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remove whitespace in expo_chemical and normalize tables to nanobot
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Anita Caron authored and anitacaron committed Jan 24, 2024
1 parent 9e0d0db commit b003a91
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Showing 15 changed files with 108 additions and 109 deletions.
Empty file modified src/ontology/_nanobot
100644 → 100755
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2 changes: 1 addition & 1 deletion src/ontology/src/schema/column.tsv
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Expand Up @@ -115,4 +115,4 @@ expo_org defined_class_name ontology_label
expo_org stressor ontology_id
food_ingestion defined_class ontology_id
food_ingestion defined_class_name ontology_label
food_ingestion stressor ontology_id
food_ingestion stressor ontology_id
2 changes: 1 addition & 1 deletion src/ontology/src/schema/datatype.tsv
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Expand Up @@ -10,4 +10,4 @@ html_type word in('text', 'textarea', 'search', 'radio', 'number', 'select') an
ontology_id nonspace match(/\w+:\w+/) CURIE that does not begin or end with whitespace TEXT TEXT
ontology_label trimmed_text match(/[^\s]+.+[^\s]/) label that does not begin or end with whitespace text
trimmed_text text exclude(/^\s+|\s+$/) text that does not begin or end with whitespace
nonspace trimmed_text exclude(/\s/) text without whitespace
nonspace trimmed_text exclude(/\s/) text without whitespace
2 changes: 1 addition & 1 deletion src/ontology/src/schema/table.tsv
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Expand Up @@ -29,4 +29,4 @@ expo_med_action_r ../patterns/data/default/exposure_to_medical_action_route.tsv
expo_med_action ../patterns/data/default/exposure_to_medical_action.tsv
expo_occ ../patterns/data/default/exposure_to_occupation.tsv
expo_org ../patterns/data/default/exposure_to_organism.tsv
food_ingestion ../patterns/data/default/food_ingestion.tsv
food_ingestion ../patterns/data/default/food_ingestion.tsv
2 changes: 1 addition & 1 deletion src/patterns/data/default/exposure_to_behavior.tsv
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Expand Up @@ -29,4 +29,4 @@ ECTO:6000030 exposure to hunting NBO:0009003
ECTO:0001082 exposure to alcohol consumption NCIT:C16273
ECTO:6000033 exposure to travel NCIT:C53462
ECTO:6000031 exposure to strenuous exercise NCIT:C39773
ECTO:6000032 exposure to weight bearing NCIT:C178214
ECTO:6000032 exposure to weight bearing NCIT:C178214
72 changes: 36 additions & 36 deletions src/patterns/data/default/exposure_to_change.tsv
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@@ -1,36 +1,36 @@
defined_class defined_class_name attribute degree
ECTO:0001055 exposure to decreased air temperature ENVO:09200001 PATO:0001997
ECTO:4000000 exposure to change PATO:0000001 PATO:0000069
ECTO:4000002 exposure to increased salt CHEBI:24866 PATO:0000470
ECTO:4000003 exposure to decreased salt CHEBI:24866 PATO:0001997
ECTO:4000004 exposure to increased methane CHEBI:16183 PATO:0000470
ECTO:4000005 exposure to decreased methane CHEBI:16183 PATO:0001997
ECTO:4000006 exposure to increased glucose CHEBI:17234 PATO:0000470
ECTO:4000007 exposure to increased fructose CHEBI:28757 PATO:0000470
ECTO:4000008 exposure to increased sucrose CHEBI:17992 PATO:0000470
ECTO:4000009 exposure to increased protein CHEBI:36080 PATO:0000470
ECTO:4000010 exposure to increased monosaccharide CHEBI:35381 PATO:0000470
ECTO:4000011 exposure to increased cholesterol CHEBI:16113 PATO:0000470
ECTO:4000012 exposure to increased triglyceride CHEBI:17855 PATO:0000470
ECTO:4000013 exposure to increased low-density lipoprotein CHEBI:39026 PATO:0000470
ECTO:4000014 exposure to increased high-density lipoprotein CHEBI:39025 PATO:0000470
ECTO:4000015 exposure to decreased glucose CHEBI:17234 PATO:0001997
ECTO:4000016 exposure to decreased fructose CHEBI:28757 PATO:0001997
ECTO:4000017 exposure to decreased sucrose CHEBI:17992 PATO:0001997
ECTO:4000018 exposure to decreased protein CHEBI:36080 PATO:0001997
ECTO:4000019 exposure to decreased monosaccharide CHEBI:35381 PATO:0001997
ECTO:4000020 exposure to decreased cholesterol CHEBI:16113 PATO:0001997
ECTO:4000021 exposure to decreased triglyceride CHEBI:17855 PATO:0001997
ECTO:4000022 exposure to decreased low-density lipoprotein CHEBI:39026 PATO:0001997
ECTO:4000023 exposure to decreased high-density lipoprotein CHEBI:39025 PATO:0001997
ECTO:4000024 exposure to increased air pressure ENVO:09200011 PATO:0000470
ECTO:4000035 exposure to increased water pressure ENVO:3100033 PATO:0000470
ECTO:4000036 exposure to decreased air pressure ENVO:09200011 PATO:0001997
ECTO:4000033 exposure to decreased water pressure ENVO:3100033 PATO:0001997
ECTO:4000027 exposure to freezing water ENVO:00002006 PATO:0001985
ECTO:4000034 exposure to increased air temperature ENVO:09200001 PATO:0000470
ECTO:4000028 exposure to freezing air ENVO:00002005 PATO:0001985
ECTO:4000029 exposure to increased soil temperature ENVO:09200012 PATO:0000470
ECTO:4000030 exposure to decreased soil temperature ENVO:09200012 PATO:0001997
ECTO:4000031 exposure to increased water temperature ENVO:09200014 PATO:0000470
ECTO:4000032 exposure to decreased water temperature ENVO:09200014 PATO:0001997
defined_class defined_class_name attribute degree
ECTO:0001055 exposure to decreased air temperature ENVO:09200001 PATO:0001997
ECTO:4000000 exposure to change PATO:0000001 PATO:0000069
ECTO:4000002 exposure to increased salt CHEBI:24866 PATO:0000470
ECTO:4000003 exposure to decreased salt CHEBI:24866 PATO:0001997
ECTO:4000004 exposure to increased methane CHEBI:16183 PATO:0000470
ECTO:4000005 exposure to decreased methane CHEBI:16183 PATO:0001997
ECTO:4000006 exposure to increased glucose CHEBI:17234 PATO:0000470
ECTO:4000007 exposure to increased fructose CHEBI:28757 PATO:0000470
ECTO:4000008 exposure to increased sucrose CHEBI:17992 PATO:0000470
ECTO:4000009 exposure to increased protein CHEBI:36080 PATO:0000470
ECTO:4000010 exposure to increased monosaccharide CHEBI:35381 PATO:0000470
ECTO:4000011 exposure to increased cholesterol CHEBI:16113 PATO:0000470
ECTO:4000012 exposure to increased triglyceride CHEBI:17855 PATO:0000470
ECTO:4000013 exposure to increased low-density lipoprotein CHEBI:39026 PATO:0000470
ECTO:4000014 exposure to increased high-density lipoprotein CHEBI:39025 PATO:0000470
ECTO:4000015 exposure to decreased glucose CHEBI:17234 PATO:0001997
ECTO:4000016 exposure to decreased fructose CHEBI:28757 PATO:0001997
ECTO:4000017 exposure to decreased sucrose CHEBI:17992 PATO:0001997
ECTO:4000018 exposure to decreased protein CHEBI:36080 PATO:0001997
ECTO:4000019 exposure to decreased monosaccharide CHEBI:35381 PATO:0001997
ECTO:4000020 exposure to decreased cholesterol CHEBI:16113 PATO:0001997
ECTO:4000021 exposure to decreased triglyceride CHEBI:17855 PATO:0001997
ECTO:4000022 exposure to decreased low-density lipoprotein CHEBI:39026 PATO:0001997
ECTO:4000023 exposure to decreased high-density lipoprotein CHEBI:39025 PATO:0001997
ECTO:4000024 exposure to increased air pressure ENVO:09200011 PATO:0000470
ECTO:4000035 exposure to increased water pressure ENVO:3100033 PATO:0000470
ECTO:4000036 exposure to decreased air pressure ENVO:09200011 PATO:0001997
ECTO:4000033 exposure to decreased water pressure ENVO:3100033 PATO:0001997
ECTO:4000027 exposure to freezing water ENVO:00002006 PATO:0001985
ECTO:4000034 exposure to increased air temperature ENVO:09200001 PATO:0000470
ECTO:4000028 exposure to freezing air ENVO:00002005 PATO:0001985
ECTO:4000029 exposure to increased soil temperature ENVO:09200012 PATO:0000470
ECTO:4000030 exposure to decreased soil temperature ENVO:09200012 PATO:0001997
ECTO:4000031 exposure to increased water temperature ENVO:09200014 PATO:0000470
ECTO:4000032 exposure to decreased water temperature ENVO:09200014 PATO:0001997
4 changes: 2 additions & 2 deletions src/patterns/data/default/exposure_to_chemical.tsv
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Expand Up @@ -15,7 +15,7 @@ ECTO:9000013 exposure to thiazolidinediones CHEBI:50990
ECTO:9000014 exposure to verapamil CHEBI:9948
ECTO:0002002 exposure to steroid CHEBI:35341
ECTO:9000016 exposure to hydrogen chloride CHEBI:17883
ECTO:9000017 exposure to sulfuric acid CHEBI:26836
ECTO:9000017 exposure to sulfuric acid CHEBI:26836
ECTO:9000018 exposure to phosphoric acid CHEBI:26078
ECTO:9000019 exposure to acetic acid CHEBI:15366
ECTO:9000020 exposure to nitric acid CHEBI:48107
Expand Down Expand Up @@ -916,7 +916,7 @@ ECTO:9000967 exposure to aldicarb CHEBI:2555
ECTO:9000968 exposure to (+)-trans-allethrin CHEBI:39118
ECTO:9000969 exposure to allyl alcohol CHEBI:16605
ECTO:9000970 exposure to Allyl chloride CHEBI:82379
ECTO:9000971 exposure to aluminium metal CHEBI:33629
ECTO:9000971 exposure to aluminium metal CHEBI:33629
ECTO:9000972 exposure to aluminium phosphide CHEBI:38495
ECTO:9000973 exposure to aluminium oxide CHEBI:30187
ECTO:9000974 exposure to 2-Aminoanthraquinone CHEBI:34258
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2 changes: 1 addition & 1 deletion src/patterns/data/default/exposure_to_chemical_medium.tsv
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Expand Up @@ -14,4 +14,4 @@ ECTO:0090012 exposure to paraquat in soil CHEBI:34905 ENVO:00001998
ECTO:0090013 exposure to paraquat in water CHEBI:34905 ENVO:00002006
ECTO:0090014 exposure to DDT in air CHEBI:16130 ENVO:00002005
ECTO:0090015 exposure to DDT in soil CHEBI:16130 ENVO:00001998
ECTO:0090016 exposure to DDT in water CHEBI:16130 ENVO:00002006
ECTO:0090016 exposure to DDT in water CHEBI:16130 ENVO:00002006
2 changes: 1 addition & 1 deletion src/patterns/data/default/exposure_to_construction.tsv
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Expand Up @@ -24,4 +24,4 @@ ECTO:5000006 exposure to gold mine ENVO:00002168
ECTO:5000007 exposure to coal mine ENVO:00002169
ECTO:5000001 exposure to sidewalks ENVO:01001279
ECTO:5000002 exposure to public swimming pool ENVO:01000967
ECTO:1000042 exposure to day care building ENVO:01000927
ECTO:1000042 exposure to day care building ENVO:01000927
1 change: 0 additions & 1 deletion src/patterns/data/default/exposure_to_disposition.tsv
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@@ -1,4 +1,3 @@
defined_class defined_class_name stressor
ECTO:0500000 exposure to environmental disposition ENVO:01000452
ECTO:1000006 exposure to radiation shielding disposition ENVO:01001195

2 changes: 1 addition & 1 deletion src/patterns/data/default/exposure_to_environmental_condition.tsv
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@@ -1,4 +1,4 @@
defined_class defined_class_name stressor
ECTO:1000000 exposure to environmental condition ENVO:01000203
ECTO:1000020 exposure to weather ENVO:01001078
ECTO:1000032 exposure to air conditioning unit ENVO:00002874
ECTO:1000032 exposure to air conditioning unit ENVO:00002874
2 changes: 1 addition & 1 deletion src/patterns/data/default/exposure_to_environmental_quality.tsv
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Expand Up @@ -8,4 +8,4 @@ ECTO:0000980 exposure to temperature of air in surroundings ENVO:09200001
ECTO:4000001 exposure to increased temperature PATO:0001305
ECTO:0001057 exposure to decreased temperature PATO:0001306
ECTO:4000025 exposure to increased pressure PATO:0001576
ECTO:4000026 exposure to decreased pressure PATO:0001575
ECTO:4000026 exposure to decreased pressure PATO:0001575
2 changes: 1 addition & 1 deletion src/patterns/data/default/exposure_to_geographic_feature.tsv
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Expand Up @@ -4,4 +4,4 @@ ECTO:5000003 exposure to mine drainage ENVO:00001996
ECTO:5000004 exposure to acid mine drainage ENVO:00001997
ECTO:5000005 exposure to gold mine drainage ENVO:00002112
ECTO:5000008 exposure to petting zoo ENVO:01000923
ECTO:5000009 exposure to campground ENVO:01000935
ECTO:5000009 exposure to campground ENVO:01000935
120 changes: 60 additions & 60 deletions src/patterns/data/default/exposure_to_medical_action.tsv
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@@ -1,60 +1,60 @@
defined_class defined_class_name stressor
ECTO:2000000 exposure to medical action MAXO:0000001
ECTO:2000001 exposure to medication for hypertension MAXO:0000321
ECTO:2000002 exposure to dyslipidemic agent therapy MAXO:0000189
ECTO:2000003 exposure to blood glucose regulator therapy MAXO:0000175
ECTO:2000004 exposure to theraputic insulin treatment MAXO:0000259
ECTO:2000005 exposure to hormone replacement therapy MAXO:0000282
ECTO:2000006 exposure to estrogen modification therapy MAXO:0000287
ECTO:2000007 exposure to platelet aggregation inhibitors MAXO:0000180
ECTO:2000008 exposure to antiarrythmic agents MAXO:0000185
ECTO:2000009 exposure to antipsychotic medication MAXO:0000166
ECTO:2000010 exposure to calcium channel blocker treatment MAXO:0000434
ECTO:2000011 exposure to NSAIDs MAXO:0000221
ECTO:2000012 exposure to H2 blockers MAXO:0000269
ECTO:2000013 exposure to theraputic diuretics MAXO:0000165
ECTO:2000014 exposure to anticholinergic bronchodilators MAXO:0000317
ECTO:2000015 exposure to corticosteroid therapy MAXO:0000640
ECTO:2000016 exposure to MAO inhibitor MAXO:0000213
ECTO:2000017 exposure to antidepressants MAXO:0000160
ECTO:2000018 exposure to phosphodiesterase inhibitors MAXO:0000318
ECTO:2000019 exposure to proton pump inhibitors MAXO:0000272
ECTO:2000020 exposure to progestin treatment MAXO:0000288
ECTO:2000021 exposure to drugs to treat Parkinsons MAXO:0000157
ECTO:2000022 exposure to vasodilators MAXO:0000191
ECTO:2000023 exposure to sympathomimetic bronchodilators MAXO:0000319
ECTO:2000024 exposure to tricyclic antidepressants MAXO:0000215
ECTO:2000025 exposure to thyroid-modifying hormonal therapy MAXO:0000284
ECTO:2000027 exposure to anticoagulants MAXO:0000178
ECTO:2000028 exposure to sartans MAXO:0000190
ECTO:2000029 exposure to alpha-blockers MAXO:0000184
ECTO:2000030 exposure to cholinesterase inhibitor MAXO:0000210
ECTO:2000031 exposure to theraputic tranquilizers MAXO:0001023
ECTO:2000032 exposure to beta-blockers MAXO:0000187
ECTO:2000034 exposure to antileukotriene agents MAXO:0000315
ECTO:2000035 exposure to glycemic agents MAXO:0000258
ECTO:2000036 exposure to antigout agent MAXO:0000164
ECTO:2000037 exposure to diagnostic imaging NCIT:C16502
ECTO:2000038 exposure to ultrasound tomography NCIT:C116448
ECTO:2000039 exposure to positron emission tomography NCIT:C17007
ECTO:2000040 exposure to radiography NCIT:C38101
ECTO:2000041 exposure to mammography NCIT:C16818
ECTO:2000042 exposure to xeroradiography NCIT:C17263
ECTO:2000043 exposure to myelography NCIT:C20175
ECTO:2000044 exposure to bronchography NCIT:C38040
ECTO:2000045 exposure to cystography NCIT:C38049
ECTO:2000046 exposure to vaginography NCIT:C38096
ECTO:2000047 exposure to abdominal radiography NCIT:C38102
ECTO:2000048 exposure to chest radiography NCIT:C38103
ECTO:2000049 exposure to cholangiography NCIT:C61508
ECTO:2000050 exposure to total body radiography NCIT:C96640
ECTO:2000051 exposure to angiography NCIT:C20080
ECTO:2000052 exposure to radioactivity NCIT:C17054
ECTO:2000053 exposure to Human Papillomavirus Infection NCIT:C27851
ECTO:2000054 exposure to surgery MAXO:0000004
ECTO:2000055 exposure to kidney implantation MAXO:0010043
ECTO:2000056 exposure to transplant surgery MAXO:0000068
ECTO:2000057 exposure to pharmacotherapy MAXO:0000058
ECTO:2000058 exposure to blood transfusion MAXO:0000756
ECTO:2000059 exposure to anesthetics MAXO:0000170
ECTO:2000060 exposure to neck radiograph procedure MAXO:0010355
defined_class defined_class_name stressor
ECTO:2000000 exposure to medical action MAXO:0000001
ECTO:2000001 exposure to medication for hypertension MAXO:0000321
ECTO:2000002 exposure to dyslipidemic agent therapy MAXO:0000189
ECTO:2000003 exposure to blood glucose regulator therapy MAXO:0000175
ECTO:2000004 exposure to theraputic insulin treatment MAXO:0000259
ECTO:2000005 exposure to hormone replacement therapy MAXO:0000282
ECTO:2000006 exposure to estrogen modification therapy MAXO:0000287
ECTO:2000007 exposure to platelet aggregation inhibitors MAXO:0000180
ECTO:2000008 exposure to antiarrythmic agents MAXO:0000185
ECTO:2000009 exposure to antipsychotic medication MAXO:0000166
ECTO:2000010 exposure to calcium channel blocker treatment MAXO:0000434
ECTO:2000011 exposure to NSAIDs MAXO:0000221
ECTO:2000012 exposure to H2 blockers MAXO:0000269
ECTO:2000013 exposure to theraputic diuretics MAXO:0000165
ECTO:2000014 exposure to anticholinergic bronchodilators MAXO:0000317
ECTO:2000015 exposure to corticosteroid therapy MAXO:0000640
ECTO:2000016 exposure to MAO inhibitor MAXO:0000213
ECTO:2000017 exposure to antidepressants MAXO:0000160
ECTO:2000018 exposure to phosphodiesterase inhibitors MAXO:0000318
ECTO:2000019 exposure to proton pump inhibitors MAXO:0000272
ECTO:2000020 exposure to progestin treatment MAXO:0000288
ECTO:2000021 exposure to drugs to treat Parkinsons MAXO:0000157
ECTO:2000022 exposure to vasodilators MAXO:0000191
ECTO:2000023 exposure to sympathomimetic bronchodilators MAXO:0000319
ECTO:2000024 exposure to tricyclic antidepressants MAXO:0000215
ECTO:2000025 exposure to thyroid-modifying hormonal therapy MAXO:0000284
ECTO:2000027 exposure to anticoagulants MAXO:0000178
ECTO:2000028 exposure to sartans MAXO:0000190
ECTO:2000029 exposure to alpha-blockers MAXO:0000184
ECTO:2000030 exposure to cholinesterase inhibitor MAXO:0000210
ECTO:2000031 exposure to theraputic tranquilizers MAXO:0001023
ECTO:2000032 exposure to beta-blockers MAXO:0000187
ECTO:2000034 exposure to antileukotriene agents MAXO:0000315
ECTO:2000035 exposure to glycemic agents MAXO:0000258
ECTO:2000036 exposure to antigout agent MAXO:0000164
ECTO:2000037 exposure to diagnostic imaging NCIT:C16502
ECTO:2000038 exposure to ultrasound tomography NCIT:C116448
ECTO:2000039 exposure to positron emission tomography NCIT:C17007
ECTO:2000040 exposure to radiography NCIT:C38101
ECTO:2000041 exposure to mammography NCIT:C16818
ECTO:2000042 exposure to xeroradiography NCIT:C17263
ECTO:2000043 exposure to myelography NCIT:C20175
ECTO:2000044 exposure to bronchography NCIT:C38040
ECTO:2000045 exposure to cystography NCIT:C38049
ECTO:2000046 exposure to vaginography NCIT:C38096
ECTO:2000047 exposure to abdominal radiography NCIT:C38102
ECTO:2000048 exposure to chest radiography NCIT:C38103
ECTO:2000049 exposure to cholangiography NCIT:C61508
ECTO:2000050 exposure to total body radiography NCIT:C96640
ECTO:2000051 exposure to angiography NCIT:C20080
ECTO:2000052 exposure to radioactivity NCIT:C17054
ECTO:2000053 exposure to Human Papillomavirus Infection NCIT:C27851
ECTO:2000054 exposure to surgery MAXO:0000004
ECTO:2000055 exposure to kidney implantation MAXO:0010043
ECTO:2000056 exposure to transplant surgery MAXO:0000068
ECTO:2000057 exposure to pharmacotherapy MAXO:0000058
ECTO:2000058 exposure to blood transfusion MAXO:0000756
ECTO:2000059 exposure to anesthetics MAXO:0000170
ECTO:2000060 exposure to neck radiograph procedure MAXO:0010355
2 changes: 1 addition & 1 deletion src/patterns/data/default/exposure_to_organism.tsv
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Expand Up @@ -9,4 +9,4 @@ ECTO:3000010 exposure to human patient OPMI:0000417
ECTO:3000006 exposure to Toxoplasma gondii NCBITaxon:5811
ECTO:3000007 exposure to Listeria NCBITaxon:1637
ECTO:3000008 exposure to Salmonella NCBITaxon:590
ECTO:3000009 exposure to Escherichia coli NCBITaxon:562
ECTO:3000009 exposure to Escherichia coli NCBITaxon:562

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