(define-theory Molecular-Biology (Substances Biologic-Functions Representation))

(in-theory 'Molecular-Biology)


(DEFINE-RELATION BINDING-TARGET-OF (?A ?B) :IFF-DEF
 (AND (= (INVERSE BINDS-WITH) BINDING-TARGET-OF)
      (ENTITY ?A)
      (OBJECT ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE BINDING-TARGET-OF OBJECT)
      (DOMAIN BINDING-TARGET-OF ENTITY)))
(DEFINE-RELATION BINDS-WITH (?A ?B) :DEF (OPERATES-ON ?A ?B)
 :AXIOM-CONSTRAINTS
 (AND (RANGE BINDS-WITH MATERIAL-OBJECT)
      (DOMAIN BINDS-WITH MATERIAL-OBJECT)))
(DEFINE-RELATION FORMS-SYMBOLIC-SEQUENCE (?A ?B) :DEF
 (AND (TOPO-MORPHOLOGICAL-RELATION ?A ?B)
      (EXISTS (?C) (AND (FORMS-SEQUENCE ?A ?C) (REPRESENTED-BY ?C ?B)))))
(DEFINE-RELATION RECOGNIZED-BY (?A ?B) :IFF-DEF
 (AND (= (INVERSE RECOGNIZES) RECOGNIZED-BY)
      (ENTITY ?A)
      (OBJECT ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE RECOGNIZED-BY OBJECT)
      (DOMAIN RECOGNIZED-BY ENTITY)))
(DEFINE-RELATION RECOGNIZES (?A ?B) :DEF (OPERATES-ON ?A ?B)
 :AXIOM-CONSTRAINTS
 (AND (RANGE RECOGNIZES MATERIAL-OBJECT)
      (DOMAIN RECOGNIZES MATERIAL-OBJECT)))
(DEFINE-RELATION SYMBOLIC-SEQUENCE-OF (?A ?B) :IFF-DEF
 (AND (= (INVERSE FORMS-SYMBOLIC-SEQUENCE)
         SYMBOLIC-SEQUENCE-OF)
      (ABSTRACTION ?A)
      (OBJECT ?B))
 :AXIOM-CONSTRAINTS
 (AND (RANGE SYMBOLIC-SEQUENCE-OF OBJECT)
      (DOMAIN SYMBOLIC-SEQUENCE-OF ABSTRACTION)))
(DEFINE-CLASS AMINO-ACID (?SELF)
:DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (PRIME-COMPONENT-OF ?SELF ?A) (PROTEIN ?A)))))
(DEFINE-CLASS AMINO-ACID-PEPTIDE-OR-PROTEIN (?SELF)
 "Amino acids and chains of amino acids connected by peptide." :IFF-DEF
 (AND (THING ?SELF)
      (OR (AMINO-ACID ?SELF) (PEPTIDE-BOND ?SELF) (PROTEIN ?SELF)))
 :AXIOM-DEF
 (PROBLEM AMINO-ACID-PEPTIDE-OR-PROTEIN
  "Investigate: amino-acid vs. chain of a.a. vs. peptide vs. protein. See also
<Amino-Acid-Sequence>. Possible splitting?"))
(DEFINE-CLASS AMINO-ACID-SEQUENCE (?SELF)
 "The sequence of amino acids as arrayed in chains, sheets, etc., 
within the protein molecule. It is of fundamental importance in determining protein structure."
 :DEF
 (AND (MOLECULAR-SEQUENCE ?SELF)
      (EXISTS (?A) (AND (SYMBOLIC-SEQUENCE-OF ?SELF ?A) (AMINO-ACID ?A)))
      (EXISTS (?B)
              (AND (REPRESENTS ?SELF ?B)
                   (OR (GENE-OR-GENOME ?B)
                       (AMINO-ACID-PEPTIDE-OR-PROTEIN ?B))))))
(DEFINE-CLASS BIOCHEMICAL-REACTION (?SELF)
:DEF
 (AND (CHEMICAL-REACTION ?SELF)
      (EXISTS (?A) (AND (EMBODIED-IN ?SELF ?A) (BIOLOGIC-OBJECT ?A)))))
(DEFINE-CLASS CARBOHYDRATE-SEQUENCE (?SELF)
 "The sequence of carbohydrates within polysaccharides, glycoproteins, and 
glycolipids."
 :DEF
 (AND (MOLECULAR-SEQUENCE ?SELF)
      (EXISTS (?A) (AND (SYMBOLIC-SEQUENCE-OF ?SELF ?A) (CARBOHYDRATE ?A)))
      (EXISTS (?B)
              (AND (REPRESENTS ?SELF ?B)
                   (OR (POLYSACCHARIDE ?B)
                       (GLYCOPROTEIN ?B)
                       (GLYCOLIPID ?B))))))
(DEFINE-CLASS GENE-OR-GENOME (?SELF)
 "A specific sequence, or in the case of the genome the complete 
sequence of nucleotides along a molecule of DNA or RNA (in the case of some viruses) which 
represent the functional units of heredity."
 :DEF
 (AND (MOLECULAR-ANATOMICAL-STRUCTURE ?SELF)
      (EXISTS (?A)
              (AND (FINER-GRAIN-PART-OF ?SELF ?A)
                   (OR (TISSUE ?A)
                       (CELL-COMPONENT ?A)
                       (CELL ?A)
                       (BODY-PART ?A))))
      (EXISTS (?B)
              (AND (EMBODIES ?SELF ?B) (MOLECULAR-PHYSIOLOGIC-FUNCTION ?B)))
      (EXISTS (?C)
              (AND (STRICTLY-DEPENDS-ON ?SELF ?C) (MOLECULAR-SEQUENCE ?C))))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF AFFECTS PHYSIOLOGIC-FUNCTION)
      (VALUE-TYPE ?SELF COMPONENT GENE-OR-GENOME)
      (EXISTS (?D) (AND (REPRESENTED-BY ?SELF ?D) (NUCLEOTIDE-SEQUENCE ?D))))
 :AXIOM-DEF
 (AND (PROBLEM GENE-OR-GENOME
       "USN NL definition has gene as a sequence, but templates have it as an
anatomical structure having a nucleotide sequence as property. Here is the known ambiguity
of structure and description. In ON9, gene is a structure, and it is represented by a nucleotide
sequence.")
      (MAPPING GENE-OR-GENOME
       "This should be split into GENE and GENOME. Gene should be splitted
into GENE and ALLELE.")))
(DEFINE-CLASS GENETIC-FUNCTION (?SELF)
 "Functions of or related to the maintenance, translation or expression 
of the genetic material."
 :DEF
 (AND (MOLECULAR-PHYSIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A) (AND (EMBODIED-IN ?SELF ?A) (GENE-OR-GENOME ?A))))
 :CONSTRAINTS
 (AND (VALUE-TYPE ?SELF PRODUCT CELL-COMPONENT)
      (VALUE-TYPE ?SELF RESULT GENETIC-FUNCTION)))
(DEFINE-CLASS GLYCOSIDIC-COMPOUND (?SELF)
:IFF-DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A)
              (AND (PRODUCT-OF ?SELF ?A)
                   (AND (SPLITTING ?A)
                        (EXISTS (?B)
                                (AND (EMBODIED-IN ?A ?B) (NUCLEOTIDE ?B))))))))
(DEFINE-CLASS MOLECULAR-BIOLOGY-RESEARCH-TECHNIQUE (?SELF)
 "Any of the techniques used in the study of or the directed modification of the 
gene complement of a living organism."
 :DEF
 (AND (RESEARCH-ACTIVITY ?SELF)
      (EXISTS (?A)
              (AND (CONVENTIONAL-WITHIN ?SELF ?A) (MOLECULAR-BIOLOGY ?A))))
 :CONSTRAINTS
 (EXISTS (?B)
         (AND (SUPPORTS ?SELF ?B)
              (OR (THERAPEUTIC-OR-PREVENTIVE-PROCEDURE ?B)
                  (DIAGNOSTIC-PROCEDURE ?B)))))
(DEFINE-CLASS MOLECULAR-PHYSIOLOGIC-FUNCTION (?SELF)
 "A physiologic function occurring at the molecular level." :DEF
 (AND (PHYSIOLOGIC-FUNCTION ?SELF)
      (VALUE-CARDINALITY ?SELF _MOLECULAR 1)))
(DEFINE-CLASS MOLECULAR-SEQUENCE (?SELF)
 "A broad type for grouping the collected sequences of amino acids, 
carbohydrates, and nucleotide sequences. Descriptions of these sequences are generally reported in the 
published literature and/or are deposited in and maintained by databanks such as GenBank, European 
Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence 
repositories."
 :DEF
 (AND (EXPRESSION ?SELF)
      (EXISTS (?A)
              (AND (SYMBOLIC-SEQUENCE-OF ?SELF ?A)
                   (OR (AMINO-ACID ?A) (CARBOHYDRATE ?A) (NUCLEOTIDE ?A)))))
 :AXIOM-DEF
 (PROBLEM MOLECULAR-SEQUENCE
  "What is a molecular sequence as a spatial concept? a special kind of 
region? an anatomical structure at molecular layer? Here we support the view of MS as a special 
expression representing some molecular object having amino-acids, carbohydrates, or nucleotides 
as elements."))
(DEFINE-CLASS NUCLEIC-ACID (?SELF)
:DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (PRIME-COMPONENT ?SELF ?A) (NUCLEOTIDE ?A)))))
(DEFINE-CLASS NUCLEIC-ACID-NUCLEOSIDE-OR-NUCLEOTIDE (?SELF)
 "A complex compound of high molecular weight occurring in living cells. 
These are basically of two types, ribonucleic (RNA) and deoxyribo-nucleic (DNA) acids, both of which 
consist of nucleotides (nucleoside phosphates linked together by phosphate bridges)."
 :IFF-DEF
 (AND (THING ?SELF)
      (OR (NUCLEIC-ACID ?SELF) (NUCLEOSIDE ?SELF) (NUCLEOTIDE ?SELF)))
 :AXIOM-DEF
 (PROBLEM NUCLEIC-ACID-NUCLEOSIDE-OR-NUCLEOTIDE
  "The following definition assumes a splitting between Nucleic Acid, Nucleoside,
and Nucleotide, which is not in the NL description provided by USN98."))
(DEFINE-CLASS NUCLEOSIDE (?SELF)
:DEF
 (AND (GLYCOSIDIC-COMPOUND ?SELF)
      (VALUE-CARDINALITY ?SELF COMPONENT 1)
      (VALUE-CARDINALITY ?SELF COMPONENT 1)))
(DEFINE-CLASS NUCLEOTIDE (?SELF)
:DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (VALUE-CARDINALITY ?SELF COMPONENT 1)
      (VALUE-CARDINALITY ?SELF COMPONENT 1)
      (VALUE-CARDINALITY ?SELF COMPONENT 1)))
(DEFINE-CLASS NUCLEOTIDE-SEQUENCE (?SELF)
 "The sequence of purines and pyrimidines in nucleic acids and polynucleotides. 
Included here are nucleotide-rich regions, conserved sequence, and DNA transforming region."
 :DEF
 (AND (MOLECULAR-SEQUENCE ?SELF)
      (EXISTS (?A)
              (AND (SYMBOLIC-SEQUENCE-OF ?SELF ?A)
                   (OR (PURINE ?A) (PYRIMIDINE ?A))))
      (EXISTS (?B)
              (AND (REPRESENTS ?SELF ?B)
                   (OR (GENE-OR-GENOME ?B)
                       (NUCLEIC-ACID-NUCLEOSIDE-OR-NUCLEOTIDE ?B)
                       (POLYNUCLEOTIDE ?B)))))
 :CONSTRAINTS (VALUE-TYPE ?SELF PART-OF NUCLEOTIDE-SEQUENCE))
(DEFINE-CLASS PEPTIDE-BOND (?SELF)
:DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (PRIME-COMPONENT-OF ?SELF ?A) (PROTEIN ?A)))
      (EXISTS (?B) (AND (INTERCONNECTS ?SELF ?B) (AMINO-ACID ?B)))))
(DEFINE-CLASS POLYNUCLEOTIDE (?SELF)
:DEF
 (AND (ORGANIC-CHEMICAL ?SELF)
      (EXISTS (?A) (AND (POLYMER-OF ?SELF ?A) (NUCLEOTIDE ?A)))))
(DEFINE-CLASS PURINE (?SELF)
:DEF (ORGANIC-CHEMICAL ?SELF))
(DEFINE-CLASS PYRIMIDINE (?SELF)
:DEF (ORGANIC-CHEMICAL ?SELF))
(DEFINE-CLASS REPLICATION (?SELF)
:DEF
 (AND (MOLECULAR-PHYSIOLOGIC-FUNCTION ?SELF)
      (EXISTS (?A) (AND (EMBODIED-IN ?SELF ?A) (BIOLOGIC-OBJECT ?A)))
      (EXISTS (?B)
              (AND (PRODUCT ?SELF ?B)
                   (AND (ANATOMICAL-STRUCTURE ?B)
                        (EXISTS (?C)
                                (AND (COPY-OF ?B ?C)
                                     (ANATOMICAL-STRUCTURE ?C)))))))
 :AXIOM-DEF
 (FURTHER-MODELLING REPLICATION
  "For coreference: (:same-as embodied-in representation:copy)."))