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