# -*- coding: utf-8 -*-
# copyright 2012 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr -- mailto:contact@logilab.fr
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 2.1 of the License, or (at your option)
# any later version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License along
# with this program. If not, see <http://www.gnu.org/licenses/>.
"""cubicweb-diseasome schema"""
from yams.buildobjs import EntityType, SubjectRelation, String, Int
class Disease(EntityType):
"""Disease entity definition.
A Disease entity is characterized by several attributes which are
defined by URIs:
- a name, which we define as a CubicWeb / Yams String object
- a label, also defined as a Yams String
- a class degree, defined as a Yams Int (that is, an integer)
- a degree, also defined as a Yams Int
- size, also defined as an Int
- classes, defined as a set containing zero, one or several objects
identified by their URIs, that is, objects of type ``ExternalUri``
- subtype_of, defined as a set containing zero, one or several
objects of type ``Disease``
- associated_genes, defined as a set containing zero, one or several
objects of type ``Gene``, that is, of genes associated to the
disease
- possible_drugs, defined as a set containing zero, one or several
objects, identified by their URIs, that is, of type ``ExternalUri``
- omim and omim_page are identifiers in the OMIM (Online Mendelian
Inheritance in Man) database, which contains an inventory of "human
genes and genetic phenotypes"
(see http://http://www.ncbi.nlm.nih.gov/omim). Given that a disease
only has unique omim and omim_page identifiers, when it has them,
these attributes have been defined through relations such that
for each disease there is at most one omim and one omim_page.
Each such identifier is defined through a URI, that is, through
an ``ExternalUri`` entity.
That is, these relations are of cardinality "?*". For optimization
purposes, one might be tempted to defined them as inlined, by setting
the ``inlined`` keyword argument to ``True``.
- chromosomal_location is also defined through a relation of
cardinality "?*", since any disease has at most one chromosomal
location associated to it.
- same_as is also defined through a URI, and hence through a
relation having ``ExternalUri`` entities as objects.
For more information on this data set and the data set itself,
please consult http://datahub.io/dataset/fu-berlin-diseasome.
"""
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/name
name = String(maxsize=256, fulltextindexed=True)
# Corresponds to http://www.w3.org/2000/01/rdf-schema#label
label = String(maxsize=512, fulltextindexed=True)
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/classDegree
class_degree = Int()
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/degree
degree = Int()
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/size
size = Int()
#Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/class
classes = SubjectRelation('ExternalUri', cardinality='**')
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/diseaseSubtypeOf
subtype_of = SubjectRelation('Disease', cardinality='**')
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/associatedGene
associated_genes = SubjectRelation('Gene', cardinality='**')
#Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/possibleDrug
possible_drugs = SubjectRelation('ExternalUri', cardinality='**')
#Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/omim
omim = SubjectRelation('ExternalUri', cardinality='?*', inlined=True)
#Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/omimPage
omim_page = SubjectRelation('ExternalUri', cardinality='?*', inlined=True)
#Corresponds to 'http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/chromosomalLocation'
chromosomal_location = SubjectRelation('ExternalUri', cardinality='?*',
inlined=True)
#Corresponds to http://www.w3.org/2002/07/owl#sameAs
same_as = SubjectRelation('ExternalUri', cardinality='**')
class Gene(EntityType):
"""Gene entity defintion.
A gene is characterized by the following attributes:
- label, defined through a Yams String.
- bio2rdf_symbol, also defined as a Yams String, since it is
just an identifier.
- gene_id is a URI identifying a gene, hence it is defined
as a relation with an ``ExternalUri`` object.
- a pair of unique identifiers in the HUGO Gene Nomenclature
Committee (http://http://www.genenames.org/). They are defined
as ``ExternalUri`` entities as well.
- same_as is also defined through a URI, and hence through a
relation having ``ExternalUri`` entities as objects.
"""
# Corresponds to http://www.w3.org/2000/01/rdf-schema#label
label = String(maxsize=512, fulltextindexed=True)
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/geneId
gene_id = SubjectRelation('ExternalUri', cardinality='**')
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/hgncId
hgnc_id = SubjectRelation('ExternalUri', cardinality='**')
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/hgncIdPage
hgnc_page = SubjectRelation('ExternalUri', cardinality='**')
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
# diseasome/bio2rdfSymbol
bio2rdf_symbol = String(maxsize=64, fulltextindexed=True)
#Corresponds to http://www.w3.org/2002/07/owl#sameAs
same_as = SubjectRelation('ExternalUri', cardinality='**')