEUROREACTIVE-SUBSTANCE-OR-BIOGENIC-AMINE (?SELF)
 "A biologic factor whose activities affect or play a role in the functioning 
of the nervous system. Included here are catecholamines, neuroregulators, neurophysins, etc."
 :DEF
 (AND (BIOLOGICALLY-ACTIVE-SUBSTANCE ?SELF)
      (EXISTS (?A) (AND (AFFECTS ?SELF ?A) (NERVOUS-SYSTEM ?A)))))
(DEFINE-CLASS OXIDOREDUCTASES (?SELF)
:DEF (ENZYME ?SELF))
(DEFINE-CLASS PHARMACOLOGIC-SUBSTANCE (?SELF)
 "A substance used in the treatment, diagnosis, prevention, or analysis of 
normal and abnormal body function. This includes substances that occur naturally in the body and are 
administered therapeutically."
 :DEF
 (AND (CHEMICAL-VIEWED-FUNCTIONALLY ?SELF)
      (VALUE-TYPE ?SELF TREATMENT-RESOURCE-OF HEALTH-CONDITION)
      (VALUE-TYPE ?SELF DIAGNOSTIC-RESOURCE-OF HEALTH-CONDITION)
      (VALUE-TYPE ?SELF PREVENTS BIOLOGIC-FUNCTION))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF DISRUPTS PHYSIOLOGIC-FUNCTION)
      (VALUE-TYPE ?SELF ALTERS ANATOMICAL-STRUCTURE)
      (VALUE-TYPE ?SELF COMPLICATES BIOLOGIC-FUNCTION)))
(DEFINE-CLASS PROSTAGLANDIN (?SELF)
 "A member of the group of physiologically active compounds derived from arachidonic 
acid. Members of the group play major roles in the reproductive process, smooth muscle stimulation, blood pressure 
levels, inflammation, etc. Included here are prostacyclins, thromboxanes, and leukotrienes."
 :DEF
 (AND (BIOLOGICALLY-ACTIVE-SUBSTANCE ?SELF)
      (EXISTS (?A) (AND (DERIVATIVE-OF ?SELF ?A) (ARACHIDONIC-ACID ?A))))
 :AXIOM-DEF
 (AND (OBSOLETE PROSTAGLANDIN "1997 edition.")
      (PROBLEM PROSTAGLANDIN
       "Consider that in USN98 there is 'eicosanoid', that might include this.")))
(DEFINE-CLASS RECEPTOR (?SELF)
 "A specific structure or site on the cell surface or within its cytoplasm 
that recognizes and binds with other specific molecules. These include the proteins on the surface of an 
immunocompetent cell that binds with antigens, or proteins found on the surface molecules that bind with 
hormones or neurotransmitters and react with other molecules that respond in a specific way. Ex. Adenosine 
A2 Receptor; Antigen p150,95; T-Cell Receptors alpha-Chain."
 :DEF
 (AND (BIOLOGICALLY-ACTIVE-SUBSTANCE ?SELF)
      (EXISTS (?A)
              (AND (CONSTITUENT-MATERIAL-OF ?SELF ?A)
                   (OR (CELL-WALL ?A) (CYTOPLASM ?A))))
      (MINIMUM-SLOT-CARDINALITY ?SELF RECOGNIZES 1)
      (MINIMUM-SLOT-CARDINALITY ?SELF BINDS-WITH 1)))
(DEFINE-CLASS TRANSFERASES (?SELF)
:DEF (ENZYME ?SELF))
(DEFINE-CLASS VITAMIN (?SELF)
 "A substance, usually an organic chemical complex, present in natural 
products or made synthetically, which is essential in the diet of man or other higher animals. 
Included here are vitamin precursors and provitamins."
 :DEF
 (AND (BIOLOGICALLY-ACTIVE-SUBSTANCE ?SELF)
      (EXISTS (?A)
              (AND (RESOURCE-OF ?SELF ?A)
                   (AND (DIET ?A)
                        (EXISTS (?B) (AND (PERFORMED-BY ?A ?B) (HUMAN ?B))))))))