added small fun ontology for examples : Cytology

examples/cytology/Cytology.thy

@@ -0,0 +1,53 @@
+theory Cytology
+  imports "Isabelle_DOF.scholarly_paper"
+begin
+
+text\<open>A small example ontology for demonstration purposes.
+     The presentation follows closely: \<^url>\<open>https://www.youtube.com/watch?v=URUJD5NEXC8\<close>.\<close>
+
+
+datatype protein = filaments | motor_proteins | rna |dna |nucleolus
+
+
+onto_class organelles =   description :: string
+
+onto_class ribosomes = organelles +       description :: string
+   
+onto_class mytochondria = organelles +    description :: string
+
+onto_class golgi_apparatus = organelles + description :: string
+
+onto_class lysosome = organelles + description :: string
+
+
+text\<open>the control center of the cell:\<close>
+onto_class nucleus = organelles +  
+       description :: string
+       components  :: "protein list" <= "[nucleolus]" 
+
+definition is_nucleus 
+  where "is_nucleus org \<equiv>  \<exists> tg d ta da . org  =  nucleus.make tg d ta da"
+find_theorems (300) name:"Cytology" name:"nucleus"
+
+
+onto_class cell = 
+    name             :: string
+    membrane         :: string   <= "\<open>The outer boundary of the cell\<close>"
+    cytoplasm        :: string   <= "\<open>The outer boundary of the cell\<close>"
+    cytoskeleton     :: string   <= "\<open>includes the thread-like microfilaments\<close>"
+    genetic_material :: "protein list" <= "[rna, dna]"
+
+text\<open>Cells are devided into two categories: \<^emph>\<open>procaryotic\<close> cells (unicellular organisms some 
+bacteria) without a substructuring in organelles and \<^emph>\<open>eucaryotic\<close> cells, as occurring in 
+pluricellular organisms\<close>
+
+onto_class procaryotic_cells = cell +
+    name :: string
+
+onto_class eucaryotic_cells = cell + 
+    organelles :: "organelles list"
+(*
+invariant has_nucleus :: "\<lambda>\<sigma>::eucaryotic_cells. \<exists> org \<in> set (organelles \<sigma>). is_nucleus org"
+*)
+ 
+end