(define-theory Substances (Meronymy Physical-Concepts))

(in-theory 'Substances)


(DEFINE-RELATION CATALYZED-BY (?A ?B) :IFF-DEF
 (= (INVERSE CATALYZES) CATALYZED-BY))
(DEFINE-RELATION CATALYZES (?A ?B) :DEF
 (AND (CHEMICAL-RELATION ?A ?B) (FAVORS ?A ?B)) :AXIOM-CONSTRAINTS
 (AND (RANGE CATALYZES CHEMICAL-REACTION)
      (DOMAIN CATALYZES SUBSTANCE)))
(DEFINE-RELATION DERIVATIVE (?A ?B) :IFF-DEF
 (= (INVERSE DERIVATIVE-OF) DERIVATIVE))
(DEFINE-RELATION DERIVATIVE-OF (?A ?B)
 "Some substance is a to-actor of a process
which has an in-actor which is a material object. In other words: in chemistry, a substance 
structurally related to another or that can be made from the other substance. This is used 
only for structural relationships. This does not include functional relationships such as 
metabolite of, by product of, nor analog of."
 :DEF (CHEMICAL-RELATION ?A ?B) :AXIOM-CONSTRAINTS
 (AND (RANGE DERIVATIVE-OF MATERIAL-OBJECT)
      (DOMAIN DERIVATIVE-OF SUBSTANCE)))
(DEFINE-RELATION INHIBITED-BY (?A ?B) :IFF-DEF
 (= (INVERSE INHIBITS) INHIBITED-BY))
(DEFINE-RELATION INHIBITS (?A ?B) :DEF
 (AND (CHEMICAL-RELATION ?A ?B) (PREVENTS ?A ?B)) :AXIOM-CONSTRAINTS
 (AND (RANGE INHIBITS NATURAL-PROCESS)
      (DOMAIN INHIBITS SUBSTANCE)))
(DEFINE-RELATION ION (?A ?B) :IFF-DEF
 (AND (= (INVERSE ION-OF) ION)
      (CHEMICAL-ELEMENT ?A)
      (ELEMENT-ION-OR-ISOTOPE ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE ION ELEMENT-ION-OR-ISOTOPE)
      (DOMAIN ION CHEMICAL-ELEMENT)))
(DEFINE-RELATION ION-OF (?A ?B) :DEF
 (AND (EXISTS ?Z
       (AND (ELECTRON ?Z) (COMPONENT-OF ?Z ?B) (ABSENT-IN ?Z ?A)))
      (CHEMICAL-RELATION ?A ?B)
      (ELEMENT-ION-OR-ISOTOPE ?A)
      (CHEMICAL-ELEMENT ?B)))
(DEFINE-RELATION ISOTOPE (?A ?B) :IFF-DEF
 (AND (= (INVERSE ISOTOPE-OF) ISOTOPE)
      (CHEMICAL-ELEMENT ?A)
      (ELEMENT-ION-OR-ISOTOPE ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE ISOTOPE ELEMENT-ION-OR-ISOTOPE)
      (DOMAIN ISOTOPE CHEMICAL-ELEMENT)))
(DEFINE-RELATION ISOTOPE-OF (?A ?B)
 "Used to denote the form of element having the same atomic number 
(i.e., the same number of protons), but differing in atomic weight or mass due to the presence 
of one or more additional neutrons. Both for stable and radioactive isotopes."
 :DEF
 (AND (EXISTS (?Z ?W)
       (AND (VALUE-FILLER ?Z)
            (VALUE-FILLER ?W)
            (ATOMIC-MASS-VALUE ?A ?Z)
            (ATOMIC-MASS-VALUE ?B ?W)
            (DIFFERENT ?Z ?W)))
      (CHEMICAL-RELATION ?A ?B)
      (ELEMENT-ION-OR-ISOTOPE ?A)
      (CHEMICAL-ELEMENT ?B)))
(DEFINE-RELATION POLYMER (?A ?B) :IFF-DEF
 (= (INVERSE POLYMER-OF) POLYMER))
(DEFINE-RELATION POLYMER-OF (?A ?B) :DEF (CHEMICAL-RELATION ?A ?B))
(DEFINE-RELATION TRANSFORMATION-OF (?A ?B) :IFF-DEF
 (AND (= (INVERSE TRANSFORMS-INTO) TRANSFORMATION-OF)
      (ENTITY ?A)
      (ENTITY ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE TRANSFORMATION-OF ENTITY)
      (DOMAIN TRANSFORMATION-OF ENTITY)))
(DEFINE-RELATION TRANSFORMS-INTO (?A ?B)
 "A substance trasforms into another
when its duration-value meets the duration value of the other.
Moreover, the second strictly depends on the first."
 :DEF
 (AND (EXISTS (?Z ?W)
       (AND (INTERVAL ?Z)
            (INTERVAL ?W)
            (DURING ?Z ?A)
            (DURING ?W ?B)
            (MEETS ?Z ?W)))
      (CHEMICAL-RELATION ?A ?B)
      (STRICTLY-NECESSARY-TO ?A ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE TRANSFORMS-INTO SUBSTANCE)
      (DOMAIN TRANSFORMS-INTO SUBSTANCE)))
(DEFINE-CLASS ALKALOID (?SELF)
 "A basic, nitrogen-containing compound of plant origin. Included here are 
aporphines, cinchona, curare, ergot, opium, belladonna, rauwolfia, and vinca alkaloids, among others."
 :DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (DERIVATIVE-OF ?SELF ?A) (PLANT ?A)))
      (EXISTS (?B) (AND (COMPONENT ?SELF ?B) (NITROGEN ?B))))
 :AXIOM-DEF (OBSOLETE ALKALOID "1997 edition."))
(DEFINE-CLASS ARACHIDONIC-ACID (?SELF)
:DEF (ORGANIC-CHEMICAL ?SELF))
(DEFINE-CLASS CARBIDE (?SELF)
:DEF
 (INORGANIC-HYDROCARBON-DERIVATIVE ?SELF))
(DEFINE-CLASS CARBOHYDRATE (?SELF)
 "A compound consisting of carbon, hydrogen, and oxygen in 
which the hydrogen/oxygen ratio is the same as in water, and in which repeating units 
are joined through oxygen linkages. Carbohydrates are generally characterized as sugars 
and include mono-, di-, oligo-, and polysaccharides, glycosides, glycans, and starches. 
Included here are sugar phosphates. Excluded are glycolipids."
 :DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (PRIME-COMPONENT ?SELF ?A) (CARBON ?A)))
      (EXISTS (?B) (AND (PRIME-COMPONENT ?SELF ?B) (HYDROGEN ?B)))
      (EXISTS (?C) (AND (PRIME-COMPONENT ?SELF ?C) (OXYGEN ?C)))
      (EXISTS (?D)
              (AND (PART ?SELF ?D)
                   (AND (ATOMIC-UNIT ?D)
                        (EXISTS (?E)
                                (AND (INTERCONNECTED-BY ?D ?E)
                                     (OXYGEN-LINKAGE ?E))))))))
(DEFINE-CLASS CARBON (?SELF)
:DEF (CHEMICAL-ELEMENT ?SELF))
(DEFINE-CLASS CARBON-17 (?SELF)
:DEF
 (AND (ELEMENT-ION-OR-ISOTOPE ?SELF)
      (EXISTS (?A) (AND (ISOTOPE-OF ?SELF ?A) (CARBON ?A)))))
(DEFINE-CLASS CARBON-DISULFIDE (?SELF)
:DEF
 (INORGANIC-HYDROCARBON-DERIVATIVE ?SELF))
(DEFINE-CLASS CARBONATE (?SELF)
:DEF
 (INORGANIC-HYDROCARBON-DERIVATIVE ?SELF))
(DEFINE-CLASS CELLULOSE (?SELF)
:DEF (POLYSACCHARIDE ?SELF))
(DEFINE-CLASS CHEMICAL (?SELF)
 "USN: Chemicals are viewed from two distinct perspectives in the network, 
functionally and structurally. Almost every chemical term is assigned at least two types, one from the 
structure hierarchy and at least one from the function hierarchy."
 :DEF
 (AND (SUBSTANCE ?SELF)
      (EXISTS (?A)
              (AND (PRIME-COMPONENT ?SELF ?A) (ELEMENT-ION-OR-ISOTOPE ?A))))
 :AXIOM-DEF
 (MAPPING CHEMICAL
  "It is not true that in the Metathesurus almost every chemical term is assigned 
at least two types (actually: 23717 Organic-Chemical-only instances, 3413 Carbohydrate-only inst., 39748 
Amino-Acid-Peptide-or-Protein-only instances, etc.
In ON9.2, due to its ontology of meta-level categories, a preferential basic view should be chosen, and 
the structural view is at the lower (material) granularity, on which the functional (teleological) 
granularity depends. For this reason, Chemical-Viewed-Structurally is merged with Chemical."))
(DEFINE-CLASS CHEMICAL-COMPOUND (?SELF)
 "A chemical viewed from the perspective of its structural characteristics. 
Included here are terms which can mean either a salt, an ion, or a compound (e.g., 'Bromates' and 
'Bromides').
  USN: Chemicals are viewed from two distinct perspectives in the network, 
functionally and structurally. Almost every chemical term is assigned at least two types, one from the 
structure hierarchy and at least one from the function hierarchy."
 :IFF-DEF (CHEMICAL ?SELF))
(DEFINE-CLASS CHEMICAL-VIEWED-STRUCTURALLY (?SELF)
 "A chemical viewed from the perspective of its structural characteristics. 
Included here are terms which can mean either a salt, an ion, or a compound (e.g., 'Bromates' and 
'Bromides')."
 :IFF-DEF (CHEMICAL ?SELF))
(DEFINE-CLASS CHEMICAL-ELEMENT (?SELF)
:DEF
 (ELEMENT-ION-OR-ISOTOPE ?SELF))
(DEFINE-CLASS CHEMICAL-REACTION (?SELF)
:DEF
 (AND (MOLECULAR-FUNCTION ?SELF)
      (EXISTS (?A)
              (AND (EMBODIED-IN ?SELF ?A)
                   (AND (SUBSTANCE ?A)
                        (EXISTS (?B)
                                (AND (TRANSFORMS-INTO ?A ?B)
                                     (SUBSTANCE ?B))))))))
(DEFINE-CLASS CHEMICAL-VIEWED-FUNCTIONALLY (?SELF)
 "A chemical viewed from the perspective of its functional characteristics or 
pharmacological activities."
 :DEF
 (AND (CHEMICAL ?SELF) (MINIMUM-SLOT-CARDINALITY ?SELF ACTOR-OF 1))
 :AXIOM-DEF
 (MAPPING CHEMICAL-VIEWED-FUNCTIONALLY
  "This concept has not a complete (:is) definition, since an automatic classification
is not wanted for every chemical bearing an actor role."))
(DEFINE-CLASS CHLOROPHYLL (?SELF)
:DEF (ORGANIC-CHEMICAL ?SELF))
(DEFINE-CLASS CYANATE (?SELF)
:DEF
 (INORGANIC-HYDROCARBON-DERIVATIVE ?SELF))
(DEFINE-CLASS CYANIDE (?SELF)
:DEF
 (INORGANIC-HYDROCARBON-DERIVATIVE ?SELF))
(DEFINE-CLASS EICOSANOID (?SELF)
 "A compound structurally related to arachidonic acid. Included here are arachidonic 
acid, eicosanoic acid, and saturated or unsaturated derivatives of each."
 :DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (ARACHIDONIC-ACID ?A)))))
(DEFINE-CLASS ELEMENT-ION-OR-ISOTOPE (?SELF)
 "One of the 109 presently known fundamental substances that comprise all matter at 
and above the atomic level. This includes elemental metals, rare gases, and most abundant naturally occurring 
radioactive elements, as well as the ionic counterparts of elements (NA+, Cl-), and the less abundant isotopic 
forms. This does not include organic ions such as iodoacetate to which the type 'Organic Chemical' is assigned.
Aluminum; Carbon; Radioisotopes; Chromium Isotopes; Cobalt Radioisotopes; Deuterium. Group terms such as sulfates 
would be assigned to the type 'Chemical Viewed Structurally'. Substances such as aluminum chloride would be 
assigned the type 'Inorganic Chemical'. Technetium Tc 99m Aggregated Albumin would not receive this type."
 :DEF
 (AND (SUBSTANCE ?SELF)
      (EXISTS (?A)
              (AND (CONSTITUENT-MATERIAL-OF ?SELF ?A) (MATERIAL-OBJECT ?A))))
 :CONSTRAINTS (VALUE-TYPE ?SELF CONSTITUENT-MATERIAL INCOHERENT)
 :AXIOM-DEF
 (MAPPING ELEMENT-ION-OR-ISOTOPE
  "ION and ISOTOPE should be reified properties (THE ionic counterpart of an element and
THE isotopic forms)."))
(DEFINE-CLASS ETHER-LINKED-LIPID (?SELF)
:DEF (LIPID ?SELF))
(DEFINE-CLASS FAT-SUBSTANCE (?SELF)
:DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (DERIVATIVE-OF ?SELF ?A) (GLYCEROL ?A)))))
(DEFINE-CLASS GLYCEROL (?SELF)
:DEF (ORGANIC-CHEMICAL ?SELF))
(DEFINE-CLASS GLYCOLIPID (?SELF)
:DEF
 (AND (LIPID ?SELF) (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (CARBOHYDRATE ?A)))))
(DEFINE-CLASS GLYCOPROTEIN (?SELF)
:DEF
 (AND (PROTEIN ?SELF) (MINIMUM-SLOT-CARDINALITY ?SELF COMPONENT 1)))
(DEFINE-CLASS HYDROCARBON (?SELF)
:DEF (ORGANIC-CHEMICAL ?SELF))
(DEFINE-CLASS HYDROCARBON-DERIVATIVE (?SELF)
:IFF-DEF
 (AND (CHEMICAL ?SELF)
      (EXISTS (?A) (AND (DERIVATIVE-OF ?SELF ?A) (HYDROCARBON ?A)))
      (FORALL (?A ?B)
       (=> (AND (DERIVATIVE-OF ?SELF ?A) (DERIVATIVE-OF ?SELF ?B))
        (= ?A ?B)))))
(DEFINE-CLASS HYDROGEN (?SELF)
:DEF (CHEMICAL-ELEMENT ?SELF))
(DEFINE-CLASS INORGANIC-CHEMICAL (?SELF)
 "Compounds of chemical elements, excluding the hydrocarbons and their 
derivatives (except carbides, carbonates, cyanides, cyanates and carbon disulfide). Generally inorganic 
compounds contain ionic bonds. Included here are inorganic acids and salts, alloys, alkalies, and minerals. 
Ammonia; Aluminum Hydroxide; Carbonic Acid."
 :DEF (CHEMICAL ?SELF))
(DEFINE-CLASS INORGANIC-HYDROCARBON-DERIVATIVE (?SELF)
:IFF-DEF
 (AND (INORGANIC-CHEMICAL ?SELF)
      (VALUE-CARDINALITY ?SELF DERIVATIVE-OF 1)
      (VALUE-TYPE ?SELF DERIVATIVE-OF HYDROCARBON)))
(DEFINE-CLASS LACTAM (?SELF)
 "A cyclic amide, usually with 4- or 5-membered rings that may or may not be 
fused to other rings, as in compounds structurally related to the penicillins and cephalosporins."
 :DEF (ORGANIC-CHEMICAL ?SELF) :AXIOM-DEF (OBSOLETE LACTAM "1997 edition."))
(DEFINE-CLASS LIPID (?SELF)
 "A fat or fat-derived substance, such as fatty acids, fatty alcohols, and waxes.
Included here are glyco- and  phospholipids."
 :DEF
 (AND (THING ?SELF)
      (OR (FAT-SUBSTANCE ?SELF)
          (AND (ORGANIC-CHEMICAL ?SELF)
               (EXISTS (?A)
                       (AND (DERIVATIVE-OF ?SELF ?A) (FAT-SUBSTANCE ?A)))))))
(DEFINE-CLASS MOLECULAR-FUNCTION (?SELF)
:DEF
 (AND (NATURAL-PROCESS ?SELF)
      (VALUE-CARDINALITY ?SELF _MOLECULAR 1)))
(DEFINE-CLASS NITROGEN (?SELF)
:DEF (CHEMICAL-ELEMENT ?SELF))
(DEFINE-CLASS ORGANIC-CHEMICAL (?SELF)
 "The general class of carbon-containing compounds, usually based on carbon chains 
or rings, and also containing hydrogen (hydrocarbons), with or without nitrogen, oxygen, or other elements.
The bonding between elements is generally covalent."
 :DEF
 (AND (CHEMICAL ?SELF)
      (EXISTS (?A) (AND (PRIME-COMPONENT ?SELF ?A) (CARBON ?A)))
      (EXISTS (?B) (AND (PRIME-COMPONENT ?SELF ?B) (HYDROGEN ?B)))))
(DEFINE-CLASS ORGANIC-HYDROCARBON-DERIVATIVE (?SELF)
:IFF-DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (VALUE-CARDINALITY ?SELF DERIVATIVE-OF 1)
      (VALUE-TYPE ?SELF DERIVATIVE-OF HYDROCARBON)))
(DEFINE-CLASS ORGANOPHOSPHORUS-COMPOUND (?SELF)
 "An organic compound containing phosphorus as a constituent. Included here are 
organic phosphinic, phosphonic and phosphoric acid derivatives and their thiophosphorus counterparts.
Excluded are phospholipids and sugar phosphates."
 :IFF-DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (PHOSPHORUS ?A)))
      (NOT (PHOSPHOLIPID ?SELF))
      (NOT (SUGAR-PHOSPHATE ?SELF)))
)
(DEFINE-CLASS OXYGEN (?SELF)
:DEF (CHEMICAL-ELEMENT ?SELF))
(DEFINE-CLASS OXYGEN-LINKAGE (?SELF)
:DEF (ATOMIC-UNIT ?SELF))
(DEFINE-CLASS PEPTIDOGLYCAN (?SELF)
:DEF (POLYSACCHARIDE ?SELF))
(DEFINE-CLASS PHOSPHATE (?SELF)
:DEF (CHEMICAL ?SELF))
(DEFINE-CLASS PHOSPHOLIPID (?SELF)
:DEF
 (AND (LIPID ?SELF) (EXISTS (?A) (AND (COMPONENT ?SELF ?A) (PHOSPHORUS ?A)))))
(DEFINE-CLASS PHOSPHORUS (?SELF)
:DEF (CHEMICAL-ELEMENT ?SELF))
(DEFINE-CLASS POLYSACCHARIDE (?SELF)
:DEF (CARBOHYDRATE ?SELF))
(DEFINE-CLASS PROTEIN (?SELF)
:DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (PRIME-COMPONENT ?SELF ?A) (CARBON ?A)))
      (EXISTS (?B) (AND (PRIME-COMPONENT ?SELF ?B) (NITROGEN ?B)))
      (EXISTS (?C) (AND (PRIME-COMPONENT ?SELF ?C) (HYDROGEN ?C)))
      (EXISTS (?D) (AND (PRIME-COMPONENT ?SELF ?D) (OXYGEN ?D)))))
(DEFINE-CLASS SPLITTING (?SELF)
:DEF
 (AND (MOLECULAR-FUNCTION ?SELF)
      (EXISTS (?A) (AND (EMBODIED-IN ?SELF ?A) (SUBSTANCE ?A)))
      (EXISTS (?B) (AND (PRODUCT ?SELF ?B) (SUBSTANCE ?B)))))
(DEFINE-CLASS STEROID (?SELF)
 "One of a group of polycyclic, 17-carbon-atom, fused-ring compounds occurring both 
in natural and synthetic forms. Included here are naturally occurring and synthetic steroids, bufanolides, 
cardanolides, homosteroids, norsteroids, and secosteroids."
 :DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (VALUE-CARDINALITY ?SELF _POLYCYCLIC 1)
      (VALUE-CARDINALITY ?SELF _FUSED-RING 1)
      (EXISTS (?A) (AND (PRIME-COMPONENT ?SELF ?A) (CARBON-17 ?A))))
 :AXIOM-DEF (OBSOLETE STEROID "1997 edition. Should search for 98 substitute."))
(DEFINE-CLASS SUGAR (?SELF)
:DEF (CARBOHYDRATE ?SELF))
(DEFINE-CLASS SUGAR-PHOSPHATE (?SELF)
:DEF (PHOSPHATE ?SELF))
(DEFINE-CLASS SULFUR (?SELF)
:DEF (CHEMICAL-ELEMENT ?SELF))
(DEFINE-CLASS WATER (?SELF)
:DEF
 (AND (CHEMICAL ?SELF)
      (EXISTS (?A) (AND (PRIME-COMPONENT ?SELF ?A) (HYDROGEN ?A)))
      (EXISTS (?B) (AND (PRIME-COMPONENT ?SELF ?B) (OXYGEN ?B)))))