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Workflow
The following workflow defines all tasks necessary to upload, preprocess, share, and map a new data dictionary.
- Upload cohort data
- Open Google Sheet
- Run automated mapping for new data dictionary
- Share Google Sheet with submitter
- Prepare data dictionary for build
- Run automated validation
- Build data dictionary
- View results
- Add data dictionary to Version Control
- Prepare git commit (click on Commit in Version menu)
- Push changes to GitHub (click on Push in Version menu), and make pull request.
- Delete Google sheet (Caution, cannot be undone)
IHCC Data Admin Tasks
Console
Press a button above to execute an action.
Exit status of last command unknown. The server may have restarted before it could complete.
$ make -f Makefile automated_mapping
make cogs_pull
make[1]: Entering directory '/workspace'
cogs fetch
cogs pull
make[1]: Leaving directory '/workspace'
cp build/terminology.tsv templates/cogs.tsv
make build/suggestions_cogs.tsv
make[1]: Entering directory '/workspace'
python3 src/mapping-suggest/id-generator-templates.py -t templates/cogs.tsv -m build/metadata.tsv
Generating IDs for data dictionary: EB
mkdir -p build/intermediate
python3 src/mapping-suggest/mapping-suggest-zooma.py -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -o build/intermediate/cogs_mapping_suggestions_zooma.tsv
Zooma config: {'zooma_annotate': 'https://test.mapping.ihccglobal.app/zooma/v2/api/services/annotate?propertyValue=', 'oxo_mapping': 'https://test.mapping.ihccglobal.app/api/mappings?fromId=', 'ols_term': 'https://test.registry.ihccglobal.app/api/terms?iri=', 'ols_oboid': 'https://test.registry.ihccglobal.app/api/terms?obo_id=', 'min_match_probability': 0.1, 'rescale_nlp_matches': {'low': 0, 'high': 0.9}, 'zooma_confidence_mappings': {'LOW': 0.51, 'MEDIUM': 0.76, 'GOOD': 0.98, 'HIGH': 1}}
Zooma matching successful. First twenty results:
term match confidence
0 Person GECKO:0000066 0.76
1 Person GECKO:0000055 0.76
2 Person GECKO:0000120 0.76
3 Sample GECKO:0000052 0.98
4 Nationality GECKO:0000064 1.00
5 Education GECKO:0000065 1.00
6 Smoking GECKO:0000068 1.00
7 Alcohol GECKO:0000069 1.00
8 Sleep GECKO:0000071 0.98
9 Health GECKO:0000126 0.98
curl -L -o build/gecko.owl http://purl.obolibrary.org/obo/gecko/views/ihcc-gecko.owl
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 349 100 349 0 0 1216 0 --:--:-- --:--:-- --:--:-- 1216
100 105k 100 105k 0 0 199k 0 --:--:-- --:--:-- --:--:-- 199k
curl -Lk -o build/robot.jar https://build.obolibrary.io/job/ontodev/job/robot/job/master/lastSuccessfulBuild/artifact/bin/robot.jar
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 77.1M 0 434k 0 0 361k 0 0:03:38 0:00:01 0:03:37 361k
17 77.1M 17 13.1M 0 0 6438k 0 0:00:12 0:00:02 0:00:10 6438k
43 77.1M 43 33.2M 0 0 10.7M 0 0:00:07 0:00:03 0:00:04 10.7M
70 77.1M 70 54.0M 0 0 13.1M 0 0:00:05 0:00:04 0:00:01 13.1M
94 77.1M 94 72.6M 0 0 14.2M 0 0:00:05 0:00:05 --:--:-- 14.7M
100 77.1M 100 77.1M 0 0 14.5M 0 0:00:05 0:00:05 --:--:-- 18.7M
java -jar build/robot.jar --prefixes src/prefixes.json query --input build/gecko.owl --query src/queries/ihcc-mapping-gecko.sparql build/intermediate/gecko-xrefs-sparql.csv
python3 src/mapping-suggest/mapping-suggest-nlp.py -z data/ihcc-mapping-suggestions-zooma.tsv -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -g build/intermediate/gecko-xrefs-sparql.csv -o build/intermediate/cogs_mapping_suggestions_nlp.tsv
/usr/local/lib/python3.8/dist-packages/sklearn/linear_model/_stochastic_gradient.py:173: FutureWarning: The loss 'log' was deprecated in v1.1 and will be removed in version 1.3. Use `loss='log_loss'` which is equivalent.
warnings.warn(
Term ID Label
0 EB:0000001 Person.skood
1 EB:0000002 Person.gender
2 EB:0000003 Person.birthDate
3 EB:0000004 Person.birthYear
4 EB:0000005 Person.agreementDate
NLP matching successful. First twenty results:
term match confidence
0 ObjectiveInformation.weight CMO:0000012 0.838854
1 ObjectiveInformation.bmi CMO:0000021 0.671333
2 ObjectiveInformation.waist CMO:0000021 0.270120
3 ObjectiveInformation.hip CMO:0000021 0.280370
4 ObjectiveInformation.height CMO:0000106 0.685548
5 Sample.vkood GECKO:0000052 0.197468
6 Sample.visitNumber GECKO:0000052 0.197468
7 PhysicalExercise.code GECKO:0000052 0.402314
8 ProfessionalSportPast.code GECKO:0000052 0.402314
9 ProfessionalSport.code GECKO:0000052 0.402314
10 HormonalContraceptiveUsed.code GECKO:0000052 0.402314
11 HormonalContraceptiveUsedV1.code GECKO:0000052 0.402314
12 HormonalMedicationMenopause.code GECKO:0000052 0.402314
13 HormonalMedicationMenopauseV1.code GECKO:0000052 0.402314
14 Health.movement GECKO:0000052 0.105140
15 Health.selfcare GECKO:0000052 0.105140
16 Health.commonActivities GECKO:0000052 0.105140
17 Health.painDiscomfort GECKO:0000052 0.105140
18 Health.anxietyDepression GECKO:0000052 0.105140
19 MedicationsForTroubledBreathing.code GECKO:0000052 0.402314
python3 src/mapping-suggest/mapping-suggest-zooma.py -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -p WORD_BOUNDARY -o build/intermediate/cogs_mapping_suggestions_zooma_clean.tsv
Zooma config: {'zooma_annotate': 'https://test.mapping.ihccglobal.app/zooma/v2/api/services/annotate?propertyValue=', 'oxo_mapping': 'https://test.mapping.ihccglobal.app/api/mappings?fromId=', 'ols_term': 'https://test.registry.ihccglobal.app/api/terms?iri=', 'ols_oboid': 'https://test.registry.ihccglobal.app/api/terms?obo_id=', 'min_match_probability': 0.1, 'rescale_nlp_matches': {'low': 0, 'high': 0.9}, 'zooma_confidence_mappings': {'LOW': 0.51, 'MEDIUM': 0.76, 'GOOD': 0.98, 'HIGH': 1}}
Zooma matching successful. First twenty results:
term match confidence
0 Person.gender GECKO:0000066 0.98
1 Nationality.nationality GECKO:0000064 0.98
2 Education.highestEducationLevel GECKO:0000065 0.76
3 Education.highestEducationLevel UBERON:0000105 0.76
4 Education.highestEducationLevel GECKO:0000065 0.76
5 EatingHabits.eatingHabit GECKO:0000072 0.98
6 Smoking.smokingStatus GECKO:0000068 0.98
7 OtherDrugs.usingOtherDrugs GECKO:0000094 0.98
8 OtherDrugs.otherDrugs GECKO:0000094 0.98
9 ObjectiveInformation.weight GECKO:0000114 0.98
10 Person GECKO:0000066 0.76
11 Person GECKO:0000055 0.76
12 Person GECKO:0000120 0.76
13 Person GECKO:0000066 0.76
14 Person GECKO:0000055 0.76
15 Person GECKO:0000120 0.76
16 Sample GECKO:0000052 0.98
17 Sample GECKO:0000052 0.98
18 Nationality GECKO:0000064 1.00
19 Nationality GECKO:0000064 1.00
python3 src/mapping-suggest/mapping-suggest-nlp.py -z data/ihcc-mapping-suggestions-zooma.tsv -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -g build/intermediate/gecko-xrefs-sparql.csv -p WORD_BOUNDARY -o build/intermediate/cogs_mapping_suggestions_nlp_clean.tsv
/usr/local/lib/python3.8/dist-packages/sklearn/linear_model/_stochastic_gradient.py:173: FutureWarning: The loss 'log' was deprecated in v1.1 and will be removed in version 1.3. Use `loss='log_loss'` which is equivalent.
warnings.warn(
Term ID Label
0 EB:0000001 Person.skood
1 EB:0000002 Person.gender
2 EB:0000003 Person.birthDate
3 EB:0000004 Person.birthYear
4 EB:0000005 Person.agreementDate
NLP matching successful. First twenty results:
term ... confidence
0 VisualDecadence.leftEyeDioptry ... 0.113617
1 CardiovascularDiseasesAdditional.leftVentricle... ... 0.373521
2 PersonPortrait.lastWeight ... 0.292623
3 ObjectiveInformation.weight ... 0.169248
4 ObjectiveInformation.weightMeasurement ... 0.129824
5 PersonPortrait.lastBmi ... 0.179169
6 PersonPortrait.bmiDate ... 0.177605
7 PersonPortrait.bmiSource ... 0.161873
8 ObjectiveInformation.bmi ... 0.131411
9 ObjectiveInformation.armCircumference ... 0.129845
10 ObjectiveInformation.waistHipMeasurement ... 0.190083
11 PersonPortrait.lastHeight ... 0.169324
12 ObjectiveInformation.height ... 0.100642
13 PersonPortrait.bmiSource ... 0.121913
14 PersonPortrait.smokingSource ... 0.100888
15 PersonPortrait.educationSource ... 0.132881
16 PersonPortrait.settlementRegionType ... 0.170828
17 Sample.vkood ... 0.172990
18 Sample.visitNumber ... 0.175211
19 InformedConsent.icDate ... 0.132590
[20 rows x 3 columns]
python3 src/mapping-suggest/mapping-suggest-zooma.py -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -p HIERARCHY -o build/intermediate/cogs_mapping_suggestions_zooma_hierarchy.tsv
Zooma config: {'zooma_annotate': 'https://test.mapping.ihccglobal.app/zooma/v2/api/services/annotate?propertyValue=', 'oxo_mapping': 'https://test.mapping.ihccglobal.app/api/mappings?fromId=', 'ols_term': 'https://test.registry.ihccglobal.app/api/terms?iri=', 'ols_oboid': 'https://test.registry.ihccglobal.app/api/terms?obo_id=', 'min_match_probability': 0.1, 'rescale_nlp_matches': {'low': 0, 'high': 0.9}, 'zooma_confidence_mappings': {'LOW': 0.51, 'MEDIUM': 0.76, 'GOOD': 0.98, 'HIGH': 1}}
Zooma matching successful. First twenty results:
term match confidence
0 Person.gender GECKO:0000060 1.00
1 Person.birthDate PATO:0000011 0.98
2 PersonPortrait.nationality GECKO:0000064 1.00
3 DiagnosisConsolidated.icd10 MONDO:0004992 0.76
4 DiagnosisConsolidated.icd10 MONDO:0005084 0.76
5 DiagnosisConsolidated.icd10 MONDO:0000001 0.76
6 DiagnosisConsolidated.icd10 MONDO:0004995 0.76
7 DiagnosisConsolidated.icd10 GECKO:0000052 0.76
8 Nationality.nationality GECKO:0000064 1.00
9 PhysicalExercise.code GECKO:0000073 0.76
10 PhysicalExercise.code GECKO:0000064 0.76
11 PhysicalExercise.code GECKO:0000052 0.76
12 PhysicalExercise.code MONDO:0000001 0.76
13 PhysicalExercise.code GECKO:0000060 0.76
14 ProfessionalSportPast.code GECKO:0000073 0.76
15 ProfessionalSportPast.code GECKO:0000064 0.76
16 ProfessionalSportPast.code GECKO:0000052 0.76
17 ProfessionalSportPast.code MONDO:0000001 0.76
18 ProfessionalSportPast.code GECKO:0000060 0.76
19 ProfessionalSport.code GECKO:0000073 0.76
python3 src/mapping-suggest/mapping-suggest-nlp.py -z data/ihcc-mapping-suggestions-zooma.tsv -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -g build/intermediate/gecko-xrefs-sparql.csv -p HIERARCHY -o build/intermediate/cogs_mapping_suggestions_nlp_hierarchy.tsv
/usr/local/lib/python3.8/dist-packages/sklearn/linear_model/_stochastic_gradient.py:173: FutureWarning: The loss 'log' was deprecated in v1.1 and will be removed in version 1.3. Use `loss='log_loss'` which is equivalent.
warnings.warn(
Term ID Label
0 EB:0000001 Person.skood
1 EB:0000002 Person.gender
2 EB:0000003 Person.birthDate
3 EB:0000004 Person.birthYear
4 EB:0000005 Person.agreementDate
NLP matching successful. First twenty results:
term match confidence
0 ObjectiveInformation.weight CMO:0000012 0.838672
1 ObjectiveInformation.bmi CMO:0000021 0.674691
2 ObjectiveInformation.waist CMO:0000021 0.266867
3 ObjectiveInformation.hip CMO:0000021 0.270046
4 ObjectiveInformation.height CMO:0000106 0.681883
5 PhysicalExercise.code GECKO:0000052 0.404556
6 ProfessionalSportPast.code GECKO:0000052 0.404556
7 ProfessionalSport.code GECKO:0000052 0.404556
8 HormonalContraceptiveUsed.code GECKO:0000052 0.404556
9 HormonalContraceptiveUsedV1.code GECKO:0000052 0.404556
10 HormonalMedicationMenopause.code GECKO:0000052 0.404556
11 HormonalMedicationMenopauseV1.code GECKO:0000052 0.404556
12 MedicationsForTroubledBreathing.code GECKO:0000052 0.404556
13 DiseasesDiagnosed.code GECKO:0000052 0.404556
14 MedicationsUsedForDisease.code GECKO:0000052 0.404556
15 MedicationPackagesUsedForDisease.code GECKO:0000052 0.404556
16 ConcurrentDiagnoses.code GECKO:0000052 0.404556
17 RespiratoryDiseasesMedications.code GECKO:0000052 0.404556
18 DiabetesComplications.code GECKO:0000052 0.404556
19 DiabetesMedications.code GECKO:0000052 0.404556
python3 src/mapping-suggest/mapping-suggest-zooma.py -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -p DEFINITION -o build/intermediate/cogs_mapping_suggestions_zooma_definition.tsv
Zooma config: {'zooma_annotate': 'https://test.mapping.ihccglobal.app/zooma/v2/api/services/annotate?propertyValue=', 'oxo_mapping': 'https://test.mapping.ihccglobal.app/api/mappings?fromId=', 'ols_term': 'https://test.registry.ihccglobal.app/api/terms?iri=', 'ols_oboid': 'https://test.registry.ihccglobal.app/api/terms?obo_id=', 'min_match_probability': 0.1, 'rescale_nlp_matches': {'low': 0, 'high': 0.9}, 'zooma_confidence_mappings': {'LOW': 0.51, 'MEDIUM': 0.76, 'GOOD': 0.98, 'HIGH': 1}}
Zooma matching successful. First twenty results:
term match confidence
0 Person.gender GECKO:0000060 1.00
1 Person.birthDate PATO:0000011 0.98
2 Person.birthYear GECKO:0000066 0.98
3 Person.deathDate STATO:0000093 1.00
4 PersonPortrait.nationality GECKO:0000064 1.00
5 PersonPortrait.lastEducation GECKO:0000065 0.98
6 PersonPortrait.residencyRegion GECKO:0000064 1.00
7 Nationality.nationality GECKO:0000064 1.00
8 SpareTimeActivities.shoppingPerWeek GECKO:0000131 0.76
9 SpareTimeActivities.shoppingPerWeek GECKO:0000104 0.76
10 SpareTimeActivities.cleaningPerWeek GECKO:0000052 0.76
11 SpareTimeActivities.cleaningPerWeek MONDO:0004992 0.76
12 SpareTimeActivities.cleaningPerWeek GECKO:0000060 0.76
13 SpareTimeActivities.physicalExercisePerWeek OGMS:0000020 0.98
14 SpareTimeActivities.readingPerWeek CMO:0000294 0.76
15 SpareTimeActivities.readingPerWeek CMO:0000003 0.76
16 TobaccoLast12Months.smokeProd GECKO:0000068 0.98
17 TobaccoUsually.smokeProd GECKO:0000068 0.98
18 TobaccoLastMonth.smokeProd GECKO:0000068 0.98
19 TobaccoYearBeforeQuitting.smokeProd GECKO:0000068 0.98
python3 src/mapping-suggest/mapping-suggest-nlp.py -z data/ihcc-mapping-suggestions-zooma.tsv -c src/mapping-suggest/mapping-suggest-config.yml -t templates/cogs.tsv -g build/intermediate/gecko-xrefs-sparql.csv -p DEFINITION -o build/intermediate/cogs_mapping_suggestions_nlp_definition.tsv
/usr/local/lib/python3.8/dist-packages/sklearn/linear_model/_stochastic_gradient.py:173: FutureWarning: The loss 'log' was deprecated in v1.1 and will be removed in version 1.3. Use `loss='log_loss'` which is equivalent.
warnings.warn(
Term ID Label
0 EB:0000001 Person.skood
1 EB:0000002 Person.gender
2 EB:0000003 Person.birthDate
3 EB:0000004 Person.birthYear
4 EB:0000005 Person.agreementDate
NLP matching successful. First twenty results:
term match confidence
0 PersonPortrait.lastWeight CMO:0000012 0.238107
1 ObjectiveInformation.weight CMO:0000012 0.776581
2 PersonPortrait.lastBmi CMO:0000021 0.159028
3 PersonPortrait.bmiSource CMO:0000021 0.111194
4 ObjectiveInformation.bmi CMO:0000021 0.624277
5 ObjectiveInformation.waist CMO:0000021 0.244291
6 ObjectiveInformation.hip CMO:0000021 0.254484
7 PersonPortrait.lastHeight CMO:0000106 0.137902
8 ObjectiveInformation.height CMO:0000106 0.632279
9 PersonPortrait.bmiSource GECKO:0000052 0.101222
10 PersonPortrait.settlementRegionType GECKO:0000052 0.212189
11 Sample.vkood GECKO:0000052 0.186963
12 Sample.visitNumber GECKO:0000052 0.186963
13 Answerset.isFirst GECKO:0000052 0.119493
14 Answerset.visitNumber GECKO:0000052 0.123105
15 PhysicalExercise.code GECKO:0000052 0.377517
16 ProfessionalSportPast.code GECKO:0000052 0.377517
17 ProfessionalSport.code GECKO:0000052 0.377517
18 SpareTimeActivities.childcarePerWeek GECKO:0000052 0.156188
19 SpareTimeActivities.elderlyCarePerWeek GECKO:0000052 0.134551
python3 src/mapping-suggest/merge-mapping-suggestions.py -t templates/cogs.tsv -s build/intermediate/cogs_mapping_suggestions_zooma.tsv -s build/intermediate/cogs_mapping_suggestions_nlp.tsv -s build/intermediate/cogs_mapping_suggestions_zooma_clean.tsv -s build/intermediate/cogs_mapping_suggestions_nlp_clean.tsv -s build/intermediate/cogs_mapping_suggestions_zooma_hierarchy.tsv -s build/intermediate/cogs_mapping_suggestions_nlp_hierarchy.tsv -s build/intermediate/cogs_mapping_suggestions_zooma_definition.tsv -s build/intermediate/cogs_mapping_suggestions_nlp_definition.tsv -o build/suggestions_cogs.tsv
['build/intermediate/cogs_mapping_suggestions_zooma.tsv', 'build/intermediate/cogs_mapping_suggestions_nlp.tsv', 'build/intermediate/cogs_mapping_suggestions_zooma_clean.tsv', 'build/intermediate/cogs_mapping_suggestions_nlp_clean.tsv', 'build/intermediate/cogs_mapping_suggestions_zooma_hierarchy.tsv', 'build/intermediate/cogs_mapping_suggestions_nlp_hierarchy.tsv', 'build/intermediate/cogs_mapping_suggestions_zooma_definition.tsv', 'build/intermediate/cogs_mapping_suggestions_nlp_definition.tsv']
Mapping suggestions files concat:
term ... confidence
0 Person ... 0.760000
1 Person ... 0.760000
2 Person ... 0.760000
3 Sample ... 0.980000
4 Nationality ... 1.000000
5 Education ... 1.000000
6 Smoking ... 1.000000
7 Alcohol ... 1.000000
8 Sleep ... 0.980000
9 Health ... 0.980000
0 ObjectiveInformation.weight ... 0.838854
1 ObjectiveInformation.bmi ... 0.671333
2 ObjectiveInformation.waist ... 0.270120
3 ObjectiveInformation.hip ... 0.280370
4 ObjectiveInformation.height ... 0.685548
5 Sample.vkood ... 0.197468
6 Sample.visitNumber ... 0.197468
7 PhysicalExercise.code ... 0.402314
8 ProfessionalSportPast.code ... 0.402314
9 ProfessionalSport.code ... 0.402314
[20 rows x 4 columns]
Merging suggestions successful. First twenty results:
Term ID ... Comment
0 EB:0000001 ... NaN
1 EB:0000002 ... NaN
2 EB:0000003 ... NaN
3 EB:0000004 ... NaN
4 EB:0000005 ... NaN
5 EB:0000006 ... NaN
6 EB:0000007 ... NaN
7 EB:0000008 ... NaN
8 EB:0000009 ... NaN
9 EB:0000010 ... NaN
10 EB:0000011 ... NaN
11 EB:0000012 ... Person's last measurements, smoking status and...
12 EB:0000013 ... Person's last measurements, smoking status and...
13 EB:0000014 ... Person's last measurements, smoking status and...
14 EB:0000015 ... Person's last measurements, smoking status and...
15 EB:0000016 ... Person's last measurements, smoking status and...
16 EB:0000017 ... Person's last measurements, smoking status and...
17 EB:0000018 ... Person's last measurements, smoking status and...
18 EB:0000019 ... Person's last measurements, smoking status and...
19 EB:0000020 ... Person's last measurements, smoking status and...
[20 rows x 8 columns]
make[1]: Leaving directory '/workspace'
cp build/suggestions_cogs.tsv build/terminology.tsv
rm -f templates/cogs.tsv
make cogs-apply-data-validation
make[1]: Entering directory '/workspace'
java -jar build/robot.jar --prefixes src/prefixes.json export \
--input build/gecko.owl \
--header "LABEL" \
--export build/gecko_labels.tsv
python3 src/mapping-suggest/create-data-validation.py build/terminology.tsv build/gecko_labels.tsv build/cogs-data-validation.tsv build/cogs-info-table.tsv
ERROR:root:'disease or disorder' suggested on row 32 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 85 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 92 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 94 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 265 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 266 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 267 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 268 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 332 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 335 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 339 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 341 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 342 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 359 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 371 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 373 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 374 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 397 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 405 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 465 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 466 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 467 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 468 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 469 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 470 is not a GECKO term
ERROR:root:'disease or disorder' suggested on row 475 is not a GECKO term
cogs apply build/cogs-data-validation.tsv
make[1]: Leaving directory '/workspace'
make cogs-apply-info-table
make[1]: Entering directory '/workspace'
cogs apply build/cogs-info-table.tsv
make[1]: Leaving directory '/workspace'
cogs push