author | Julien Cristau <julien.cristau@logilab.fr> |
Mon, 24 Nov 2014 17:43:29 +0100 | |
changeset 10047 | a1fde2d343b6 |
parent 9702 | c2108dbfb508 |
permissions | -rw-r--r-- |
8836
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
1 |
# -*- coding: utf-8 -*- |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
2 |
# copyright 2012 LOGILAB S.A. (Paris, FRANCE), all rights reserved. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
3 |
# contact http://www.logilab.fr -- mailto:contact@logilab.fr |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
4 |
# |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
5 |
# This program is free software: you can redistribute it and/or modify it under |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
6 |
# the terms of the GNU Lesser General Public License as published by the Free |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
7 |
# Software Foundation, either version 2.1 of the License, or (at your option) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
8 |
# any later version. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
9 |
# |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
10 |
# This program is distributed in the hope that it will be useful, but WITHOUT |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
11 |
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
12 |
# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
13 |
# details. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
14 |
# |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
15 |
# You should have received a copy of the GNU Lesser General Public License along |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
16 |
# with this program. If not, see <http://www.gnu.org/licenses/>. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
17 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
18 |
"""cubicweb-diseasome schema""" |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
19 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
20 |
from yams.buildobjs import EntityType, SubjectRelation, String, Int |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
21 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
22 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
23 |
class Disease(EntityType): |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
24 |
"""Disease entity definition. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
25 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
26 |
A Disease entity is characterized by several attributes which are |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
27 |
defined by URIs: |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
28 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
29 |
- a name, which we define as a CubicWeb / Yams String object |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
30 |
- a label, also defined as a Yams String |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
31 |
- a class degree, defined as a Yams Int (that is, an integer) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
32 |
- a degree, also defined as a Yams Int |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
33 |
- size, also defined as an Int |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
34 |
- classes, defined as a set containing zero, one or several objects |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
35 |
identified by their URIs, that is, objects of type ``ExternalUri`` |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
36 |
- subtype_of, defined as a set containing zero, one or several |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
37 |
objects of type ``Disease`` |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
38 |
- associated_genes, defined as a set containing zero, one or several |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
39 |
objects of type ``Gene``, that is, of genes associated to the |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
40 |
disease |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
41 |
- possible_drugs, defined as a set containing zero, one or several |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
42 |
objects, identified by their URIs, that is, of type ``ExternalUri`` |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
43 |
- omim and omim_page are identifiers in the OMIM (Online Mendelian |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
44 |
Inheritance in Man) database, which contains an inventory of "human |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
45 |
genes and genetic phenotypes" |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
46 |
(see http://http://www.ncbi.nlm.nih.gov/omim). Given that a disease |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
47 |
only has unique omim and omim_page identifiers, when it has them, |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
48 |
these attributes have been defined through relations such that |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
49 |
for each disease there is at most one omim and one omim_page. |
9702 | 50 |
Each such identifier is defined through a URI, that is, through |
8836
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
51 |
an ``ExternalUri`` entity. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
52 |
That is, these relations are of cardinality "?*". For optimization |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
53 |
purposes, one might be tempted to defined them as inlined, by setting |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
54 |
the ``inlined`` keyword argument to ``True``. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
55 |
- chromosomal_location is also defined through a relation of |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
56 |
cardinality "?*", since any disease has at most one chromosomal |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
57 |
location associated to it. |
9702 | 58 |
- same_as is also defined through a URI, and hence through a |
8836
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
59 |
relation having ``ExternalUri`` entities as objects. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
60 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
61 |
For more information on this data set and the data set itself, |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
62 |
please consult http://datahub.io/dataset/fu-berlin-diseasome. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
63 |
""" |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
64 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
65 |
# diseasome/name |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
66 |
name = String(maxsize=256, fulltextindexed=True) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
67 |
# Corresponds to http://www.w3.org/2000/01/rdf-schema#label |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
68 |
label = String(maxsize=512, fulltextindexed=True) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
69 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
70 |
# diseasome/classDegree |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
71 |
class_degree = Int() |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
72 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
73 |
# diseasome/degree |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
74 |
degree = Int() |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
75 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
76 |
# diseasome/size |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
77 |
size = Int() |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
78 |
#Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
79 |
# diseasome/class |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
80 |
classes = SubjectRelation('ExternalUri', cardinality='**') |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
81 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
82 |
# diseasome/diseaseSubtypeOf |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
83 |
subtype_of = SubjectRelation('Disease', cardinality='**') |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
84 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
85 |
# diseasome/associatedGene |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
86 |
associated_genes = SubjectRelation('Gene', cardinality='**') |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
87 |
#Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
88 |
# diseasome/possibleDrug |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
89 |
possible_drugs = SubjectRelation('ExternalUri', cardinality='**') |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
90 |
#Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
91 |
# diseasome/omim |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
92 |
omim = SubjectRelation('ExternalUri', cardinality='?*', inlined=True) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
93 |
#Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
94 |
# diseasome/omimPage |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
95 |
omim_page = SubjectRelation('ExternalUri', cardinality='?*', inlined=True) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
96 |
#Corresponds to 'http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
97 |
# diseasome/chromosomalLocation' |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
98 |
chromosomal_location = SubjectRelation('ExternalUri', cardinality='?*', |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
99 |
inlined=True) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
100 |
#Corresponds to http://www.w3.org/2002/07/owl#sameAs |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
101 |
same_as = SubjectRelation('ExternalUri', cardinality='**') |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
102 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
103 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
104 |
class Gene(EntityType): |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
105 |
"""Gene entity defintion. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
106 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
107 |
A gene is characterized by the following attributes: |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
108 |
|
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
109 |
- label, defined through a Yams String. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
110 |
- bio2rdf_symbol, also defined as a Yams String, since it is |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
111 |
just an identifier. |
9702 | 112 |
- gene_id is a URI identifying a gene, hence it is defined |
8836
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
113 |
as a relation with an ``ExternalUri`` object. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
114 |
- a pair of unique identifiers in the HUGO Gene Nomenclature |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
115 |
Committee (http://http://www.genenames.org/). They are defined |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
116 |
as ``ExternalUri`` entities as well. |
9702 | 117 |
- same_as is also defined through a URI, and hence through a |
8836
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
118 |
relation having ``ExternalUri`` entities as objects. |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
119 |
""" |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
120 |
# Corresponds to http://www.w3.org/2000/01/rdf-schema#label |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
121 |
label = String(maxsize=512, fulltextindexed=True) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
122 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
123 |
# diseasome/geneId |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
124 |
gene_id = SubjectRelation('ExternalUri', cardinality='**') |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
125 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
126 |
# diseasome/hgncId |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
127 |
hgnc_id = SubjectRelation('ExternalUri', cardinality='**') |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
128 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
129 |
# diseasome/hgncIdPage |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
130 |
hgnc_page = SubjectRelation('ExternalUri', cardinality='**') |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
131 |
# Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/ |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
132 |
# diseasome/bio2rdfSymbol |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
133 |
bio2rdf_symbol = String(maxsize=64, fulltextindexed=True) |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
134 |
#Corresponds to http://www.w3.org/2002/07/owl#sameAs |
8a57802d40d3
[cubicweb/doc] Add tutorial on data import in CubicWeb.
Vladimir Popescu <vladimir.popescu@logilab.fr>
parents:
diff
changeset
|
135 |
same_as = SubjectRelation('ExternalUri', cardinality='**') |