# QUERIES ####################################################################################

# Each query has the semantics defined in a comment property. The canonical way of doing this
# is to define the semantics as an equivalent condition, but in order to get the answers 
# we would need to execute the OPPL inferred step, which does not work properly (TODO: check this)

# Superclass of all the queries

ADD Class: query;

# Query 1: Proteins acting in the mitotic S phase (At) ############################################

ADD Class: query_1;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins acting in the mitotic S phase";ADD oppl_query "participates_in some (CCO_P0000014 or (part_of some CCO_P0000014))";

SELECT subClassOf participates_in some (CCO_P0000014 or (part_of some CCO_P0000014));ADD subClassOf query_1;

# Query 2: Location of proteins acting in the mitotic S phase (At) #################################

ADD Class: query_2;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Location of proteins acting in the mitotic S phase";ADD oppl_query "location_of some (participates_in some (CCO_P0000014 or (part_of some CCO_P0000014)));ADD subClassOf query_2";

SELECT subClassOf location_of some (participates_in some (CCO_P0000014 or (part_of some CCO_P0000014)));ADD subClassOf query_2;

# Query 3: Proteins participating in processes before mitosis  (At) #################################

ADD Class: query_3;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins participating in processes before mitotic M";ADD oppl_query "participates_in some (precedes some CCO_P0000017 or part_of some (precedes some CCO_P0000017))";

SELECT subClassOf participates_in some (precedes some CCO_P0000017 or part_of some (precedes some CCO_P0000017));ADD subClassOf query_3;

# Query 4: Proteins participating in Mitosis and any process before mitosis in mitotic cell cycle 

ADD Class: query_4;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins participating in Mitosis and any process before mitosis in mitotic cell cycle";ADD oppl_query "participates_in some (precedes some (CCO_P0000017 or (part_of some (precedes some CCO_P0000017)))) and participates_in some (CCO_P0000017 or part_of some CCO_P0000017)";

SELECT subClassOf participates_in some (precedes some (CCO_P0000017 or (part_of some (precedes some CCO_P0000017)))) and participates_in some (CCO_P0000017 or part_of some CCO_P0000017);ADD subClassOf query_4;

# Query 4_1: Proteins participating in Mitosis and any process inmediatelly before mitosis in mitotic cell cycle 

ADD Class: query_4_1;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins participating in Mitosis and any process inmedieatelly before mitosis in mitotic cell cycle";ADD oppl_query "participates_in some (inmediately_precedes some (CCO_P0000017 or (part_of some (inmediately_precedes some CCO_P0000017)))) and participates_in some (CCO_P0000017 or part_of some CCO_P0000017)";

SELECT subClassOf participates_in some (inmediately_precedes some (CCO_P0000017 or (part_of some (inmediately_precedes some CCO_P0000017)))) and participates_in some (CCO_P0000017 or part_of some CCO_P0000017);ADD subClassOf query_4_1;

# Query 4_2: Proteins participating in G2 and any process before G2 in meiotic cell cycle 

ADD Class: query_4_2;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins participating in G2 and any process before G2 in meiotic cell cycle";ADD oppl_query "participates_in some (precedes some (CCO_P0000326 or (part_of some (precedes some CCO_P0000326)))) and participates_in some (CCO_P0000326 or part_of some CCO_P0000326)";

SELECT subClassOf participates_in some (precedes some (CCO_P0000326 or (part_of some (precedes some CCO_P0000326)))) and participates_in some (CCO_P0000326 or part_of some CCO_P0000326);ADD subClassOf query_4_2;

# Query 4_3: Proteins participating in any process before G2 in meiotic cell cycle 

ADD Class: query_4_3;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins participating in any process before G2 in meiotic cell cycle";ADD oppl_query "participates_in some (precedes some (CCO_P0000326 or (part_of some (precedes some CCO_P0000326))))";

SELECT subClassOf participates_in some (precedes some (CCO_P0000326 or (part_of some (precedes some CCO_P0000326))));ADD subClassOf query_4_3;

# Query 5: Proteins interacting

ADD Class: query_5;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins interacting";ADD oppl_query "CCO_U0000005 and participates_in some CCO_Y0000001";

SELECT subClassOf CCO_U0000005 and participates_in some CCO_Y0000001;ADD subClassOf query_5; 

# Query 6: Proteins located in a known place

ADD Class: query_6;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins located in a known place";ADD oppl_query "CCO_U0000005 and (located_in some CCO_C0000200) or (located_in some (part_of some CCO_C0000200))";

SELECT subClassOf CCO_U0000005 and (located_in some CCO_C0000200) or (located_in some (part_of some CCO_C0000200));ADD subClassOf query_6; 

# Query 7: Proteins interacting in a known place

ADD Class: query_7;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins interacting in a known place";ADD oppl_query "CCO_U0000005 and ((located_in some CCO_C0000200) or (located_in some (part_of some CCO_C0000200))) and participates_in some CCO_Y0000001";

SELECT subClassOf CCO_U0000005 and ((located_in some CCO_C0000200) or (located_in some (part_of some CCO_C0000200))) and participates_in some CCO_Y0000001;ADD subClassOf query_7; 

# Query 8: Proteins interacting in the cytoplasm

ADD Class: query_8;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins interacting in the cytoplasm";ADD oppl_query "CCO_U0000005 and ((located_in some (part_of some CCO_C0000324)) or (located_in some CCO_C0000324)) and participates_in some CCO_Y0000001";

SELECT subClassOf CCO_U0000005 and ((located_in some (part_of some CCO_C0000324)) or (located_in some CCO_C0000324)) and participates_in some CCO_Y0000001;ADD subClassOf query_8; 

# Query 9: Proteins interacting in the cytoplasm and nucleus

ADD Class: query_9;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins interacting in the cytoplasm and nucleus";ADD oppl_query "CCO_U0000005 and ((located_in some (part_of some CCO_C0000323)) or (located_in some CCO_C0000323)) and ((located_in some (part_of some CCO_C0000252)) or (located_in some CCO_C0000252)) and participates_in some CCO_Y0000001";

SELECT subClassOf CCO_U0000005 and ((located_in some (part_of some CCO_C0000323)) or (located_in some CCO_C0000323)) and ((located_in some (part_of some CCO_C0000252)) or (located_in some CCO_C0000252)) and participates_in some CCO_Y0000001;ADD subClassOf query_9; 

# Query 10: Proteins interacting in the nucleus

ADD Class: query_10;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins interacting in the nucleus";ADD oppl_query "CCO_U0000005 and ((located_in some (part_of some CCO_C0000252)) or (located_in some CCO_C0000252)) and participates_in some CCO_Y0000001";

SELECT subClassOf CCO_U0000005 and ((located_in some (part_of some CCO_C0000252)) or (located_in some CCO_C0000252)) and participates_in some CCO_Y0000001;ADD subClassOf query_10;

# Query 11: Proteins located in the chloroplast

ADD Class: query_11;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins located in the chloroplast";ADD oppl_query "CCO_U0000005 and ((located_in some (part_of some CCO_C0000636)) or (located_in some CCO_C0000636))";

SELECT subClassOf CCO_U0000005 and ((located_in some (part_of some CCO_C0000636)) or (located_in some CCO_C0000636));ADD subClassOf query_11;

# Query 12: Proteins located in the membrane

ADD Class: query_12;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins located in the membrane";ADD oppl_query "CCO_U0000005 and ((located_in some (part_of some CCO_C0000766)) or (located_in some CCO_C0000766))";

SELECT subClassOf CCO_U0000005 and ((located_in some (part_of some CCO_C0000766)) or (located_in some CCO_C0000766));ADD subClassOf query_12;

# Query 13: Proteins located in the mitochondrion

ADD Class: query_13;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins located in the mitochondrion";ADD oppl_query "CCO_U0000005 and ((located_in some (part_of some CCO_C0000325)) or (located_in some CCO_C0000325))";

SELECT subClassOf CCO_U0000005 and ((located_in some (part_of some CCO_C0000325)) or (located_in some CCO_C0000325));ADD subClassOf query_13;

# Query 14: Proteins located in nucleus and cytoplasm: travelling?

ADD Class: query_14;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins located in nucleus and cytoplasm: travelling?";ADD oppl_query "CCO_U0000005 and (located_in some (part_of some CCO_C0000323 or CCO_C0000323)) and (located_in some (part_of some CCO_C0000252 or CCO_C0000252))";

SELECT subClassOf CCO_U0000005 and (located_in some (part_of some CCO_C0000323 or CCO_C0000323)) and (located_in some (part_of some CCO_C0000252 or CCO_C0000252));ADD subClassOf query_14;