/
gen_data_queries.php
executable file
·461 lines (434 loc) · 25.2 KB
/
gen_data_queries.php
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
<?php
/**
* Copyright (C) 2010 DIYgenomics diygenomics.org
* Copyright (C) 2010 Melanie Swan mxswan@gmail
* Copyright (C) 2010 Marat Nepomnyashy maratbn@gmail
* All rights reserved.
*
* Module: gen_data_queries.php
*
* Description: This module is intended to contain all the utility
* functions involving database queries.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
* Neither the name of the DIYgenomics nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
* THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
/**
* Returns an array of conditions that the user can browse through.
*/
function queryArrayConditions() {
/* QUERY THE DATABASE - QUERY 3(CONDITIONS LIST)
Returns a list like this:
1 Alzheimer's disease
2 Atrial fibrillation
3 Breast cancer
4 Celiac disease
5 Colorectal cancer
6 Crohn's disease
7 Diabetes (type 1)
8 Diabetes (type 2)
9 Glaucoma
10 Heart attack
11 Lung cancer
12 Lupus
13 Macular degeneration
14 Multiple sclerosis
15 Obesity
16 Prostate cancer
17 Psoriasis
18 Restless legs syndrome
19 Rheumatoid arthritis
20 Ulcerative colitis
*/
$QueryConditions = mysql_query("SELECT 2_conditions.Primary, 2_conditions.Condition FROM 2_conditions;")
or die("<p>Unable to query a database table for conditions. Error code: " . mysql_errno() . "</p>");
//READ QUERY 3 RESULTS INTO ARRAY
// conditions holds rows {condition_ix, condition_name}
$Conditions = array();
while ($CondRow = mysql_fetch_array($QueryConditions)) {
$Conditions[] = $CondRow;
}
return $Conditions;
}
/**
* This function queries the database for the data associated with the specified health condition id, and
* returns that data in a hierarchial data structure.
*
* The data structure looks like this:
*
* {
* entities: ["Navigenics", "deCODEme"],
* entities_keyed: {
* "Navigenics": {
* "entity": "Navigenics",
* "entity_cond_url": "http://www.navigenics.com/demo/for_scientists/d/alzheimers_disease/"
* },
* "deCODEme": {
* "entity": "deCODEme",
* "entity_cond_url": "http://demo.decodeme.com/health-watch/details/ALZ"
* }
* },
* studies: ["17474819", "9343467", "19734902"],
* studies_keyed: {
* "17474819": {
* "number": 1,
* "pubmedid": "17474819",
* "url": "http://www.ncbi.nlm.nih.gov/pubmed/17474819",
* "citation": "Coon KD et al.; A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease; J ClinPsychiatry; 2007 Apr;68(4):613-8."
* },
* "9343467": {
* "number": 2,
* "pubmedid": "9343467",
* "url": "http://www.ncbi.nlm.nih.gov/pubmed/9343467",
* "citation": "Farrer LA et al.; Effects of age sex and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium; JAMA; 1997 Oct 22-29;278(16):1349-56."
* },
* "19734902": {
* "number": 3,
* "pubmedid": "19734902",
* "url": "http://www.ncbi.nlm.nih.gov/pubmed/19734902",
* "citation": "Harold D et al.; Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease; Nat Genet; 2009 Oct;41(10):1088-93."
* }
* },
* variants: ["rs11136000", "rs429358", "rs7412"],
* variants_keyed: {
* "rs11136000": {
* "dbSNP_normal": "C",
* "dbSNP_risk": "T",
* "dbSNP_sample_1": "T",
* "dbSNP_sample_2": "T",
* "gene": "CLU",
* "gene_url": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=CLU",
* "locus": "8p21.1",
* "locus_url": "http://www.ncbi.nlm.nih.gov/Omim/getmap.cgi?chromosome=8p21.1",
* "studies": ["19734902"],
* "studies_keyed": {
* "19734902": [
* "entities": [
* "deCODEme": true
* ]
* ]
* },
* "variant": "rs11136000",
* "variant_url": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs11136000"
* },
* "rs429358": {
* "dbSNP_normal": "C",
* "dbSNP_risk": "T",
* "dbSNP_sample_1": "",
* "dbSNP_sample_2": "",
* "gene": "APOE",
* "gene_url": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=APOE",
* "locus": "19q13.32",
* "locus_url": "http://www.ncbi.nlm.nih.gov/Omim/getmap.cgi?chromosome=19q13.32",
* "studies": ["17474819", "9343467"],
* "studies_keyed": {
* "17474819": [
* "entities": [
* "Navigenics": true
* ]
* ],
* "9343467": [
* "entities": [
* "deCODEme": true
* ]
* ]
* },
* "variant": "rs429358",
* "variant_url": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs429358"
* },
* "rs7412": {
* "dbSNP_normal": "C",
* "dbSNP_risk": "T",
* "dbSNP_sample_1": "T",
* "dbSNP_sample_2": "T",
* "gene": "APOE",
* "gene_url": "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=APOE",
* "locus": "19q13.32",
* "locus_url": "http://www.ncbi.nlm.nih.gov/Omim/getmap.cgi?chromosome=19q13.32",
* "studies": ["17474819", "9343467"],
* "studies_keyed": {
* "17474819": [
* "entities": [
* "Navigenics": true
* ]
* ],
* "9343467": [
* "entities": [
* "deCODEme": true
* ]
* ]
* },
* "variant": "rs7412",
* "variant_url": "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs7412"
* }
* }
* }
*/
function queryDataForCondition($idCondition) {
$strQueryStudiesInfo = "SELECT 1_studies.PMID,"
. " 1_studies.PMID_URL,"
. " 1_studies.Citation,"
. " 3_variants.Variant,"
. " 3_variants.Variant_URL,"
. " 3_variants.Locus,"
. " 3_variants.Locus_URL,"
. " 3_variants.Gene,"
. " 3_variants.Gene_URL,"
. " 3_variants.dbSNP_normal,"
. " 3_variants.dbSNP_risk,"
. " 3_variants.23andMe_1,"
. " 3_variants.23andMe_2,"
. " 3_variants.23andMe_normal,"
. " 3_variants.23andMe_risk,"
. " 3_variants.Rank,"
. " 4_entities.Entity"
. " FROM 1_studies"
. " JOIN 8_map_variant_condition_entity_study ON 1_studies.Primary = 8_map_variant_condition_entity_study.Study_index"
. " JOIN 3_variants ON 3_variants.Primary = 8_map_variant_condition_entity_study.Variant_index"
. " JOIN 4_entities ON 4_entities.Primary = 8_map_variant_condition_entity_study.Entity_index"
. " WHERE 8_map_variant_condition_entity_study.Condition_index = " . $idCondition
. " ORDER BY 1_studies.Citation";
$resultQueryStudiesInfo = mysql_query($strQueryStudiesInfo)
or die("<p>Unable to query the database for studies information. Error code: " . mysql_errno() . "</p>");
$mapDataCurrentCondition = array(
'entities' => array(),
'entities_keyed' => array(),
'studies' => array(),
'studies_keyed' => array(),
'variants' => array(),
'variants_keyed' => array());
while ($arrStudyInfo = mysql_fetch_array($resultQueryStudiesInfo)) {
$field_pubmedid = $arrStudyInfo[0];
$field_url = $arrStudyInfo[1];
$field_citation = $arrStudyInfo[2];
$field_variant = $arrStudyInfo[3];
$field_variant_url = $arrStudyInfo[4];
$field_locus = $arrStudyInfo[5];
$field_locus_url = $arrStudyInfo[6];
$field_gene = $arrStudyInfo[7];
$field_gene_url = $arrStudyInfo[8];
$field_dbSNP_normal = $arrStudyInfo[9];
$field_dbSNP_risk = $arrStudyInfo[10];
$field_23andMe_1 = $arrStudyInfo[11];
$field_23andMe_2 = $arrStudyInfo[12];
$field_23andMe_normal = $arrStudyInfo[13];
$field_23andMe_risk = $arrStudyInfo[14];
$field_rank = $arrStudyInfo[15];
$field_entity = $arrStudyInfo[16];
if (!$mapDataCurrentCondition['entities_keyed'][$field_entity]) {
$mapDataCurrentCondition['entities_keyed'][$field_entity] = array(
'entity' => $field_entity);
$mapDataCurrentCondition['entities'][] = $field_entity;
}
if (!$mapDataCurrentCondition['studies_keyed'][$field_pubmedid]) {
$mapDataCurrentCondition['studies'][] = $field_pubmedid;
$mapDataCurrentCondition['studies_keyed'][$field_pubmedid] = array(
'number' => count($mapDataCurrentCondition['studies']),
'pubmedid' => $field_pubmedid,
'url' => $field_url,
'citation' => $field_citation);
}
if (!$mapDataCurrentCondition['variants_keyed'][$field_variant]) {
$mapDataCurrentCondition['variants_keyed'][$field_variant] = array(
'gene' => $field_gene,
'gene_url' => $field_gene_url,
'locus' => $field_locus,
'locus_url' => $field_locus_url,
'studies' => array(),
'variant' => $field_variant,
'variant_url' => $field_variant_url,
'dbSNP_normal' => $field_dbSNP_normal,
'dbSNP_risk' => $field_dbSNP_risk,
'dbSNP_sample_1' => $field_23andMe_1,
'dbSNP_sample_2' => $field_23andMe_2,
'23andMe_normal' => $field_23andMe_normal,
'23andMe_risk' => $field_23andMe_risk,
'rank' => $field_rank);
$mapDataCurrentCondition['variants'][] = $field_variant;
}
if (!$mapDataCurrentCondition['variants_keyed'][$field_variant]['studies_keyed'][$field_pubmedid]) {
$mapDataCurrentCondition['variants_keyed'][$field_variant]['studies_keyed'][$field_pubmedid]
= array(
'entities' => array());
$mapDataCurrentCondition['variants_keyed'][$field_variant]['studies'][] = $field_pubmedid;
}
if (!$mapDataCurrentCondition['variants_keyed'][$field_variant]['studies_keyed'][$field_pubmedid]['entities'][$field_entity]) {
$mapDataCurrentCondition['variants_keyed'][$field_variant]['studies_keyed'][$field_pubmedid]['entities'][$field_entity]
= true;
}
}
//SORT BY LOCUS
usort(
$mapDataCurrentCondition['variants'],
function($strVariant1, $strVariant2) use ($mapDataCurrentCondition) {
$cmp = strnatcmp(
$mapDataCurrentCondition['variants_keyed'][$strVariant1]['locus'],
$mapDataCurrentCondition['variants_keyed'][$strVariant2]['locus']);
if ($cmp <> 0) return $cmp;
return strcmp($strVariant1, $strVariant2);
});
// Query the disease / condition URLs from the database:
$strQueryDiseaseURLs = "SELECT 4_entities.Entity, 6_map_entity_condition.URL"
. " FROM 6_map_entity_condition JOIN 4_entities"
. " WHERE Condition_index = " . $idCondition . " AND 6_map_entity_condition.Entity_index = 4_entities.Primary";
$resultQueryDiseaseURLs = mysql_query($strQueryDiseaseURLs)
or die("<p>Unable to query the database for conditions. Error code: " . mysql_errno() . "</p>");
// Process the query results into the current condition data:
while ($arrDiseaseURL = mysql_fetch_array($resultQueryDiseaseURLs)) {
$field_entity = $arrDiseaseURL[0];
$field_entity_cond_url = $arrDiseaseURL[1];
if ($mapDataCurrentCondition['entities_keyed'][$field_entity]) {
$mapDataCurrentCondition['entities_keyed'][$field_entity]['entity_cond_url'] = $field_entity_cond_url;
}
}
return $mapDataCurrentCondition;
}
/**
* Queries the database for the data containing all the information on all the conditions
* and their associated variants and related studies, and returns that data in a hierarchial
* data structure.
*
* The data structure looks like this:
*
* {
* conditions: [
* "Alzheimer's disease",
* "Atrial fibrillation",
* "Breast cancer",
* "Celiac disease",
* "Colorectal cancer",
* "Crohn"s disease",
* "Diabetes (type 1)",
* "Diabetes (type 2)",
* "Glaucoma",
* "Heart attack",
* "Lung cancer",
* "Lupus",
* "Macular degeneration",
* "Multiple sclerosis",
* "Obesity",
* "Prostate cancer",
* "Psoriasis",
* "Restless legs syndrome",
* "Rheumatoid arthritis",
* "Ulcerative colitis"
* ],
* conditions_keyed: {
* "Alzheimer's disease": {
* id: 1,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Atrial fibrillation": {
* id: 2,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Breast cancer": {
* id: 3,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Celiac disease": {
* id: 4,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Colorectal cancer": {
* id: 5,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Crohn"s disease": {
* id: 6,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Diabetes (type 1)": {
* id: 7,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Diabetes (type 2)": {
* id: 8,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Glaucoma": {
* id: 9,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Heart attack": {
* id: 10,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Lung cancer": {
* id: 11,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Lupus": {
* id: 12,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Macular degeneration": {
* id: 13,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Multiple sclerosis": {
* id: 14,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Obesity": {
* id: 15,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Prostate cancer": {
* id: 16,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Psoriasis": {
* id: 17,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Restless legs syndrome": {
* id: 18,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Rheumatoid arthritis": {
* id: 19,
* condition_data: // data structure from queryDataForCondition(id)
* },
* "Ulcerative colitis": {
* id: 20,
* condition_data: // data structure from queryDataForCondition(id)
* }
* }
* }
*/
function queryDataForConditionsAll() {
$arrConditions = queryArrayConditions();
$mapDataConditions = array(
'conditions' => array(),
'conditions_keyed' => array());
foreach ($arrConditions as $arrCondition) {
$idCondition = $arrCondition[0];
$strCondition = $arrCondition[1];
$mapDataConditions['conditions'][] = $strCondition;
$mapDataConditions['conditions_keyed'][$strCondition] = array(
'id' => $idCondition,
'condition_data' => queryDataForCondition($idCondition));
}
return $mapDataConditions;
}
?>