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adding neo4j rag
This commit is contained in:
Karthik Soman
101
data/rag_comparison_data.csv
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data/rag_comparison_data.csv
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disease_name,gene_name,gwas_pvalue,question
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childhood-onset asthma,RORA,2e-37,What is the GWAS p-value for the association between childhood-onset asthma and RORA?
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skin benign neoplasm,SHANK2,5e-08,What is the GWAS p-value for the association between SHANK2 and skin benign neoplasm?
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hypertrophic cardiomyopathy,AMBRA1,1e-16,Is hypertrophic cardiomyopathy associated with AMBRA1?
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lung adenocarcinoma,CYP2A6,8e-11,What is the GWAS p-value for the association between CYP2A6 and lung adenocarcinoma?
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idiopathic generalized epilepsy,RYR2,3e-09,Is idiopathic generalized epilepsy associated with RYR2?
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gastric fundus cancer,PLCE1,2e-22,What is the GWAS p-value for the association between PLCE1 and gastric fundus cancer?
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hypertrophic cardiomyopathy,VTI1A,4e-12,Is VTI1A associated with hypertrophic cardiomyopathy?
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peptic ulcer disease,TTC33,5e-25,Is peptic ulcer disease associated with TTC33?
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multiple sclerosis,TSPAN31,2e-09,Is multiple sclerosis associated with TSPAN31?
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large intestine cancer,ABHD12B,7e-09,What is the GWAS p-value for the association between ABHD12B and large intestine cancer?
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prostate carcinoma,ESR2,7e-12,What is the GWAS p-value for the association between ESR2 and prostate carcinoma?
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inflammatory bowel disease,SH2B3,1e-09,What is the GWAS p-value for the association between inflammatory bowel disease and SH2B3?
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mastocytosis,FTCD,1e-09,What is the GWAS p-value for the association between mastocytosis and FTCD?
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major depressive disorder,FURIN,3e-19,What is the GWAS p-value for the association between FURIN and major depressive disorder?
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testicular cancer,TERT,8e-15,Is testicular cancer associated with TERT?
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type 2 diabetes mellitus,SLC24A3,3e-17,Is SLC24A3 associated with type 2 diabetes mellitus?
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celiac disease,PLEK,8e-09,Is celiac disease associated with PLEK?
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endometrial carcinoma,CPVL,2e-08,What is the GWAS p-value for the association between endometrial carcinoma and CPVL?
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allergic disease,ZNF652,1e-15,Is allergic disease associated with ZNF652?
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systemic lupus erythematosus,ELF3,4e-09,What is the GWAS p-value for the association between systemic lupus erythematosus and ELF3?
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hemorrhoid,GMDS,2e-31,Is GMDS associated with hemorrhoid?
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rheumatoid arthritis,DPP4,2e-21,What is the GWAS p-value for the association between rheumatoid arthritis and DPP4?
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colon carcinoma,SMAD7,3e-08,What is the GWAS p-value for the association between SMAD7 and colon carcinoma?
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pulmonary hypertension,PKIA,2e-09,What is the GWAS p-value for the association between PKIA and pulmonary hypertension?
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autoimmune thyroiditis,TNFRSF14,2e-11,What is the GWAS p-value for the association between autoimmune thyroiditis and TNFRSF14?
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psoriatic arthritis,CNTNAP2,5e-28,Is psoriatic arthritis associated with CNTNAP2?
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primary biliary cholangitis,CCDC88B,1e-10,Is primary biliary cholangitis associated with CCDC88B?
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otosclerosis,MARK3,3e-18,Is MARK3 associated with otosclerosis?
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large intestine cancer,RHPN2,4e-41,What is the GWAS p-value for the association between RHPN2 and large intestine cancer?
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anxiety disorder,NTRK2,7e-09,Is anxiety disorder associated with NTRK2?
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atopic dermatitis,RERE,6e-16,Is atopic dermatitis associated with RERE?
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asthma,PRR5L,6e-12,Is PRR5L associated with asthma?
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gastric fundus cancer,GON4L,1e-15,What is the GWAS p-value for the association between gastric fundus cancer and GON4L?
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type 2 diabetes mellitus,DNAH1,7e-21,Is type 2 diabetes mellitus associated with DNAH1?
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schizophrenia,SLC17A3,3e-20,What is the GWAS p-value for the association between schizophrenia and SLC17A3?
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inflammatory bowel disease,FADS2,2e-15,What is the GWAS p-value for the association between inflammatory bowel disease and FADS2?
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opiate dependence,ADGRV1,2e-09,Is opiate dependence associated with ADGRV1?
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attention deficit hyperactivity disorder,ST3GAL3,8e-14,What is the GWAS p-value for the association between attention deficit hyperactivity disorder and ST3GAL3?
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cataract,C3orf49,2e-11,Is C3orf49 associated with cataract?
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duodenal ulcer,PLD1,5e-08,What is the GWAS p-value for the association between PLD1 and duodenal ulcer?
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chronic obstructive pulmonary disease,CHRNA3,5e-28,What is the GWAS p-value for the association between CHRNA3 and chronic obstructive pulmonary disease?
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pancreatic carcinoma,CCDC68,5e-09,What is the GWAS p-value for the association between pancreatic carcinoma and CCDC68?
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primary biliary cholangitis,HLA-DPB1,2e-22,Is HLA-DPB1 associated with primary biliary cholangitis?
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atopic dermatitis,GABPB2,2e-88,Is atopic dermatitis associated with GABPB2?
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systemic lupus erythematosus,HIP1,6e-62,What is the GWAS p-value for the association between HIP1 and systemic lupus erythematosus?
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hypothyroidism,TIMMDC1,3e-09,Is hypothyroidism associated with TIMMDC1?
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degenerative myopia,MIPEP,2e-16,What is the GWAS p-value for the association between degenerative myopia and MIPEP?
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alcoholic pancreatitis,CASP9,6e-09,Is alcoholic pancreatitis associated with CASP9?
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lung squamous cell carcinoma,PDS5B,9e-12,Is lung squamous cell carcinoma associated with PDS5B?
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common variable immunodeficiency,CLEC16A,2e-09,What is the GWAS p-value for the association between CLEC16A and common variable immunodeficiency?
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lung non-small cell carcinoma,TERT,1e-42,Is TERT associated with lung non-small cell carcinoma?
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cardiovascular system disease,PSMD3,1e-20,Is PSMD3 associated with cardiovascular system disease?
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gestational diabetes,CCND2,3e-12,What is the GWAS p-value for the association between gestational diabetes and CCND2?
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major depressive disorder,TMEM106B,8e-24,Is TMEM106B associated with major depressive disorder?
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keratoconus,COL6A1,9e-12,What is the GWAS p-value for the association between COL6A1 and keratoconus?
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chronic lymphocytic leukemia,RREB1,1e-08,Is chronic lymphocytic leukemia associated with RREB1?
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prostate carcinoma,PARPBP,3e-13,Is PARPBP associated with prostate carcinoma?
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testicular germ cell cancer,ZFP64,3e-12,What is the GWAS p-value for the association between testicular germ cell cancer and ZFP64?
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psoriasis,KLF13,9e-10,What is the GWAS p-value for the association between KLF13 and psoriasis?
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coronary artery disease,ADGRL3,3e-23,Is coronary artery disease associated with ADGRL3?
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abdominal obesity-metabolic syndrome 1,JMJD1C,2e-14,What is the GWAS p-value for the association between abdominal obesity-metabolic syndrome 1 and JMJD1C?
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type 1 diabetes mellitus,CUX2,1e-16,Is CUX2 associated with type 1 diabetes mellitus?
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type 2 diabetes mellitus,KCNK16,4e-17,What is the GWAS p-value for the association between KCNK16 and type 2 diabetes mellitus?
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type 1 diabetes mellitus,DGKQ,6e-09,Is type 1 diabetes mellitus associated with DGKQ?
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refractive error,SIX6,2e-16,What is the GWAS p-value for the association between SIX6 and refractive error?
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Parkinson's disease,MAP4K4,8e-13,What is the GWAS p-value for the association between MAP4K4 and Parkinson's disease?
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autism spectrum disorder,DCC,3e-08,Is autism spectrum disorder associated with DCC?
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multiple sclerosis,NR1D1,9e-14,Is multiple sclerosis associated with NR1D1?
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coronary artery disease,SMAD3,1e-19,Is coronary artery disease associated with SMAD3?
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prostate carcinoma,ANO7,8e-43,What is the GWAS p-value for the association between ANO7 and prostate carcinoma?
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ovarian carcinoma,FGFR2,4e-254,What is the GWAS p-value for the association between FGFR2 and ovarian carcinoma?
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lymphoid leukemia,BMF,1e-10,What is the GWAS p-value for the association between BMF and lymphoid leukemia?
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skin melanoma,CYP1B1,3e-16,Is skin melanoma associated with CYP1B1?
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myositis,ATP6V1G2,6e-49,What is the GWAS p-value for the association between myositis and ATP6V1G2?
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melanoma,SPG7,9e-26,What is the GWAS p-value for the association between SPG7 and melanoma?
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type 2 diabetes mellitus,EYA2,6e-19,Is EYA2 associated with type 2 diabetes mellitus?
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carpal tunnel syndrome,SERPINA1,3e-24,What is the GWAS p-value for the association between SERPINA1 and carpal tunnel syndrome?
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substance-related disorder,FUT2,3e-19,What is the GWAS p-value for the association between substance-related disorder and FUT2?
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open-angle glaucoma,PLEKHA7,9e-15,Is open-angle glaucoma associated with PLEKHA7?
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myocardial infarction,ZNF831,1e-08,What is the GWAS p-value for the association between myocardial infarction and ZNF831?
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squamous cell carcinoma,IRF4,1e-169,Is IRF4 associated with squamous cell carcinoma?
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Parkinson's disease,WDHD1,4e-16,What is the GWAS p-value for the association between WDHD1 and Parkinson's disease?
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cataract,TOP1,1e-11,Is cataract associated with TOP1?
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atrial fibrillation,AGBL4,3e-09,What is the GWAS p-value for the association between atrial fibrillation and AGBL4?
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otosclerosis,SEMA4D,4e-09,What is the GWAS p-value for the association between otosclerosis and SEMA4D?
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hypothyroidism,RAD51B,2e-11,What is the GWAS p-value for the association between hypothyroidism and RAD51B?
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childhood-onset asthma,SPSB1,4e-18,What is the GWAS p-value for the association between SPSB1 and childhood-onset asthma?
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major depressive disorder,ATG7,5e-08,Is major depressive disorder associated with ATG7?
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alopecia,WNT10A,2e-16,Is WNT10A associated with alopecia?
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inflammatory bowel disease,IL27,1e-21,Is inflammatory bowel disease associated with IL27?
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tonsillitis,TNFRSF13B,8e-26,What is the GWAS p-value for the association between tonsillitis and TNFRSF13B?
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cleft lip,SFI1,3e-08,What is the GWAS p-value for the association between cleft lip and SFI1?
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multiple sclerosis,INAVA,6e-21,What is the GWAS p-value for the association between multiple sclerosis and INAVA?
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esophageal carcinoma,CASP8,1e-08,Is esophageal carcinoma associated with CASP8?
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skin melanoma,GPRC5A,8e-15,Is skin melanoma associated with GPRC5A?
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lung squamous cell carcinoma,BRCA2,1e-15,Is lung squamous cell carcinoma associated with BRCA2?
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systemic lupus erythematosus,HLA-DRA,2e-60,What is the GWAS p-value for the association between HLA-DRA and systemic lupus erythematosus?
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type 2 diabetes mellitus,UBE2E2,2e-42,Is type 2 diabetes mellitus associated with UBE2E2?
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allergic rhinitis,HLA-DQA1,1e-43,What is the GWAS p-value for the association between HLA-DQA1 and allergic rhinitis?
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systemic lupus erythematosus,HLA-DQA1,1e-54,What is the GWAS p-value for the association between systemic lupus erythematosus and HLA-DQA1?
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101
data/results/neo4j_rag_output.csv
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101
data/results/neo4j_rag_output.csv
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disease_name,gene_name,gwas_pvalue,question,neo4j_rag_answer,total_tokens_used
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childhood-onset asthma,RORA,2e-37,What is the GWAS p-value for the association between childhood-onset asthma and RORA?,The GWAS p-value for the association between childhood-onset asthma and RORA is 2e-37.,8015
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skin benign neoplasm,SHANK2,5e-08,What is the GWAS p-value for the association between SHANK2 and skin benign neoplasm?,The GWAS p-value for the association between SHANK2 and skin benign neoplasm is 5e-08.,8022
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hypertrophic cardiomyopathy,AMBRA1,1e-16,Is hypertrophic cardiomyopathy associated with AMBRA1?,"Yes, hypertrophic cardiomyopathy is associated with AMBRA1.",7996
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lung adenocarcinoma,CYP2A6,8e-11,What is the GWAS p-value for the association between CYP2A6 and lung adenocarcinoma?,The GWAS p-value for the association between CYP2A6 and lung adenocarcinoma is 8e-11.,8034
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idiopathic generalized epilepsy,RYR2,3e-09,Is idiopathic generalized epilepsy associated with RYR2?,"Yes, idiopathic generalized epilepsy is associated with RYR2.",7992
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gastric fundus cancer,PLCE1,2e-22,What is the GWAS p-value for the association between PLCE1 and gastric fundus cancer?,The GWAS p-value for the association between PLCE1 and gastric fundus cancer is 2e-22.,8020
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hypertrophic cardiomyopathy,VTI1A,4e-12,Is VTI1A associated with hypertrophic cardiomyopathy?,"I'm sorry, but I don't have the information to answer that question.",7983
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peptic ulcer disease,TTC33,5e-25,Is peptic ulcer disease associated with TTC33?,"Yes, peptic ulcer disease is associated with TTC33, which is a gene located on chromosome 5 and is also known as tetratricopeptide repeat domain 33.",8317
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multiple sclerosis,TSPAN31,2e-09,Is multiple sclerosis associated with TSPAN31?,"Yes, multiple sclerosis is associated with TSPAN31.",7981
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large intestine cancer,ABHD12B,7e-09,What is the GWAS p-value for the association between ABHD12B and large intestine cancer?,,7857
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prostate carcinoma,ESR2,7e-12,What is the GWAS p-value for the association between ESR2 and prostate carcinoma?,The GWAS p-value for the association between ESR2 and prostate carcinoma is 7e-12.,8011
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inflammatory bowel disease,SH2B3,1e-09,What is the GWAS p-value for the association between inflammatory bowel disease and SH2B3?,The GWAS p-value for the association between inflammatory bowel disease and SH2B3 is 1e-09.,8019
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mastocytosis,FTCD,1e-09,What is the GWAS p-value for the association between mastocytosis and FTCD?,The GWAS p-value for the association between mastocytosis and FTCD is 1e-09.,8014
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major depressive disorder,FURIN,3e-19,What is the GWAS p-value for the association between FURIN and major depressive disorder?,The GWAS p-value for the association between FURIN and major depressive disorder is 3e-19.,8014
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testicular cancer,TERT,8e-15,Is testicular cancer associated with TERT?,"Yes, testicular cancer is associated with TERT.",7981
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type 2 diabetes mellitus,SLC24A3,3e-17,Is SLC24A3 associated with type 2 diabetes mellitus?,"Yes, the gene SLC24A3, also known as solute carrier family 24 member 3, which is located on chromosome 20, is associated with type 2 diabetes mellitus.",8194
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celiac disease,PLEK,8e-09,Is celiac disease associated with PLEK?,"Yes, celiac disease is associated with PLEK. PLEK, or pleckstrin, is a gene located on chromosome 2. This association is based on information from the Disease Ontology and Entrez Gene sources.",8412
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endometrial carcinoma,CPVL,2e-08,What is the GWAS p-value for the association between endometrial carcinoma and CPVL?,The GWAS p-value for the association between endometrial carcinoma and CPVL is 2e-08.,8196
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allergic disease,ZNF652,1e-15,Is allergic disease associated with ZNF652?,"Yes, the allergic disease is associated with ZNF652, which is a zinc finger protein.",8128
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systemic lupus erythematosus,ELF3,4e-09,What is the GWAS p-value for the association between systemic lupus erythematosus and ELF3?,The GWAS p-value for the association between systemic lupus erythematosus and ELF3 is 4e-09.,8028
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hemorrhoid,GMDS,2e-31,Is GMDS associated with hemorrhoid?,"No, GMDS is not associated with hemorrhoids.",7979
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rheumatoid arthritis,DPP4,2e-21,What is the GWAS p-value for the association between rheumatoid arthritis and DPP4?,The GWAS p-value for the association between rheumatoid arthritis and DPP4 is 2e-21.,8019
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colon carcinoma,SMAD7,3e-08,What is the GWAS p-value for the association between SMAD7 and colon carcinoma?,The GWAS p-value for the association between SMAD7 and colon carcinoma is 3e-08.,8010
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pulmonary hypertension,PKIA,2e-09,What is the GWAS p-value for the association between PKIA and pulmonary hypertension?,The GWAS p-value for the association between PKIA and pulmonary hypertension is 2e-09.,8008
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autoimmune thyroiditis,TNFRSF14,2e-11,What is the GWAS p-value for the association between autoimmune thyroiditis and TNFRSF14?,The GWAS p-value for the association between autoimmune thyroiditis and TNFRSF14 is 2e-11.,8019
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psoriatic arthritis,CNTNAP2,5e-28,Is psoriatic arthritis associated with CNTNAP2?,"I'm sorry, but I don't have the information to answer that question.",7988
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primary biliary cholangitis,CCDC88B,1e-10,Is primary biliary cholangitis associated with CCDC88B?,"Yes, primary biliary cholangitis is associated with CCDC88B.",7998
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otosclerosis,MARK3,3e-18,Is MARK3 associated with otosclerosis?,"Yes, the gene MARK3, which stands for microtubule affinity regulating kinase 3, is associated with the disease otosclerosis.",8149
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large intestine cancer,RHPN2,4e-41,What is the GWAS p-value for the association between RHPN2 and large intestine cancer?,The GWAS p-value for the association between RHPN2 and large intestine cancer is 4e-41.,8018
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anxiety disorder,NTRK2,7e-09,Is anxiety disorder associated with NTRK2?,"Yes, anxiety disorder is associated with NTRK2, which is the neurotrophic receptor tyrosine kinase 2.",8159
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atopic dermatitis,RERE,6e-16,Is atopic dermatitis associated with RERE?,"Yes, atopic dermatitis is associated with RERE.",7985
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asthma,PRR5L,6e-12,Is PRR5L associated with asthma?,"Yes, the gene PRR5L, also known as proline rich 5 like, which is located on chromosome 11, is associated with the disease asthma.",8146
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gastric fundus cancer,GON4L,1e-15,What is the GWAS p-value for the association between gastric fundus cancer and GON4L?,The GWAS p-value for the association between gastric fundus cancer and GON4L is 1e-15.,8024
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type 2 diabetes mellitus,DNAH1,7e-21,Is type 2 diabetes mellitus associated with DNAH1?,"Yes, type 2 diabetes mellitus is associated with DNAH1.",7994
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schizophrenia,SLC17A3,3e-20,What is the GWAS p-value for the association between schizophrenia and SLC17A3?,The GWAS p-value for the association between schizophrenia and SLC17A3 is 3e-20.,8016
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inflammatory bowel disease,FADS2,2e-15,What is the GWAS p-value for the association between inflammatory bowel disease and FADS2?,The GWAS p-value for the association between inflammatory bowel disease and FADS2 is 2e-15.,8015
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opiate dependence,ADGRV1,2e-09,Is opiate dependence associated with ADGRV1?,"Yes, opiate dependence is associated with ADGRV1.",7988
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attention deficit hyperactivity disorder,ST3GAL3,8e-14,What is the GWAS p-value for the association between attention deficit hyperactivity disorder and ST3GAL3?,The GWAS p-value for the association between attention deficit hyperactivity disorder and ST3GAL3 is 8e-14.,8030
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cataract,C3orf49,2e-11,Is C3orf49 associated with cataract?,"Yes, the gene C3orf49, also known as chromosome 3 open reading frame 49, is associated with the disease cataract.",8149
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duodenal ulcer,PLD1,5e-08,What is the GWAS p-value for the association between PLD1 and duodenal ulcer?,The GWAS p-value for the association between PLD1 and duodenal ulcer is 5e-08.,8018
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chronic obstructive pulmonary disease,CHRNA3,5e-28,What is the GWAS p-value for the association between CHRNA3 and chronic obstructive pulmonary disease?,"I'm sorry, but I don't have the information to answer that question.",8009
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pancreatic carcinoma,CCDC68,5e-09,What is the GWAS p-value for the association between pancreatic carcinoma and CCDC68?,The GWAS p-value for the association between pancreatic carcinoma and CCDC68 is 5e-09.,8012
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primary biliary cholangitis,HLA-DPB1,2e-22,Is HLA-DPB1 associated with primary biliary cholangitis?,"Yes, HLA-DPB1 is associated with primary biliary cholangitis.",8004
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atopic dermatitis,GABPB2,2.0000000000000001e-88,Is atopic dermatitis associated with GABPB2?,"Yes, atopic dermatitis is associated with GABPB2.",7992
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systemic lupus erythematosus,HIP1,5.999999999999999e-62,What is the GWAS p-value for the association between HIP1 and systemic lupus erythematosus?,The GWAS p-value for the association between HIP1 and systemic lupus erythematosus is 6e-62.,8027
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hypothyroidism,TIMMDC1,3e-09,Is hypothyroidism associated with TIMMDC1?,"Yes, hypothyroidism is associated with TIMMDC1.",7993
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degenerative myopia,MIPEP,2e-16,What is the GWAS p-value for the association between degenerative myopia and MIPEP?,,7851
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alcoholic pancreatitis,CASP9,6e-09,Is alcoholic pancreatitis associated with CASP9?,"Yes, alcoholic pancreatitis is associated with CASP9.",7985
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lung squamous cell carcinoma,PDS5B,9e-12,Is lung squamous cell carcinoma associated with PDS5B?,"Yes, lung squamous cell carcinoma is associated with PDS5B.",7994
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common variable immunodeficiency,CLEC16A,2e-09,What is the GWAS p-value for the association between CLEC16A and common variable immunodeficiency?,The GWAS p-value for the association between CLEC16A and common variable immunodeficiency is 2e-09.,8030
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lung non-small cell carcinoma,TERT,9.999999999999999e-43,Is TERT associated with lung non-small cell carcinoma?,"No, TERT is not associated with lung non-small cell carcinoma.",7988
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cardiovascular system disease,PSMD3,1e-20,Is PSMD3 associated with cardiovascular system disease?,"Yes, the gene PSMD3, which is the proteasome 26S subunit, non-ATPase 3, is associated with cardiovascular system disease.",8174
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gestational diabetes,CCND2,3e-12,What is the GWAS p-value for the association between gestational diabetes and CCND2?,"I'm sorry, but the GWAS p-value for the association between gestational diabetes and CCND2 is not available.",8011
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major depressive disorder,TMEM106B,8.000000000000001e-24,Is TMEM106B associated with major depressive disorder?,"Yes, the gene TMEM106B, which stands for transmembrane protein 106B and is located on chromosome 7, is associated with major depressive disorder.",8153
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keratoconus,COL6A1,9e-12,What is the GWAS p-value for the association between COL6A1 and keratoconus?,The GWAS p-value for the association between COL6A1 and keratoconus is 9e-12.,8022
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chronic lymphocytic leukemia,RREB1,1e-08,Is chronic lymphocytic leukemia associated with RREB1?,"Yes, chronic lymphocytic leukemia is associated with RREB1.",7997
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prostate carcinoma,PARPBP,3e-13,Is PARPBP associated with prostate carcinoma?,"Yes, the gene PARPBP is associated with prostate carcinoma.",8117
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testicular germ cell cancer,ZFP64,3e-12,What is the GWAS p-value for the association between testicular germ cell cancer and ZFP64?,The GWAS p-value for the association between testicular germ cell cancer and ZFP64 is 3e-12.,8022
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psoriasis,KLF13,9e-10,What is the GWAS p-value for the association between KLF13 and psoriasis?,"I'm sorry, but I don't have the information to answer that question.",7991
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coronary artery disease,ADGRL3,3e-23,Is coronary artery disease associated with ADGRL3?,"Yes, coronary artery disease is associated with ADGRL3.",7990
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abdominal obesity-metabolic syndrome 1,JMJD1C,2e-14,What is the GWAS p-value for the association between abdominal obesity-metabolic syndrome 1 and JMJD1C?,The GWAS p-value for the association between abdominal obesity-metabolic syndrome 1 and JMJD1C is 2e-14.,8040
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type 1 diabetes mellitus,CUX2,1e-16,Is CUX2 associated with type 1 diabetes mellitus?,"Yes, the gene CUX2 (cut like homeobox 2) located on chromosome 12 is associated with type 1 diabetes mellitus.",8156
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type 2 diabetes mellitus,KCNK16,4e-17,What is the GWAS p-value for the association between KCNK16 and type 2 diabetes mellitus?,The GWAS p-value for the association between KCNK16 and type 2 diabetes mellitus is 4e-17.,8027
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type 1 diabetes mellitus,DGKQ,6e-09,Is type 1 diabetes mellitus associated with DGKQ?,"Yes, type 1 diabetes mellitus is associated with DGKQ.",7996
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refractive error,SIX6,2e-16,What is the GWAS p-value for the association between SIX6 and refractive error?,The GWAS p-value for the association between SIX6 and refractive error is 2e-16.,8012
|
||||
Parkinson's disease,MAP4K4,8e-13,What is the GWAS p-value for the association between MAP4K4 and Parkinson's disease?,The GWAS p-value for the association between MAP4K4 and Parkinson's disease is 8e-13.,8019
|
||||
autism spectrum disorder,DCC,3e-08,Is autism spectrum disorder associated with DCC?,"Yes, autism spectrum disorder is associated with DCC.",7981
|
||||
multiple sclerosis,NR1D1,9e-14,Is multiple sclerosis associated with NR1D1?,"Yes, multiple sclerosis is associated with NR1D1.",7985
|
||||
coronary artery disease,SMAD3,1e-19,Is coronary artery disease associated with SMAD3?,"Yes, coronary artery disease is associated with SMAD3.",7987
|
||||
prostate carcinoma,ANO7,8e-43,What is the GWAS p-value for the association between ANO7 and prostate carcinoma?,"I'm sorry, but I don't have the information to answer that question.",7991
|
||||
ovarian carcinoma,FGFR2,4.0000000000000004e-254,What is the GWAS p-value for the association between FGFR2 and ovarian carcinoma?,,7861
|
||||
lymphoid leukemia,BMF,1e-10,What is the GWAS p-value for the association between BMF and lymphoid leukemia?,,7869
|
||||
skin melanoma,CYP1B1,3e-16,Is skin melanoma associated with CYP1B1?,"I'm sorry, but I don't have the information to answer that question.",7980
|
||||
myositis,ATP6V1G2,6e-49,What is the GWAS p-value for the association between myositis and ATP6V1G2?,The GWAS p-value for the association between myositis and ATP6V1G2 is 6e-49.,8027
|
||||
melanoma,SPG7,9e-26,What is the GWAS p-value for the association between SPG7 and melanoma?,"I'm sorry, but I don't have the information to answer that question.",7992
|
||||
type 2 diabetes mellitus,EYA2,6e-19,Is EYA2 associated with type 2 diabetes mellitus?,"I'm sorry, but I don't have the information to answer that question.",7982
|
||||
carpal tunnel syndrome,SERPINA1,3e-24,What is the GWAS p-value for the association between SERPINA1 and carpal tunnel syndrome?,The GWAS p-value for the association between SERPINA1 and carpal tunnel syndrome is 3e-24.,8022
|
||||
substance-related disorder,FUT2,3e-19,What is the GWAS p-value for the association between substance-related disorder and FUT2?,The GWAS p-value for the association between substance-related disorder and FUT2 is 3e-19.,8015
|
||||
open-angle glaucoma,PLEKHA7,9e-15,Is open-angle glaucoma associated with PLEKHA7?,"Yes, open-angle glaucoma is associated with PLEKHA7.",7999
|
||||
myocardial infarction,ZNF831,1e-08,What is the GWAS p-value for the association between myocardial infarction and ZNF831?,The GWAS p-value for the association between myocardial infarction and ZNF831 is 1e-08.,8023
|
||||
squamous cell carcinoma,IRF4,1e-169,Is IRF4 associated with squamous cell carcinoma?,"I'm sorry, but I don't have the information to answer that question.",7976
|
||||
Parkinson's disease,WDHD1,4e-16,What is the GWAS p-value for the association between WDHD1 and Parkinson's disease?,The GWAS p-value for the association between WDHD1 and Parkinson's disease is 4e-16.,8016
|
||||
cataract,TOP1,1e-11,Is cataract associated with TOP1?,"Yes, cataract is associated with TOP1.",7980
|
||||
atrial fibrillation,AGBL4,3e-09,What is the GWAS p-value for the association between atrial fibrillation and AGBL4?,The GWAS p-value for the association between atrial fibrillation and AGBL4 is 3e-09.,8021
|
||||
otosclerosis,SEMA4D,4e-09,What is the GWAS p-value for the association between otosclerosis and SEMA4D?,The GWAS p-value for the association between otosclerosis and SEMA4D is 4e-09.,8017
|
||||
hypothyroidism,RAD51B,2e-11,What is the GWAS p-value for the association between hypothyroidism and RAD51B?,The GWAS p-value for the association between hypothyroidism and RAD51B is 2e-11.,8018
|
||||
childhood-onset asthma,SPSB1,4e-18,What is the GWAS p-value for the association between SPSB1 and childhood-onset asthma?,The GWAS p-value for the association between SPSB1 and childhood-onset asthma is 4e-18.,8022
|
||||
major depressive disorder,ATG7,5e-08,Is major depressive disorder associated with ATG7?,"Yes, major depressive disorder is associated with ATG7.",7985
|
||||
alopecia,WNT10A,2e-16,Is WNT10A associated with alopecia?,"Yes, the gene WNT10A, which is located on chromosome 2, is associated with the condition alopecia.",8138
|
||||
inflammatory bowel disease,IL27,1e-21,Is inflammatory bowel disease associated with IL27?,"Yes, inflammatory bowel disease is associated with IL27.",7981
|
||||
tonsillitis,TNFRSF13B,7.999999999999999e-26,What is the GWAS p-value for the association between tonsillitis and TNFRSF13B?,The GWAS p-value for the association between tonsillitis and TNFRSF13B is 8e-26.,8022
|
||||
cleft lip,SFI1,3e-08,What is the GWAS p-value for the association between cleft lip and SFI1?,The GWAS p-value for the association between cleft lip and SFI1 is 3e-08.,8014
|
||||
multiple sclerosis,INAVA,6e-21,What is the GWAS p-value for the association between multiple sclerosis and INAVA?,The GWAS p-value for the association between multiple sclerosis and INAVA is 6e-21.,8006
|
||||
esophageal carcinoma,CASP8,1e-08,Is esophageal carcinoma associated with CASP8?,"Yes, esophageal carcinoma is associated with CASP8.",7988
|
||||
skin melanoma,GPRC5A,8e-15,Is skin melanoma associated with GPRC5A?,"I'm sorry, but I don't have the information to answer that question.",7983
|
||||
lung squamous cell carcinoma,BRCA2,1e-15,Is lung squamous cell carcinoma associated with BRCA2?,"Yes, lung squamous cell carcinoma is associated with BRCA2.",7993
|
||||
systemic lupus erythematosus,HLA-DRA,2.0000000000000002e-60,What is the GWAS p-value for the association between HLA-DRA and systemic lupus erythematosus?,The GWAS p-value for the association between HLA-DRA and systemic lupus erythematosus is 2e-60.,8035
|
||||
type 2 diabetes mellitus,UBE2E2,1.9999999999999998e-42,Is type 2 diabetes mellitus associated with UBE2E2?,"Yes, type 2 diabetes mellitus is associated with UBE2E2.",8003
|
||||
allergic rhinitis,HLA-DQA1,1e-43,What is the GWAS p-value for the association between HLA-DQA1 and allergic rhinitis?,The GWAS p-value for the association between HLA-DQA1 and allergic rhinitis is 1e-43.,8027
|
||||
systemic lupus erythematosus,HLA-DQA1,9.999999999999999e-55,What is the GWAS p-value for the association between systemic lupus erythematosus and HLA-DQA1?,The GWAS p-value for the association between systemic lupus erythematosus and HLA-DQA1 is 1e-54.,8039
|
||||
|
1206
notebooks/neo4j_rag_using_langchain.ipynb
Normal file
1206
notebooks/neo4j_rag_using_langchain.ipynb
Normal file
File diff suppressed because it is too large
Load Diff
@@ -1,172 +0,0 @@
|
||||
{
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 8,
|
||||
"id": "a67d5fcb",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"from langchain.chains import GraphCypherQAChain\n",
|
||||
"from langchain.chat_models import ChatOpenAI\n",
|
||||
"from langchain.graphs import Neo4jGraph\n",
|
||||
"from langchain.callbacks import get_openai_callback\n",
|
||||
"from dotenv import load_dotenv\n",
|
||||
"import os\n",
|
||||
"import openai\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 2,
|
||||
"id": "1f500648",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"LLM_MODEL = 'gpt-4-32k'\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "4b35a99d",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"id": "64733a91",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"def get_neo4j_cypher_rag_chain():\n",
|
||||
" load_dotenv(os.path.join(os.path.expanduser('~'), '.spoke_neo4j_config.env'))\n",
|
||||
" username = os.environ.get('NEO4J_USER')\n",
|
||||
" password = os.environ.get('NEO4J_PSW')\n",
|
||||
" url = os.environ.get('NEO4J_URI')\n",
|
||||
" database = os.environ.get('NEO4J_DB')\n",
|
||||
"\n",
|
||||
" graph = Neo4jGraph(\n",
|
||||
" url=url, \n",
|
||||
" username=username, \n",
|
||||
" password=password,\n",
|
||||
" database = database\n",
|
||||
" )\n",
|
||||
"\n",
|
||||
" load_dotenv(os.path.join(os.path.expanduser('~'), '.gpt_config.env'))\n",
|
||||
" API_KEY = os.environ.get('API_KEY')\n",
|
||||
" API_VERSION = os.environ.get('API_VERSION')\n",
|
||||
" RESOURCE_ENDPOINT = os.environ.get('RESOURCE_ENDPOINT')\n",
|
||||
" openai.api_type = \"azure\"\n",
|
||||
" openai.api_key = API_KEY\n",
|
||||
" openai.api_base = RESOURCE_ENDPOINT\n",
|
||||
" openai.api_version = API_VERSION\n",
|
||||
" chat_deployment_id = LLM_MODEL\n",
|
||||
" chat_model_id = chat_deployment_id\n",
|
||||
" temperature = 0\n",
|
||||
" chat_model = ChatOpenAI(openai_api_key=API_KEY, \n",
|
||||
" engine=chat_deployment_id, \n",
|
||||
" temperature=temperature)\n",
|
||||
" chain = GraphCypherQAChain.from_llm(\n",
|
||||
" chat_model, \n",
|
||||
" graph=graph, \n",
|
||||
" verbose=True, \n",
|
||||
" validate_cypher=True,\n",
|
||||
" return_intermediate_steps=True\n",
|
||||
" )\n",
|
||||
" return chain"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 6,
|
||||
"id": "115f2da3",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stderr",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"WARNING! engine is not default parameter.\n",
|
||||
" engine was transferred to model_kwargs.\n",
|
||||
" Please confirm that engine is what you intended.\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"CPU times: user 88.4 ms, sys: 14.2 ms, total: 103 ms\n",
|
||||
"Wall time: 50.2 s\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"%%time\n",
|
||||
"neo4j_rag_chain = get_neo4j_cypher_rag_chain()\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 9,
|
||||
"id": "d4525903",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"\n",
|
||||
"\n",
|
||||
"\u001b[1m> Entering new GraphCypherQAChain chain...\u001b[0m\n",
|
||||
"Generated Cypher:\n",
|
||||
"\u001b[32;1m\u001b[1;3mMATCH (d:Disease {name: \"multiple sclerosis\"})-[:ASSOCIATES_DaG]->(g:Gene)\n",
|
||||
"RETURN g.name\u001b[0m\n",
|
||||
"Full Context:\n",
|
||||
"\u001b[32;1m\u001b[1;3m[{'g.name': 'IL4'}, {'g.name': 'BTNL2'}, {'g.name': 'TGFB1'}, {'g.name': 'CBLB'}, {'g.name': 'CD6'}, {'g.name': 'OS9'}, {'g.name': 'TBX6'}, {'g.name': 'ESPN'}, {'g.name': 'IKZF3'}, {'g.name': 'AFF1'}]\u001b[0m\n",
|
||||
"\n",
|
||||
"\u001b[1m> Finished chain.\u001b[0m\n",
|
||||
"The genes associated with multiple sclerosis are IL4, BTNL2, TGFB1, CBLB, CD6, OS9, TBX6, ESPN, IKZF3, and AFF1.\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"question = 'What are the genes associated with multiple sclerosis?'\n",
|
||||
"with get_openai_callback() as cb:\n",
|
||||
" out = neo4j_rag_chain.run(query=question, return_final_only=False)\n",
|
||||
" print(out)\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "b4bb5881",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
}
|
||||
],
|
||||
"metadata": {
|
||||
"kernelspec": {
|
||||
"display_name": "Python 3 (ipykernel)",
|
||||
"language": "python",
|
||||
"name": "python3"
|
||||
},
|
||||
"language_info": {
|
||||
"codemirror_mode": {
|
||||
"name": "ipython",
|
||||
"version": 3
|
||||
},
|
||||
"file_extension": ".py",
|
||||
"mimetype": "text/x-python",
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.10.9"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
"nbformat_minor": 5
|
||||
}
|
||||
@@ -2,21 +2,49 @@
|
||||
"cells": [
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 5,
|
||||
"id": "d7c48327",
|
||||
"execution_count": 108,
|
||||
"id": "403d179c",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"from neo4j import GraphDatabase, basic_auth\n",
|
||||
"from dotenv import load_dotenv\n",
|
||||
"import os\n",
|
||||
"\n"
|
||||
"import pickle\n",
|
||||
"import random\n",
|
||||
"import pandas as pd\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "80ee9a49",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Set number of questions to generate"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 7,
|
||||
"id": "6f3963aa",
|
||||
"execution_count": 109,
|
||||
"id": "fa80e37b",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"N_QUESTIONS = 100\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "ac046718",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Load KG credentials"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 110,
|
||||
"id": "8d41be45",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
@@ -27,10 +55,146 @@
|
||||
"database = os.environ.get('NEO4J_DB')\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "cf3354e7",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Load disease names stored in vectorDB"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 111,
|
||||
"id": "2ec9d667",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"with open('../data/disease_with_relation_to_genes.pickle', 'rb') as f:\n",
|
||||
" disease_names = pickle.load(f)\n",
|
||||
" "
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "654a9a58",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Extract GWAS Disease-Gene relation from the KG"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 112,
|
||||
"id": "c280e781",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"CPU times: user 159 ms, sys: 20.2 ms, total: 179 ms\n",
|
||||
"Wall time: 1.64 s\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"%%time\n",
|
||||
"\n",
|
||||
"auth = basic_auth(username, password)\n",
|
||||
"sdb = GraphDatabase.driver(url, auth=auth)\n",
|
||||
"\n",
|
||||
"gwas_query = '''\n",
|
||||
" MATCH (d:Disease)-[r:ASSOCIATES_DaG]->(g:Gene)\n",
|
||||
" WHERE r.sources = ['GWAS']\n",
|
||||
" WITH d, g, r.gwas_pvalue AS pvalue\n",
|
||||
" ORDER BY pvalue\n",
|
||||
" WITH d, COLLECT(g)[0] AS gene_with_lowest_pvalue, pvalue\n",
|
||||
" RETURN d.name AS disease_name, gene_with_lowest_pvalue.name AS gene_name, pvalue\n",
|
||||
"'''\n",
|
||||
"\n",
|
||||
"with sdb.session() as session:\n",
|
||||
" with session.begin_transaction() as tx:\n",
|
||||
" result = tx.run(gwas_query)\n",
|
||||
" out_list = []\n",
|
||||
" for row in result:\n",
|
||||
" out_list.append((row['disease_name'], row['gene_name'], row['pvalue']))\n",
|
||||
"\n",
|
||||
"gwas_disease_names = pd.DataFrame(out_list, columns=['disease_name', 'gene_name', 'gwas_pvalue']).drop_duplicates()\n",
|
||||
"sdb.close()\n",
|
||||
"\n",
|
||||
"gwas_disease_names = gwas_disease_names[gwas_disease_names.disease_name.isin(disease_names)]\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "0db2757f",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Create test questions from the extracted relationships"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 113,
|
||||
"id": "9fe85753",
|
||||
"metadata": {},
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"CPU times: user 96.1 ms, sys: 1.15 ms, total: 97.3 ms\n",
|
||||
"Wall time: 96.5 ms\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"source": [
|
||||
"%%time\n",
|
||||
"\n",
|
||||
"template_questions = [\n",
|
||||
" 'Is {} associated with {}?',\n",
|
||||
" 'What is the GWAS p-value for the association between {} and {}?' \n",
|
||||
"]\n",
|
||||
"\n",
|
||||
"test_questions = []\n",
|
||||
"random.seed(42)\n",
|
||||
"for index,row in gwas_disease_names.iterrows():\n",
|
||||
" selected_question = random.choice(template_questions)\n",
|
||||
" if random.random() < 0.5:\n",
|
||||
" test_questions.append(selected_question.format(row['disease_name'], row['gene_name']))\n",
|
||||
" else:\n",
|
||||
" test_questions.append(selected_question.format(row['gene_name'], row['disease_name']))\n",
|
||||
"\n",
|
||||
"gwas_disease_names.loc[:,'question'] = test_questions\n",
|
||||
"\n",
|
||||
"gwas_disease_names_selected = gwas_disease_names.sample(N_QUESTIONS, random_state=42)\n",
|
||||
"\n",
|
||||
"\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "markdown",
|
||||
"id": "06eed996",
|
||||
"metadata": {},
|
||||
"source": [
|
||||
"## Save the test data"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": 114,
|
||||
"id": "7f02bb5b",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": [
|
||||
"gwas_disease_names_selected.to_csv('../data/rag_comparison_data.csv', index=False)\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"cell_type": "code",
|
||||
"execution_count": null,
|
||||
"id": "43615aca",
|
||||
"id": "6e04d6ea",
|
||||
"metadata": {},
|
||||
"outputs": [],
|
||||
"source": []
|
||||
|
||||
@@ -145,7 +145,7 @@
|
||||
"source": [
|
||||
"question = 'What are the genes associated with multiple sclerosis?'\n",
|
||||
"question=\"Which gene has stronger association with the disease 'liver benign neoplasm', is it PNPLA3 or HLA-B?\"\n",
|
||||
"question='What is the clinical phase of levodopa treating parkinson disease?'\n",
|
||||
"question='What is the clinical phase of levodopa in treating parkinson disease?'\n",
|
||||
"with get_openai_callback() as cb:\n",
|
||||
" out = chain.run(query=question, return_final_only=False)\n",
|
||||
" print(out)\n"
|
||||
|
||||
Reference in New Issue
Block a user