line |
stmt |
bran |
cond |
sub |
pod |
time |
code |
1
|
|
|
|
|
|
|
#!/usr/bin/perl |
2
|
|
|
|
|
|
|
# |
3
|
|
|
|
|
|
|
# @File Interface.pm.pm |
4
|
|
|
|
|
|
|
# @Author andriy |
5
|
|
|
|
|
|
|
# @Created Aug 1, 2016 10:33:50 AM |
6
|
|
|
|
|
|
|
# |
7
|
|
|
|
|
|
|
|
8
|
|
|
|
|
|
|
=head1 NAME |
9
|
|
|
|
|
|
|
SemRep::Interface - A suite of Perl modules that utilize path information |
10
|
|
|
|
|
|
|
present in the Semantic Medline Database in order to calculate the semantic |
11
|
|
|
|
|
|
|
association between two concepts in the UMLS. |
12
|
|
|
|
|
|
|
|
13
|
|
|
|
|
|
|
|
14
|
|
|
|
|
|
|
=head1 INSTALL |
15
|
|
|
|
|
|
|
To install the module, run the following magic commands: |
16
|
|
|
|
|
|
|
|
17
|
|
|
|
|
|
|
perl Makefile.PL |
18
|
|
|
|
|
|
|
make |
19
|
|
|
|
|
|
|
make test |
20
|
|
|
|
|
|
|
make install |
21
|
|
|
|
|
|
|
|
22
|
|
|
|
|
|
|
This will install the module in the standard location. You will, most |
23
|
|
|
|
|
|
|
probably, require root privileges to install in standard system |
24
|
|
|
|
|
|
|
directories. To install in a non-standard directory, specify a prefix |
25
|
|
|
|
|
|
|
during the 'perl Makefile.PL' stage as: |
26
|
|
|
|
|
|
|
|
27
|
|
|
|
|
|
|
perl Makefile.PL PREFIX=/home/sid |
28
|
|
|
|
|
|
|
|
29
|
|
|
|
|
|
|
It is possible to modify other parameters during installation. The |
30
|
|
|
|
|
|
|
details of these can be found in the ExtUtils::MakeMaker |
31
|
|
|
|
|
|
|
documentation. However, it is highly recommended not messing around |
32
|
|
|
|
|
|
|
with other parameters, unless you know what you're doing. |
33
|
|
|
|
|
|
|
|
34
|
|
|
|
|
|
|
=head1 DESCRIPTION |
35
|
|
|
|
|
|
|
This package provides a Perl interface to |
36
|
|
|
|
|
|
|
|
37
|
|
|
|
|
|
|
=head1 DATABASE SETUP |
38
|
|
|
|
|
|
|
The interface assumes you have installed the Semantic Medline Database onto your |
39
|
|
|
|
|
|
|
MYSQL server and in addition, followed the steps present in the INSTALL file to |
40
|
|
|
|
|
|
|
create the appropriate auxilary tables in order to speed up program runtime. |
41
|
|
|
|
|
|
|
The name of the database can be passed through during program runtime but will |
42
|
|
|
|
|
|
|
default to 'SemMedDB' if no parameter is given. |
43
|
|
|
|
|
|
|
|
44
|
|
|
|
|
|
|
The SemMedDB database must contain the following tables: |
45
|
|
|
|
|
|
|
1. CONCEPT |
46
|
|
|
|
|
|
|
2. CONCEPT_SEMTYPE |
47
|
|
|
|
|
|
|
3. PREDICATION_ARGUMENT |
48
|
|
|
|
|
|
|
4. PREDICATION |
49
|
|
|
|
|
|
|
5. SENTENCE_PREDICATION |
50
|
|
|
|
|
|
|
6. SENTENCE |
51
|
|
|
|
|
|
|
7. CITATIONS |
52
|
|
|
|
|
|
|
8. PREDICATION_AGGREGATE |
53
|
|
|
|
|
|
|
9. DISTINCT_PREDICATION_AGGREGATE * |
54
|
|
|
|
|
|
|
|
55
|
|
|
|
|
|
|
*The table 'DISTINCT_PREDICATION_AGGREGATE' does not install alongside the |
56
|
|
|
|
|
|
|
Semantic Medline Database via the .SQL file provided on their website. Steps |
57
|
|
|
|
|
|
|
must be followed in the INSTALL file to set-up this table. Failure to do so |
58
|
|
|
|
|
|
|
will cause fatal errors at runtime. |
59
|
|
|
|
|
|
|
|
60
|
|
|
|
|
|
|
A script inside the INSTALL file details the steps needed to generate |
61
|
|
|
|
|
|
|
the required auxilary tables. These steps are to be done following the Semantic |
62
|
|
|
|
|
|
|
Medline Database install and may take up to several days to complete due to the |
63
|
|
|
|
|
|
|
size of the database. |
64
|
|
|
|
|
|
|
|
65
|
|
|
|
|
|
|
=head1 INITIALIZING THE MODULE |
66
|
|
|
|
|
|
|
|
67
|
|
|
|
|
|
|
To create an instance of the interface module, using default values |
68
|
|
|
|
|
|
|
for all configuration options: |
69
|
|
|
|
|
|
|
|
70
|
|
|
|
|
|
|
use SemRep::Interface; |
71
|
|
|
|
|
|
|
my $interface = new SemRep::Interface(); |
72
|
|
|
|
|
|
|
|
73
|
|
|
|
|
|
|
=cut |
74
|
|
|
|
|
|
|
|
75
|
|
|
|
|
|
|
package SemMed::Interface; |
76
|
1
|
|
|
1
|
|
14482
|
use strict; |
|
1
|
|
|
|
|
2
|
|
|
1
|
|
|
|
|
27
|
|
77
|
1
|
|
|
1
|
|
3
|
use warnings; |
|
1
|
|
|
|
|
2
|
|
|
1
|
|
|
|
|
25
|
|
78
|
1
|
|
|
1
|
|
356
|
use SemMed::Interface::GraphTraversal; |
|
0
|
|
|
|
|
|
|
|
0
|
|
|
|
|
|
|
79
|
|
|
|
|
|
|
use SemMed::Interface::DataAccess; |
80
|
|
|
|
|
|
|
|
81
|
|
|
|
|
|
|
|
82
|
|
|
|
|
|
|
use vars qw($VERSION); |
83
|
|
|
|
|
|
|
|
84
|
|
|
|
|
|
|
$VERSION = '0.01'; |
85
|
|
|
|
|
|
|
|
86
|
|
|
|
|
|
|
my $connection = ""; |
87
|
|
|
|
|
|
|
my $gt = ""; |
88
|
|
|
|
|
|
|
|
89
|
|
|
|
|
|
|
my @includedPredicates= (); #only this predicates will be used in the traversal |
90
|
|
|
|
|
|
|
my @excludedPredicates = (); #these predicates will be excluded in the traversal |
91
|
|
|
|
|
|
|
|
92
|
|
|
|
|
|
|
# method to create a new SemRep::Interface object |
93
|
|
|
|
|
|
|
# input : $SemMedLoginParams <- reference to hash containing SemMed login parameter |
94
|
|
|
|
|
|
|
# $AssociationLoginParams <- reference to hash containing the UMLS::Association login parameters |
95
|
|
|
|
|
|
|
# output: |
96
|
|
|
|
|
|
|
sub new { |
97
|
|
|
|
|
|
|
|
98
|
|
|
|
|
|
|
my $self = {}; |
99
|
|
|
|
|
|
|
my $class = shift; |
100
|
|
|
|
|
|
|
my $SemMedLoginParams = shift; #hash containing the SemMed login parameters |
101
|
|
|
|
|
|
|
my $AssociationLoginParams = shift; #hash containing the UMLS::Association login parameters |
102
|
|
|
|
|
|
|
bless($self, $class); |
103
|
|
|
|
|
|
|
|
104
|
|
|
|
|
|
|
$connection = new DataAccess($SemMedLoginParams, $AssociationLoginParams); |
105
|
|
|
|
|
|
|
$gt = new GraphTraversal($connection); |
106
|
|
|
|
|
|
|
|
107
|
|
|
|
|
|
|
return $self; |
108
|
|
|
|
|
|
|
} |
109
|
|
|
|
|
|
|
|
110
|
|
|
|
|
|
|
####################################### |
111
|
|
|
|
|
|
|
|
112
|
|
|
|
|
|
|
=head3 findPathLength |
113
|
|
|
|
|
|
|
|
114
|
|
|
|
|
|
|
description: |
115
|
|
|
|
|
|
|
|
116
|
|
|
|
|
|
|
Utilizes a breadth first search to find the path length from a source_concept to a destination_concept |
117
|
|
|
|
|
|
|
|
118
|
|
|
|
|
|
|
input: |
119
|
|
|
|
|
|
|
|
120
|
|
|
|
|
|
|
$source_concept <- string containing the concept id of the cui to start seraching from |
121
|
|
|
|
|
|
|
$destination_concept <- string containing the concept id you are searching for |
122
|
|
|
|
|
|
|
|
123
|
|
|
|
|
|
|
output: |
124
|
|
|
|
|
|
|
|
125
|
|
|
|
|
|
|
length of path <- Non-negative Integer indicating length of path between the two concepts |
126
|
|
|
|
|
|
|
|
127
|
|
|
|
|
|
|
example: |
128
|
|
|
|
|
|
|
|
129
|
|
|
|
|
|
|
#finds path length between Heart and Myocardial Infarction |
130
|
|
|
|
|
|
|
use SemRep::Interface; |
131
|
|
|
|
|
|
|
my $interface = new SemRep::Interface(); |
132
|
|
|
|
|
|
|
|
133
|
|
|
|
|
|
|
my $pathlength = $interface->findPathLength("C0018787", "C0027061"); |
134
|
|
|
|
|
|
|
|
135
|
|
|
|
|
|
|
|
136
|
|
|
|
|
|
|
=cut |
137
|
|
|
|
|
|
|
sub findPathLength{ |
138
|
|
|
|
|
|
|
|
139
|
|
|
|
|
|
|
my $self = shift; |
140
|
|
|
|
|
|
|
my $source_cui = shift; |
141
|
|
|
|
|
|
|
my $destination_cui = shift; |
142
|
|
|
|
|
|
|
return $gt->findPath($source_cui, $destination_cui, \@includedPredicates, \@excludedPredicates); |
143
|
|
|
|
|
|
|
|
144
|
|
|
|
|
|
|
} |
145
|
|
|
|
|
|
|
|
146
|
|
|
|
|
|
|
####################################### |
147
|
|
|
|
|
|
|
|
148
|
|
|
|
|
|
|
=head3 findPathSCore |
149
|
|
|
|
|
|
|
|
150
|
|
|
|
|
|
|
description: |
151
|
|
|
|
|
|
|
|
152
|
|
|
|
|
|
|
Function utilizing a breadth first search along with UMLS::Association to find the aggregate association score |
153
|
|
|
|
|
|
|
along the path between source_concept and destination_concept |
154
|
|
|
|
|
|
|
|
155
|
|
|
|
|
|
|
input: |
156
|
|
|
|
|
|
|
|
157
|
|
|
|
|
|
|
$source_concept <- string containing the concept id of the cui to start seraching from |
158
|
|
|
|
|
|
|
$destination_concept <- string containing the concept id you are searching for |
159
|
|
|
|
|
|
|
$measure <- string containing the UMLS::Association statistic measure to aggregate along paths. |
160
|
|
|
|
|
|
|
|
161
|
|
|
|
|
|
|
output: |
162
|
|
|
|
|
|
|
|
163
|
|
|
|
|
|
|
Aggregate association score <- Non-negative float indicating the aggregate path score |
164
|
|
|
|
|
|
|
|
165
|
|
|
|
|
|
|
example: |
166
|
|
|
|
|
|
|
|
167
|
|
|
|
|
|
|
#finds aggregate association score between Heart and Myocardial Infarction |
168
|
|
|
|
|
|
|
use SemRep::Interface; |
169
|
|
|
|
|
|
|
my $interface = new SemRep::Interface(); |
170
|
|
|
|
|
|
|
|
171
|
|
|
|
|
|
|
my $score = $interface->findPathLength("C0018787", "C0027061", "tscore"); |
172
|
|
|
|
|
|
|
|
173
|
|
|
|
|
|
|
|
174
|
|
|
|
|
|
|
=cut |
175
|
|
|
|
|
|
|
sub findPathScore{ |
176
|
|
|
|
|
|
|
|
177
|
|
|
|
|
|
|
my $self = shift; |
178
|
|
|
|
|
|
|
my $source_cui = shift; |
179
|
|
|
|
|
|
|
my $destination_cui = shift; |
180
|
|
|
|
|
|
|
my $measure = shift; |
181
|
|
|
|
|
|
|
return $gt->findPathScore($source_cui, $destination_cui, $measure, \@includedPredicates, \@excludedPredicates); |
182
|
|
|
|
|
|
|
|
183
|
|
|
|
|
|
|
} |
184
|
|
|
|
|
|
|
|
185
|
|
|
|
|
|
|
############################# |
186
|
|
|
|
|
|
|
|
187
|
|
|
|
|
|
|
|
188
|
|
|
|
|
|
|
sub addIncludedPredicates{ |
189
|
|
|
|
|
|
|
my $self = shift; |
190
|
|
|
|
|
|
|
my $predicates = shift; |
191
|
|
|
|
|
|
|
push @includedPredicates, @$predicates; |
192
|
|
|
|
|
|
|
} |
193
|
|
|
|
|
|
|
|
194
|
|
|
|
|
|
|
############################# |
195
|
|
|
|
|
|
|
|
196
|
|
|
|
|
|
|
sub clearIncludedPredicates{ |
197
|
|
|
|
|
|
|
my $self = shift; |
198
|
|
|
|
|
|
|
@includedPredicates = (); |
199
|
|
|
|
|
|
|
} |
200
|
|
|
|
|
|
|
|
201
|
|
|
|
|
|
|
############################# |
202
|
|
|
|
|
|
|
|
203
|
|
|
|
|
|
|
sub addExcludedPredicates{ |
204
|
|
|
|
|
|
|
my $self = shift; |
205
|
|
|
|
|
|
|
my $predicates = shift; |
206
|
|
|
|
|
|
|
push @excludedPredicates, @$predicates; |
207
|
|
|
|
|
|
|
} |
208
|
|
|
|
|
|
|
|
209
|
|
|
|
|
|
|
############################# |
210
|
|
|
|
|
|
|
|
211
|
|
|
|
|
|
|
sub clearExcludedPredicates{ |
212
|
|
|
|
|
|
|
my $self = shift; |
213
|
|
|
|
|
|
|
@excludedPredicates = (); |
214
|
|
|
|
|
|
|
} |
215
|
|
|
|
|
|
|
|
216
|
|
|
|
|
|
|
|
217
|
|
|
|
|
|
|
|
218
|
|
|
|
|
|
|
|
219
|
|
|
|
|
|
|
1; |
220
|
|
|
|
|
|
|
|
221
|
|
|
|
|
|
|
|
222
|
|
|
|
|
|
|
|
223
|
|
|
|
|
|
|
|
224
|
|
|
|
|
|
|
|
225
|
|
|
|
|
|
|
|
226
|
|
|
|
|
|
|
|
227
|
|
|
|
|
|
|
|
228
|
|
|
|
|
|
|
|
229
|
|
|
|
|
|
|
|
230
|
|
|
|
|
|
|
|
231
|
|
|
|
|
|
|
|
232
|
|
|
|
|
|
|
|