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commit 4048b1ef8c5755b2c64784e34e5c3ce274e2f866 1 parent d9b14ec
Chris Mungall authored November 15, 2010
30  README
@@ -10,6 +10,9 @@ This documentation is intended to be read via pldoc
10 10
 
11 11
 See INSTALL.txt
12 12
 
  13
+You can bypass installation and use the 'thea' script directly. See
  14
+below.
  15
+
13 16
 ---++ Overview
14 17
 
15 18
 The module owl2_io.pl provides a means of loading and saving OWL2
@@ -47,6 +50,23 @@ reasoners can be plugged in, both native prolog and non-prolog (the
47 50
 latter accessed seamlessly via either owl2_owllink.pl or
48 51
 owl2_java_owlapi.pl).
49 52
 
  53
+---++ Command Line Usage
  54
+
  55
+The script "thea" in the bin directory should work from anywhere, with
  56
+no installation of thea modules required.
  57
+
  58
+Type
  59
+
  60
+==
  61
+thea --help
  62
+==
  63
+
  64
+for full instructions. Many complex operations can be chained on the
  65
+command line.
  66
+
  67
+See also the other wrapper scripts in the bin directory
  68
+
  69
+See Command_Line_Usage.txt for more details
50 70
 
51 71
 ---++ Further Reading
52 72
 
@@ -63,15 +83,17 @@ See also the apps/ directory for example applications.
63 83
   * owl2_xml.pl -- support for OWL-XML
64 84
   * owl2_manchester_paser.pl -- incomplete support for Manchester syntax
65 85
   * owl2_plsyn.pl -- infix prolog syntax for OWL
66  
- * owl2_model.pl
  86
+ * owl2_model.pl -- definition of prolog predicates used to embed OWL
67 87
  * swrl.pl
68  
- * owl2_model.pl
69  
- * owl2_reasoner.pl
  88
+  * swrl_rdf_hooks.pl -- allows SWRL to be parsed by owl2_from_rdf.pl
  89
+ * owl2_reasoner.pl -- pluggable reasoner framework
70 90
   * owl2_rl_rules.pl
71 91
   * owl2_graph_reasoner.pl
72 92
  * owl2_java_owlapi.pl (requires JPL)
73 93
  * owl2_owllink.pl
74  
-
  94
+ * owl2_util.pl -- misc utilities
  95
+ * owl2_popl.pl -- prolog ontology processing language
  96
+ * owl2_metamodel.pl -- information about OWL axiom types
75 97
 
76 98
 ---++ Reasoning support
77 99
 
7  owl2_from_rdf.pl
@@ -69,6 +69,7 @@
69 69
 
70 70
 :- use_module(owl2_model).
71 71
 
  72
+:- use_module(library(debug)).
72 73
 :- use_module(library('semweb/rdf_db')).
73 74
 :- use_module(library('semweb/rdf_edit')).
74 75
 :- use_module(library('semweb/rdfs')).
@@ -214,7 +215,7 @@
214 215
         % see email to JanW July-1-2009
215 216
         forall((test_use_owl(S,P,BNode),
216 217
                 atom(BNode),
217  
-                sub_string(BNode,0,2,_,'__'),
  218
+                sub_atom(BNode,0,2,_,'__'),
218 219
                 test_use_owl(BNode,'http://www.w3.org/1999/02/22-rdf-syntax-ns#datatype',literal(_))),
219 220
                (   use_owl(S,P,BNode,datatype_fix),
220 221
                    use_owl(BNode,'http://www.w3.org/1999/02/22-rdf-syntax-ns#datatype',literal(_)),
@@ -335,7 +336,7 @@
335 336
 
336 337
 rdf_load_stream(URL,Ontology,BaseURI,Imports) :-
337 338
 	BaseURI = URL,
338  
-  	(   sub_string(URL,0,4,_,'http')
  339
+  	(   sub_atom(URL,0,4,_,'http')
339 340
         ->  catch((http_open(URL,RDF_Stream,[]),
340 341
 	      rdf_load(RDF_Stream,[if(true),base_uri(BaseURI),blank_nodes(noshare),
341 342
 				   result(Action, Triples, MD5),register_namespaces(true)]),
@@ -595,7 +596,7 @@
595 596
 
596 597
 is_bnode(C) :-
597 598
 	atom(C),
598  
-	sub_string(C,0,2,_,'__').
  599
+	sub_atom(C,0,2,_,'__').
599 600
 
600 601
 % Table 11. Parsing Object Property Expressions
601 602
 
1  owl2_io.pl
@@ -9,6 +9,7 @@
9 9
            convert_axioms/5
10 10
           ]).
11 11
 
  12
+:- use_module(library(debug)).
12 13
 :- use_module(owl2_model,[consult_axioms/1, axiom/1]).
13 14
 
14 15
 %% load_axioms_hook(+File,+Fmt,+Opts)
96  owl2_java_owlapi.pl
@@ -924,70 +924,80 @@
924 924
 
925 925
 ---+ Synopsis
926 926
 
927  
-using OWLAPI to save files:
928  
-  
  927
+using a reasoner:
  928
+
929 929
 ==
930  
-[owl2_model].
931  
-[owl2_java_owlapi].
932  
-[owl2_from_rdf].
933  
-owl_parse_rdf('testfiles/Hydrology.owl'), % parse using prolog/thea
934  
-create_factory(Man,Fac),
935  
-build_ontology(Man,Fac,Ont),
936  
-save_ontology(Man,Ont,'file:///tmp/foo'). % save using owlapi
  930
+reasoner_test :-
  931
+        initialize_reasoner(pellet,R),
  932
+        forall(reasoner_ask(subClassOf(A,B)),
  933
+               format('~w SubClassOf ~w~n',[A,B])).
937 934
 ==  
938 935
 
939  
-using a reasoner:
  936
+To use this interactively, make sure to start-up prolog with JPL and
  937
+everything in your classpath. You can use the thea-jpl wrapper script.
  938
+
  939
+To start a prolog session:
940 940
 
941 941
 ==
942  
-create_reasoner(Man,pellet,Reasoner),
943  
-create_factory(Man,Fac),
944  
-build_ontology(Man,Fac,Ont),
945  
-reasoner_classify(Reasoner,Man,Ont),
946  
-save_ontology(Man,Ont,'file:///tmp/foo').
947  
-==  
  942
+thea-jpl --prolog
  943
+==
  944
+
  945
+To query reasoner results:
948 946
 
949 947
 ==
950  
-[owl2_model].
951  
-[owl2_java_owlapi].
952  
-[owl2_from_rdf].
953  
-owl_parse_rdf('testfiles/music_ontology.owl'),
954  
-create_factory(Man,Fac),
955  
-build_ontology(Man,Fac,Ont),
956  
-writeln(classifying),
957  
-create_reasoner(Man,pellet,Reasoner),
958  
-reasoner_classify(Reasoner,Man,Ont),
959  
-writeln(classified),
960  
-class(C),
961  
-writeln(c=C),
962  
-reasoner_subClassOf(Reasoner,Fac,C,P),
963  
-writeln(p=P).
964  
-==  
  948
+thea-jpl --reasoner pellet testfiles/pizza.owl --reasoner-ask "subClassOf(A,B)"
  949
+==
  950
+
  951
+---+ Details
  952
+
  953
+This module is intended to interface with the OWLAPI
965 954
 
966  
-queries:
  955
+  http://owlapi.sourceforge.net/
  956
+
  957
+This provides access to reasoners such as Pellet and FaCT++, as well
  958
+as OWLAPI parsers and renderers. You can also use this if you want
  959
+additional capabilities provided by the OWLAPI.
  960
+
  961
+
  962
+---+ Hooks
  963
+
  964
+It provides hooks into both owl2_reasoner.pl and owl2_io.pl
  965
+
  966
+---++ I/O Hooks
  967
+
  968
+You can use the format =|owlapi(Format)|= to use the OWLAPI for
  969
+reading or writing. E.g.
967 970
 
968 971
 ==
969  
-someValuesFrom('http://purl.org/ontology/mo/performed','http://purl.org/ontology/mo/Performance')
  972
+save_axioms('my.owl',owlapi(manchester)).
970 973
 ==
971 974
 
972  
----+ Use
  975
+Supported values:
973 976
 
974  
-  JPL Required
  977
+ * owlapi(manchester)
  978
+ * owlapi(owlxml)
  979
+ * owlapi(owlrdf)
975 980
 
976  
-  Set your CLASSPATH to include owlapi-bin.jar, pellet.jar, ...
  981
+ More can be added easily on request
977 982
 
978  
-  start SWI
  983
+---++ Reasoner Hooks
  984
+
  985
+You can use any of
  986
+
  987
+ * pellet
  988
+ * factpp
  989
+ * hermit
  990
+
  991
+As arguments to reasoner_initialize/2.
979 992
 
980  
----+ Details
981 993
 
982  
-  This module is intended to interface with the OWLAPI
983 994
 
984  
-  http://owlapi.sourceforge.net/
985 995
 
986  
-  This provides access to reasoners such as Pellet and FaCT++
  996
+---+ Pre-Requisites
987 997
 
988  
-  JPL is required for this module
  998
+JPL is required for this module
989 999
 
990  
-  Note that this module is not required for the rest of Thea2
  1000
+Note that this module is not required for the rest of Thea2
991 1001
 
992 1002
 @author  Chris Mungall
993 1003
 @version $Revision$
72  owl2_plsyn.pl
@@ -121,10 +121,15 @@
121 121
 	\+ ((ontologyAxiom(Ont,H),
122 122
 	     member(Ont,Onts))).
123 123
 
  124
+%% plsyn_owl(?Pl,?Owl)
  125
+% as plsyn_owl/3
124 126
 plsyn_owl(Pl,Owl) :-
125 127
 	plsyn_owl(Pl,Owl,[]).
126 128
 
127  
-%% plsyn_owl(+Pl,?Owl,+Opts:list)
  129
+%% plsyn_owl(?Pl,?Owl,+Opts:list)
  130
+%
  131
+% convert between a plsyn prolog term and an owl2_model.pl prolog term.
  132
+% either one of Pl or Owl must be ground
128 133
 plsyn_owl(Pl,Owl,Opts) :-
129 134
 	select(use_labels,Opts,Opts2),
130 135
 	!,
@@ -347,7 +352,7 @@
347 352
 convenience predicates declared infix in order to resemble Manchester
348 353
 Syntax.
349 354
 
350  
-The following prolog file
  355
+The following is a valid plsyn file:
351 356
 
352 357
 ==
353 358
 ontology(spicy).
@@ -356,7 +361,7 @@
356 361
 pizza_with_4_cheeses == pizza and hasPart exactly 4 of cheese.
357 362
 ==
358 363
 
359  
-Can be loaded like this:
  364
+This file can be loaded via load_axioms/2 like this:
360 365
 
361 366
 ==
362 367
 load_axioms('myfile.plsyn',plsyn).
@@ -371,7 +376,66 @@
371 376
 We are forced to introduce an extra keyword 'of' for cardinality
372 377
 expressions to make this parseable by prolog.
373 378
 
374  
-
375 379
 TODO: show translation table
376 380
 
  381
+---++ Infix Predicate Symbols for Axioms
  382
+
  383
+  * < --- subClassOf/2
  384
+  * @< --- subPropertyOf/2
  385
+  * == --- equivalentClasses/1
  386
+  * = --- sameIndividual/1
  387
+  * \= --- differentIndividuals/1
  388
+  * :: --- classAssertion/2
  389
+ 
  390
+---++ Property Characteristic Prefix Predicates
  391
+
  392
+the following are all declared prefix
  393
+
  394
+  * transitive --- transitiveProperty/1
  395
+  * symmetric --- symmetricProperty/1
  396
+  * reflexive --- reflexiveProperty/1
  397
+  * functional --- functionalProperty/1
  398
+
  399
+---++ Other Infix Predicates
  400
+
  401
+  * inverseOf --- inverseProperties/2
  402
+
  403
+---++ Class Expressions
  404
+
  405
+  * and --- intersectionOf
  406
+  * or --- unionOf
  407
+  * some --- someValuesFrom
  408
+  * only --- allValuesFrom
  409
+  * value --- hasValue
  410
+  * not --- complementOf (prefix)
  411
+  * exactly --- exactCardinality
  412
+  * min --- minCardinality
  413
+  * max --- maxCardinality
  414
+  * of --- required when making QCRs. E.g. exactly 5 of finger
  415
+
  416
+ ---++ Property Expressions
  417
+
  418
+ Use the '*' symbol. For example
  419
+
  420
+ ==
  421
+ uncleOf @< fatherOf * brotherOf.
  422
+ ==
  423
+
  424
+ ---++ Uses
  425
+
  426
+ plsyn makes it easier to mix OWL ontologies and ontology templates into prolog programs.
  427
+
  428
+For example, consider the following failure-driven loop to add an OWL
  429
+axiom with a complex nested expression for all facts of a 4-argument predicate:
  430
+
  431
+==
  432
+generate_ownership_assertions :-
  433
+        owns(Person,Number,Thing,Loc),
  434
+        plsyn_owl( owns exactly Number of (Thing and located_in value Loc) :: Person, OwlAxiom),
  435
+        assert_axiom(OwlAxiom),
  436
+        fail.
  437
+==
  438
+
  439
+The owl2_popl.pl module facilitates this kind of translation
  440
+
377 441
 */
5  owl2_rl_rules.pl
@@ -17,7 +17,6 @@
17 17
 
18 18
 This module implements the OWL2 RL rule-based reasoninng
19 19
 
20  
-
21 20
 ---+ Details
22 21
 
23 22
 See http://www.w3.org/TR/2008/WD-owl2-profiles-20081202/#Reasoning_in_OWL_2_RL_and_RDF_Graphs_using_Rules
@@ -73,7 +72,9 @@
73 72
 
74 73
 u_assert(X) :-
75 74
 	call(X),!.
76  
-u_assert(X) :- assert(X).
  75
+u_assert(X) :-
  76
+        debug(rl_rules,'asserting : ~w',[X]),
  77
+        assert(X).
77 78
 
78 79
 
79 80
 
19  owl2_util.pl
@@ -16,11 +16,14 @@
16 16
            remove_ns/2,
17 17
            replace_ns_prefix/4,
18 18
            use_label_as_IRI/2,
  19
+           get_IRI_from_label/2,
19 20
            use_labels_for_IRIs/0,
20 21
            use_safe_labels_for_IRIs/0,
  22
+           replace_labels_with_IRIs/0,
21 23
            use_numeric_IRIs_for_classes/2,
22 24
            prefix_IRIs/1,
23 25
            translate_IRIs/1,
  26
+           translate_IRIs/2,
24 27
            map_IRIs/3,
25 28
            assume_entity_declarations/0,
26 29
            use_class_labels_as_synonyms/1,
@@ -211,6 +214,9 @@
211 214
 use_safe_labels_for_IRIs:-
212 215
         translate_IRIs(use_safe_label_as_IRI).
213 216
 
  217
+replace_labels_with_IRIs:-
  218
+        translate_IRIs(get_IRI_from_label).
  219
+
214 220
 remove_ns(IRI,X) :-
215 221
         concat_atom([_,X],'#',IRI),
216 222
         !.
@@ -250,6 +256,11 @@
250 256
         !.
251 257
 use_label_as_IRI(X,X).
252 258
 
  259
+get_IRI_from_label(X,IRI) :- labelAnnotation_value(IRI,X),!.
  260
+get_IRI_from_label(X,X).
  261
+
  262
+
  263
+
253 264
 use_property_as_IRI(Prop,IRI,NewIRI) :-
254 265
         anyPropertyAssertion(Prop,IRI,Literal),
255 266
 	Literal=literal(type(_,Val)),
@@ -282,6 +293,14 @@
282 293
         maplist(retract_axiom,Axioms),
283 294
         maplist(assert_axiom,Axioms2).
284 295
 
  296
+:- module_transparent translate_IRIs/2.
  297
+translate_IRIs(Goal,Ontology):-
  298
+        findall(A,ontologyAxiom(Ontology,A),Axioms),
  299
+        maplist(map_IRIs(Goal),Axioms,Axioms2),
  300
+        maplist(retract_axiom,Axioms),
  301
+        forall(member(A,Axioms2),
  302
+               assert_axiom(A,Ontology)).
  303
+
285 304
 %% map_IRIs(+MapGoal,+AxiomIn,?AxiomOut)
286 305
 :- module_transparent map_IRIs/3.
287 306
 map_IRIs(_,[],[]) :- !.
134  z1.txt
... ...
@@ -0,0 +1,134 @@
  1
+sim(big_left_ear,retina_degenerates,has_quality some morphology and has_quality some quality and part_of some head).
  2
+sim(big_left_ear,retina_degenerates,has_quality some morphology and part_of some head).
  3
+sim(big_left_ear,deformed_right_ear,ear and organ and has_quality some morphology and has_quality some quality and part_of some head).
  4
+sim(big_left_ear,deformed_right_ear,ear and organ and has_quality some morphology and part_of some head).
  5
+sim(big_left_ear,deformed_right_ear,ear and organ and has_quality some morphology).
  6
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology and organ and has_quality some quality and part_of some head).
  7
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology and organ and has_quality some quality).
  8
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology and organ and part_of some head).
  9
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology and has_quality some quality and organ and part_of some head).
  10
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology and has_quality some quality and part_of some head).
  11
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology and part_of some head and organ and has_quality some quality).
  12
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology and part_of some head).
  13
+sim(big_left_ear,deformed_right_ear,ear and part_of some head and organ and has_quality some morphology).
  14
+sim(big_left_ear,deformed_right_ear,ear and part_of some head and has_quality some morphology and organ and has_quality some quality).
  15
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology).
  16
+sim(big_left_ear,deformed_right_ear,has_quality some morphology and ear and organ and has_quality some quality and part_of some head).
  17
+sim(big_left_ear,deformed_right_ear,has_quality some morphology and ear and organ and has_quality some quality).
  18
+sim(big_left_ear,deformed_right_ear,has_quality some morphology and ear and has_quality some quality and organ and part_of some head).
  19
+sim(big_left_ear,deformed_right_ear,has_quality some morphology and ear and has_quality some quality and part_of some head).
  20
+sim(big_left_ear,deformed_right_ear,has_quality some morphology and ear and part_of some head and organ and has_quality some quality).
  21
+sim(big_left_ear,deformed_right_ear,has_quality some morphology and ear and has_quality some quality).
  22
+sim(retina_degenerates,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and has_quality some quality and part_of some nervous_system).
  23
+sim(retina_degenerates,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and part_of some nervous_system).
  24
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some brain).
  25
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and (has_quality some morphology or has_part some has_quality some morphology)and part_of some brain and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  26
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and (has_quality some morphology or has_part some has_quality some morphology)and part_of some brain).
  27
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and (has_quality some quality or has_part some has_quality some quality)and part_of some brain).
  28
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some brain and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  29
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some brain and (has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system).
  30
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some brain and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  31
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some brain).
  32
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates,part_of some brain and (has_quality some degenerated or has_part some has_quality some degenerated)and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  33
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates,part_of some brain and (has_quality some degenerated or has_part some has_quality some degenerated)and (has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system).
  34
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates,part_of some brain and (has_quality some degenerated or has_part some has_quality some degenerated)and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  35
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates,part_of some brain and (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some nervous_system).
  36
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some brain).
  37
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some hippocampus).
  38
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  39
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and part_of some brain and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  40
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and part_of some hippocampus and (has_quality some quality or has_part some has_quality some quality)and part_of some brain).
  41
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and part_of some hippocampus and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  42
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and part_of some hippocampus and part_of some brain and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  43
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and part_of some brain).
  44
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and part_of some hippocampus).
  45
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system).
  46
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some brain and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  47
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some brain and (has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system).
  48
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some hippocampus and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some brain).
  49
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some hippocampus and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  50
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some hippocampus and (has_quality some morphology or has_part some has_quality some morphology)and part_of some brain and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  51
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some hippocampus and (has_quality some morphology or has_part some has_quality some morphology)and part_of some brain).
  52
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some hippocampus and (has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system).
  53
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some hippocampus and part_of some brain and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  54
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and part_of some hippocampus and part_of some brain and (has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system).
  55
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)).
  56
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and ca2 and (has_quality some quality or has_part some has_quality some quality)and part_of some brain).
  57
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and ca2 and (has_quality some quality or has_part some has_quality some quality)and part_of some hippocampus).
  58
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and ca2 and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  59
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and ca2 and part_of some brain and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  60
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and ca2 and part_of some hippocampus and (has_quality some quality or has_part some has_quality some quality)and part_of some brain).
  61
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and ca2 and part_of some hippocampus and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  62
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and ca2 and part_of some hippocampus and part_of some brain and (has_quality some quality or has_part some has_quality some quality)and part_of some nervous_system).
  63
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and ca2 and (has_quality some quality or has_part some has_quality some quality)).
  64
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  65
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  66
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  67
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  68
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  69
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  70
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  71
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  72
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  73
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  74
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  75
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  76
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  77
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  78
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  79
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  80
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  81
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  82
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  83
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  84
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  85
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  86
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  87
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  88
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  89
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  90
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  91
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  92
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  93
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  94
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  95
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  96
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  97
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  98
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  99
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  100
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  101
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  102
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  103
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  104
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  105
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  106
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  107
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  108
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  109
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  110
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  111
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  112
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  113
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  114
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  115
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and (part_of some neuron or has_part some part_of some neuron)and part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some cell or has_part some part_of some cell)).
  116
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and (part_of some cell or has_part some part_of some cell)).
  117
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and (part_of some neuron or has_part some part_of some neuron)).
  118
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some neuron or has_part some part_of some neuron)and (has_quality some quality or has_part some has_quality some quality)and (part_of some cell or has_part some part_of some cell)).
  119
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some cell or has_part some part_of some cell)).
  120
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some neuron or has_part some part_of some neuron)).
  121
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system and (part_of some neuron or has_part some part_of some neuron)and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and (part_of some cell or has_part some part_of some cell)).
  122
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system and (part_of some neuron or has_part some part_of some neuron)and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some cell or has_part some part_of some cell)).
  123
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and (part_of some axon or has_part some part_of some axon)).
  124
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon)and (has_quality some quality or has_part some has_quality some quality)and (part_of some cell or has_part some part_of some cell)).
  125
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon)and (has_quality some quality or has_part some has_quality some quality)and (part_of some neuron or has_part some part_of some neuron)).
  126
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon)and (part_of some neuron or has_part some part_of some neuron)and (has_quality some quality or has_part some has_quality some quality)and (part_of some cell or has_part some part_of some cell)).
  127
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon)).
  128
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (part_of some axon or has_part some part_of some axon)and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and (part_of some cell or has_part some part_of some cell)).
  129
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (part_of some axon or has_part some part_of some axon)and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and (part_of some neuron or has_part some part_of some neuron)).
  130
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (part_of some axon or has_part some part_of some axon)and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some neuron or has_part some part_of some neuron)and (has_quality some quality or has_part some has_quality some quality)and (part_of some cell or has_part some part_of some cell)).
  131
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (part_of some axon or has_part some part_of some axon)and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some cell or has_part some part_of some cell)).
  132
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (part_of some axon or has_part some part_of some axon)and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some neuron or has_part some part_of some neuron)).
  133
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (part_of some axon or has_part some part_of some axon)and (part_of some neuron or has_part some part_of some neuron)and (has_quality some morphology or has_part some has_quality some morphology)and (has_quality some quality or has_part some has_quality some quality)and (part_of some cell or has_part some part_of some cell)).
  134
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,part_of some nervous_system and (part_of some axon or has_part some part_of some axon)and (part_of some neuron or has_part some part_of some neuron)and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some cell or has_part some part_of some cell)).
43  z2.txt
... ...
@@ -0,0 +1,43 @@
  1
+sim(big_left_ear,retina_degenerates,has_quality some morphology and part_of some head).
  2
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology).
  3
+sim(retina_degenerates,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and part_of some nervous_system).
  4
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some brain).
  5
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)).
  6
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon)).
  7
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system).
  8
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system).
  9
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_ca3,has_part some (axon_terminal and has_quality some degenerated)and part_of some hippocampus).
  10
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_ca3,has_part some (axon_terminal and has_quality some degenerated)).
  11
+sim(axon_terminals_degenerated_in_ca2,deformed_hippocampus, (hippocampus or part_of some hippocampus)and (has_quality some morphology or has_part some has_quality some morphology)).
  12
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_sn,has_part some axon_terminal and has_part some has_quality some degenerated).
  13
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_sn,has_part some (axon_terminal and has_quality some degenerated)).
  14
+sim(deformed_ca2,retina_degenerates,has_quality some morphology and part_of some brain).
  15
+sim(deformed_ca2,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and part_of some nervous_system).
  16
+sim(deformed_ca2,deformed_hippocampus, (hippocampus or part_of some hippocampus)and has_quality some deformed).
  17
+sim(lewy_bodies_in_sn,lewy_bodies_in_sn2, (lewy_body or has_part some lewy_body)and (sn or part_of some sn)).
  18
+sim(deformed_right_ear,retina_degenerates,has_quality some morphology and part_of some head).
  19
+sim(axon_terminals_degenerated_in_ca3,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some brain).
  20
+sim(axon_terminals_degenerated_in_ca3,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and part_of some hippocampus).
  21
+sim(axon_terminals_degenerated_in_ca3,thin_mm_in_axon_of_dn_of_sn, (has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon)).
  22
+sim(axon_terminals_degenerated_in_ca3,thin_mm_in_axon_of_dn_of_sn, (has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system).
  23
+sim(axon_terminals_degenerated_in_ca3,thin_mm_in_axon_of_dn_of_sn, (part_of some axon or has_part some part_of some axon)and part_of some nervous_system).
  24
+sim(axon_terminals_degenerated_in_ca3,deformed_hippocampus, (hippocampus or part_of some hippocampus)and (has_quality some morphology or has_part some has_quality some morphology)).
  25
+sim(axon_terminals_degenerated_in_ca3,axon_terminals_degenerated_in_sn,has_part some axon_terminal and has_part some has_quality some degenerated).
  26
+sim(axon_terminals_degenerated_in_ca3,axon_terminals_degenerated_in_sn,has_part some (axon_terminal and has_quality some degenerated)).
  27
+sim(atrophied_hippocampus,retina_degenerates,has_quality some degenerated and part_of some brain).
  28
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_ca2, (hippocampus or part_of some hippocampus)and (has_quality some degenerated or has_part some has_quality some degenerated)).
  29
+sim(atrophied_hippocampus,deformed_ca2, (hippocampus or part_of some hippocampus)and has_quality some morphology).
  30
+sim(atrophied_hippocampus,thin_mm_in_axon_of_dn_of_sn,has_quality some decreased and has_quality some morphology).
  31
+sim(atrophied_hippocampus,thin_mm_in_axon_of_dn_of_sn,has_quality some decreased and part_of some nervous_system).
  32
+sim(atrophied_hippocampus,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and part_of some nervous_system).
  33
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_ca3, (hippocampus or part_of some hippocampus)and (has_quality some degenerated or has_part some has_quality some degenerated)).
  34
+sim(atrophied_hippocampus,deformed_hippocampus,hippocampus and has_quality some morphology).
  35
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_sn, (has_quality some degenerated or has_part some has_quality some degenerated)and (part_of some nervous_system or has_part some part_of some nervous_system)).
  36
+sim(deformed_hippocampus,retina_degenerates,has_quality some morphology and part_of some brain).
  37
+sim(deformed_hippocampus,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and part_of some nervous_system).
  38
+sim(axon_terminals_degenerated_in_sn,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and (part_of some nervous_system or has_part some part_of some nervous_system)).
  39
+sim(axon_terminals_degenerated_in_sn,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and (part_of some nervous_system or has_part some part_of some nervous_system)).
  40
+sim(axon_terminals_degenerated_in_sn,thin_mm_in_axon_of_dn_of_sn, (sn or part_of some sn)and (has_quality some morphology or has_part some has_quality some morphology)).
  41
+sim(axon_terminals_degenerated_in_sn,thin_mm_in_axon_of_dn_of_sn, (sn or part_of some sn)and (part_of some axon or has_part some part_of some axon)).
  42
+sim(axon_terminals_degenerated_in_sn,thin_mm_in_axon_of_dn_of_sn, (has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon)).
  43
+sim(axon_terminals_degenerated_in_sn,deformed_hippocampus, (has_quality some morphology or has_part some has_quality some morphology)and (part_of some nervous_system or has_part some part_of some nervous_system)).
44  z3.txt
... ...
@@ -0,0 +1,44 @@
  1
+sim(big_left_ear,retina_degenerates,has_quality some morphology and part_of some head).
  2
+sim(big_left_ear,deformed_right_ear,ear and has_quality some morphology).
  3
+sim(big_left_ear,small_green_left_eye, (left and has_quality some size)and (left and part_of some head)and has_quality some size and part_of some head).
  4
+sim(big_left_ear,deformed_blue_right_eye,has_quality some morphology and part_of some head).
  5
+sim(retina_degenerates,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and part_of some nervous_system).
  6
+sim(retina_degenerates,small_green_left_eye, (eye or part_of some eye)and has_quality some morphology).
  7
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some brain).
  8
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,ca2 and (has_quality some morphology or has_part some has_quality some morphology)).
  9
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn, ((has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon))and ((has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system)and (part_of some axon or has_part some part_of some axon)and part_of some nervous_system).
  10
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_ca3,has_part some (axon_terminal and has_quality some degenerated)and part_of some hippocampus).
  11
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_ca3,has_part some (axon_terminal and has_quality some degenerated)).
  12
+sim(axon_terminals_degenerated_in_ca2,deformed_hippocampus, (hippocampus or part_of some hippocampus)and (has_quality some morphology or has_part some has_quality some morphology)).
  13
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_sn,has_part some axon_terminal and has_part some has_quality some degenerated).
  14
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_sn,has_part some (axon_terminal and has_quality some degenerated)).
  15
+sim(deformed_ca2,retina_degenerates,has_quality some morphology and part_of some brain).
  16
+sim(deformed_ca2,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and part_of some nervous_system).
  17
+sim(deformed_ca2,deformed_hippocampus, (hippocampus or part_of some hippocampus)and has_quality some deformed).
  18
+sim(lewy_bodies_in_sn,lewy_bodies_in_sn2, (lewy_body or has_part some lewy_body)and (sn or part_of some sn)).
  19
+sim(deformed_right_ear,retina_degenerates,has_quality some morphology and part_of some head).
  20
+sim(deformed_right_ear,small_green_left_eye,has_quality some morphology and part_of some head).
  21
+sim(axon_terminals_degenerated_in_ca3,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and part_of some brain).
  22
+sim(axon_terminals_degenerated_in_ca3,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and part_of some hippocampus).
  23
+sim(axon_terminals_degenerated_in_ca3,thin_mm_in_axon_of_dn_of_sn, ((has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon))and ((has_quality some morphology or has_part some has_quality some morphology)and part_of some nervous_system)and (part_of some axon or has_part some part_of some axon)and part_of some nervous_system).
  24
+sim(axon_terminals_degenerated_in_ca3,deformed_hippocampus, (hippocampus or part_of some hippocampus)and (has_quality some morphology or has_part some has_quality some morphology)).
  25
+sim(axon_terminals_degenerated_in_ca3,axon_terminals_degenerated_in_sn,has_part some axon_terminal and has_part some has_quality some degenerated).
  26
+sim(axon_terminals_degenerated_in_ca3,axon_terminals_degenerated_in_sn,has_part some (axon_terminal and has_quality some degenerated)).
  27
+sim(atrophied_hippocampus,retina_degenerates,has_quality some degenerated and part_of some brain).
  28
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_ca2, (hippocampus or part_of some hippocampus)and (has_quality some degenerated or has_part some has_quality some degenerated)).
  29
+sim(atrophied_hippocampus,deformed_ca2, (hippocampus or part_of some hippocampus)and has_quality some morphology).
  30
+sim(atrophied_hippocampus,thin_mm_in_axon_of_dn_of_sn, (has_quality some decreased and has_quality some morphology)and (has_quality some decreased and part_of some nervous_system)and has_quality some morphology and part_of some nervous_system).
  31
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_ca3, (hippocampus or part_of some hippocampus)and (has_quality some degenerated or has_part some has_quality some degenerated)).
  32
+sim(atrophied_hippocampus,deformed_hippocampus,hippocampus and has_quality some morphology).
  33
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_sn, (has_quality some degenerated or has_part some has_quality some degenerated)and (part_of some nervous_system or has_part some part_of some nervous_system)).
  34
+sim(atrophied_hippocampus,small_green_left_eye,has_quality some decreased and has_quality some size).
  35
+sim(deformed_hippocampus,retina_degenerates,has_quality some morphology and part_of some brain).
  36
+sim(deformed_hippocampus,thin_mm_in_axon_of_dn_of_sn,has_quality some morphology and part_of some nervous_system).
  37
+sim(axon_terminals_degenerated_in_sn,retina_degenerates, (has_quality some degenerated or has_part some has_quality some degenerated)and (part_of some nervous_system or has_part some part_of some nervous_system)).
  38
+sim(axon_terminals_degenerated_in_sn,deformed_ca2, (has_quality some morphology or has_part some has_quality some morphology)and (part_of some nervous_system or has_part some part_of some nervous_system)).
  39
+sim(axon_terminals_degenerated_in_sn,thin_mm_in_axon_of_dn_of_sn, ((sn or part_of some sn)and (has_quality some morphology or has_part some has_quality some morphology))and ((sn or part_of some sn)and (part_of some axon or has_part some part_of some axon))and (has_quality some morphology or has_part some has_quality some morphology)and (part_of some axon or has_part some part_of some axon)).
  40
+sim(axon_terminals_degenerated_in_sn,deformed_hippocampus, (has_quality some morphology or has_part some has_quality some morphology)and (part_of some nervous_system or has_part some part_of some nervous_system)).
  41
+sim(small_green_left_eye,thin_mm_in_axon_of_dn_of_sn,has_quality some decreased and has_quality some morphology).
  42
+sim(deformed_blue_right_eye,retina_degenerates, (eye or part_of some eye)and has_quality some morphology).
  43
+sim(deformed_blue_right_eye,deformed_right_ear, (right and has_quality some deformed)and (right and part_of some head)and has_quality some deformed and part_of some head).
  44
+sim(deformed_blue_right_eye,small_green_left_eye, (eye and has_quality some color)and (eye and has_quality some morphology)and has_quality some color and has_quality some morphology).
44  z3b.txt
... ...
@@ -0,0 +1,44 @@
  1
+sim(big_left_ear,retina_degenerates,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,head)]))
  2
+sim(big_left_ear,deformed_right_ear,intersectionOf([ear,someValuesFrom(has_quality,morphology)]))
  3
+sim(big_left_ear,small_green_left_eye,intersectionOf([intersectionOf([left,someValuesFrom(has_quality,size)]),intersectionOf([left,someValuesFrom(part_of,head)]),intersectionOf([someValuesFrom(has_quality,size),someValuesFrom(part_of,head)])]))
  4
+sim(big_left_ear,deformed_blue_right_eye,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,head)]))
  5
+sim(retina_degenerates,thin_mm_in_axon_of_dn_of_sn,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,nervous_system)]))
  6
+sim(retina_degenerates,small_green_left_eye,intersectionOf([unionOf([eye,someValuesFrom(part_of,eye)]),someValuesFrom(has_quality,morphology)]))
  7
+sim(axon_terminals_degenerated_in_ca2,retina_degenerates,intersectionOf([unionOf([someValuesFrom(has_quality,degenerated),someValuesFrom(has_part,someValuesFrom(has_quality,degenerated))]),someValuesFrom(part_of,brain)]))
  8
+sim(axon_terminals_degenerated_in_ca2,deformed_ca2,intersectionOf([ca2,unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))])]))
  9
+sim(axon_terminals_degenerated_in_ca2,thin_mm_in_axon_of_dn_of_sn,intersectionOf([intersectionOf([unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))]),unionOf([someValuesFrom(part_of,axon),someValuesFrom(has_part,someValuesFrom(part_of,axon))])]),intersectionOf([unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))]),someValuesFrom(part_of,nervous_system)]),intersectionOf([unionOf([someValuesFrom(part_of,axon),someValuesFrom(has_part,someValuesFrom(part_of,axon))]),someValuesFrom(part_of,nervous_system)])]))
  10
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_ca3,intersectionOf([someValuesFrom(has_part,intersectionOf([axon_terminal,someValuesFrom(has_quality,degenerated)])),someValuesFrom(part_of,hippocampus)]))
  11
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_ca3,someValuesFrom(has_part,intersectionOf([axon_terminal,someValuesFrom(has_quality,degenerated)])))
  12
+sim(axon_terminals_degenerated_in_ca2,deformed_hippocampus,intersectionOf([unionOf([hippocampus,someValuesFrom(part_of,hippocampus)]),unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))])]))
  13
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_sn,intersectionOf([someValuesFrom(has_part,axon_terminal),someValuesFrom(has_part,someValuesFrom(has_quality,degenerated))]))
  14
+sim(axon_terminals_degenerated_in_ca2,axon_terminals_degenerated_in_sn,someValuesFrom(has_part,intersectionOf([axon_terminal,someValuesFrom(has_quality,degenerated)])))
  15
+sim(deformed_ca2,retina_degenerates,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,brain)]))
  16
+sim(deformed_ca2,thin_mm_in_axon_of_dn_of_sn,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,nervous_system)]))
  17
+sim(deformed_ca2,deformed_hippocampus,intersectionOf([unionOf([hippocampus,someValuesFrom(part_of,hippocampus)]),someValuesFrom(has_quality,deformed)]))
  18
+sim(lewy_bodies_in_sn,lewy_bodies_in_sn2,intersectionOf([unionOf([lewy_body,someValuesFrom(has_part,lewy_body)]),unionOf([sn,someValuesFrom(part_of,sn)])]))
  19
+sim(deformed_right_ear,retina_degenerates,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,head)]))
  20
+sim(deformed_right_ear,small_green_left_eye,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,head)]))
  21
+sim(axon_terminals_degenerated_in_ca3,retina_degenerates,intersectionOf([unionOf([someValuesFrom(has_quality,degenerated),someValuesFrom(has_part,someValuesFrom(has_quality,degenerated))]),someValuesFrom(part_of,brain)]))
  22
+sim(axon_terminals_degenerated_in_ca3,deformed_ca2,intersectionOf([unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))]),someValuesFrom(part_of,hippocampus)]))
  23
+sim(axon_terminals_degenerated_in_ca3,thin_mm_in_axon_of_dn_of_sn,intersectionOf([intersectionOf([unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))]),unionOf([someValuesFrom(part_of,axon),someValuesFrom(has_part,someValuesFrom(part_of,axon))])]),intersectionOf([unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))]),someValuesFrom(part_of,nervous_system)]),intersectionOf([unionOf([someValuesFrom(part_of,axon),someValuesFrom(has_part,someValuesFrom(part_of,axon))]),someValuesFrom(part_of,nervous_system)])]))
  24
+sim(axon_terminals_degenerated_in_ca3,deformed_hippocampus,intersectionOf([unionOf([hippocampus,someValuesFrom(part_of,hippocampus)]),unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))])]))
  25
+sim(axon_terminals_degenerated_in_ca3,axon_terminals_degenerated_in_sn,intersectionOf([someValuesFrom(has_part,axon_terminal),someValuesFrom(has_part,someValuesFrom(has_quality,degenerated))]))
  26
+sim(axon_terminals_degenerated_in_ca3,axon_terminals_degenerated_in_sn,someValuesFrom(has_part,intersectionOf([axon_terminal,someValuesFrom(has_quality,degenerated)])))
  27
+sim(atrophied_hippocampus,retina_degenerates,intersectionOf([someValuesFrom(has_quality,degenerated),someValuesFrom(part_of,brain)]))
  28
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_ca2,intersectionOf([unionOf([hippocampus,someValuesFrom(part_of,hippocampus)]),unionOf([someValuesFrom(has_quality,degenerated),someValuesFrom(has_part,someValuesFrom(has_quality,degenerated))])]))
  29
+sim(atrophied_hippocampus,deformed_ca2,intersectionOf([unionOf([hippocampus,someValuesFrom(part_of,hippocampus)]),someValuesFrom(has_quality,morphology)]))
  30
+sim(atrophied_hippocampus,thin_mm_in_axon_of_dn_of_sn,intersectionOf([intersectionOf([someValuesFrom(has_quality,decreased),someValuesFrom(has_quality,morphology)]),intersectionOf([someValuesFrom(has_quality,decreased),someValuesFrom(part_of,nervous_system)]),intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,nervous_system)])]))
  31
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_ca3,intersectionOf([unionOf([hippocampus,someValuesFrom(part_of,hippocampus)]),unionOf([someValuesFrom(has_quality,degenerated),someValuesFrom(has_part,someValuesFrom(has_quality,degenerated))])]))
  32
+sim(atrophied_hippocampus,deformed_hippocampus,intersectionOf([hippocampus,someValuesFrom(has_quality,morphology)]))
  33
+sim(atrophied_hippocampus,axon_terminals_degenerated_in_sn,intersectionOf([unionOf([someValuesFrom(has_quality,degenerated),someValuesFrom(has_part,someValuesFrom(has_quality,degenerated))]),unionOf([someValuesFrom(part_of,nervous_system),someValuesFrom(has_part,someValuesFrom(part_of,nervous_system))])]))
  34
+sim(atrophied_hippocampus,small_green_left_eye,intersectionOf([someValuesFrom(has_quality,decreased),someValuesFrom(has_quality,size)]))
  35
+sim(deformed_hippocampus,retina_degenerates,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,brain)]))
  36
+sim(deformed_hippocampus,thin_mm_in_axon_of_dn_of_sn,intersectionOf([someValuesFrom(has_quality,morphology),someValuesFrom(part_of,nervous_system)]))
  37
+sim(axon_terminals_degenerated_in_sn,retina_degenerates,intersectionOf([unionOf([someValuesFrom(has_quality,degenerated),someValuesFrom(has_part,someValuesFrom(has_quality,degenerated))]),unionOf([someValuesFrom(part_of,nervous_system),someValuesFrom(has_part,someValuesFrom(part_of,nervous_system))])]))
  38
+sim(axon_terminals_degenerated_in_sn,deformed_ca2,intersectionOf([unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))]),unionOf([someValuesFrom(part_of,nervous_system),someValuesFrom(has_part,someValuesFrom(part_of,nervous_system))])]))
  39
+sim(axon_terminals_degenerated_in_sn,thin_mm_in_axon_of_dn_of_sn,intersectionOf([intersectionOf([unionOf([sn,someValuesFrom(part_of,sn)]),unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))])]),intersectionOf([unionOf([sn,someValuesFrom(part_of,sn)]),unionOf([someValuesFrom(part_of,axon),someValuesFrom(has_part,someValuesFrom(part_of,axon))])]),intersectionOf([unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))]),unionOf([someValuesFrom(part_of,axon),someValuesFrom(has_part,someValuesFrom(part_of,axon))])])]))
  40
+sim(axon_terminals_degenerated_in_sn,deformed_hippocampus,intersectionOf([unionOf([someValuesFrom(has_quality,morphology),someValuesFrom(has_part,someValuesFrom(has_quality,morphology))]),unionOf([someValuesFrom(part_of,nervous_system),someValuesFrom(has_part,someValuesFrom(part_of,nervous_system))])]))
  41
+sim(small_green_left_eye,thin_mm_in_axon_of_dn_of_sn,intersectionOf([someValuesFrom(has_quality,decreased),someValuesFrom(has_quality,morphology)]))
  42
+sim(deformed_blue_right_eye,retina_degenerates,intersectionOf([unionOf([eye,someValuesFrom(part_of,eye)]),someValuesFrom(has_quality,morphology)]))
  43
+sim(deformed_blue_right_eye,deformed_right_ear,intersectionOf([intersectionOf([right,someValuesFrom(has_quality,deformed)]),intersectionOf([right,someValuesFrom(part_of,head)]),intersectionOf([someValuesFrom(has_quality,deformed),someValuesFrom(part_of,head)])]))
  44
+sim(deformed_blue_right_eye,small_green_left_eye,intersectionOf([intersectionOf([eye,someValuesFrom(has_quality,color)]),intersectionOf([eye,someValuesFrom(has_quality,morphology)]),intersectionOf([someValuesFrom(has_quality,color),someValuesFrom(has_quality,morphology)])]))

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