ontology.gql

define

#
# Entities
#

gene sub entity
	plays annotatedEntity
	plays identified
	plays encoder
	plays interactingGene
	plays contained
	has geneId
    has locusTag
    has chromosome
    has location
    has description
    has type
    has symbol
    has fullName;
#    has otherDesignations
#    has nomenclatureStatus;

go sub entity
	plays functionalAnnotation
	has goId
	has name
	has namespace
	has definition
	has comment;

protein sub entity
	plays annotatedEntity
	plays contained
	plays identified
	plays encoded
	has name
	has fullName
	has alternativeName
	has sequence
	has sequenceLength
	has sequenceMass
	has proteinGene
	has function
	has proteinPathway
	has subunit
	has tissue
	has ptm
	has similarity;

pathway sub entity
	plays annotatedEntity
	plays container
	has pathwayId
	has name
	has disease
	has summation;

mirna sub entity
	plays precursor
	plays upRegulator
	plays downRegulator
	plays contained
	has accession
	has name
	has description
	has comment
	has sequence;
	
mirnaMature sub mirna
	plays mature
	plays mutated
	plays interactingMiRNA
	plays mirnaWithSNP
	has product
	has location;

mirnaSNP sub entity
	plays snp
	has snpId
	has chr
	has mirStart
	has mirEnd
	has lostNum
	has gainNum;
	
cancer sub entity
	plays upRegulated
	plays downRegulated
	plays byCancer
	has name;
	
proteinAccession sub entity
	plays identifier
	has accession;

geneName sub entity
	plays identifier
	has name;

interaction sub entity
	plays interacting
	has database
	has experiments
	has supportType;
	

#
# Relations
#

annotation sub relationship
	relates functionalAnnotation
	relates annotatedEntity
	has evidence
	has qualifier
	has category;

containing sub relationship
	relates container
	relates contained;
	
precursorOf sub relationship
	relates precursor
	relates mature;

regulation sub relationship is-abstract
	relates regulator
	relates regulated;

upRegulation sub regulation
	relates upRegulator
	relates upRegulated;

downRegulation sub regulation
	relates downRegulator
	relates downRegulated;

snpMutation sub relationship
	relates mutated
	relates snp;
	
entityReference sub relationship
	relates identifier
	relates identified;

encoding sub relationship
	relates encoder
	relates encoded;

interactionMiRNA sub relationship
	relates interactingMiRNA
	relates interacting;

interactionGene sub relationship
	relates interacting
	relates interactingGene;
	
matureWithSNPsByCancer sub relationship
	relates byCancer
	relates mirnaWithSNP;
	
	
#
# Roles
#

functionalAnnotation sub role;
annotatedEntity sub role;
container sub role;
contained sub role;
precursor sub role;
mature sub role;
mutated sub role;
snp sub role;

regulator sub role;
regulated sub role;
upRegulator sub regulator;
upRegulated sub regulated;
downRegulator sub regulator;
downRegulated sub regulated;

identifier sub role;
identified sub role;

encoder sub role;
encoded sub role;

interacting sub role;
interactingMiRNA sub role;
interactingGene sub role;

byCancer sub role;
mirnaWithSNP sub role;

#
# attributes
#

ID sub attribute datatype string is-abstract;

# common attributes
location sub attribute datatype string;
description sub attribute datatype string;
symbol sub attribute datatype string;
name sub attribute datatype string;
fullName sub attribute datatype string;
comment sub attribute datatype string;
accession sub attribute datatype string;

# gene
geneId sub ID;
locusTag sub attribute datatype string;
chromosome sub attribute datatype string;
type sub attribute datatype string;
# otherDesignations sub attribute datatype string;
# nomenclatureStatus sub attribute datatype string;

# go
goId sub ID;
namespace sub attribute datatype string;
definition sub attribute datatype string;

# protein
alternativeName sub name;
proteinGene sub attribute datatype string;
function sub attribute datatype string;
proteinPathway sub attribute datatype string;
subunit sub attribute datatype string;
tissue sub attribute datatype string;
ptm sub attribute datatype string;
similarity sub attribute datatype string;
sequenceLength sub attribute datatype long;
sequenceMass sub attribute datatype long;

# pathway
pathwayId sub ID;
disease sub attribute datatype string;
summation sub attribute datatype string;

# annotation
evidence sub attribute datatype string;
qualifier sub attribute datatype string;
category sub attribute datatype string;

# mirna
product sub attribute datatype string;
sequence sub attribute datatype string;

# mirnaSNP
snpId sub ID;
chr sub attribute datatype string;
mirStart sub attribute datatype long;
mirEnd sub attribute datatype long;
lostNum sub attribute datatype long;
gainNum sub attribute datatype long;

# interaction
database sub attribute datatype string;
experiments sub attribute datatype string;
supportType sub attribute datatype string;