author | Sylvain Thénault <sylvain.thenault@logilab.fr> |
Tue, 07 Jan 2014 16:19:18 +0100 | |
changeset 9366 | bcbc92223b35 |
parent 8930 | 6a02be304486 |
child 9702 | c2108dbfb508 |
permissions | -rw-r--r-- |
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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 |
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# |
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# 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 |
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# Software Foundation, either version 2.1 of the License, or (at your option) |
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# any later version. |
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# |
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# 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 |
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# details. |
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# |
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# 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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class Disease(EntityType): |
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"""Disease entity definition. |
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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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- 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 an 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 an URI, and hence through a |
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relation having ``ExternalUri`` entities as objects. |
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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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103 |
|
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class Gene(EntityType): |
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"""Gene entity defintion. |
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106 |
|
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A gene is characterized by the following attributes: |
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108 |
|
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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 an 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 an 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='**') |