owl2_to_progol.pl

/* -*- Mode: Prolog -*- */

:- module(owl2_to_progol,
          [
           write_progol_mode_decls/1,
           write_progol_facts/3
           ]).

:- use_module(owl2_model).
:- use_module(owl2_basic_reasoner).

:- multifile owl2_io:save_axioms_hook/3.
owl2_io:save_axioms_hook(File,progol,Opts) :-
        (   nonvar(File)
        ->  tell(File)
        ;   true),
        member(mode_decls(Roots),Opts),
        write_progol_mode_decls(Roots),
        member(head(Head),Opts),
        member(goal(Goal),Opts),
        member(type(TypeDecl),Opts),
        write_progol_facts(Head,Goal,TypeDecl),
        told.

%% write_progol_facts(+Head:term,+Goal:callable,+TypeDecl:term)
%
% writes instance data for use as ILP training set. Also generates
% type declarations.
%
% Training set is written as unit clauses using Head. Facts
% are generated using Goal
%
% This is designed to be used in conjunction with a DLP
% program generated by owl2_to_prolog_dlp
%
% classAssertion/2 is treated as a unary predicate
% propertyAssertion/2 is treated as a binary predicate
% (see the Grosof translation in owl2_to_prolog_dlp)
% TODO: combine these?
%
% Example: write_progol_facts(has_disease_type(H,DT), (propertyAssertion(inheres_in,D,H),classAssertion(D,DT)), disease_type(DT))
% writes:
% =|has_disease_type(human1,alzheimers). ... disease_type(alzheimers)|=
write_progol_facts(Head,Goal,TypeDecl) :-
        format('% Type declarations:~n'),
        setof(TypeDecl,Goal^Goal,TypeDecls),
        nl,
        format('% Facts:~n'),
        forall(member(TypeDecl,TypeDecls),
               format('~q.~n',[TypeDecl])),
        forall(Goal,format('~q.~n',[Head])).

%% write_progol_mode_decls(+Roots:list)
%
% progol typing system means we have a general type for everything
%
% Roots is a list of classes. A mode declaration is made for
% every class subsumed by each Root in Roots. We use unary class predicates
% for instantiation
%
% Example:
% =|:- modeb(1,brainstem(+object))?|=
write_progol_mode_decls(Roots) :-
        forall(class(X),
               write_progol_mode_decl(class(X),Roots)).

write_progol_mode_decl(class(X),Roots) :-
        entailed(subClassOf(X,Root)),
        member(Root,Roots),
        format(':- modeb(1,~q(+~q))?~n',[X,Root]),
        !.
write_progol_mode_decl(_,_).

/** <module> generates ProGol ILP programs from OWL2 ontologies

  ---+ Synopsis

==
:- use_module(bio(owl2_to_progol)).
:- use_module(bio(owl2_io)).

% 
demo:-
  load_axioms('data.rdf'),  % classAssertion/2 and propertyAssertion/3
  load_axioms('ont.owl'),   % 
  tell('foo.progol'),
  use_labels_for_IRIs,
  write_progol_mode_decls(['Biomaterial object',quality,'Quality',dependent_continuant,disease,'Disease']),
  write_progol_facts(has_disease_type(H,DT),
                           (   propertyAssertion(inheres_in,D,H),
                               classAssertion(DT,D),
                               entailed(subClassOf(DT,'Neurodegenerative disease'))),
                           disease_type(DT)),
  told.

==

---+ Details

Alpha/experimental

Depends on owl2_basic_reasoner which is also alpha

---++

TODO - add hooks for owl2_io

*/