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RichardZhu52 commited on
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Delete opentarget_tools.json

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  1. opentarget_tools.json +0 -2166
opentarget_tools.json DELETED
@@ -1,2166 +0,0 @@
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- [
2
- {
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- "name": "get_associated_targets_by_disease_efoId",
4
- "description": "Find targets associated with a specific disease or phenotype based on efoId.",
5
- "label": [
6
- "Disease",
7
- "Phenotype",
8
- "Target",
9
- "Association",
10
- "OpenTarget",
11
- "GraphQL"
12
- ],
13
- "parameter": {
14
- "type": "object",
15
- "properties": {
16
- "efoId": {
17
- "type": "string",
18
- "description": "The efoId of a disease or phenotype.",
19
- "required": true
20
- }
21
- }
22
- },
23
- "query_schema": "\nquery associatedTargets($efoId: String!) {\n disease(efoId: $efoId) {\n id\n name\n associatedTargets {\n count\n rows {\n target {\n id\n approvedSymbol\n }\n score\n }\n }\n }\n}\n",
24
- "type": "OpenTarget"
25
- },
26
- {
27
- "name": "get_associated_diseases_phenotypes_by_target_ensemblID",
28
- "description": "Find diseases or phenotypes associated with a specific target using ensemblId.",
29
- "label": [
30
- "Target",
31
- "Disease",
32
- "Phenotype",
33
- "Association",
34
- "OpenTarget",
35
- "GraphQL"
36
- ],
37
- "parameter": {
38
- "type": "object",
39
- "properties": {
40
- "ensemblId": {
41
- "type": "string",
42
- "description": "The ensemblId of a target.",
43
- "required": true
44
- }
45
- }
46
- },
47
- "query_schema": "\nquery associatedDiseases($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n associatedDiseases {\n count\n rows {\n disease {\n id\n name\n }\n datasourceScores {\n id\n score\n }\n }\n }\n }\n}\n",
48
- "type": "OpenTarget"
49
- },
50
- {
51
- "name": "target_disease_evidence",
52
- "description": "Explore evidence that supports a specific target-disease association. Input is disease efoId and target ensemblID.",
53
- "label": [
54
- "Target",
55
- "Disease",
56
- "Evidence",
57
- "Association",
58
- "OpenTarget",
59
- "GraphQL"
60
- ],
61
- "parameter": {
62
- "type": "object",
63
- "properties": {
64
- "efoId": {
65
- "type": "string",
66
- "description": "The efoId of a disease or phenotype.",
67
- "required": true
68
- },
69
- "ensemblId": {
70
- "type": "string",
71
- "description": "The ensemblId of a target.",
72
- "required": true
73
- }
74
- }
75
- },
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- "query_schema": "\nquery targetDiseaseEvidence($efoId: String!, $ensemblId: String!) {\n disease(efoId: $efoId) {\n id\n name\n evidences(datasourceIds: [\"intogen\"], ensemblIds: [$ensemblId]) {\n count\n rows {\n disease {\n id\n name\n }\n diseaseFromSource\n target {\n id\n approvedSymbol\n }\n mutatedSamples {\n functionalConsequence {\n id\n label\n }\n numberSamplesTested\n numberMutatedSamples\n }\n resourceScore\n significantDriverMethods\n cohortId\n cohortShortName\n cohortDescription\n }\n }\n }\n}\n",
77
- "type": "OpenTarget"
78
- },
79
- {
80
- "name": "get_drug_warnings_by_chemblId",
81
- "description": "Retrieve warnings for a specific drug using ChEMBL ID.",
82
- "parameter": {
83
- "type": "object",
84
- "properties": {
85
- "chemblId": {
86
- "type": "string",
87
- "description": "The ChEMBL ID of the drug.",
88
- "required": true
89
- }
90
- }
91
- },
92
- "query_schema": "\n query drugWarnings($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n drugWarnings {\n warningType\n description\n country\n year\n toxicityClass\n chemblIds\n efoIdForWarningClass\n references {\n id\n source\n url\n }\n }\n }\n }\n ",
93
- "label": [
94
- "Drug",
95
- "AdverseEvents",
96
- "SafetyLiability",
97
- "OpenTarget",
98
- "GraphQL",
99
- "Warnings",
100
- "Safety",
101
- "Withdrawal",
102
- "Toxicity"
103
- ],
104
- "type": "OpenTarget"
105
- },
106
- {
107
- "name": "get_drug_mechanisms_of_action_by_chemblId",
108
- "description": "Retrieve the mechanisms of action associated with a specific drug using chemblId.",
109
- "parameter": {
110
- "type": "object",
111
- "properties": {
112
- "chemblId": {
113
- "type": "string",
114
- "description": "The ChEMBL ID of the drug.",
115
- "required": true
116
- }
117
- }
118
- },
119
- "query_schema": "\n query drugMechanismsOfAction($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n mechanismsOfAction {\n rows {\n mechanismOfAction\n actionType\n targetName\n targets {\n id\n approvedSymbol\n }\n }\n }\n }\n }\n ",
120
- "label": [
121
- "Drug",
122
- "MechanismsOfAction",
123
- "Target",
124
- "Pharmacology",
125
- "ChemblId",
126
- "OpenTarget",
127
- "GraphQL"
128
- ],
129
- "type": "OpenTarget"
130
- },
131
- {
132
- "name": "get_associated_drugs_by_disease_efoId",
133
- "description": "Retrieve known drugs associated with a specific disease by disease efoId.",
134
- "parameter": {
135
- "type": "object",
136
- "properties": {
137
- "efoId": {
138
- "type": "string",
139
- "description": "The EFO ID of the disease.",
140
- "required": true
141
- },
142
- "size": {
143
- "type": "integer",
144
- "description": "Number of entries to fetch, recomanding a large number to avoid missing drugs.",
145
- "required": true
146
- }
147
- }
148
- },
149
- "query_schema": "\n query diseaseKnownDrugs($efoId: String!, $size: Int!, $freeTextQuery: String) {\n disease(efoId: $efoId) {\n id\n name\n knownDrugs(size: $size, freeTextQuery: $freeTextQuery) {\n count\n rows {\n drug {\n id\n name\n tradeNames\n maximumClinicalTrialPhase\n isApproved\n hasBeenWithdrawn\n }\n phase\n status\n mechanismOfAction\n target {\n id\n approvedSymbol\n }\n }\n }\n }\n }\n ",
150
- "examples": [
151
- {
152
- "question": "Please list the drugs associated with the disease with efoId 'EFO_0005548' and filter by 'dopamine'.",
153
- "query": {
154
- "name": "get_associated_drugs_by_disease_efoId",
155
- "arguments": {
156
- "efoId": "EFO_0005548",
157
- "size": 10,
158
- "freeTextQuery": "dopamine"
159
- }
160
- }
161
- }
162
- ],
163
- "label": [
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- "OpenTarget",
165
- "Disease",
166
- "Drug",
167
- "Pagination",
168
- "GraphQL"
169
- ],
170
- "type": "OpenTarget"
171
- },
172
- {
173
- "name": "get_similar_entities_by_disease_efoId",
174
- "description": "Retrieve similar entities for a given disease efoId using a model trained with PubMed.",
175
- "parameter": {
176
- "type": "object",
177
- "properties": {
178
- "efoId": {
179
- "type": "string",
180
- "description": "The EFO ID of the disease.",
181
- "required": true
182
- },
183
- "threshold": {
184
- "type": "number",
185
- "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
186
- "required": true
187
- },
188
- "size": {
189
- "type": "integer",
190
- "description": "Number of similar entities to fetch.",
191
- "required": true
192
- }
193
- }
194
- },
195
- "query_schema": "\n query diseaseSimilarEntities($efoId: String!, $threshold: Float!, $size: Int!) {\n disease(efoId: $efoId) {\n id\n name\n similarEntities(threshold: $threshold, size: $size) {\n id\n category\n score\n object {\n ... on Disease {\n id\n name\n }\n ... on Target {\n id\n approvedSymbol\n }\n ... on Drug {\n id\n name\n }\n }\n }\n }\n }\n ",
196
- "label": [
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- "Disease",
198
- "Similarity",
199
- "Model",
200
- "Entities",
201
- "OpenTarget",
202
- "GraphQL"
203
- ],
204
- "type": "OpenTarget"
205
- },
206
- {
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- "name": "get_similar_entities_by_drug_chemblId",
208
- "description": "Retrieve similar entities for a given drug chemblId using a model trained with PubMed.",
209
- "parameter": {
210
- "type": "object",
211
- "properties": {
212
- "chemblId": {
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- "type": "string",
214
- "description": "The chemblId of the disease.",
215
- "required": true
216
- },
217
- "threshold": {
218
- "type": "number",
219
- "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
220
- "required": true
221
- },
222
- "size": {
223
- "type": "integer",
224
- "description": "Number of similar entities to fetch.",
225
- "required": true
226
- }
227
- }
228
- },
229
- "query_schema": "\n query diseaseSimilarEntities($chemblId: String!, $threshold: Float!, $size: Int!) {\n drug(chemblId: $chemblId) {\n id\n name\n similarEntities(threshold: $threshold, size: $size) {\n id\n category\n score\n object {\n ... on Disease {\n id\n name\n }\n ... on Target {\n id\n approvedSymbol\n }\n ... on Drug {\n id\n name\n }\n }\n }\n }\n }\n ",
230
- "label": [
231
- "Drug",
232
- "Similarity",
233
- "Model",
234
- "Entities",
235
- "OpenTarget",
236
- "GraphQL"
237
- ],
238
- "type": "OpenTarget"
239
- },
240
- {
241
- "name": "get_similar_entities_by_target_ensemblID",
242
- "description": "Retrieve similar entities for a given target ensemblID using a model trained with PubMed.",
243
- "parameter": {
244
- "type": "object",
245
- "properties": {
246
- "ensemblId": {
247
- "type": "string",
248
- "description": "The ensemblID of the disease.",
249
- "required": true
250
- },
251
- "threshold": {
252
- "type": "number",
253
- "description": "Threshold similarity between 0 and 1. Only results above threshold are returned.",
254
- "required": true
255
- },
256
- "size": {
257
- "type": "integer",
258
- "description": "Number of similar entities to fetch.",
259
- "required": true
260
- }
261
- }
262
- },
263
- "query_schema": "\n query diseaseSimilarEntities($ensemblId: String!, $threshold: Float!, $size: Int!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n similarEntities(threshold: $threshold, size: $size) {\n id\n category\n score\n object {\n ... on Disease {\n id\n name\n }\n ... on Target {\n id\n approvedSymbol\n }\n ... on Drug {\n id\n name\n }\n }\n }\n }\n }\n ",
264
- "label": [
265
- "Disease",
266
- "Similarity",
267
- "Model",
268
- "Entities",
269
- "OpenTarget",
270
- "GraphQL"
271
- ],
272
- "type": "OpenTarget"
273
- },
274
- {
275
- "name": "get_associated_phenotypes_by_disease_efoId",
276
- "description": "Find HPO phenotypes asosciated with the specified disease efoId.",
277
- "parameter": {
278
- "type": "object",
279
- "properties": {
280
- "efoId": {
281
- "type": "string",
282
- "description": "The efoId of a disease or phenotype.",
283
- "required": true
284
- }
285
- }
286
- },
287
- "query_schema": "query diseaseAnnotation($efoId: String!) {\n disease(efoId: $efoId) {\n id\n name\n phenotypes {\n rows {\n phenotypeHPO {\n id\n name\n description\n namespace\n }\n phenotypeEFO {\n id\n name\n }\n }\n }\n }\n}",
288
- "label": [
289
- "Disease",
290
- "OpenTarget",
291
- "GraphQL",
292
- "Phenotype",
293
- "Symptoms",
294
- "Clinical signs"
295
- ],
296
- "type": "OpenTarget"
297
- },
298
- {
299
- "name": "get_drug_withdrawn_blackbox_status_by_chemblId",
300
- "description": "Find withdrawn and black-box warning statuses for a specific drug by chemblId.",
301
- "parameter": {
302
- "type": "object",
303
- "properties": {
304
- "chemblId": {
305
- "type": "array",
306
- "items": {
307
- "type": "string"
308
- },
309
- "description": "The chemblId of a drug.",
310
- "required": true
311
- }
312
- }
313
- },
314
- "query_schema": "\n query drugWithdrawnWarningData($chemblId: String!) {\n drug(chemblId: $chemblId) {\n name\n id\n hasBeenWithdrawn\n blackBoxWarning\n }\n }\n ",
315
- "label": [
316
- "Drug",
317
- "SafetyWarnings",
318
- "Withdrawal",
319
- "OpenTarget",
320
- "GraphQL"
321
- ],
322
- "type": "OpenTarget"
323
- },
324
- {
325
- "name": "search_category_counts_by_query_string",
326
- "description": "Get the count of entries in each entity category (disease, target, drug) based on a query string.",
327
- "parameter": {
328
- "type": "object",
329
- "properties": {
330
- "queryString": {
331
- "type": "string",
332
- "description": "The search string for querying information.",
333
- "required": true
334
- }
335
- }
336
- },
337
- "query_schema": "\n query searchCategoryCounts($queryString: String!) {\n search(queryString: $queryString) {\n aggregations {\n total\n entities {\n total\n name\n }\n }\n }\n }\n ",
338
- "label": [
339
- "OpenTarget",
340
- "GraphQL",
341
- "SearchResults",
342
- "Search",
343
- "Query",
344
- "Counts",
345
- "Categories"
346
- ],
347
- "type": "OpenTarget"
348
- },
349
- {
350
- "name": "get_disease_id_description_by_name",
351
- "description": "Retrieve the efoId and additional details of a disease based on its name.",
352
- "parameter": {
353
- "type": "object",
354
- "properties": {
355
- "diseaseName": {
356
- "type": "string",
357
- "description": "The name of the disease to search for.",
358
- "required": true
359
- }
360
- }
361
- },
362
- "query_schema": "\n query getDiseaseIdByName($diseaseName: String!) {\n search(queryString: $diseaseName, entityNames: [\"disease\"]) {\n hits {\n id\n name\n description\n }\n }\n }\n ",
363
- "label": [
364
- "Disease",
365
- "Identification",
366
- "Search",
367
- "Name",
368
- "Disease",
369
- "OpenTarget",
370
- "GraphQL"
371
- ],
372
- "type": "OpenTarget"
373
- },
374
- {
375
- "name": "get_drug_id_description_by_name",
376
- "description": "Fetch the drug chemblId and description based on the drug name.",
377
- "parameter": {
378
- "type": "object",
379
- "properties": {
380
- "drugName": {
381
- "type": "string",
382
- "description": "The name of the drug for which the ID is required.",
383
- "required": true
384
- }
385
- }
386
- },
387
- "query_schema": "\n query getDrugIdByName($drugName: String!) {\n search(queryString: $drugName, entityNames: [\"drug\"]) {\n hits {\n id\n name\n description\n }\n }\n }\n ",
388
- "label": [
389
- "Identification",
390
- "Search",
391
- "Name",
392
- "Drug",
393
- "OpenTarget",
394
- "GraphQL"
395
- ],
396
- "type": "OpentargetToolDrugNameMatch"
397
- },
398
- {
399
- "name": "get_drug_indications_by_chemblId",
400
- "description": "Fetch indications (treatable phenotypes/diseases) for a given drug chemblId.",
401
- "parameter": {
402
- "type": "object",
403
- "properties": {
404
- "chemblId": {
405
- "type": "string",
406
- "description": "The chemblId of the drug for which to retrieve treatable phenotypes information.",
407
- "required": true
408
- }
409
- }
410
- },
411
- "query_schema": "\n query drugIndications($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n indications {\n rows {\n disease {\n id\n name\n }\n maxPhaseForIndication\n references {\n source\n ids\n }\n }\n }\n }\n }\n ",
412
- "label": [
413
- "Drug",
414
- "Indications",
415
- "Disease",
416
- "Treatment",
417
- "OpenTarget",
418
- "GraphQL"
419
- ],
420
- "type": "OpenTarget"
421
- },
422
- {
423
- "name": "get_target_gene_ontology_by_ensemblID",
424
- "description": "Retrieve Gene Ontology annotations for a specific target by Ensembl ID.",
425
- "parameter": {
426
- "type": "object",
427
- "properties": {
428
- "ensemblId": {
429
- "type": "string",
430
- "description": "The Ensembl ID of the target for which to retrieve Gene Ontology annotations.",
431
- "required": true
432
- }
433
- }
434
- },
435
- "query_schema": "\n query targetGeneOntology($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n geneOntology {\n aspect\n evidence\n geneProduct\n source\n term {\n id\n name\n }\n }\n }\n }\n ",
436
- "examples": [
437
- {
438
- "question": "Can you retrieve the Gene Ontology annotations for the target with Ensembl ID 'ENSG00000136492'?",
439
- "query": {
440
- "name": "get_target_gene_ontology_by_ensemblID",
441
- "arguments": {
442
- "ensemblId": "ENSG00000136492"
443
- }
444
- }
445
- },
446
- {
447
- "question": "What are the Gene Ontology annotations for the target identified by Ensembl ID 'ENSG00000138653'?",
448
- "query": {
449
- "name": "get_target_gene_ontology_by_ensemblID",
450
- "arguments": {
451
- "ensemblId": "ENSG00000138653"
452
- }
453
- }
454
- },
455
- {
456
- "question": "Please provide the Gene Ontology annotations for the target with Ensembl ID 'ENSG00000186162'.",
457
- "query": {
458
- "name": "get_target_gene_ontology_by_ensemblID",
459
- "arguments": {
460
- "ensemblId": "ENSG00000186162"
461
- }
462
- }
463
- }
464
- ],
465
- "label": [
466
- "Target",
467
- "GeneOntology",
468
- "OpenTarget",
469
- "GraphQL"
470
- ],
471
- "type": "OpenTarget"
472
- },
473
- {
474
- "name": "get_target_homologues_by_ensemblID",
475
- "description": "Fetch homologues for a specific target by Ensembl ID.",
476
- "parameter": {
477
- "type": "object",
478
- "properties": {
479
- "ensemblId": {
480
- "type": "string",
481
- "description": "The Ensembl ID of the target for which to retrieve homologues.",
482
- "required": true
483
- }
484
- }
485
- },
486
- "query_schema": "\n query targetHomologues($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n homologues {\n homologyType\n queryPercentageIdentity\n speciesId\n speciesName\n targetGeneId\n targetGeneSymbol\n targetPercentageIdentity\n isHighConfidence\n }\n }\n }\n ",
487
- "examples": [
488
- {
489
- "question": "Can you fetch homologues for the target with Ensembl ID 'ENSG00000100033'?",
490
- "query": {
491
- "name": "get_target_homologues_by_ensemblID",
492
- "arguments": {
493
- "ensemblId": "ENSG00000100033"
494
- }
495
- }
496
- },
497
- {
498
- "question": "What are the homologues for the target identified by Ensembl ID 'ENSG00000288534'?",
499
- "query": {
500
- "name": "get_target_homologues_by_ensemblID",
501
- "arguments": {
502
- "ensemblId": "ENSG00000288534"
503
- }
504
- }
505
- },
506
- {
507
- "question": "Please provide the homologues for the target with Ensembl ID 'ENSG00000198937'.",
508
- "query": {
509
- "name": "get_target_homologues_by_ensemblID",
510
- "arguments": {
511
- "ensemblId": "ENSG00000198937"
512
- }
513
- }
514
- }
515
- ],
516
- "label": [
517
- "OpenTarget",
518
- "Target Information",
519
- "GraphQL",
520
- "Homologue"
521
- ],
522
- "type": "OpenTarget"
523
- },
524
- {
525
- "name": "get_target_safety_profile_by_ensemblID",
526
- "description": "Retrieve known target safety liabilities for a specific target Ensembl ID.",
527
- "parameter": {
528
- "type": "object",
529
- "properties": {
530
- "ensemblId": {
531
- "type": "string",
532
- "description": "The Ensembl ID of the target for which to retrieve safety liabilities.",
533
- "required": true
534
- }
535
- }
536
- },
537
- "query_schema": "\n query targetSafetyLiabilities($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n safetyLiabilities {\n event\n eventId\n biosamples {\n cellFormat\n cellLabel\n tissueLabel\n tissueId\n }\n effects {\n dosing\n direction\n }\n studies {\n name\n type\n description\n }\n datasource\n literature\n }\n }\n }\n ",
538
- "examples": [
539
- {
540
- "question": "Can you provide the safety liabilities for the target with Ensembl ID 'ENSG00000175274'?",
541
- "query": {
542
- "name": "target_safety_liabilities",
543
- "arguments": {
544
- "ensemblId": "ENSG00000175274"
545
- }
546
- }
547
- },
548
- {
549
- "question": "What are the known safety effects for the target identified by Ensembl ID 'ENSG00000226446'?",
550
- "query": {
551
- "name": "target_safety_liabilities",
552
- "arguments": {
553
- "ensemblId": "ENSG00000226446"
554
- }
555
- }
556
- },
557
- {
558
- "question": "Please retrieve the safety risk information for the target with Ensembl ID 'ENSG00000151929'.",
559
- "query": {
560
- "name": "target_safety_liabilities",
561
- "arguments": {
562
- "ensemblId": "ENSG00000151929"
563
- }
564
- }
565
- }
566
- ],
567
- "label": [
568
- "Target",
569
- "SafetyLiability",
570
- "OpenTarget",
571
- "GraphQL",
572
- "Safety",
573
- "Liabilities"
574
- ],
575
- "type": "OpenTarget"
576
- },
577
- {
578
- "name": "get_biological_mouse_models_by_ensemblID",
579
- "description": "Retrieve biological mouse models, including allelic compositions and genetic backgrounds, for a specific target.",
580
- "parameter": {
581
- "type": "object",
582
- "properties": {
583
- "ensemblId": {
584
- "type": "string",
585
- "description": "The Ensembl ID of the target.",
586
- "required": true
587
- }
588
- }
589
- },
590
- "query_schema": "\n query fetchBiologicalModels($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n mousePhenotypes {\n biologicalModels {\n allelicComposition\n geneticBackground\n id\n literature\n }\n }\n }\n }\n ",
591
- "examples": [
592
- {
593
- "question": "What are the allelic compositions and genetic backgrounds for the target identified by Ensembl ID 'ENSG00000196639'?",
594
- "query": {
595
- "name": "get_biological_mouse_models_by_ensemblID",
596
- "arguments": {
597
- "ensemblId": "ENSG00000196639"
598
- }
599
- }
600
- },
601
- {
602
- "question": "Please provide the biological models for the target with the Ensembl ID 'ENSG00000171862'.",
603
- "query": {
604
- "name": "get_biological_mouse_models_by_ensemblID",
605
- "arguments": {
606
- "ensemblId": "ENSG00000171862"
607
- }
608
- }
609
- }
610
- ],
611
- "label": [
612
- "OpenTarget",
613
- "Target Information",
614
- "BiologicalModels",
615
- "GraphQL"
616
- ],
617
- "type": "OpenTarget"
618
- },
619
- {
620
- "name": "get_target_genomic_location_by_ensemblID",
621
- "description": "Retrieve genomic location data for a specific target, including chromosome, start, end, and strand.",
622
- "parameter": {
623
- "type": "object",
624
- "properties": {
625
- "ensemblId": {
626
- "type": "string",
627
- "description": "The Ensembl ID of the target for which to retrieve genomic location information.",
628
- "required": true
629
- }
630
- }
631
- },
632
- "query_schema": "\n query targetGenomicLocation($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n genomicLocation {\n chromosome\n start\n end\n strand\n }\n }\n }\n ",
633
- "examples": [
634
- {
635
- "question": "Can you provide the genomic location for the target with Ensembl ID 'ENSG00000114098'?",
636
- "query": {
637
- "name": "get_target_genomic_location_by_ensemblID",
638
- "arguments": {
639
- "ensemblId": "ENSG00000114098"
640
- }
641
- }
642
- },
643
- {
644
- "question": "What is the genomic location data for the target identified by Ensembl ID 'ENSG00000231404'?",
645
- "query": {
646
- "name": "get_target_genomic_location_by_ensemblID",
647
- "arguments": {
648
- "ensemblId": "ENSG00000231404"
649
- }
650
- }
651
- },
652
- {
653
- "question": "Please retrieve the genomic location information for the target with Ensembl ID 'ENSG00000167258'.",
654
- "query": {
655
- "name": "get_target_genomic_location_by_ensemblID",
656
- "arguments": {
657
- "ensemblId": "ENSG00000167258"
658
- }
659
- }
660
- }
661
- ],
662
- "label": [
663
- "Target",
664
- "GenomicLocation",
665
- "OpenTarget",
666
- "GraphQL"
667
- ],
668
- "type": "OpenTarget"
669
- },
670
- {
671
- "name": "get_target_subcellular_locations_by_ensemblID",
672
- "description": "Retrieve information about subcellular locations for a specific target ensemblID.",
673
- "parameter": {
674
- "type": "object",
675
- "properties": {
676
- "ensemblId": {
677
- "type": "string",
678
- "description": "The ensemblId of a target.",
679
- "required": true
680
- }
681
- }
682
- },
683
- "query_schema": "\n query targetSubcellularLocations($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n subcellularLocations {\n location\n source\n termSL\n labelSL\n }\n }\n }\n ",
684
- "examples": [
685
- {
686
- "question": "Can you provide the subcellular locations for the target with Ensembl ID 'ENSG00000121898'?",
687
- "query": {
688
- "name": "get_target_subcellular_locations_by_ensemblID",
689
- "arguments": {
690
- "ensemblId": "ENSG00000121898"
691
- }
692
- }
693
- },
694
- {
695
- "question": "What are the subcellular locations for the target identified by Ensembl ID 'ENSG00000274286'?",
696
- "query": {
697
- "name": "get_target_subcellular_locations_by_ensemblID",
698
- "arguments": {
699
- "ensemblId": "ENSG00000274286"
700
- }
701
- }
702
- },
703
- {
704
- "question": "Please retrieve the subcellular location information for the target with Ensembl ID 'ENSG00000171843'.",
705
- "query": {
706
- "name": "get_target_subcellular_locations_by_ensemblID",
707
- "arguments": {
708
- "ensemblId": "ENSG00000171843"
709
- }
710
- }
711
- }
712
- ],
713
- "label": [
714
- "Target",
715
- "Subcellular Locations",
716
- "GraphQL",
717
- "OpenTarget"
718
- ],
719
- "type": "OpenTarget"
720
- },
721
- {
722
- "name": "get_target_synonyms_by_ensemblID",
723
- "description": "Retrieve synonyms for specified target, including alternative names and symbols, using given ensemblID.",
724
- "parameter": {
725
- "type": "object",
726
- "properties": {
727
- "ensemblId": {
728
- "type": "string",
729
- "description": "The Ensembl ID of the target.",
730
- "required": true
731
- }
732
- }
733
- },
734
- "query_schema": "\n query retrieveTargetSynonyms($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n synonyms {\n label\n source\n }\n symbolSynonyms {\n label\n source\n }\n nameSynonyms {\n label\n source\n }\n }\n }\n ",
735
- "examples": [
736
- {
737
- "question": "Can you retrieve synonyms for the target with the Ensembl ID 'ENSG00000188986'?",
738
- "query": {
739
- "name": "get_target_synonyms_by_ensemblID",
740
- "arguments": {
741
- "ensemblId": "ENSG00000188986"
742
- }
743
- }
744
- },
745
- {
746
- "question": "What are the alternative names and symbols for the target identified by Ensembl ID 'ENSG00000269335'?",
747
- "query": {
748
- "name": "get_target_synonyms_by_ensemblID",
749
- "arguments": {
750
- "ensemblId": "ENSG00000269335"
751
- }
752
- }
753
- },
754
- {
755
- "question": "Please provide the synonyms for the target with Ensembl ID 'ENSG00000141052'.",
756
- "query": {
757
- "name": "get_target_synonyms_by_ensemblID",
758
- "arguments": {
759
- "ensemblId": "ENSG00000141052"
760
- }
761
- }
762
- }
763
- ],
764
- "label": [
765
- "OpenTarget",
766
- "Target Information",
767
- "GraphQL",
768
- "Target"
769
- ],
770
- "type": "OpenTarget"
771
- },
772
- {
773
- "name": "get_target_tractability_by_ensemblID",
774
- "description": "Retrieve tractability assessments, including modality and values, for a specific target ensembl ID.",
775
- "parameter": {
776
- "type": "object",
777
- "properties": {
778
- "ensemblId": {
779
- "type": "string",
780
- "description": "The Ensembl ID of the target.",
781
- "required": true
782
- }
783
- }
784
- },
785
- "query_schema": "\n query targetTractabilityAssessment($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n tractability {\n label\n modality\n value\n }\n }\n }\n ",
786
- "examples": [
787
- {
788
- "question": "Can you retrieve the tractability assessment for the target with Ensembl ID 'ENSG00000141736'?",
789
- "query": {
790
- "name": "get_target_tractability_by_ensemblID",
791
- "arguments": {
792
- "ensemblId": "ENSG00000141736"
793
- }
794
- }
795
- },
796
- {
797
- "question": "What are the tractability assessments for the target identified by Ensembl ID 'ENSG00000169249'?",
798
- "query": {
799
- "name": "get_target_tractability_by_ensemblID",
800
- "arguments": {
801
- "ensemblId": "ENSG00000169249"
802
- }
803
- }
804
- },
805
- {
806
- "question": "Please provide the tractability assessment details for the target with Ensembl ID 'ENSG00000122548'.",
807
- "query": {
808
- "name": "get_target_tractability_by_ensemblID",
809
- "arguments": {
810
- "ensemblId": "ENSG00000122548"
811
- }
812
- }
813
- }
814
- ],
815
- "label": [
816
- "Target",
817
- "Tractability",
818
- "OpenTarget",
819
- "Target Information",
820
- "GraphQL"
821
- ],
822
- "type": "OpenTarget"
823
- },
824
- {
825
- "name": "get_target_classes_by_ensemblID",
826
- "description": "Retrieve the target classes associated with a specific target ensemblID.",
827
- "parameter": {
828
- "type": "object",
829
- "properties": {
830
- "ensemblId": {
831
- "type": "string",
832
- "description": "The Ensembl ID of the target.",
833
- "required": true
834
- }
835
- }
836
- },
837
- "query_schema": "\n query fetchTargetClasses($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n targetClass {\n id\n label\n level\n }\n }\n }\n ",
838
- "examples": [
839
- {
840
- "question": "Can you retrieve the target classes for the target with Ensembl ID 'ENSG00000185324'?",
841
- "query": {
842
- "name": "get_target_classes_by_ensemblID",
843
- "arguments": {
844
- "ensemblId": "ENSG00000185324"
845
- }
846
- }
847
- },
848
- {
849
- "question": "What are the target classes associated with the Ensembl ID 'ENSG00000141646'?",
850
- "query": {
851
- "name": "get_target_classes_by_ensemblID",
852
- "arguments": {
853
- "ensemblId": "ENSG00000141646"
854
- }
855
- }
856
- },
857
- {
858
- "question": "Please provide the target classes for the target identified by Ensembl ID 'ENSG00000141736'.",
859
- "query": {
860
- "name": "get_target_classes_by_ensemblID",
861
- "arguments": {
862
- "ensemblId": "ENSG00000141736"
863
- }
864
- }
865
- }
866
- ],
867
- "label": [
868
- "OpenTarget",
869
- "Target Information",
870
- "GraphQL",
871
- "Target"
872
- ],
873
- "type": "OpenTarget"
874
- },
875
- {
876
- "name": "get_target_enabling_packages_by_ensemblID",
877
- "description": "Retrieve the Target Enabling Packages (TEP) associated with a specific target ensemblID.",
878
- "parameter": {
879
- "type": "object",
880
- "properties": {
881
- "ensemblId": {
882
- "type": "string",
883
- "description": "The Ensembl ID of the target.",
884
- "required": true
885
- }
886
- }
887
- },
888
- "query_schema": "\n query fetchTargetEnablingPackages($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n tep {\n name\n uri\n therapeuticArea\n description\n }\n }\n }\n ",
889
- "examples": [
890
- {
891
- "question": "Can you retrieve the Target Enabling Packages for the target with Ensembl ID 'ENSG00000167258'?",
892
- "query": {
893
- "name": "get_target_enabling_packages_by_ensemblID",
894
- "arguments": {
895
- "ensemblId": "ENSG00000167258"
896
- }
897
- }
898
- }
899
- ],
900
- "label": [
901
- "OpenTarget",
902
- "Target Information",
903
- "GraphQL",
904
- "Target"
905
- ],
906
- "type": "OpenTarget"
907
- },
908
- {
909
- "name": "get_target_interactions_by_ensemblID",
910
- "description": "Retrieve interaction data for a specific target ensemblID, including interaction partners and evidence.",
911
- "label": [
912
- "Target",
913
- "Interaction",
914
- "Evidence",
915
- "GraphQL",
916
- "Pagination",
917
- "OpenTarget"
918
- ],
919
- "parameter": {
920
- "type": "object",
921
- "properties": {
922
- "ensemblId": {
923
- "type": "string",
924
- "description": "The Ensembl ID of the target.",
925
- "required": true
926
- },
927
- "page": {
928
- "type": "object",
929
- "properties": {
930
- "index": {
931
- "type": "integer",
932
- "description": "The index of the page to retrieve.",
933
- "required": true
934
- },
935
- "size": {
936
- "type": "integer",
937
- "description": "The number of items per page.",
938
- "required": true
939
- }
940
- },
941
- "description": "Pagination parameters.",
942
- "required": false
943
- }
944
- }
945
- },
946
- "query_schema": "\n query targetInteractions($ensemblId: String!, $page: Pagination!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n interactions(page: $page) {\n count\n rows {\n intA\n targetA {\n id\n approvedSymbol\n }\n intB\n targetB {\n id\n approvedSymbol\n }\n score\n sourceDatabase\n evidences {\n evidenceScore\n pubmedId\n interactionDetectionMethodShortName\n }\n }\n }\n }\n }\n ",
947
- "examples": [
948
- {
949
- "question": "Can you retrieve interaction data for the target with Ensembl ID 'ENSG00000134508' from the source database 'BioGRID'?",
950
- "query": {
951
- "name": "target_interactions",
952
- "arguments": {
953
- "ensemblId": "ENSG00000134508",
954
- "page": {
955
- "index": 1,
956
- "size": 10
957
- }
958
- }
959
- }
960
- },
961
- {
962
- "question": "What are the interaction partners and evidence for the target identified by Ensembl ID 'ENSG00000276601'?",
963
- "query": {
964
- "name": "target_interactions",
965
- "arguments": {
966
- "ensemblId": "ENSG00000276601",
967
- "page": {
968
- "index": 2,
969
- "size": 5
970
- }
971
- }
972
- }
973
- },
974
- {
975
- "question": "Please provide the interaction data for the target with Ensembl ID 'ENSG00000287061' on the first page with 20 items per page.",
976
- "query": {
977
- "name": "target_interactions",
978
- "arguments": {
979
- "ensemblId": "ENSG00000287061",
980
- "page": {
981
- "index": 1,
982
- "size": 20
983
- }
984
- }
985
- }
986
- }
987
- ],
988
- "type": "OpenTarget"
989
- },
990
- {
991
- "name": "get_disease_ancestors_parents_by_efoId",
992
- "description": "Retrieve the disease ancestors and parents in the ontology using the disease EFO ID.",
993
- "parameter": {
994
- "type": "object",
995
- "properties": {
996
- "efoId": {
997
- "type": "string",
998
- "description": "The EFO ID of the disease.",
999
- "required": true
1000
- }
1001
- }
1002
- },
1003
- "query_schema": "\n query getDiseaseDetailsByEfoId($efoId: String!) {\n disease(efoId: $efoId) {\n id\n name\n ancestors\n parents {\n id\n name\n }\n }\n }\n ",
1004
- "label": [
1005
- "OpenTarget",
1006
- "Disease",
1007
- "Disease Information",
1008
- "GraphQL"
1009
- ],
1010
- "type": "OpenTarget"
1011
- },
1012
- {
1013
- "name": "get_disease_descendants_children_by_efoId",
1014
- "description": "Retrieve the disease descendants and children in the ontology using the disease EFO ID.",
1015
- "parameter": {
1016
- "type": "object",
1017
- "properties": {
1018
- "efoId": {
1019
- "type": "string",
1020
- "description": "The EFO ID of the disease.",
1021
- "required": true
1022
- }
1023
- }
1024
- },
1025
- "query_schema": "\n query getDiseaseDetailsByEfoId($efoId: String!) {\n disease(efoId: $efoId) {\n id\n name\n descendants\n children {\n id\n name\n }\n }\n }\n",
1026
- "label": [
1027
- "OpenTarget",
1028
- "Disease",
1029
- "Disease Information",
1030
- "GraphQL"
1031
- ],
1032
- "type": "OpenTarget"
1033
- },
1034
- {
1035
- "name": "get_disease_locations_by_efoId",
1036
- "description": "Retrieve the disease's direct location and indirect location disease terms and IDs using the disease EFO ID.",
1037
- "parameter": {
1038
- "type": "object",
1039
- "properties": {
1040
- "efoId": {
1041
- "type": "string",
1042
- "description": "The EFO ID of the disease.",
1043
- "required": true
1044
- }
1045
- }
1046
- },
1047
- "query_schema": "\n query getDiseaseDetailsByEfoId($efoId: String!) {\n disease(efoId: $efoId) {\n id\n name\n directLocationIds\n indirectLocationIds\n directLocations {\n id\n name\n }\n indirectLocations {\n id\n name\n }\n }\n }\n ",
1048
- "label": [
1049
- "OpenTarget",
1050
- "Disease",
1051
- "Disease Information",
1052
- "GraphQL"
1053
- ],
1054
- "type": "OpenTarget"
1055
- },
1056
- {
1057
- "name": "get_disease_synonyms_by_efoId",
1058
- "description": "Retrieve disease synonyms by its EFO ID.",
1059
- "parameter": {
1060
- "type": "object",
1061
- "properties": {
1062
- "efoId": {
1063
- "type": "string",
1064
- "description": "The EFO ID of the disease.",
1065
- "required": true
1066
- }
1067
- }
1068
- },
1069
- "query_schema": "\n query getDiseaseDetailsByEfoId($efoId: String!) {\n disease(efoId: $efoId) {\n id\n name\n synonyms {\n relation\n terms\n }\n }\n }\n",
1070
- "label": [
1071
- "OpenTarget",
1072
- "Disease",
1073
- "Disease Information",
1074
- "GraphQL"
1075
- ],
1076
- "type": "OpenTarget"
1077
- },
1078
- {
1079
- "name": "get_disease_description_by_efoId",
1080
- "description": "Retrieve disease description, name, database cros references, obsolete terms, and whether it's a therapeutic area, all using the specified efoId.",
1081
- "parameter": {
1082
- "type": "object",
1083
- "properties": {
1084
- "efoId": {
1085
- "type": "string",
1086
- "description": "The EFO ID of the disease.",
1087
- "required": true
1088
- }
1089
- }
1090
- },
1091
- "query_schema": "\n query getDiseaseDetailsByEfoId($efoId: String!) {\n disease(efoId: $efoId) {\n id\n name\n description\n dbXRefs\n obsoleteTerms\n isTherapeuticArea\n }\n }\n ",
1092
- "examples": [
1093
- {
1094
- "question": "Can you provide detailed information about the disease with the EFO ID 'MONDO_0000030'?",
1095
- "query": {
1096
- "name": "get_disease_description_by_efoId",
1097
- "arguments": {
1098
- "efoId": "MONDO_0000030"
1099
- }
1100
- }
1101
- },
1102
- {
1103
- "question": "What are the details of the disease identified by the EFO ID 'EFO_0007468'?",
1104
- "query": {
1105
- "name": "get_disease_description_by_efoId",
1106
- "arguments": {
1107
- "efoId": "EFO_0007468"
1108
- }
1109
- }
1110
- },
1111
- {
1112
- "question": "Please retrieve information about the disease with the EFO ID 'Orphanet_217563'.",
1113
- "query": {
1114
- "name": "get_disease_description_by_efoId",
1115
- "arguments": {
1116
- "efoId": "Orphanet_217563"
1117
- }
1118
- }
1119
- }
1120
- ],
1121
- "label": [
1122
- "OpenTarget",
1123
- "Disease",
1124
- "Disease Information",
1125
- "GraphQL"
1126
- ],
1127
- "type": "OpenTarget"
1128
- },
1129
- {
1130
- "name": "get_disease_therapeutic_areas_by_efoId",
1131
- "description": "Retrieve the therapeutic areas associated with a specific disease efoId.",
1132
- "parameter": {
1133
- "type": "object",
1134
- "properties": {
1135
- "efoId": {
1136
- "type": "string",
1137
- "description": "The EFO ID of the disease.",
1138
- "required": true
1139
- }
1140
- }
1141
- },
1142
- "query_schema": "\n query diseaseTherapeuticAreas($efoId: String!) {\n disease(efoId: $efoId) {\n id\n name\n therapeuticAreas {\n id\n name\n }\n }\n }\n ",
1143
- "examples": [
1144
- {
1145
- "question": "What therapeutic areas are linked to the disease with the efoId 'MONDO_0016474'?",
1146
- "query": {
1147
- "name": "get_disease_therapeutic_areas_by_efoId",
1148
- "arguments": {
1149
- "efoId": "MONDO_0016474"
1150
- }
1151
- }
1152
- },
1153
- {
1154
- "question": "Can you provide the therapeutic areas associated with the disease identified by efoId 'Orphanet_2579'?",
1155
- "query": {
1156
- "name": "get_disease_therapeutic_areas_by_efoId",
1157
- "arguments": {
1158
- "efoId": "Orphanet_2579"
1159
- }
1160
- }
1161
- },
1162
- {
1163
- "question": "Please list the therapeutic areas for the disease with the efoId 'MONDO_0000873'.",
1164
- "query": {
1165
- "name": "get_disease_therapeutic_areas_by_efoId",
1166
- "arguments": {
1167
- "efoId": "MONDO_0000873"
1168
- }
1169
- }
1170
- }
1171
- ],
1172
- "label": [
1173
- "OpenTarget",
1174
- "Disease",
1175
- "TherapeuticArea",
1176
- "GraphQL"
1177
- ],
1178
- "type": "OpenTarget"
1179
- },
1180
- {
1181
- "name": "get_drug_adverse_events_by_chemblId",
1182
- "description": "Retrieve significant adverse events reported for a specific drug chemblId.",
1183
- "parameter": {
1184
- "type": "object",
1185
- "properties": {
1186
- "chemblId": {
1187
- "type": "string",
1188
- "description": "The ChEMBL ID of the drug.",
1189
- "required": true
1190
- },
1191
- "page": {
1192
- "type": "object",
1193
- "properties": {
1194
- "index": {
1195
- "type": "integer",
1196
- "description": "Index of the page to fetch, starting from 0.",
1197
- "required": true
1198
- },
1199
- "size": {
1200
- "type": "integer",
1201
- "description": "Number of entries per page.",
1202
- "required": true
1203
- }
1204
- },
1205
- "description": "Pagination settings.",
1206
- "required": false
1207
- }
1208
- }
1209
- },
1210
- "query_schema": "\n query drugAdverseEvents($chemblId: String!, $page: Pagination!) {\n drug(chemblId: $chemblId) {\n id\n name\n adverseEvents(page: $page) {\n count\n criticalValue\n rows {\n name\n meddraCode\n count\n logLR\n }\n }\n }\n }\n ",
1211
- "label": [
1212
- "Drug",
1213
- "AdverseEvents",
1214
- "Safety",
1215
- "Reporting",
1216
- "Pagination",
1217
- "OpenTarget",
1218
- "GraphQL",
1219
- "AdverseEvents"
1220
- ],
1221
- "type": "OpenTarget"
1222
- },
1223
- {
1224
- "name": "get_known_drugs_by_drug_chemblId",
1225
- "description": "Get a list of known drugs and associated information using the specified chemblId.",
1226
- "parameter": {
1227
- "type": "object",
1228
- "properties": {
1229
- "chemblId": {
1230
- "type": "string",
1231
- "description": "The ChEMBL ID of the drug.",
1232
- "required": true
1233
- }
1234
- }
1235
- },
1236
- "query_schema": "\n query retrieveMultipleDrugsInfo($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n knownDrugs {\n uniqueDrugs\n uniqueDiseases\n uniqueTargets\n count\n cursor\n rows {\n approvedSymbol\n approvedName\n label\n prefName\n drugType\n targetId\n diseaseId\n drugId\n phase\n mechanismOfAction\n status\n targetClass\n references {\n source\n ids\n urls\n }\n ctIds\n urls {\n url\n name\n }\n disease {\n id\n name\n }\n target {\n id\n approvedSymbol\n }\n drug {\n id\n name\n }\n }\n }\n }\n }\n ",
1237
- "label": [
1238
- "OpenTarget",
1239
- "Drug",
1240
- "Drug Information",
1241
- "GraphQL"
1242
- ],
1243
- "type": "OpenTarget"
1244
- },
1245
- {
1246
- "name": "get_parent_child_molecules_by_drug_chembl_ID",
1247
- "description": "Get parent and child molecules of specified drug chemblId.",
1248
- "parameter": {
1249
- "type": "object",
1250
- "properties": {
1251
- "chemblId": {
1252
- "type": "string",
1253
- "description": "The ChEMBL ID of the drug.",
1254
- "required": true
1255
- }
1256
- }
1257
- },
1258
- "query_schema": "\n query retrieveMultipleDrugsInfo($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n parentMolecule {\n id\n name\n }\n childMolecules {\n id\n name\n }\n }\n }\n ",
1259
- "label": [
1260
- "OpenTarget",
1261
- "Drug",
1262
- "Drug Information",
1263
- "GraphQL"
1264
- ],
1265
- "type": "OpenTarget"
1266
- },
1267
- {
1268
- "name": "get_approved_indications_by_drug_chemblId",
1269
- "description": "Retrieve detailed information about multiple drugs using a list of ChEMBL IDs.",
1270
- "parameter": {
1271
- "type": "object",
1272
- "properties": {
1273
- "chemblId": {
1274
- "type": "string",
1275
- "description": "The ChEMBL ID of the drug.",
1276
- "required": true
1277
- }
1278
- }
1279
- },
1280
- "query_schema": "\n query retrieveMultipleDrugsInfo($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n approvedIndications\n }\n }\n ",
1281
- "label": [
1282
- "OpenTarget",
1283
- "Drug",
1284
- "Drug Information",
1285
- "GraphQL"
1286
- ],
1287
- "type": "OpenTarget"
1288
- },
1289
- {
1290
- "name": "get_drug_description_by_chemblId",
1291
- "description": "Get drug name, year of first approval, type, cross references, and max clinical trial phase based on specified chemblId.",
1292
- "parameter": {
1293
- "type": "object",
1294
- "properties": {
1295
- "chemblId": {
1296
- "type": "string",
1297
- "description": "The ChEMBL ID of the drug.",
1298
- "required": true
1299
- }
1300
- }
1301
- },
1302
- "query_schema": "\n query retrieveMultipleDrugsInfo($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n yearOfFirstApproval\n drugType\n crossReferences {\n source\n reference\n }\n maximumClinicalTrialPhase\n }\n }\n ",
1303
- "label": [
1304
- "OpenTarget",
1305
- "Drug",
1306
- "Drug Information",
1307
- "GraphQL"
1308
- ],
1309
- "type": "OpenTarget"
1310
- },
1311
- {
1312
- "name": "get_drug_synonyms_by_chemblId",
1313
- "description": "Retrieve the synonyms associated with a specific drug chemblId.",
1314
- "parameter": {
1315
- "type": "object",
1316
- "properties": {
1317
- "chemblId": {
1318
- "type": "string",
1319
- "description": "The ChEMBL ID of the drug.",
1320
- "required": true
1321
- }
1322
- }
1323
- },
1324
- "query_schema": "\n query drugSynonyms($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n synonyms\n }\n }\n ",
1325
- "examples": [
1326
- {
1327
- "question": "Can you provide the synonyms for the drug with ChEMBL ID 'CHEMBL2021430'?",
1328
- "query": {
1329
- "name": "drug_synget_drug_synonyms_by_chemblIdonyms",
1330
- "arguments": {
1331
- "chemblId": "CHEMBL2021430"
1332
- }
1333
- }
1334
- },
1335
- {
1336
- "question": "What are the synonyms associated with the drug identified by ChEMBL ID 'CHEMBL295698'?",
1337
- "query": {
1338
- "name": "get_drug_synonyms_by_chemblId",
1339
- "arguments": {
1340
- "chemblId": "CHEMBL295698"
1341
- }
1342
- }
1343
- },
1344
- {
1345
- "question": "Please list the synonyms for the drug that has the ChEMBL ID 'CHEMBL1084617'.",
1346
- "query": {
1347
- "name": "get_drug_synonyms_by_chemblId",
1348
- "arguments": {
1349
- "chemblId": "CHEMBL1084617"
1350
- }
1351
- }
1352
- }
1353
- ],
1354
- "label": [
1355
- "OpenTarget",
1356
- "Drug Information",
1357
- "Drug",
1358
- "GraphQL"
1359
- ],
1360
- "type": "OpenTarget"
1361
- },
1362
- {
1363
- "name": "get_drug_trade_names_by_chemblId",
1364
- "description": "Retrieve the trade names associated with a specific drug chemblId.",
1365
- "parameter": {
1366
- "type": "object",
1367
- "properties": {
1368
- "chemblId": {
1369
- "type": "string",
1370
- "description": "The ChEMBL ID of the drug.",
1371
- "required": true
1372
- }
1373
- }
1374
- },
1375
- "query_schema": "\n query drugTradeNames($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n tradeNames\n }\n }\n ",
1376
- "examples": [
1377
- {
1378
- "question": "What are the trade names for the drug with ChEMBL ID 'CHEMBL25'?",
1379
- "query": {
1380
- "name": "get_drug_trade_names_by_chemblId",
1381
- "arguments": {
1382
- "chemblId": "CHEMBL25"
1383
- }
1384
- }
1385
- },
1386
- {
1387
- "question": "Can you provide the trade names associated with the drug identified by ChEMBL ID 'CHEMBL1201613'?",
1388
- "query": {
1389
- "name": "get_drug_trade_names_by_chemblId",
1390
- "arguments": {
1391
- "chemblId": "CHEMBL1201613"
1392
- }
1393
- }
1394
- },
1395
- {
1396
- "question": "Please list the trade names for the drug that has the ChEMBL ID 'CHEMBL3182621'.",
1397
- "query": {
1398
- "name": "get_drug_trade_names_by_chemblId",
1399
- "arguments": {
1400
- "chemblId": "CHEMBL3182621"
1401
- }
1402
- }
1403
- }
1404
- ],
1405
- "label": [
1406
- "Drug",
1407
- "OpenTarget",
1408
- "Drug Information",
1409
- "GraphQL"
1410
- ],
1411
- "type": "OpenTarget"
1412
- },
1413
- {
1414
- "name": "get_drug_approval_status_by_chemblId",
1415
- "description": "Retrieve the approval status of a specific drug chemblId.",
1416
- "parameter": {
1417
- "type": "object",
1418
- "properties": {
1419
- "chemblId": {
1420
- "type": "string",
1421
- "description": "The ChEMBL ID of the drug.",
1422
- "required": true
1423
- }
1424
- }
1425
- },
1426
- "query_schema": "\n query drugApprovalStatus($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n isApproved\n }\n }\n ",
1427
- "examples": [
1428
- {
1429
- "question": "What is the approval status of the drug with ChEMBL ID 'CHEMBL2103799'?",
1430
- "query": {
1431
- "name": "get_drug_approval_status_by_chemblId",
1432
- "arguments": {
1433
- "chemblId": "CHEMBL2103799"
1434
- }
1435
- }
1436
- },
1437
- {
1438
- "question": "Can you tell me if the drug identified by ChEMBL ID 'CHEMBL1684' is approved?",
1439
- "query": {
1440
- "name": "get_drug_approval_status_by_chemblId",
1441
- "arguments": {
1442
- "chemblId": "CHEMBL1684"
1443
- }
1444
- }
1445
- },
1446
- {
1447
- "question": "Please provide the approval status for the drug with ChEMBL ID 'CHEMBL1086997'.",
1448
- "query": {
1449
- "name": "get_drug_approval_status_by_chemblId",
1450
- "arguments": {
1451
- "chemblId": "CHEMBL1086997"
1452
- }
1453
- }
1454
- }
1455
- ],
1456
- "label": [
1457
- "Drug",
1458
- "Drug Information",
1459
- "GraphQL",
1460
- "OpenTarget"
1461
- ],
1462
- "type": "OpenTarget"
1463
- },
1464
- {
1465
- "name": "get_chemical_probes_by_target_ensemblID",
1466
- "description": "Retrieve chemical probes associated with a specific target using its ensemblID.",
1467
- "parameter": {
1468
- "type": "object",
1469
- "properties": {
1470
- "ensemblId": {
1471
- "type": "string",
1472
- "description": "The Ensembl ID of the target for which to retrieve chemical probes.",
1473
- "required": true
1474
- }
1475
- }
1476
- },
1477
- "query_schema": "\n query getTargetChemicalProbes($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n chemicalProbes {\n id\n control\n drugId\n mechanismOfAction\n isHighQuality\n origin\n probeMinerScore\n probesDrugsScore\n scoreInCells\n scoreInOrganisms\n targetFromSourceId\n urls {\n niceName\n url\n }\n }\n }\n }\n ",
1478
- "examples": [
1479
- {
1480
- "question": "Can you retrieve the chemical probes for the target with Ensembl ID 'ENSG00000163515'?",
1481
- "query": {
1482
- "name": "get_chemical_probes_by_target_ensemblID",
1483
- "arguments": {
1484
- "ensemblId": "ENSG00000163515"
1485
- }
1486
- }
1487
- },
1488
- {
1489
- "question": "What chemical probes are associated with the target identified by Ensembl ID 'ENSG00000157916'?",
1490
- "query": {
1491
- "name": "get_chemical_probes_by_target_ensemblID",
1492
- "arguments": {
1493
- "ensemblId": "ENSG00000157916"
1494
- }
1495
- }
1496
- },
1497
- {
1498
- "question": "Please list the chemical probes linked to the target with Ensembl ID 'ENSG00000253563'.",
1499
- "query": {
1500
- "name": "get_chemical_probes_by_target_ensemblID",
1501
- "arguments": {
1502
- "ensemblId": "ENSG00000253563"
1503
- }
1504
- }
1505
- }
1506
- ],
1507
- "label": [
1508
- "OpenTarget",
1509
- "Drug Information",
1510
- "ChemicalProbe",
1511
- "GraphQL"
1512
- ],
1513
- "type": "OpenTarget"
1514
- },
1515
- {
1516
- "name": "drug_pharmacogenomics_data",
1517
- "description": "Retrieve pharmacogenomics data for a specific drug, including evidence levels and genotype annotations.",
1518
- "label": [
1519
- "Drug",
1520
- "Pharmacogenomics",
1521
- "Evidence",
1522
- "Genotype",
1523
- "Pagination",
1524
- "OpenTarget",
1525
- "GraphQL"
1526
- ],
1527
- "parameter": {
1528
- "type": "object",
1529
- "properties": {
1530
- "chemblId": {
1531
- "type": "string",
1532
- "description": "The ChEMBL ID of the drug.",
1533
- "required": true
1534
- },
1535
- "page": {
1536
- "type": "object",
1537
- "description": "Pagination options.",
1538
- "properties": {
1539
- "index": {
1540
- "type": "integer",
1541
- "description": "Pagination index.",
1542
- "required": true
1543
- },
1544
- "size": {
1545
- "type": "integer",
1546
- "description": "Number of records to fetch per page.",
1547
- "required": true
1548
- }
1549
- },
1550
- "required": false
1551
- }
1552
- }
1553
- },
1554
- "query_schema": "\n query drugPharmacogenomicsData($chemblId: String!, $page: Pagination!) {\n drug(chemblId: $chemblId) {\n id\n name\n pharmacogenomics(page: $page) {\n datasourceId\n datatypeId\n genotype\n evidenceLevel\n genotypeAnnotationText\n genotypeId\n haplotypeFromSourceId\n haplotypeId\n literature\n pgxCategory\n phenotypeFromSourceId\n phenotypeText\n studyId\n targetFromSourceId\n variantFunctionalConsequenceId\n variantRsId\n isDirectTarget\n variantFunctionalConsequence {\n id\n label\n }\n drugs {\n drugId\n drug {\n name\n }\n }\n target {\n id\n approvedSymbol\n }\n }\n }\n }\n ",
1555
- "examples": [
1556
- {
1557
- "question": "Can you provide the pharmacogenomics data for the drug with ChEMBL ID 'CHEMBL23261'?",
1558
- "query": {
1559
- "name": "drug_pharmacogenomics_data",
1560
- "arguments": {
1561
- "chemblId": "CHEMBL23261",
1562
- "page": {
1563
- "index": 1,
1564
- "size": 10
1565
- }
1566
- }
1567
- }
1568
- },
1569
- {
1570
- "question": "What are the genotype annotations and evidence levels for the drug identified by ChEMBL ID 'CHEMBL1497'?",
1571
- "query": {
1572
- "name": "drug_pharmacogenomics_data",
1573
- "arguments": {
1574
- "chemblId": "CHEMBL1497",
1575
- "page": {
1576
- "index": 2,
1577
- "size": 5
1578
- }
1579
- }
1580
- }
1581
- },
1582
- {
1583
- "question": "Retrieve the pharmacogenomics data for the drug with ChEMBL ID 'CHEMBL4455124', including evidence levels.",
1584
- "query": {
1585
- "name": "drug_pharmacogenomics_data",
1586
- "arguments": {
1587
- "chemblId": "CHEMBL4455124",
1588
- "page": {
1589
- "index": 3,
1590
- "size": 15
1591
- }
1592
- }
1593
- }
1594
- }
1595
- ],
1596
- "type": "OpenTarget"
1597
- },
1598
- {
1599
- "name": "get_associated_drugs_by_target_ensemblID",
1600
- "description": "Get known drugs associated with a specific target ensemblID, including clinical trial phase and mechanism of action of the drugs.",
1601
- "parameter": {
1602
- "type": "object",
1603
- "properties": {
1604
- "ensemblId": {
1605
- "type": "string",
1606
- "description": "The Ensembl ID of the target.",
1607
- "required": true
1608
- },
1609
- "size": {
1610
- "type": "integer",
1611
- "description": "Number of entries to fetch.",
1612
- "required": true
1613
- },
1614
- "cursor": {
1615
- "type": "string",
1616
- "description": "Cursor for pagination.",
1617
- "required": false
1618
- }
1619
- }
1620
- },
1621
- "query_schema": "\n query targetKnownDrugs($ensemblId: String!, $size: Int!, $cursor: String) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n knownDrugs(size: $size, cursor: $cursor) {\n count\n rows {\n drug {\n id\n name\n tradeNames\n maximumClinicalTrialPhase\n isApproved\n hasBeenWithdrawn\n }\n phase\n status\n mechanismOfAction\n disease {\n id\n name\n }\n }\n }\n }\n }\n ",
1622
- "examples": [
1623
- {
1624
- "question": "Can you retrieve known drugs associated with the target having Ensembl ID 'ENSG00000141736' and fetch 10 entries?",
1625
- "query": {
1626
- "name": "get_associated_drugs_by_target_ensemblID",
1627
- "arguments": {
1628
- "ensemblId": "ENSG00000141736",
1629
- "size": 10
1630
- }
1631
- }
1632
- },
1633
- {
1634
- "question": "What are the known drugs for the target with Ensembl ID 'ENSG00000184182', and can you provide 5 entries?",
1635
- "query": {
1636
- "name": "get_associated_drugs_by_target_ensemblID",
1637
- "arguments": {
1638
- "ensemblId": "ENSG00000184182",
1639
- "size": 5
1640
- }
1641
- }
1642
- },
1643
- {
1644
- "question": "Please list the known drugs associated with the target identified by Ensembl ID 'ENSG00000104884', and fetch 15 entries. Use the cursor 'abc123' for pagination.",
1645
- "query": {
1646
- "name": "get_associated_drugs_by_target_ensemblID",
1647
- "arguments": {
1648
- "ensemblId": "ENSG00000104884",
1649
- "size": 15,
1650
- "cursor": "abc123"
1651
- }
1652
- }
1653
- }
1654
- ],
1655
- "label": [
1656
- "Target",
1657
- "Drug",
1658
- "MechanismsOfAction",
1659
- "Pagination",
1660
- "OpenTarget",
1661
- "GraphQL"
1662
- ],
1663
- "type": "OpenTarget"
1664
- },
1665
- {
1666
- "name": "get_associated_diseases_by_drug_chemblId",
1667
- "description": "Retrieve the list of diseases associated with a specific drug chemblId based on clinical trial data or post-marketed drugs.",
1668
- "parameter": {
1669
- "type": "object",
1670
- "properties": {
1671
- "chemblId": {
1672
- "type": "string",
1673
- "description": "The ChEMBL ID of the drug.",
1674
- "required": true
1675
- }
1676
- }
1677
- },
1678
- "query_schema": "\n query fetchLinkedDiseasesForDrug($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n linkedDiseases {\n count\n rows {\n id\n name\n description\n }\n }\n }\n }\n ",
1679
- "examples": [
1680
- {
1681
- "question": "Can you retrieve the list of diseases linked to the drug with ChEMBL ID 'CHEMBL3137349'?",
1682
- "query": {
1683
- "name": "get_associated_diseases_by_drug_chemblId",
1684
- "arguments": {
1685
- "chemblId": "CHEMBL3137349"
1686
- }
1687
- }
1688
- },
1689
- {
1690
- "question": "What diseases are associated with the drug identified by ChEMBL ID 'CHEMBL1389'?",
1691
- "query": {
1692
- "name": "get_associated_diseases_by_drug_chemblId",
1693
- "arguments": {
1694
- "chemblId": "CHEMBL1389"
1695
- }
1696
- }
1697
- },
1698
- {
1699
- "question": "Please provide the diseases linked to the drug that has the ChEMBL ID 'CHEMBL2109266'.",
1700
- "query": {
1701
- "name": "get_associated_diseases_by_drug_chemblId",
1702
- "arguments": {
1703
- "chemblId": "CHEMBL2109266"
1704
- }
1705
- }
1706
- }
1707
- ],
1708
- "label": [
1709
- "Drug",
1710
- "Disease",
1711
- "OpenTarget",
1712
- "Drug Information",
1713
- "GraphQL"
1714
- ],
1715
- "type": "OpenTarget"
1716
- },
1717
- {
1718
- "name": "get_associated_targets_by_drug_chemblId",
1719
- "description": "Retrieve the list of targets linked to a specific drug chemblId based on its mechanism of action.",
1720
- "parameter": {
1721
- "type": "object",
1722
- "properties": {
1723
- "chemblId": {
1724
- "type": "string",
1725
- "description": "The ChEMBL ID of the drug.",
1726
- "required": true
1727
- }
1728
- }
1729
- },
1730
- "query_schema": "\n query fetchLinkedTargetsForDrug($chemblId: String!) {\n drug(chemblId: $chemblId) {\n id\n name\n linkedTargets {\n count\n rows {\n id\n approvedSymbol\n approvedName\n }\n }\n }\n }\n ",
1731
- "examples": [
1732
- {
1733
- "question": "Can you retrieve the list of targets linked to the drug with ChEMBL ID 'CHEMBL459008'?",
1734
- "query": {
1735
- "name": "get_associated_targets_by_drug_chemblId",
1736
- "arguments": {
1737
- "chemblId": "CHEMBL459008"
1738
- }
1739
- }
1740
- },
1741
- {
1742
- "question": "What are the targets associated with the drug identified by ChEMBL ID 'CHEMBL1800955'?",
1743
- "query": {
1744
- "name": "get_associated_targets_by_drug_chemblId",
1745
- "arguments": {
1746
- "chemblId": "CHEMBL1800955"
1747
- }
1748
- }
1749
- },
1750
- {
1751
- "question": "Please provide the list of targets for the drug with ChEMBL ID 'CHEMBL32'.",
1752
- "query": {
1753
- "name": "get_associated_targets_by_drug_chemblId",
1754
- "arguments": {
1755
- "chemblId": "CHEMBL32"
1756
- }
1757
- }
1758
- }
1759
- ],
1760
- "label": [
1761
- "Drug",
1762
- "Target",
1763
- "MechanismsOfAction",
1764
- "OpenTarget",
1765
- "GraphQL"
1766
- ],
1767
- "type": "OpenTarget"
1768
- },
1769
- {
1770
- "name": "multi_entity_search_by_query_string",
1771
- "description": "Perform a multi-entity search based on a query string, filtering by entity names and pagination settings.",
1772
- "parameter": {
1773
- "type": "object",
1774
- "properties": {
1775
- "queryString": {
1776
- "type": "string",
1777
- "description": "The search string for querying information.",
1778
- "required": true
1779
- },
1780
- "entityNames": {
1781
- "type": "array",
1782
- "items": {
1783
- "type": "string"
1784
- },
1785
- "description": "List of entity names to search for (e.g., target, disease, drug).",
1786
- "required": false
1787
- },
1788
- "page": {
1789
- "type": "object",
1790
- "properties": {
1791
- "index": {
1792
- "type": "integer",
1793
- "description": "Pagination index.",
1794
- "required": "True"
1795
- },
1796
- "size": {
1797
- "type": "integer",
1798
- "description": "Pagination size.",
1799
- "required": "True"
1800
- }
1801
- },
1802
- "description": "Pagination settings with index and size.",
1803
- "required": false
1804
- }
1805
- }
1806
- },
1807
- "query_schema": "\n query multiEntitySearch($queryString: String!, $entityNames: [String!], $page: Pagination) {\n search(queryString: $queryString, entityNames: $entityNames, page: $page) {\n total\n hits {\n id\n entity\n description\n name\n score\n }\n }\n }\n ",
1808
- "examples": [
1809
- {
1810
- "question": "Can you search for information on the drug 'Aspirin' and the disease 'Hypertension'?",
1811
- "query": {
1812
- "name": "multi_entity_search_by_query_string",
1813
- "arguments": {
1814
- "queryString": "Aspirin Hypertension",
1815
- "entityNames": [
1816
- "drug",
1817
- "disease"
1818
- ],
1819
- "page": {
1820
- "index": 1,
1821
- "size": 10
1822
- }
1823
- }
1824
- }
1825
- },
1826
- {
1827
- "question": "Please find details about the target 'BRCA1' with pagination settings of index 2 and size 5.",
1828
- "query": {
1829
- "name": "multi_entity_search_by_query_string",
1830
- "arguments": {
1831
- "queryString": "BRCA1",
1832
- "entityNames": [
1833
- "target"
1834
- ],
1835
- "page": {
1836
- "index": 2,
1837
- "size": 5
1838
- }
1839
- }
1840
- }
1841
- },
1842
- {
1843
- "question": "What information is available for the disease 'Diabetes'?",
1844
- "query": {
1845
- "name": "multi_entity_search_by_query_string",
1846
- "arguments": {
1847
- "queryString": "Diabetes",
1848
- "entityNames": [
1849
- "disease"
1850
- ]
1851
- }
1852
- }
1853
- }
1854
- ],
1855
- "label": [
1856
- "Search and Mapping Functions",
1857
- "MultiEntitySearch",
1858
- "Pagination",
1859
- "OpenTarget",
1860
- "GraphQL"
1861
- ],
1862
- "type": "OpenTarget"
1863
- },
1864
- {
1865
- "name": "get_gene_ontology_terms_by_goID",
1866
- "description": "Retrieve Gene Ontology terms based on a list of GO IDs.",
1867
- "parameter": {
1868
- "type": "object",
1869
- "properties": {
1870
- "goIds": {
1871
- "type": "array",
1872
- "items": {
1873
- "type": "string"
1874
- },
1875
- "description": "A list of Gene Ontology (GO) IDs to fetch the corresponding terms.",
1876
- "required": true
1877
- }
1878
- }
1879
- },
1880
- "query_schema": "\n query fetchGeneOntologyTerms($goIds: [String!]!) {\n geneOntologyTerms(goIds: $goIds) {\n id\n name\n }\n }\n ",
1881
- "examples": [
1882
- {
1883
- "question": "Can you retrieve the Gene Ontology terms for the GO IDs 'GO:0008150' and 'GO:0003674'?",
1884
- "query": {
1885
- "name": "fetch_gene_ontology_terms",
1886
- "arguments": {
1887
- "goIds": [
1888
- "GO:0008150",
1889
- "GO:0003674"
1890
- ]
1891
- }
1892
- }
1893
- },
1894
- {
1895
- "question": "What are the Gene Ontology terms associated with the GO IDs 'GO:0005575', 'GO:0003674', and 'GO:0008150'?",
1896
- "query": {
1897
- "name": "fetch_gene_ontology_terms",
1898
- "arguments": {
1899
- "goIds": [
1900
- "GO:0005575",
1901
- "GO:0003674",
1902
- "GO:0008150"
1903
- ]
1904
- }
1905
- }
1906
- },
1907
- {
1908
- "question": "Please provide the Gene Ontology terms for the following GO IDs: 'GO:0008150', 'GO:0003674', 'GO:0005575', and 'GO:0003677'.",
1909
- "query": {
1910
- "name": "fetch_gene_ontology_terms",
1911
- "arguments": {
1912
- "goIds": [
1913
- "GO:0008150",
1914
- "GO:0003674",
1915
- "GO:0005575",
1916
- "GO:0003677"
1917
- ]
1918
- }
1919
- }
1920
- }
1921
- ],
1922
- "label": [
1923
- "GeneOntology",
1924
- "Data Retrieval and Aggregation",
1925
- "OpenTarget",
1926
- "GraphQL"
1927
- ],
1928
- "type": "OpenTarget"
1929
- },
1930
- {
1931
- "name": "get_target_constraint_info_by_ensemblID",
1932
- "description": "Retrieve genetic constraint information for a specific target ensemblID, including expected and observed values, and scores.",
1933
- "parameter": {
1934
- "type": "object",
1935
- "properties": {
1936
- "ensemblId": {
1937
- "type": "string",
1938
- "description": "The Ensembl ID of the target.",
1939
- "required": true
1940
- }
1941
- }
1942
- },
1943
- "query_schema": "\n query targetConstraintInfo($ensemblId: String!) {\n target(ensemblId: $ensemblId) {\n id\n approvedSymbol\n geneticConstraint {\n constraintType\n exp\n obs\n oe\n oeLower\n oeUpper\n score\n upperBin\n upperBin6\n upperRank\n }\n }\n }\n ",
1944
- "examples": [
1945
- {
1946
- "question": "Can you provide the genetic constraint information for the target with Ensembl ID 'ENSG00000135476'?",
1947
- "query": {
1948
- "name": "target_constraint_info",
1949
- "arguments": {
1950
- "ensemblId": "ENSG00000135476"
1951
- }
1952
- }
1953
- },
1954
- {
1955
- "question": "What are the expected and observed values, and scores for the target identified by Ensembl ID 'ENSG00000290763'?",
1956
- "query": {
1957
- "name": "target_constraint_info",
1958
- "arguments": {
1959
- "ensemblId": "ENSG00000290763"
1960
- }
1961
- }
1962
- },
1963
- {
1964
- "question": "Please retrieve the genetic constraint details for the target with Ensembl ID 'ENSG00000109906'.",
1965
- "query": {
1966
- "name": "target_constraint_info",
1967
- "arguments": {
1968
- "ensemblId": "ENSG00000109906"
1969
- }
1970
- }
1971
- }
1972
- ],
1973
- "label": [
1974
- "Target",
1975
- "Constraint",
1976
- "Data Retrieval and Aggregation",
1977
- "OpenTarget",
1978
- "GraphQL"
1979
- ],
1980
- "type": "OpenTarget"
1981
- },
1982
- {
1983
- "name": "get_publications_by_disease_efoId",
1984
- "description": "Retrieve publications related to a disease efoId, including PubMed IDs and publication dates.",
1985
- "parameter": {
1986
- "type": "object",
1987
- "properties": {
1988
- "entityId": {
1989
- "type": "string",
1990
- "description": "The ID of the entity (efoId).",
1991
- "required": true
1992
- },
1993
- "additionalIds": {
1994
- "type": "array",
1995
- "items": {
1996
- "type": "string"
1997
- },
1998
- "description": "List of additional IDs to include in the search.",
1999
- "required": false
2000
- },
2001
- "startYear": {
2002
- "type": "integer",
2003
- "description": "Year at the lower end of the filter.",
2004
- "required": false
2005
- },
2006
- "startMonth": {
2007
- "type": "integer",
2008
- "description": "Month at the lower end of the filter.",
2009
- "required": false
2010
- },
2011
- "endYear": {
2012
- "type": "integer",
2013
- "description": "Year at the higher end of the filter.",
2014
- "required": false
2015
- },
2016
- "endMonth": {
2017
- "type": "integer",
2018
- "description": "Month at the higher end of the filter.",
2019
- "required": false
2020
- }
2021
- }
2022
- },
2023
- "query_schema": "\n query entityPublications($entityId: String!, $additionalIds: [String!], $startYear: Int, $startMonth: Int, $endYear: Int, $endMonth: Int) {\n disease(efoId: $entityId) {\n id\n name\n literatureOcurrences(additionalIds: $additionalIds, startYear: $startYear, startMonth: $startMonth, endYear: $endYear, endMonth: $endMonth) {\n count\n filteredCount\n earliestPubYear\n rows {\n pmid\n pmcid\n publicationDate\n sentences {\n section\n matches {\n mappedId\n matchedLabel\n sectionStart\n sectionEnd\n startInSentence\n endInSentence\n matchedType\n }\n }\n }\n }\n }\n }\n ",
2024
- "examples": [
2025
- {
2026
- "question": "Can you retrieve publications related to the entity with ID 'EFO_0000400'?",
2027
- "query": {
2028
- "name": "get_publications_by_disease_efoId",
2029
- "arguments": {
2030
- "entityId": "EFO_0000400"
2031
- }
2032
- }
2033
- }
2034
- ],
2035
- "label": [
2036
- "Publications",
2037
- "Data Retrieval and Aggregation",
2038
- "GraphQL",
2039
- "OpenTarget"
2040
- ],
2041
- "type": "OpenTarget"
2042
- },
2043
- {
2044
- "name": "get_publications_by_target_ensemblID",
2045
- "description": "Retrieve publications related to a target ensemblID, including PubMed IDs and publication dates.",
2046
- "parameter": {
2047
- "type": "object",
2048
- "properties": {
2049
- "entityId": {
2050
- "type": "string",
2051
- "description": "The ID of the entity (ensemblID).",
2052
- "required": true
2053
- },
2054
- "additionalIds": {
2055
- "type": "array",
2056
- "items": {
2057
- "type": "string"
2058
- },
2059
- "description": "List of additional IDs to include in the search.",
2060
- "required": false
2061
- },
2062
- "startYear": {
2063
- "type": "integer",
2064
- "description": "Year at the lower end of the filter.",
2065
- "required": false
2066
- },
2067
- "startMonth": {
2068
- "type": "integer",
2069
- "description": "Month at the lower end of the filter.",
2070
- "required": false
2071
- },
2072
- "endYear": {
2073
- "type": "integer",
2074
- "description": "Year at the higher end of the filter.",
2075
- "required": false
2076
- },
2077
- "endMonth": {
2078
- "type": "integer",
2079
- "description": "Month at the higher end of the filter.",
2080
- "required": false
2081
- }
2082
- }
2083
- },
2084
- "query_schema": "\n query entityPublications($entityId: String!, $additionalIds: [String!], $startYear: Int, $startMonth: Int, $endYear: Int, $endMonth: Int) {\n target(ensemblId: $entityId) {\n id\n approvedSymbol\n literatureOcurrences(additionalIds: $additionalIds, startYear: $startYear, startMonth: $startMonth, endYear: $endYear, endMonth: $endMonth) {\n count\n filteredCount\n earliestPubYear\n rows {\n pmid\n pmcid\n publicationDate\n sentences {\n section\n matches {\n mappedId\n matchedLabel\n sectionStart\n sectionEnd\n startInSentence\n endInSentence\n matchedType\n }\n }\n }\n }\n }\n }\n ",
2085
- "label": [
2086
- "Publications",
2087
- "Data Retrieval and Aggregation",
2088
- "GraphQL",
2089
- "OpenTarget"
2090
- ],
2091
- "type": "OpenTarget"
2092
- },
2093
- {
2094
- "name": "get_publications_by_drug_chemblId",
2095
- "description": "Retrieve publications related to a drug chemblId, including PubMed IDs and publication dates.",
2096
- "parameter": {
2097
- "type": "object",
2098
- "properties": {
2099
- "entityId": {
2100
- "type": "string",
2101
- "description": "The ID of the entity (chemblId).",
2102
- "required": true
2103
- },
2104
- "additionalIds": {
2105
- "type": "array",
2106
- "items": {
2107
- "type": "string"
2108
- },
2109
- "description": "List of additional IDs to include in the search.",
2110
- "required": false
2111
- },
2112
- "startYear": {
2113
- "type": "integer",
2114
- "description": "Year at the lower end of the filter.",
2115
- "required": false
2116
- },
2117
- "startMonth": {
2118
- "type": "integer",
2119
- "description": "Month at the lower end of the filter.",
2120
- "required": false
2121
- },
2122
- "endYear": {
2123
- "type": "integer",
2124
- "description": "Year at the higher end of the filter.",
2125
- "required": false
2126
- },
2127
- "endMonth": {
2128
- "type": "integer",
2129
- "description": "Month at the higher end of the filter.",
2130
- "required": false
2131
- }
2132
- }
2133
- },
2134
- "query_schema": "\n query entityPublications($entityId: String!, $additionalIds: [String!], $startYear: Int, $startMonth: Int, $endYear: Int, $endMonth: Int) {\n drug(chemblId: $entityId) {\n id\n name\n literatureOcurrences(additionalIds: $additionalIds, startYear: $startYear, startMonth: $startMonth, endYear: $endYear, endMonth: $endMonth) {\n count\n filteredCount\n earliestPubYear\n rows {\n pmid\n pmcid\n publicationDate\n sentences {\n section\n matches {\n mappedId\n matchedLabel\n sectionStart\n sectionEnd\n startInSentence\n endInSentence\n matchedType\n }\n }\n }\n }\n }\n }\n ",
2135
- "label": [
2136
- "Publications",
2137
- "Data Retrieval and Aggregation",
2138
- "GraphQL",
2139
- "OpenTarget"
2140
- ],
2141
- "type": "OpenTarget"
2142
- },
2143
- {
2144
- "name": "get_target_id_description_by_name",
2145
- "description": "Get the ensemblId and description based on the target name.",
2146
- "parameter": {
2147
- "type": "object",
2148
- "properties": {
2149
- "targetName": {
2150
- "type": "string",
2151
- "description": "The name of the target for which the ID is required.",
2152
- "required": true
2153
- }
2154
- }
2155
- },
2156
- "query_schema": "\n query getTargetIdByName($targetName: String!) {\n search(queryString: $targetName, entityNames: [\"target\"]) {\n hits {\n id\n name\n description\n }\n }\n }\n ",
2157
- "label": [
2158
- "Search",
2159
- "Name",
2160
- "Target",
2161
- "OpenTarget",
2162
- "GraphQL"
2163
- ],
2164
- "type": "OpenTarget"
2165
- }
2166
- ]