# TWEAKS ########################################################################################

# Remove instance_of from RO, as in OWL doesn't make any sense

REMOVE ObjectProperty: instance_of;

# Remove symmetric from interacts_with, as it screws up pellet

SELECT ObjectProperty: interacts_with;REMOVE symmetric;

# TODO: consistency flags 

# e.g.: Every entity belongs to one organism:
# belongs_to functional or belongs max 1 in root 

# Metadata 
# Create a "metadata" class for putting all the information that does not belong to the model.
# The easiest way of doing it is to move everything under owl:Thing to under metadata and
# then move entity back to the first level
# 
# ADD Class: metadata;
# 
# SELECT subClassOf Thing;ADD subClassOf metadata;REMOVE subClassOf Thing; 
# 
# SELECT Class: CCO_U0000000;REMOVE subClassOf metadata;
#
# TODO: this does not work because as a result of doing it metadata becomes equivalent to owl:Thing (???)

# MODELLING PROPER ############################################################################

# Sequence ODP ################################################################################
# Application of the Sequence ODP (http://odps.sourceforge.net/odp/html/Sequence.html).
# This ODP allows us to query the model for things happening after or before. we apply it to
# the cell cycle from GO

# Create ne properties: inmediately_precedes and inmediately_preceded_by
# TODO: reasoning didn't work with inverses and domains/ranges 

ADD ObjectProperty: inmediately_preceded_by;ADD functional;ADD subPropertyOf preceded_by;

ADD ObjectProperty: inmediately_precedes;ADD functional;ADD subPropertyOf precedes;

# Add restrictions: in theory we should just add "inmediately_precedes" and the reasoner should
# infer the inverse relationship but it does not seem to work with the superproperty of the inverse, i.e. 
# it does not infer that A is preceded_by B if B inmediately_precedes A, which is very important for queries

# TODO: Consistency: cell cycle phase p_by and preceds extacly 1 

# Meiotic cell cycle: G1 -> S -> G2 -> M

SELECT Class: CCO_P0000325;ADD subClassOf inmediately_precedes some CCO_P0000327;

SELECT Class: CCO_P0000327;ADD subClassOf inmediately_preceded_by some CCO_P0000325;ADD subClassOf inmediately_precedes some CCO_P0000326;

SELECT Class: CCO_P0000326;ADD subClassOf inmediately_preceded_by some CCO_P0000327;ADD subClassOf inmediately_precedes some CCO_P0000117;

SELECT Class: CCO_P0000117;ADD subClassOf inmediately_preceded_by some CCO_P0000326;

# Meiotic cell cycle: MI  -> cytokinesis -> MII  -> cytokinesis

SELECT Class: CCO_P0000118;ADD subClassOf inmediately_precedes some CCO_P0000113;

SELECT Class: CCO_P0000113;ADD subClassOf inmediately_preceded_by some CCO_P0000118;ADD subClassOf inmediately_precedes some CCO_P0000126;

SELECT Class: CCO_P0000126;ADD subClassOf inmediately_preceded_by some CCO_P0000113;ADD subClassOf inmediately_precedes some CCO_P0000114;

SELECT Class: CCO_P0000114;ADD subClassOf inmediately_preceded_by some CCO_P0000126;

# Meiotic cell cycle: prophaseI -> metaphase I -> anaphase I -> telophase I

SELECT Class: CCO_P0000119;ADD subClassOf inmediately_precedes some CCO_P0000123;

SELECT Class: CCO_P0000123;ADD subClassOf inmediately_preceded_by some CCO_P0000119;ADD subClassOf inmediately_precedes some CCO_P0000124;

SELECT Class: CCO_P0000124;ADD subClassOf inmediately_preceded_by some CCO_P0000123;ADD subClassOf inmediately_precedes some CCO_P0000125;

SELECT Class: CCO_P0000125;ADD subClassOf inmediately_preceded_by some CCO_P0000124;

# Meiotic cell cycle: prophaseII -> metaphase II -> anaphase II -> telophase II

SELECT Class: CCO_P0000127;ADD subClassOf inmediately_precedes some CCO_P0000128;

SELECT Class: CCO_P0000128;ADD subClassOf inmediately_preceded_by some CCO_P0000127;ADD subClassOf inmediately_precedes some CCO_P0000129;

SELECT Class: CCO_P0000129;ADD subClassOf inmediately_preceded_by some CCO_P0000128;ADD subClassOf inmediately_precedes some CCO_P0000130;

SELECT Class: CCO_P0000130;ADD subClassOf inmediately_preceded_by some CCO_P0000129;

# Meiotic cell cycle: leptotene -> zygotene -> pachytene -> diplotene -> diakinesis

SELECT Class: CCO_P0000033;ADD subClassOf inmediately_precedes some CCO_P0000034;

SELECT Class: CCO_P0000034;ADD subClassOf inmediately_preceded_by some CCO_P0000033;ADD subClassOf inmediately_precedes some CCO_P0000035;

SELECT Class: CCO_P0000035;ADD subClassOf inmediately_preceded_by some CCO_P0000034;ADD subClassOf inmediately_precedes some CCO_P0000036;

SELECT Class: CCO_P0000036;ADD subClassOf inmediately_preceded_by some CCO_P0000035;ADD subClassOf inmediately_precedes some CCO_P0000037;

SELECT Class: CCO_P0000037;ADD subClassOf inmediately_preceded_by some CCO_P0000036;

# A few tweaks for meiotic cell cycle

# diakinesis precedes metaphase I

SELECT Class: CCO_P0000037;ADD subClassOf inmediately_precedes some CCO_P0000123;

# telophase I precedes MII

SELECT Class: CCO_P0000125;ADD subClassOf inmediately_precedes some CCO_P0000126;

# Mitotic cell cycle: G1 -> G1/S ->S -> G2 -> G2/M -> M -> M/G1 

SELECT Class: CCO_P0000011;ADD subClassOf inmediately_precedes some CCO_P0000012;

SELECT Class: CCO_P0000012;ADD subClassOf inmediately_preceded_by some CCO_P0000011;ADD subClassOf inmediately_precedes some CCO_P0000014;

SELECT Class: CCO_P0000014;ADD subClassOf inmediately_preceded_by some CCO_P0000012;ADD subClassOf inmediately_precedes some CCO_P0000015;

SELECT Class: CCO_P0000015;ADD subClassOf inmediately_preceded_by some CCO_P0000014;ADD subClassOf inmediately_precedes some CCO_P0000016;

SELECT Class: CCO_P0000016;ADD subClassOf inmediately_preceded_by some CCO_P0000015;ADD subClassOf inmediately_precedes some CCO_P0000017;

SELECT Class: CCO_P0000017;ADD subClassOf inmediately_preceded_by some CCO_P0000016;ADD subClassOf inmediately_precedes some CCO_P0000031;

SELECT Class: CCO_P0000031;ADD subClassOf inmediately_preceded_by some CCO_P0000017;

# General cell cycle: G1 -> S -> G2 -> M

SELECT Class: CCO_P0000313;ADD subClassOf inmediately_precedes some CCO_P0000315;

SELECT Class: CCO_P0000315;ADD subClassOf inmediately_preceded_by some CCO_P0000313;ADD subClassOf inmediately_precedes some CCO_P0000314;

SELECT Class: CCO_P0000314;ADD subClassOf inmediately_preceded_by some CCO_P0000315;ADD subClassOf inmediately_precedes some CCO_P0000039;

SELECT Class: CCO_P0000039;ADD subClassOf inmediately_preceded_by some CCO_P0000314;

# mitotic prophase -> prometaphase -> metaphase -> metaphase/anaphase ->anaphase -> telophase -> cytokinesis after mitosis

SELECT Class: CCO_P0000018;ADD subClassOf inmediately_precedes some CCO_P0000032;

SELECT Class: CCO_P0000032;ADD subClassOf inmediately_preceded_by some CCO_P0000018;ADD subClassOf inmediately_precedes some CCO_P0000019;

SELECT Class: CCO_P0000019;ADD subClassOf inmediately_preceded_by some CCO_P0000032;ADD subClassOf inmediately_precedes some CCO_P0000102;

SELECT Class: CCO_P0000102;ADD subClassOf inmediately_preceded_by some CCO_P0000019;ADD subClassOf inmediately_precedes some CCO_P0000020;

SELECT Class: CCO_P0000020;ADD subClassOf inmediately_preceded_by some CCO_P0000102;ADD subClassOf inmediately_precedes some CCO_P0000023;

SELECT Class: CCO_P0000023;ADD subClassOf inmediately_preceded_by some CCO_P0000020;ADD subClassOf inmediately_precedes some CCO_P0000040;

SELECT Class: CCO_P0000040;ADD subClassOf inmediately_preceded_by some CCO_P0000020;