Subject: 
       SUO: RE: suggested draft vertebrate animal Ontology.
   Date: 
       Fri, 5 Jan 2001 09:46:22 -0800
   From: 
       Ian Niles <iniles@teknowledge.com>
    To: 
       "'Horn, Graham'" <graham.horn@aihw.gov.au>,
       "Standard-Upper-Ontology (E-mail)" <standard-upper-ontology@ieee.org>




Hi Graham,

        I've just incorporated into the merged ontology the Natural Kinds
ontology developed by the ITBM-CNR folks.  I think it does a nice job of
specifying the essential axioms and taxonomic relations for high-level
categories of organisms.  Perhaps you could use this ontology as a basis for
additional biological content.  The merged, SUO-KIF version of the Natural
Kinds ontology follows.

-Ian

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;  BIOLOGICAL HIERARCHY   ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; The following formulas incorporate the content in the Natural-Kinds
ontology developed by the
;; CNR-ITBM group.  This content is essentially a set of high-level
biological categories.

(subclass-of Organism Organic)
(subclass-of Plant Organism)
(documentation Plant "An organism having cellulose cell walls, growing by
synthesis of inorganic 
substances, generally distinguished by the presence of chlorophyll, and
lacking the power of  locomotion.  Plant parts are included here as well.")

(=>
        (instance-of ?X Plant)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y CellWall-Peptidoglycan))))

(=>
        (instance-of ?X Plant)
        (exists (?Y ?Z)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Pigment)
                        (result ?Z ?Y)
                        (instance-of ?Z Photosynthesis))))

(subclass-of Animal Organism)
(documentation Animal "An organism with eukaryotic cells, and lacking stiff
cell walls, plastids  and photosynthetic pigments. The children of this type
in the network are 'Invertebrate', and  'Vertebrate'.")
(disjoint Plant Animal)

(=>
        (instance-of ?X Animal)
        (exists (?Y ?Z)
                (and
                        (component-of ?X ?Y)
                        (instance-of ?Y Cell)
                        (part-of ?Y ?Z)
                        (instance-of ?Z CellWall-NonRigid))))

(subclass-of Microorganism Organism)
(subclass-of Archaeon Microorganism)
(documentation Archaeon "A member of one of the three domains of life,
formerly called  Archaebacteria under the taxon Bacteria, but now considered
separate and distinct. Archaea are  characterized by:  1) the presence of
characteristic tRNAs and ribosomal RNAs; 2) the absence of  peptidoglycan
cell walls; 3) the presence of ether-linked lipids built from branched-chain
subunits; and 4) their occurrence in unusual habitats. While archaea
resemble bacteria in  morphology and genomic organization, they resemble
eukarya in their method of genomic  replication. Thermoproteales;
Methanospirillum; Haloferax volcanii.")

(subclass-of Bacterium Microorganism)
(documentation Bacterium "A small, typically one-celled, prokaryotic
micro-organism."))

(=>
        (instance-of ?X Bacterium)
        (cardinality (setof ?Y (and (component-of ?Y ?X) (instance-of ?Y
Cell))) 1))

(=>
        (and
                (instance-of ?X Bacterium)
                (located-at ?X ?Y))
        (instance-of ?Y Organic))

(subclass-of Virus Microorganism)
(documentation Virus "An organism consisting of a core of a single nucleic
acid enclosed in a 
protective coat of protein. A virus may replicate only inside a host living
cell. A virus  exhibits some but not all of the usual characteristics of
living things.")

(=>
        (instance-of ?X Virus)
        (cardinality (setof ?Y (and (component-of ?Y ?X) (instance-of ?Y
Molecule))) 1))

(=>
        (instance-of ?X Virus)
        (and
                (instance-of ?X Nucleic-Acid)
                (exists (?Y ?Z)
                        (and
                                (external-covering ?Y ?X)
                                (part-of ?Z ?Y)
                                (instance-of ?Z Protein)))))

(=>
        (and
                (instance-of ?X Virus)
                (instance-of ?Y Replication)
                (effector-of ?Y ?X))
        (exists (?Z)
                (and
                        (located-at ?Y ?Z)
                        (instance-of ?Z Cell))))

(=>
        (and
                (instance-of ?X Virus)
                (located-at ?X ?Y))
        (instance-of ?Y Organic))
        
                                 
(subclass-of Chlamydia Microorganism)
(documentation Chlamydia "An organism intermediate in size and complexity
between a virus and a  bacterium, and which is parasitic within the cells of
insects and ticks. Included here are all  the chlamydias, also called 'PLT'
for psittacosis-lymphogranuloma venereum-trachoma.")

(=>
        (instance-of ?X Chlamydia)
        (exists (?Y ?Z)
                (and
                        (lives-in ?X ?Y)
                        (instance-of ?Y Cell)
                        (component-of ?Y ?Z)
                        (or
                                (instance-of ?Z Insect)
                                (instance-of ?Z Tick)))))

(=>
        (and
                (instance-of ?X Chlamydia)
                (located-at ?X ?Y))
        (instance-of ?Y Organic))


(subclass-of Vertebrate Animal)
(documentation Vertebrate "An animal which has a spinal column.")

(=>
        (instance-of ?X Vertebrate)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Spinal-Column))))

(subclass-of Invertebrate Animal)
(disjoint Vertebrate Invertebrate)
(documentation Invertebrate "An animal which has no spinal column. This type
has no children 
in the network and is assigned to all invertebrate animals.")

(subclass-of Arthropod Invertebrate)
(subclass-of Arachnid Arthropod)
(subclass-of Tick Arachnid)
(subclass-of Insect Arthropod)
(subclass-of Vertebrate-ColdBlooded Vertebrate)
(subclass-of Vertebrate-WarmBlooded Vertebrate)
(disjoint Vertebrate-WarmBlooded Vertebrate-ColdBlooded)
(subclass-of Mammal Vertebrate-WarmBlooded)

(subclass-of Alga Plant)
(documentation Alga "A chiefly aquatic plant that contains chlorophyll, but
does not form 
embryos during development and lacks vascular tissue.")

(=>
        (instance-of ?X Alga)
        (exists (?Y)
                (and
                        (lives-in ?X ?Y)
                        (instance-of ?Y Water))))

(=>
        (instance-of ?X Alga)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Chlorophyll))))

(=>
        (instance-of ?X Alga)
        (has-developmental-form ?X Incoherent))

(subclass-of Amphibian Vertebrate-ColdBlooded)
(disjoint Amphibian Reptile)
(documentation Amphibian "A cold-blooded, smooth-skinned vertebrate which
characteristically  hatches as an aquatic larva, breathing by gills. When
mature, the amphibian breathes with  lungs.")

(=>
        (instance-of ?X Amphibian)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Lungs))))

(=>
        (instance-of ?X Amphibian)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Smooth-Skin))))

(=>
        (instance-of ?X Amphibian)
        (has-developmental-form ?X Aquatic-Larva))

(subclass-of Bird Vertebrate-WarmBlooded)
(disjoint Bird Mammal)
(documentation Bird "A vertebrate having a constant body temperature and
characterized by 
the presence of feathers.")

(=>
        (instance-of ?X Bird)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Plumage)))) 

(subclass-of Fish Vertebrate-ColdBlooded)
(disjoint Fish Reptile)
(documentation Fish "A cold-blooded aquatic vertebrate characterized by fins
and breathing by  gills. Included here are fishes having either a bony
skeleton, such as a perch, or a  cartilaginous skeleton, such as a shark, or
those lacking a jaw, such as a lamprey or hagfish.")

(=>
        (instance-of ?X Fish)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Gills)))) 

(=>
        (instance-of ?X Fish)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Fin)))) 

(=>
        (instance-of ?X Fish
        (exists (?Y)
                (and
                        (lives-in ?Y ?X)
                        (instance-of ?Y Water))))

(subclass-of Fungus Plant)
(documentation Fungus "A eukaryotic organism characterized by the absence of
chlorophyll and the 
presence of a rigid cell wall. Included here are both slime molds and true
fungi such as yeasts,  molds, mildews, and mushrooms.")

(=>
        (instance-of ?X Fungus)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Cell-Eurkaryotic))))

(=>
        (instance-of ?X Fungus)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y CellWall-Rigid))))

(=>
        (and
                (instance-of ?X Fungus)
                (located-at ?X ?Y))
        (instance-of ?Y Organic))
        
(subclass-of Human Mammal)
(documentation Human "Modern man, the only remaining species of the Homo
genus. If a term  describes a human being from the point of view of
occupational, family, social status, etc., then  a type from the 'Group'
hierarchy is assigned instead.")

(subclass-of Mammal Vertebrate-WarmBlooded)
(documentation Mammal "A vertebrate having a constant body temperature and
characterized by the  presence of hair, mammary glands and sweat glands.")

(=>
        (instance-of ?X Mammal)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Hair))))

(=>
        (instance-of ?X Mammal)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Mammary-Gland))))

(=>
        (instance-of ?X Mammal)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Sweat-Gland))))

(subclass-of Reptile Vertebrate-ColdBlooded)
(documentation Reptile "A cold-blooded vertebrate having an external
covering of scales or horny  plates.  Reptiles breathe by means of lungs and
are generally egg-laying.")

(=>
        (instance-of ?X Reptile)
        (exists (?Y)
                (and
                        (component-of ?Y ?X)
                        (instance-of ?Y Lungs))))

(=>
        (instance-of ?X Reptile)
        (exists (?Y)
                (and
                        (external-covering ?Y ?X)
                        (or
                                (instance-of ?Y Scale)
                                (instance-of ?Y Horny-Plate)))))