BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases
Paper • 2505.20321 • Published • 5
Datasets:
uuid stringlengths 4 8 | template_uuid stringclasses 40
values | question stringlengths 13 193 | answer stringlengths 29 2.2k | benchmark_query stringlengths 133 622 | execution_results stringlengths 2 1.14M | query_type stringclasses 2
values | sql_category stringclasses 26
values | bio_category stringclasses 14
values |
|---|---|---|---|---|---|---|---|---|
Q1.1450 | Q1 | Is TNFRSF4 a druggable gene? | There are currently no approved drugs targeting TNFRSF4, but there are 5 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%TNFRSF4 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_3441', 'drugName': 'Ivuxolimab', 'drugIsApproved': False, 'newLinkedTargets_string': 'TNFRSF4 (ENSG00000186827)', 'maxClinicalTrialPhase': 3}, {'UUID': 'DrugGeneTargets_v2_4001', 'drugName': 'Khk-4083', 'drugIsApproved': False, 'newLinkedTargets_string': 'TNFRSF4 (ENSG00000186827)', 'maxCl... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.78 | Q1 | Is ARAF a druggable gene? | There are currently no approved drugs targeting ARAF, but there are 3 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%ARAF %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_4331', 'drugName': 'Tovorafenib', 'drugIsApproved': False, 'newLinkedTargets_string': 'RAF1 (ENSG00000132155), BRAF (ENSG00000157764), ARAF (ENSG00000078061)', 'maxClinicalTrialPhase': 2}, {'UUID': 'DrugGeneTargets_v2_3033', 'drugName': 'Belvarafenib', 'drugIsApproved': False, 'newLinkedTa... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1016 | Q1 | Is NTSR1 a druggable gene? | There are currently no approved drugs targeting NTSR1, but there is 1 drug in a clinical trial indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%NTSR1 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_4907', 'drugName': 'Reminertant', 'drugIsApproved': False, 'newLinkedTargets_string': 'NTSR1 (ENSG00000101188)', 'maxClinicalTrialPhase': 3}] | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.664 | Q1 | Is IKBKB a druggable gene? | There are currently no approved drugs targeting IKBKB, but there are 7 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%IKBKB %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_4921', 'drugName': 'Bardoxolone Methyl', 'drugIsApproved': False, 'newLinkedTargets_string': 'NFE2L2 (ENSG00000116044), KEAP1 (ENSG00000079999), PPARG (ENSG00000132170), IKBKB (ENSG00000104365)', 'maxClinicalTrialPhase': 3}, {'UUID': 'DrugGeneTargets_v2_4920', 'drugName': 'Bardoxolone Meth... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1140 | Q1 | Is PRKCI a druggable gene? | There is 1 drug, Midostaurin, that targets PRKCI, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%PRKCI %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_5666', 'drugName': 'Midostaurin', 'drugIsApproved': True, 'newLinkedTargets_string': 'KIT (ENSG00000157404), KDR (ENSG00000128052), PDGFRB (ENSG00000113721), PDGFRA (ENSG00000134853), FLT3 (ENSG00000122025), PRKD3 (ENSG00000115825), PRKCI (ENSG00000163558), PRKCA (ENSG00000154229), PRKCG (... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.988 | Q1 | Is NOS3 a druggable gene? | There are currently no approved drugs targeting NOS3, but there are 2 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%NOS3 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_890', 'drugName': 'Tilarginine', 'drugIsApproved': False, 'newLinkedTargets_string': 'NOS1 (ENSG00000089250), NOS2 (ENSG00000007171), NOS3 (ENSG00000164867)', 'maxClinicalTrialPhase': 3}, {'UUID': 'DrugGeneTargets_v2_1662', 'drugName': 'Tilarginine Acetate', 'drugIsApproved': False, 'newLi... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1421 | Q1 | Is TFR2 a druggable gene? | There are currently no approved drugs targeting TFR2, but there are 2 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%TFR2 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_3234', 'drugName': 'Pabinafusp Alfa', 'drugIsApproved': False, 'newLinkedTargets_string': 'TFRC (ENSG00000072274), TFR2 (ENSG00000106327)', 'maxClinicalTrialPhase': 3}, {'UUID': 'DrugGeneTargets_v2_4473', 'drugName': 'E2.3', 'drugIsApproved': False, 'newLinkedTargets_string': 'TFRC (ENSG00... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1509 | Q1 | Is TUBB8B a druggable gene? | There are currently no approved drugs targeting TUBB8B, but there is 1 drug in a clinical trial indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%TUBB8B %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_3400', 'drugName': 'Abt-751', 'drugIsApproved': False, 'newLinkedTargets_string': 'TUBB4B (ENSG00000188229), TUBB1 (ENSG00000101162), TUBB3 (ENSG00000258947), TUBB4A (ENSG00000104833), TUBB8 (ENSG00000261456), TUBB (ENSG00000196230), TUBB2A (ENSG00000137267), TUBB2B (ENSG00000137285), TUBB... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1345 | Q1 | Is SELE a druggable gene? | There are currently no approved drugs targeting SELE, but there are 4 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%SELE %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_2473', 'drugName': 'Rivipansel', 'drugIsApproved': False, 'newLinkedTargets_string': 'SELE (ENSG00000007908), SELP (ENSG00000174175), SELL (ENSG00000188404)', 'maxClinicalTrialPhase': 3}, {'UUID': 'DrugGeneTargets_v2_2474', 'drugName': 'Rivipansel', 'drugIsApproved': False, 'newLinkedTarge... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1197 | Q1 | Is PTGS1 a druggable gene? | There are currently 61 approved drugs which target PTGS1, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%PTGS1 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_2814', 'drugName': 'Dipyrone', 'drugIsApproved': True, 'newLinkedTargets_string': 'PTGS2 (ENSG00000073756), PTGS1 (ENSG00000095303)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_5291', 'drugName': 'Naproxen Sodium', 'drugIsApproved': True, 'newLinkedTargets_string': 'PTGS2 (E... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1215 | Q1 | Is RELA a druggable gene? | There are currently no approved drugs targeting RELA, but there is 1 drug in a clinical trial indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%RELA %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_1568', 'drugName': 'Edasalonexent', 'drugIsApproved': False, 'newLinkedTargets_string': 'NFKB2 (ENSG00000077150), NFKB1 (ENSG00000109320), RELA (ENSG00000173039)', 'maxClinicalTrialPhase': 3}] | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.632 | Q1 | Is HTT a druggable gene? | There are currently no approved drugs targeting HTT, but there is 1 drug in a clinical trial indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%HTT %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_3493', 'drugName': 'Tominersen', 'drugIsApproved': False, 'newLinkedTargets_string': 'HTT (ENSG00000197386)', 'maxClinicalTrialPhase': 3}] | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.396 | Q1 | Is EGLN3 a druggable gene? | There is 1 drug, Roxadustat, that targets EGLN3, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%EGLN3 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_5393', 'drugName': 'Roxadustat', 'drugIsApproved': True, 'newLinkedTargets_string': 'EGLN2 (ENSG00000269858), P4HTM (ENSG00000178467), EGLN1 (ENSG00000135766), EGLN3 (ENSG00000129521)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_2677', 'drugName': 'Daprodustat', 'drugIsAppro... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1489 | Q1 | Is TSHR a druggable gene? | There are currently 2 approved drugs which target TSHR, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%TSHR %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_2659', 'drugName': 'Thyrotropin Alfa', 'drugIsApproved': True, 'newLinkedTargets_string': 'TSHR (ENSG00000165409)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_3423', 'drugName': 'Thyrotropin', 'drugIsApproved': True, 'newLinkedTargets_string': 'TSHR (ENSG00000165409)', 'maxC... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.517 | Q1 | Is GHR a druggable gene? | There are currently 6 approved drugs which target GHR, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%GHR %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_3588', 'drugName': 'Somapacitan', 'drugIsApproved': True, 'newLinkedTargets_string': 'GHR (ENSG00000112964)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_1805', 'drugName': 'Pegvisomant', 'drugIsApproved': True, 'newLinkedTargets_string': 'GHR (ENSG00000112964)', 'maxClinical... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.630 | Q1 | Is HTR6 a druggable gene? | There are currently 5 approved drugs which target HTR6, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%HTR6 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_2863', 'drugName': 'Dexfenfluramine', 'drugIsApproved': True, 'newLinkedTargets_string': 'HTR1F (ENSG00000179097), HTR2B (ENSG00000135914), HTR4 (ENSG00000164270), HTR1B (ENSG00000135312), HTR3A (ENSG00000166736), HTR1A (ENSG00000178394), HTR1D (ENSG00000179546), HTR2A (ENSG00000102468), H... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1122 | Q1 | Is PRIM1 a druggable gene? | There are currently 5 approved drugs which target PRIM1, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%PRIM1 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_4', 'drugName': 'Gemcitabine Hydrochloride', 'drugIsApproved': True, 'newLinkedTargets_string': 'POLA1 (ENSG00000101868), POLD4 (ENSG00000175482), POLD3 (ENSG00000077514), POLD1 (ENSG00000062822), POLD2 (ENSG00000106628), POLE (ENSG00000177084), POLA2 (ENSG00000014138), PRIM1 (ENSG00000198... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.31 | Q1 | Is ADORA3 a druggable gene? | There are currently 8 approved drugs which target ADORA3, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%ADORA3 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_5471', 'drugName': 'Aminophylline', 'drugIsApproved': True, 'newLinkedTargets_string': 'PDE4A (ENSG00000065989), PDE4D (ENSG00000113448), PDE4B (ENSG00000184588), PDE4C (ENSG00000105650), PDE3A (ENSG00000172572), PDE3B (ENSG00000152270), ADORA1 (ENSG00000163485), ADORA2B (ENSG00000170425),... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.50 | Q1 | Is AKT2 a druggable gene? | There are currently no approved drugs targeting AKT2, but there are 14 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%AKT2 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_2935', 'drugName': 'Ipatasertib', 'drugIsApproved': False, 'newLinkedTargets_string': 'AKT2 (ENSG00000105221), AKT3 (ENSG00000117020), AKT1 (ENSG00000142208)', 'maxClinicalTrialPhase': 3}, {'UUID': 'DrugGeneTargets_v2_6037', 'drugName': 'Capivasertib', 'drugIsApproved': False, 'newLinkedTa... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.242 | Q1 | Is CDK20 a druggable gene? | There are currently no approved drugs targeting CDK20, but there are 4 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%CDK20 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_1429', 'drugName': 'Roniciclib', 'drugIsApproved': False, 'newLinkedTargets_string': 'CDK1 (ENSG00000170312), CDK4 (ENSG00000135446), CDK2 (ENSG00000123374), CDK5 (ENSG00000164885), CDK6 (ENSG00000105810), CDK7 (ENSG00000134058), CDK3 (ENSG00000250506), CDK16 (ENSG00000102225), CDK18 (ENSG... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.431 | Q1 | Is ESR2 a druggable gene? | There are currently 22 approved drugs which target ESR2, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%ESR2 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_1689', 'drugName': 'Toremifene Citrate', 'drugIsApproved': True, 'newLinkedTargets_string': 'ESR2 (ENSG00000140009), ESR1 (ENSG00000091831)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_4127', 'drugName': 'Diethylstilbestrol Diphosphate', 'drugIsApproved': True, 'newLinkedTar... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.353 | Q1 | Is CYSLTR1 a druggable gene? | There are currently 3 approved drugs which target CYSLTR1, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%CYSLTR1 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_2453', 'drugName': 'Montelukast Sodium', 'drugIsApproved': True, 'newLinkedTargets_string': 'CYSLTR1 (ENSG00000173198)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_3211', 'drugName': 'Zafirlukast', 'drugIsApproved': True, 'newLinkedTargets_string': 'CYSLTR1 (ENSG00000173198)... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.126 | Q1 | Is C1S a druggable gene? | There are currently 2 approved drugs which target C1S, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%C1S %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_2064', 'drugName': 'Human C1-Esterase Inhibitor', 'drugIsApproved': True, 'newLinkedTargets_string': 'C1S (ENSG00000182326), F11 (ENSG00000088926), KLKB1 (ENSG00000164344), F12 (ENSG00000131187)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_3495', 'drugName': 'Sutimlimab', 'd... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.554 | Q1 | Is GRIN3B a druggable gene? | There are currently 14 approved drugs which target GRIN3B, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%GRIN3B %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_6209', 'drugName': 'Orphenadrine Citrate', 'drugIsApproved': True, 'newLinkedTargets_string': 'GRIN1 (ENSG00000176884), GRIN2A (ENSG00000183454), GRIN2B (ENSG00000273079), GRIN2D (ENSG00000105464), GRIN3B (ENSG00000116032), GRIN2C (ENSG00000161509), GRIN3A (ENSG00000198785), HRH1 (ENSG0000... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1502 | Q1 | Is TUBB2A a druggable gene? | There are currently 20 approved drugs which target TUBB2A, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%TUBB2A %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_1084', 'drugName': 'Brentuximab Vedotin', 'drugIsApproved': True, 'newLinkedTargets_string': 'TNFRSF8 (ENSG00000120949), TUBB4B (ENSG00000188229), TUBB1 (ENSG00000101162), TUBA3C (ENSG00000198033), TUBA4A (ENSG00000127824), TUBB3 (ENSG00000258947), TUBA1A (ENSG00000167552), TUBB4A (ENSG000... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.71 | Q1 | Is APH1A a druggable gene? | There are currently no approved drugs targeting APH1A, but there are 6 drugs in clinical trials indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%APH1A %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_5562', 'drugName': 'Nirogacestat', 'drugIsApproved': False, 'newLinkedTargets_string': 'APH1A (ENSG00000117362), PSENEN (ENSG00000205155), APH1B (ENSG00000138613), PSEN1 (ENSG00000080815), NCSTN (ENSG00000162736), PSEN2 (ENSG00000143801)', 'maxClinicalTrialPhase': 3}, {'UUID': 'DrugGeneTar... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1118 | Q1 | Is PPP2CA a druggable gene? | There are currently no approved drugs targeting PPP2CA, but there is 1 drug in a clinical trial indicating that it may be a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%PPP2CA %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_4335', 'drugName': 'Lb-100', 'drugIsApproved': False, 'newLinkedTargets_string': 'PPP2CA (ENSG00000113575), PPP5C (ENSG00000011485), PPP2CB (ENSG00000104695)', 'maxClinicalTrialPhase': 2}, {'UUID': 'DrugGeneTargets_v2_4336', 'drugName': 'Lb-100', 'drugIsApproved': False, 'newLinkedTargets_... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1038 | Q1 | Is PCSK9 a druggable gene? | There are currently 4 approved drugs which target PCSK9, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%PCSK9 %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_1637', 'drugName': 'Alirocumab', 'drugIsApproved': True, 'newLinkedTargets_string': 'PCSK9 (ENSG00000169174)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_4738', 'drugName': 'Inclisiran Sodium', 'drugIsApproved': True, 'newLinkedTargets_string': 'PCSK9 (ENSG00000169174)', 'ma... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
Q1.1097 | Q1 | Is PMEL a druggable gene? | There is 1 drug, Tebentafusp, that targets PMEL, indicating that it is a druggable gene. | SELECT DISTINCT UUID, drugName, drugIsApproved, newLinkedTargets_string, maxClinicalTrialPhase
FROM `{project_id}.{dataset_name}.DrugGeneTargets_ComprehensiveAnnotations_updated`
WHERE newLinkedTargets_string LIKE "%PMEL %"
ORDER BY maxClinicalTrialPhase DESC
LIMIT 100
| [{'UUID': 'DrugGeneTargets_v2_5977', 'drugName': 'Tebentafusp', 'drugIsApproved': True, 'newLinkedTargets_string': 'PMEL (ENSG00000185664)', 'maxClinicalTrialPhase': 4}, {'UUID': 'DrugGeneTargets_v2_5274', 'drugName': 'Imc-Gp100', 'drugIsApproved': False, 'newLinkedTargets_string': 'PMEL (ENSG00000185664), CD3E (ENSG00... | general | Similarity Search, Order By, Distinct | Approval Status, Genetic Target |
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BiomedSQL
Dataset Summary
BiomedSQL is a text-to-SQL benchmark designed to evaluate Large Language Models (LLMs) on scientific tabular reasoning tasks. It consists of curated question-SQL query-answer triples covering a variety of biomedical and SQL reasoning types. The benchmark challenges models to apply implicit
scientific criteria rather than simply translating syntax.
Repository Organization
- benchmark_data: contains the question-SQL query-answer triples.
- Please note that you will have to replace the
{project_id}and{dataset_name}placeholder strings in thebenchmark_querycolumn with the names of the GCP project and BigQuery dataset that you create if you wish to rerun them. Our GitHub code automatically handles this entity replacement through.envconfigurations when running experiment code.
- Please note that you will have to replace the
- db_data: contains the parquet files needed to recreate the tables in the evaluation database.
- Downloads last month
- 100
Size of downloaded dataset files:
345 MB
Size of the auto-converted Parquet files:
35.1 MB
Number of rows:
68,227