Code repository for the maintenance of the Translator API for the Broad Institute's Genetics Team comprising members of the Flannick Lab.
To deploy a dockerized version of this service, follow the following steps:
- checkout the master branch of this directory
- cd into the newly checked out directory; the two main files are
- Dockerfile - provides the commands to build the docker image
- build_docker.txt - provides the command options to build the docker image
- run the command below or modify the build_docker.txt script (or a copy of it) to set the following docker variables which are used by the Dockerfile
- fl_port - the network port that the application services
- db_host - the Mysql database host
- db_user - the Mysql database user name
- db_passwd - the Mysql database user password
- db_schema - the Mysql database schema for the application
- db_cache_schema - the Mysql database schema for the application cache (default is the same as the regular schema)
- db_results_limit - the maximum limit of how many results the service will send back (default is 150)
- tran_log_file - the location of the log file the application will log its messages to
- tran_max_query_size - this indicates how big a query size the service will accept (recommended default is 100000)
- tran_url_normalizer - the URL of the NCATS node normalizer service (default is https://nodenormalization-sri.renci.org/get_normalized_nodes)
sudo docker build \
--build-arg fl_port=8090 \
--build-arg db_host=localhost \
--build-arg db_user=root \
--build-arg db_passwd=password \
--build-arg db_schema=genetics_kp_schema \
--build-arg db_cache_schema=genetics_kp_schema \
--build-arg db_results_limit=150 \
--build-arg tran_log_file=logs/genepro.log \
--build-arg tran_max_query_size=100000 \
--build-arg tran_url_normalizer=https://nodenormalization-sri.renci.org/get_normalized_nodes \
.
- deploy the docker image making sure to open up the application port
The Genetics KP provides the following data
-
Richards method gene/phenotype associations
- Forgetta V, Jiang L, Vulpescu NA, et al. An Effector Index to Predict Causal Genes at GWAS Loci. Submitted for publication, 2020. BioRxiv
-
Magma gene/phenotype associations and Magma pathway/phenotype associations
-
Genebass - a resource of exome-based association statistics from exome sequence data from the UK Biobank
- The probability of gene/phenotype association was calculated, then only the gene/phenotype associations with a calculated probability greater than 0.15 were loaded into the database.
-
Experimental Integrated Genetics method (Flannick Lab); under development
- An extra 41 phenotypes added to the magma gene associations (from 145 to 186)
- Upgraded the API to be trapi v1.0 compatible
+--------------------------------+-------------+
| phenotype | efo_id |
+--------------------------------+-------------+
| Calcium | EFO:0004838 |
| Diastolic blood pressure | EFO:0006336 |
| Estimated bone mineral density | EFO:0009270 |
| Height | EFO:0004339 |
| Hypothyroidism | EFO:0004705 |
| LDL cholesterol | EFO:0004611 |
| Red blood cell count | EFO:0004305 |
| Systolic blood pressure | EFO:0006335 |
| Triglycerides | EFO:0004530 |
| Type 2 diabetes | EFO:0001360 |
+--------------------------------+-------------+
+--------------------------------------------------+-----------------------+
| phenotype | phenotype_ontology_id |
+--------------------------------------------------+-----------------------+
| acetate measurement | EFO:0010112 |
| acetoaetate measurement | EFO:0010111 |
| acquired aneurysmal subarachnoid hemorrhage | MONDO:0019543 |
| acute insulin response measurement | EFO:0006831 |
| adiponectin measurement | EFO:0004502 |
| age at menarche | EFO:0004703 |
| age at menopause | EFO:0004704 |
| age-related macular degeneration | EFO:0001365 |
| alanine measurement | EFO:0009765 |
| alcohol consumption measurement | EFO:0007878 |
| alkaline phosphatase measurement | EFO:0004533 |
| Alzheimer's disease | EFO:0000249 |
| amyotrophic lateral sclerosis | EFO:0000253 |
| apolipoprotein A 1 measurement | EFO:0004614 |
| apolipoprotein measurement | EFO:0004615 |
| appendicular lean mass | EFO:0004980 |
| aspartate aminotransferase measurement | EFO:0004736 |
| atrial fibrillation | EFO:0000275 |
| atrial fibrillation (disease) | MONDO:0004981 |
| atrophic macular degeneration | EFO:1001492 |
| beta-hydroxybutyric acid measurement | EFO:0010465 |
| bilirubin measurement | EFO:0004570 |
| bipolar disorder | EFO:0000289 |
| blood urea nitrogen measurement | EFO:0004741 |
| BMI-adjusted fasting blood glucose measurement | EFO:0008036 |
| BMI-adjusted fasting blood insulin measurement | EFO:0008037 |
| BMI-adjusted hip circumference | EFO:0008039 |
| BMI-adjusted waist circumference | EFO:0007789 |
| BMI-adjusted waist-hip ratio | EFO:0007788 |
| body fat percentage | EFO:0007800 |
| body height | EFO:0004339 |
| body mass index | EFO:0004340 |
| body weight | EFO:0004338 |
| bone density | EFO:0003923 |
| bone fracture | EFO:0003931 |
| brain aneurysm | MONDO:0005291 |
| C-peptide measurement | EFO:0005187 |
| C-reactive protein measurement | EFO:0004458 |
| calcium measurement | EFO:0004838 |
| cardiovascular disease | EFO:0000319 |
| cerebrovascular disorder | EFO:0003763 |
| chloride measurement | EFO:0009284 |
| chronic kidney disease | EFO:0003884 |
| chronic obstructive pulmonary disease | EFO:0000341 |
| chronotype measurement | EFO:0008328 |
| chylomicron measurement | EFO:0008596 |
| citrate measurement | EFO:0010114 |
| coronary artery disease | EFO:0000378 |
| COVID-19 | MONDO:0100096 |
| creatine kinase measurement | EFO:0004534 |
| Crohn's disease | EFO:0000384 |
| daytime rest measurement | EFO:0007828 |
| diabetic nephropathy | EFO:0000401 |
| diabetic neuropathy | EFO:1000783 |
| diabetic peripheral angiopathy | MONDO:0000960 |
| diabetic retinopathy | MONDO:0005266 |
| diastolic blood pressure | EFO:0006336 |
| diet measurement | EFO:0008111 |
| disposition index measurement | EFO:0006832 |
| end stage renal failure | MONDO:0004375 |
| erythrocyte count | EFO:0004305 |
| fasting blood glucose change measurement | EFO:0010120 |
| fasting blood glucose measurement | EFO:0004465 |
| fasting blood insulin measurement | EFO:0004466 |
| fasting C-peptide measurement | EFO:0010813 |
| fatty acid measurement | EFO:0005110 |
| femoral neck bone mineral density | EFO:0007785 |
| femoral neck size | EFO:0010076 |
| FEV/FEC ratio | EFO:0004713 |
| fibrinogen measurement | EFO:0004623 |
| fish consumption measurement | EFO:0010139 |
| forced expiratory volume | EFO:0004314 |
| glomerular filtration rate | EFO:0005208 |
| glucose measurement | EFO:0004468 |
| glucose tolerance test | EFO:0004307 |
| glutamine measurement | EFO:0009768 |
| glycerol measurement | EFO:0010115 |
| glycerophospholipid measurement | EFO:0007630 |
| glycine measurement | EFO:0009767 |
| glycoprotein measurement | EFO:0004555 |
| HbA1c measurement | EFO:0004541 |
| heart failure | EFO:0003144 |
| heart rate | EFO:0004326 |
| heel bone mineral density | EFO:0009270 |
| hemoglobin measurement | EFO:0004509 |
| high density lipoprotein cholesterol measurement | EFO:0004612 |
| hip bone size | EFO:0004844 |
| hip circumference | EFO:0005093 |
| histidine measurement | EFO:0009769 |
| HOMA-B | EFO:0004469 |
| HOMA-IR | EFO:0004501 |
| hypersomnia | EFO:0005246 |
| hypertension | EFO:0000537 |
| hypothyroidism | EFO:0004705 |
| inflammatory bowel disease | EFO:0003767 |
| insomnia | EFO:0004698 |
| insulin measurement | EFO:0004467 |
| insulin response measurement | EFO:0008473 |
| insulin secretion measurement | EFO:0008001 |
| insulin sensitivity measurement | EFO:0004471 |
| Insulinogenic index measurement | EFO:0009961 |
| intermediate density lipoprotein measurement | EFO:0008595 |
| intertrochanteric region size | EFO:0010075 |
| intracranial hemorrhage | EFO:0000551 |
| isoleucine measurement | EFO:0009793 |
| L lactate dehydrogenase measurement | EFO:0004808 |
| late-onset Alzheimers disease | EFO:1001870 |
| latent autoimmune diabetes in adults | EFO:0009706 |
| lean body mass | EFO:0004995 |
| left ventricular diastolic function measurement | EFO:0008204 |
| left ventricular ejection fraction measurement | EFO:0008373 |
| left ventricular stroke volume measurement | EFO:0010555 |
| left ventricular systolic function measurement | EFO:0008206 |
| leptin measurement | EFO:0005000 |
| leucine measurement | EFO:0009770 |
| linoleic acid measurement | EFO:0006807 |
| lipoprotein measurement | EFO:0004732 |
| lobar intracerebral hemorrhage | EFO:0010177 |
| low density lipoprotein cholesterol measurement | EFO:0004611 |
| mean arterial pressure | EFO:0006340 |
| membranous glomerulonephritis | MONDO:0005376 |
| myocardial infarction | EFO:0000612 |
| myocardial infarction (disease) | MONDO:0005068 |
| non-lobar intracerebral hemorrhage | EFO:0010178 |
| nonischemic cardiomyopathy | EFO:0009881 |
| obesity | EFO:0001073 |
| obesity disorder | MONDO:0011122 |
| omega-3 polyunsaturated fatty acid measurement | EFO:0010119 |
| omega-6 polyunsaturated fatty acid measurement | EFO:0005680 |
| open-angle glaucoma | EFO:0004190 |
| osteoarthritis | EFO:0002506 |
| osteoarthritis, hip | EFO:1000786 |
| osteoarthritis, knee | EFO:0004616 |
| P wave duration | EFO:0005094 |
| peak expiratory flow | EFO:0009718 |
| peak insulin response measurement | EFO:0008000 |
| phenylalanine measurement | EFO:0005001 |
| phosphorus measurement | EFO:0004861 |
| potassium measurement | EFO:0009283 |
| PR interval | EFO:0004462 |
| primary angle closure glaucoma | EFO:1001506 |
| proinsulin measurement | EFO:0010814 |
| proliferative diabetic retinopathy | MONDO:0001660 |
| pulse pressure measurement | EFO:0005763 |
| pyruvate measurement | EFO:0010117 |
| QRS duration | EFO:0005055 |
| remnant cholesterol measurement | EFO:0010815 |
| schizophrenia | EFO:0000692 |
| secondary hypertension | MONDO:0001200 |
| serum alanine aminotransferase measurement | EFO:0004735 |
| serum albumin measurement | EFO:0004535 |
| serum creatinine measurement | EFO:0004518 |
| serum gamma-glutamyl transferase measurement | EFO:0004532 |
| serum urea measurement | EFO:0009795 |
| severe nonproliferative diabetic retinopathy | MONDO:0004687 |
| sleep apnea measurement | EFO:0007817 |
| sleep apnea measurement during non-REM sleep | EFO:0008456 |
| sleep apnea measurement during REM sleep | EFO:0008455 |
| sleep measurement | EFO:0004870 |
| sodium measurement | EFO:0009282 |
| sphingomyelin measurement | EFO:0010118 |
| spine bone mineral density | EFO:0007701 |
| spine bone size | EFO:0004508 |
| systolic blood pressure | EFO:0006335 |
| total cholesterol measurement | EFO:0004574 |
| total cholines | EFO:0010116 |
| triglyceride measurement | EFO:0004530 |
| triglyceride:HDL cholesterol ratio | EFO:0007929 |
| trochanter size | EFO:0010074 |
| type 2 diabetes nephropathy | EFO:0004997 |
| type I diabetes mellitus | EFO:0001359 |
| type II diabetes mellitus | EFO:0001360 |
| tyrosine measurement | EFO:0005058 |
| ulcerative colitis | EFO:0000729 |
| unipolar depression | EFO:0003761 |
| urate measurement | EFO:0004531 |
| uric acid measurement | EFO:0004761 |
| urinary albumin to creatinine ratio | EFO:0007778 |
| urinary metabolite measurement | EFO:0005116 |
| valine measurement | EFO:0009792 |
| vital capacity | EFO:0004312 |
| vitamin D measurement | EFO:0004631 |
| waist circumference | EFO:0004342 |
| waist-hip ratio | EFO:0004343 |
| wet macular degeneration | EFO:0004683 |
| white matter hyperintensity measurement | EFO:0005665 |
+--------------------------------------------------+-----------------------+
+-------------------------------------------------------+-------------+
| phenotype | efo_id |
+-------------------------------------------------------+-------------+
| Adiponectin | EFO:0004502 |
| Alanine transaminase | EFO:0004735 |
| Alkaline phosphatase | EFO:0004533 |
| All diabetic kidney disease | EFO:0000401 |
| ALS | EFO:0000253 |
| Alzheimer's disease | EFO:0000249 |
| Any stroke | EFO:0000712 |
| Apnea-Hypopnea Index | EFO:0007817 |
| Apnea-Hypopnea Index in NREM sleep | EFO:0008456 |
| Apnea-Hypopnea Index in REM sleep | EFO:0008455 |
| Aspartate aminotransferase | EFO:0004736 |
| Atrial fibrillation | EFO:0000275 |
| Bipolar disorder | EFO:0000289 |
| BMI | EFO:0004340 |
| Body fat percentage | EFO:0007800 |
| Bone fracture | EFO:0003931 |
| Cerebral white matter hyperintensity volume | EFO:0005665 |
| Chronic kidney disease | EFO:0003884 |
| Chronic obstructive pulmonary disease | EFO:0000341 |
| Chronotype (morningness) | EFO:0008328 |
| Coronary artery disease | EFO:0000378 |
| Creatinine | EFO:0004518 |
| Crohn's disease | EFO:0000384 |
| Diastolic blood pressure | EFO:0006336 |
| Dihomo-gamma-linoleic acid | EFO:0008356 |
| Disposition index | EFO:0006832 |
| Estimated bone mineral density | EFO:0009270 |
| Excessive daytime sleepiness | EFO:0005246 |
| Fasting glucose | EFO:0004465 |
| Fasting glucose adj BMI | EFO:0008036 |
| Fasting insulin | EFO:0004466 |
| Fasting insulin adj BMI | EFO:0008037 |
| Fasting plasma glucose in diabetics and non-diabetics | EFO:0004465 |
| Frequent insomnia symptoms | EFO:0004698 |
| Gamma-glutamyl transferase | EFO:0004532 |
| Gamma-linolenic acid | EFO:0007762 |
| HbA1c | EFO:0004541 |
| HDL cholesterol | EFO:0004612 |
| Heart failure | EFO:0003144 |
| Heart rate | EFO:0004326 |
| Height | EFO:0004339 |
| Hip circumference | EFO:0005093 |
| Hip circumference adj BMI | EFO:0008039 |
| HOMA-B | EFO:0004469 |
| HOMA-IR | EFO:0004501 |
| Inflammatory bowel disease | EFO:0003767 |
| Insulin sensitivity | EFO:0004471 |
| Insulinogenic index | EFO:0009961 |
| Late diabetic kidney disease | EFO:0004997 |
| LDL cholesterol | EFO:0004611 |
| Leptin | EFO:0005000 |
| Linoleic acid | EFO:0006807 |
| Lobar intracranial hemorrhage | EFO:0010177 |
| Major depressive disorder | EFO:0003761 |
| Mean sleep duration | EFO:0005271 |
| Mean sleep duration, rank-normalized | EFO:0005271 |
| Naps | EFO:0007828 |
| Neuropathy in type 2 diabetics | EFO:1000783 |
| Non-HDL cholesterol | EFO:0005689 |
| Non-lobar intracranial hemorrhage | EFO:0010178 |
| Nonischemic cardiomyopathy | EFO:0009881 |
| Oleic acid | EFO:0006810 |
| P-wave duration | EFO:0005094 |
| P-wave terminal force | EFO:0008379 |
| Palmitoleic acid | EFO:0007973 |
| Pericardial adipose tissue volume | EFO:0007890 |
| Ratio visceral-subcutaneous adipose tissue volume | EFO:0004767 |
| Schizophrenia | EFO:0000692 |
| Sleep duration | EFO:0005271 |
| Subcutaneous adipose tissue volume | EFO:0004766 |
| Systolic blood pressure | EFO:0006335 |
| Total cholesterol | EFO:0004574 |
| Triglycerides | EFO:0004530 |
| Type 2 diabetes | EFO:0001360 |
| UACR in non-diabetics | EFO:0007778 |
| Ulcerative colitis | EFO:0000729 |
| Urinary albumin-to-creatinine ratio | EFO:0007778 |
| Visceral adipose tissue volume | EFO:0004765 |
| Waist circumference | EFO:0004342 |
| Waist circumference adj BMI | EFO:0007789 |
| Waist-hip ratio | EFO:0004343 |
| Waist-hip ratio adj BMI | EFO:0007788 |
+-------------------------------------------------------+-------------+
+-------------------------------------------------------+-------------+
| phenotype | efo_id |
+-------------------------------------------------------+-------------+
| Acute insulin response | EFO:0006831 |
| Adiponectin | EFO:0004502 |
| Albuminuria | EFO:0004285 |
| Alzheimer's disease | EFO:0000249 |
| Atrial fibrillation | EFO:0000275 |
| Bipolar disorder | EFO:0000289 |
| Blood urea nitrogen | EFO:0004741 |
| BMI | EFO:0004340 |
| Chronic kidney disease | EFO:0003884 |
| Chylomicrons and XXL-VLDL cholesterol | EFO:0008596 |
| Coronary artery disease | EFO:0000378 |
| Creatine kinase | EFO:0004534 |
| Creatinine | EFO:0004518 |
| Crohn's disease | EFO:0000384 |
| Diastolic blood pressure | EFO:0006336 |
| Dihomo-gamma-linoleic acid | EFO:0008356 |
| Fasting glucose | EFO:0004465 |
| Fasting glucose adj BMI | EFO:0008036 |
| Fasting insulin | EFO:0004466 |
| Fasting plasma glucose in diabetics and non-diabetics | EFO:0004465 |
| Gamma-linolenic acid | EFO:0007762 |
| HbA1c | EFO:0004541 |
| HDL cholesterol | EFO:0004612 |
| Heart failure | EFO:0003144 |
| Heart rate | EFO:0004326 |
| Height | EFO:0004339 |
| Hip circumference | EFO:0005093 |
| Hip circumference adj BMI | EFO:0008039 |
| HOMA-B | EFO:0004469 |
| Hypertension | EFO:0000537 |
| IDL cholesterol | EFO:0008595 |
| Inflammatory bowel disease | EFO:0003767 |
| LDL cholesterol | EFO:0004611 |
| Left ventricular ejection fraction | EFO:0008373 |
| Leptin | EFO:0005000 |
| Linoleic acid | EFO:0006807 |
| Mean arterial pressure | EFO:0006340 |
| Non-HDL cholesterol | EFO:0005689 |
| Nonischemic cardiomyopathy | EFO:0009881 |
| Oleic acid | EFO:0006810 |
| Omega-3 fatty acids | EFO:0010119 |
| Palmitoleic acid | EFO:0007973 |
| Peak insulin response | EFO:0008000 |
| Plasma C-reactive protein | EFO:0004458 |
| Proinsulin levels | EFO:0010814 |
| Pulse pressure | EFO:0005763 |
| Remnant cholesterol | EFO:0010815 |
| Schizophrenia | EFO:0000692 |
| Serum ApoA1 | EFO:0004614 |
| Serum ApoB | EFO:0004615 |
| Stroke volume | EFO:0010555 |
| Systolic blood pressure | EFO:0006335 |
| Total cholesterol | EFO:0004574 |
| Triglyceride-to-HDL ratio | EFO:0007929 |
| Triglycerides | EFO:0004530 |
| Type 1 diabetes | EFO:0001359 |
| Type 2 diabetes | EFO:0001360 |
| UACR in non-diabetics | EFO:0007778 |
| Ulcerative colitis | EFO:0000729 |
| Uric acid | EFO:0004761 |
| Urinary albumin-to-creatinine ratio | EFO:0007778 |
| Waist circumference | EFO:0004342 |
| Waist circumference adj BMI | EFO:0007789 |
| Waist-hip ratio | EFO:0004343 |
| Waist-hip ratio adj BMI | EFO:0007788 |
+-------------------------------------------------------+-------------+
+-------------------------------------------------------+-------------+
| phenotype | efo_id |
+-------------------------------------------------------+-------------+
| Atrial fibrillation | EFO:0000275 |
| Chronic kidney disease | EFO:0003884 |
| Coronary artery disease | EFO:0000378 |
| Fasting glucose | EFO:0004465 |
| Fasting insulin | EFO:0004466 |
| Fasting plasma glucose in diabetics and non-diabetics | EFO:0004465 |
| HbA1c | EFO:0004541 |
| HDL cholesterol | EFO:0004612 |
| LDL cholesterol | EFO:0004611 |
| Type 2 diabetes | EFO:0001360 |
+-------------------------------------------------------+-------------+