|
1 # -*- coding: utf-8 -*- |
|
2 # copyright 2012 LOGILAB S.A. (Paris, FRANCE), all rights reserved. |
|
3 # contact http://www.logilab.fr -- mailto:contact@logilab.fr |
|
4 # |
|
5 # This program is free software: you can redistribute it and/or modify it under |
|
6 # the terms of the GNU Lesser General Public License as published by the Free |
|
7 # Software Foundation, either version 2.1 of the License, or (at your option) |
|
8 # any later version. |
|
9 # |
|
10 # This program is distributed in the hope that it will be useful, but WITHOUT |
|
11 # ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
|
12 # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more |
|
13 # details. |
|
14 # |
|
15 # You should have received a copy of the GNU Lesser General Public License along |
|
16 # with this program. If not, see <http://www.gnu.org/licenses/>. |
|
17 |
|
18 """cubicweb-diseasome schema""" |
|
19 |
|
20 from yams.buildobjs import EntityType, SubjectRelation, String, Int |
|
21 from cubicweb.schemas.base import ExternalUri |
|
22 |
|
23 |
|
24 class Disease(EntityType): |
|
25 """Disease entity definition. |
|
26 |
|
27 A Disease entity is characterized by several attributes which are |
|
28 defined by URIs: |
|
29 |
|
30 - a name, which we define as a CubicWeb / Yams String object |
|
31 - a label, also defined as a Yams String |
|
32 - a class degree, defined as a Yams Int (that is, an integer) |
|
33 - a degree, also defined as a Yams Int |
|
34 - size, also defined as an Int |
|
35 - classes, defined as a set containing zero, one or several objects |
|
36 identified by their URIs, that is, objects of type ``ExternalUri`` |
|
37 - subtype_of, defined as a set containing zero, one or several |
|
38 objects of type ``Disease`` |
|
39 - associated_genes, defined as a set containing zero, one or several |
|
40 objects of type ``Gene``, that is, of genes associated to the |
|
41 disease |
|
42 - possible_drugs, defined as a set containing zero, one or several |
|
43 objects, identified by their URIs, that is, of type ``ExternalUri`` |
|
44 - omim and omim_page are identifiers in the OMIM (Online Mendelian |
|
45 Inheritance in Man) database, which contains an inventory of "human |
|
46 genes and genetic phenotypes" |
|
47 (see http://http://www.ncbi.nlm.nih.gov/omim). Given that a disease |
|
48 only has unique omim and omim_page identifiers, when it has them, |
|
49 these attributes have been defined through relations such that |
|
50 for each disease there is at most one omim and one omim_page. |
|
51 Each such identifier is defined through an URI, that is, through |
|
52 an ``ExternalUri`` entity. |
|
53 That is, these relations are of cardinality "?*". For optimization |
|
54 purposes, one might be tempted to defined them as inlined, by setting |
|
55 the ``inlined`` keyword argument to ``True``. |
|
56 - chromosomal_location is also defined through a relation of |
|
57 cardinality "?*", since any disease has at most one chromosomal |
|
58 location associated to it. |
|
59 - same_as is also defined through an URI, and hence through a |
|
60 relation having ``ExternalUri`` entities as objects. |
|
61 |
|
62 For more information on this data set and the data set itself, |
|
63 please consult http://datahub.io/dataset/fu-berlin-diseasome. |
|
64 """ |
|
65 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
66 # diseasome/name |
|
67 name = String(maxsize=256, fulltextindexed=True) |
|
68 # Corresponds to http://www.w3.org/2000/01/rdf-schema#label |
|
69 label = String(maxsize=512, fulltextindexed=True) |
|
70 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
71 # diseasome/classDegree |
|
72 class_degree = Int() |
|
73 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
74 # diseasome/degree |
|
75 degree = Int() |
|
76 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
77 # diseasome/size |
|
78 size = Int() |
|
79 #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
80 # diseasome/class |
|
81 classes = SubjectRelation('ExternalUri', cardinality='**') |
|
82 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
83 # diseasome/diseaseSubtypeOf |
|
84 subtype_of = SubjectRelation('Disease', cardinality='**') |
|
85 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
86 # diseasome/associatedGene |
|
87 associated_genes = SubjectRelation('Gene', cardinality='**') |
|
88 #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
89 # diseasome/possibleDrug |
|
90 possible_drugs = SubjectRelation('ExternalUri', cardinality='**') |
|
91 #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
92 # diseasome/omim |
|
93 omim = SubjectRelation('ExternalUri', cardinality='?*', inlined=True) |
|
94 #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
95 # diseasome/omimPage |
|
96 omim_page = SubjectRelation('ExternalUri', cardinality='?*', inlined=True) |
|
97 #Corresponds to 'http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
98 # diseasome/chromosomalLocation' |
|
99 chromosomal_location = SubjectRelation('ExternalUri', cardinality='?*', |
|
100 inlined=True) |
|
101 #Corresponds to http://www.w3.org/2002/07/owl#sameAs |
|
102 same_as = SubjectRelation('ExternalUri', cardinality='**') |
|
103 |
|
104 |
|
105 class Gene(EntityType): |
|
106 """Gene entity defintion. |
|
107 |
|
108 A gene is characterized by the following attributes: |
|
109 |
|
110 - label, defined through a Yams String. |
|
111 - bio2rdf_symbol, also defined as a Yams String, since it is |
|
112 just an identifier. |
|
113 - gene_id is an URI identifying a gene, hence it is defined |
|
114 as a relation with an ``ExternalUri`` object. |
|
115 - a pair of unique identifiers in the HUGO Gene Nomenclature |
|
116 Committee (http://http://www.genenames.org/). They are defined |
|
117 as ``ExternalUri`` entities as well. |
|
118 - same_as is also defined through an URI, and hence through a |
|
119 relation having ``ExternalUri`` entities as objects. |
|
120 """ |
|
121 # Corresponds to http://www.w3.org/2000/01/rdf-schema#label |
|
122 label = String(maxsize=512, fulltextindexed=True) |
|
123 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
124 # diseasome/geneId |
|
125 gene_id = SubjectRelation('ExternalUri', cardinality='**') |
|
126 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
127 # diseasome/hgncId |
|
128 hgnc_id = SubjectRelation('ExternalUri', cardinality='**') |
|
129 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
130 # diseasome/hgncIdPage |
|
131 hgnc_page = SubjectRelation('ExternalUri', cardinality='**') |
|
132 # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
|
133 # diseasome/bio2rdfSymbol |
|
134 bio2rdf_symbol = String(maxsize=64, fulltextindexed=True) |
|
135 #Corresponds to http://www.w3.org/2002/07/owl#sameAs |
|
136 same_as = SubjectRelation('ExternalUri', cardinality='**') |