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Improving topmed data #147

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847 changes: 847 additions & 0 deletions data/topmed_tags_v2.0.json

Large diffs are not rendered by default.

15,912 changes: 15,912 additions & 0 deletions data/topmed_variables_v2.0.csv

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14 changes: 8 additions & 6 deletions src/dug/core/parsers/topmed_tag_parser.py
Original file line number Diff line number Diff line change
@@ -55,12 +55,14 @@ def __call__(self, input_file: InputFile) -> List[Indexable]:
reader = csv.DictReader(csvfile, delimiter='\t')
for row in reader:
row = {k.strip(): v for k, v in row.items()}
elem = DugElement(elem_id=row['variable_full_accession'],
name=row['variable_name'] if 'variable_name' in row else row['variable_full_accession'],
desc=row['variable_desc'] if 'variable_name' in row else row['variable_full_accession'],
elem_type="DbGaP",
collection_id=row['study_full_accession'],
collection_name=row['study_name'])
elem = DugElement(
elem_id=row['variable_full_accession'],
name=row['variable_name'] if 'variable_name' in row else row['variable_full_accession'],
desc=row['variable_description'] if 'variable_description' in row else row['variable_full_accession'],
elem_type="DbGaP",
collection_id=row['study_full_accession'],
collection_name=row['study_name']
)

# Create DBGaP links as study/variable actions
elem.collection_action = utils.get_dbgap_study_link(study_id=elem.collection_id)
13 changes: 13 additions & 0 deletions tests/integration/data/test_tags_v2.0.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
[{
"model": "tags.tag",
"pk": 51,
"fields": {
"created": "2018-03-13t18:39:53z",
"modified": "2018-05-15t17:50:57z",
"title": "vte",
"lower_title": "vte",
"description": "qualitative indicator of venous thromboembolism (vte) status",
"instructions": "include variables that represent whether or when a subject has experienced vte. vte includes both deep venous thrombosis and pulmonary embolism. vte does not include arterial thrombosis or arterial embolism. include variables that represent prevalent and/or incident vte status. include variables that represent vte event data, including event status and time-to-event variables. include variables that indicate age at vte events, e.g. self-reported age at a vte event or followup time to a vte event. include variables indicating vte status based on any method of determination, including self report, adjudication, clinical verification, medical records, icd codes, or calculation/inference from related traits. include all instances of duplicated variables, e.g. vte variables included in multiple datasets. include variables indicating deep vein thrombosis (dvt) status, pulmonary embolism status, and vte status of unknown type. include variables that specify vte type. do not include variables that indicate possible vte treatments, e.g. surgical procedures. do not include variables that indicate medication use related to vte, e.g. anticoagulant or thrombolytic use.",
"creator": 7
}
}]
62 changes: 62 additions & 0 deletions tests/integration/data/test_variables_v2.0.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,62 @@
tag_pk tag_title variable_phv variable_full_accession dataset_full_accession study_full_accession study_name study_phs study_version created modified variable_name variable_description
51 VTE 202930 phv00202930.v1.p1 pht004030.v1.p1 phs000280.v3.p1 Atherosclerosis Risk in Communities (ARIC) 280 3 2018-04-25 13:58:00+00:00 2018-04-25 13:58:00+00:00 AFUcomp7e_G [General health]. Has a doctor ever said you had any of the following? Blood clot in a leg [deep vein thrombosis] [Annual Follow-up Questionnaire Form, AFUG]
51 VTE 202992 phv00202992.v1.p1 pht004030.v1.p1 phs000280.v3.p1 Atherosclerosis Risk in Communities (ARIC) 280 3 2018-04-25 13:58:15+00:00 2018-04-25 13:58:15+00:00 AFUcomp16d_L [General health]. Were you hospitalized for a blood clot in a leg or deep vein thrombosis at that time? [Annual Follow-up Questionnaire Form, AFUL]
51 VTE 203035 phv00203035.v1.p1 pht004030.v1.p1 phs000280.v3.p1 Atherosclerosis Risk in Communities (ARIC) 280 3 2018-04-25 13:58:28+00:00 2018-04-25 13:58:28+00:00 AFUcomp16_M [General health]. Since we last contacted you has a doctor said that you had a blood clot in a leg or deep vein thrombosis? [Annual Follow-up Questionnaire Form, AFUM]
51 VTE 207698 phv00207698.v1.p1 pht004125.v1.p1 phs000280.v3.p1 Atherosclerosis Risk in Communities (ARIC) 280 3 2018-04-25 13:58:42+00:00 2018-04-25 13:58:42+00:00 MHQA9A Has a doctor ever told you that you had a blood clot in a leg (deep vein thrombosis)? This does not include varicose veins or phlebitis. Q9A [Medical History Questionnaire, exam 4]
51 VTE 121341 phv00121341.v2.p2 pht001869.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-07-14 20:01:56+00:00 2018-07-14 20:01:56+00:00 Y01VTD VENOUS THROMBOEMBOLIC DISEASE
51 VTE 121466 phv00121466.v2.p2 pht001870.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-07-14 20:02:20+00:00 2018-07-14 20:02:20+00:00 Y00VT_PE DISCHG DIAG - VENOUS THROMB/PULMONARY EMBOL
51 VTE 121560 phv00121560.v2.p2 pht001871.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-07-14 20:03:18+00:00 2018-07-14 20:03:18+00:00 Y01VTD VENOUS THROMBOEMBOLIC DISEASE
51 VTE 273565 phv00273565.v1.p1 pht005981.v1.p1 phs000287.v6.p1 Cardiovascular Health Study (CHS) 287 6 2018-07-30 16:43:46+00:00 2018-07-30 16:43:46+00:00 vt Lite: VT case (through dec01)
51 VTE 273566 phv00273566.v1.p1 pht005981.v1.p1 phs000287.v6.p1 Cardiovascular Health Study (CHS) 287 6 2018-07-30 16:44:00+00:00 2018-07-30 16:44:00+00:00 ttoevent Days from baseline to VT or censoring (through dec01)
51 VTE 273567 phv00273567.v1.p1 pht005981.v1.p1 phs000287.v6.p1 Cardiovascular Health Study (CHS) 287 6 2018-07-30 16:44:12+00:00 2018-07-30 16:44:12+00:00 vtpehx01 LITE : Self-report of DVT or PE at baseline
51 VTE 273568 phv00273568.v1.p1 pht005981.v1.p1 phs000287.v6.p1 Cardiovascular Health Study (CHS) 287 6 2018-07-30 16:44:23+00:00 2018-07-30 16:44:23+00:00 second LITE: primary or secondary VTE by MD review (through dec01)
51 VTE 276977 phv00276977.v1.p10 pht006025.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:02:27+00:00 2018-08-09 15:02:27+00:00 EVENT1 First event Collection Interval: 1975 through 2014
51 VTE 276978 phv00276978.v1.p10 pht006025.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:02:46+00:00 2018-08-09 15:02:46+00:00 EVENT2 Second event Collection Interval: 1975 through 2014
51 VTE 276979 phv00276979.v1.p10 pht006025.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:03:15+00:00 2018-08-09 15:03:15+00:00 EVENT3 Third event Collection Interval: 1975 through 2014
51 VTE 276980 phv00276980.v1.p10 pht006025.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:03:36+00:00 2018-08-09 15:03:36+00:00 EVENT4 Fourth event Collection Interval: 1975 through 2014
51 VTE 7028 phv00007028.v1.p10 pht000028.v3.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:04:27+00:00 2018-08-09 15:04:27+00:00 FS434 VENOUS DISEASE: DEEP VEIN THROMBOSIS (BLOOD CLOTS IN LEGS OR ARMS) - LEFT
51 VTE 7029 phv00007029.v1.p10 pht000028.v3.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:04:54+00:00 2018-08-09 15:04:54+00:00 FS435 VENOUS DISEASE: DEEP VEIN THROMBOSIS (BLOOD CLOTS IN LEGS OR ARMS) - RIGHT
51 VTE 7461 phv00007461.v1.p10 pht000029.v3.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:05:33+00:00 2018-08-09 15:05:33+00:00 FT437 VENOUS DISEASE: DEEP VEIN THROMBOSIS (BLOOD CLOTS IN LEGS OR ARMS)
51 VTE 10342 phv00010342.v5.p10 pht000036.v8.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:06:29+00:00 2018-08-09 15:06:29+00:00 G220 VENOUS DISEASE: DEEP VEIN THROMBOSIS (BLOOD CLOTS IN LEGS OR ARMS) - LEFT
51 VTE 10343 phv00010343.v5.p10 pht000036.v8.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:07:13+00:00 2018-08-09 15:07:13+00:00 G221 VENOUS DISEASE: DEEP VEIN THROMBOSIS (BLOOD CLOTS IN LEGS OR ARMS) - RIGHT
51 VTE 70486 phv00070486.v1.p10 pht000692.v2.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:08:05+00:00 2018-08-09 15:08:05+00:00 FU149 VENOUS DISEASE: SINCE LAST EXAM HAVE YOU HAD A DEEP VEIN THROMBOSIS (BLOOD CLOTS IN LEGS OR ARMS)
51 VTE 70487 phv00070487.v1.p10 pht000692.v2.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:08:45+00:00 2018-08-09 15:08:45+00:00 FU150 VENOUS DISEASE: SINCE LAST EXAM HAVE YOU HAD A PULMONARY EMBOLUS (BLOOD CLOTS IN LUNGS)
51 VTE 255326 phv00255326.v1.p10 pht005142.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:09:42+00:00 2018-08-09 15:09:42+00:00 fw597 Circulatory Problems - Since the date of the last FHS exam or health update, have you seen a doctor or other healthcare provider or been hospitalized for: Blood clot or embolism in leg or lung Variable appears on Form B only Collection Interval: Original Cohort Exam 30
51 VTE 275051 phv00275051.v1.p10 pht006007.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:11:38+00:00 2018-08-09 15:11:38+00:00 FX597 Circulatory Problems (Form B) - Since your last FHS exam or health history update, have you seen a doctor or been hospitalized for blood clot or embolism in leg or lung? Collection Interval: Original Cohort Exam 31
51 VTE 275385 phv00275385.v1.p10 pht006008.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:12:11+00:00 2018-08-09 15:12:11+00:00 fy597 Circulatory Problems (Form B) - Since your last FHS exam or health update, have you seen a doctor or other healthcare provider or been hospitalized for blood clot or embolism in leg or lung? Collection Interval: Original Cohort Exam 32
51 VTE 21065 phv00021065.v4.p10 pht000074.v10.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:20:09+00:00 2018-08-09 15:20:09+00:00 G3A230 HAVE YOU EVER HAD A DEEP VEIN THROMBOSIS (BLOOD IN LEG OR ARMS)
51 VTE 273898 phv00273898.v1.p10 pht006005.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:20:31+00:00 2018-08-09 15:20:31+00:00 g3a230 Have you ever had a deep vein thrombosis (blood in leg or arms) Collection Interval: Exam 1
51 VTE 274391 phv00274391.v1.p10 pht006006.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:20:55+00:00 2018-08-09 15:20:55+00:00 g3a230 Have you ever had a deep vein thrombosis (blood in leg or arms)
51 VTE 1100 phv00001100.v1.p10 pht000010.v3.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:21:38+00:00 2018-08-09 15:21:38+00:00 FA81 HOSPITALIZED SINCE LAST EXAM FOR PULMONARY EMBOLUS
51 VTE 21066 phv00021066.v4.p10 pht000074.v10.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:22:24+00:00 2018-08-09 15:22:24+00:00 G3A231 HAVE YOU EVER HAD A PULMONARY EMBOLUS (BLOOD CLOT IN LUNGS)
51 VTE 273899 phv00273899.v1.p10 pht006005.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:22:52+00:00 2018-08-09 15:22:52+00:00 g3a231 Have you ever had a pulmonary embolus (blood clot in lungs) Collection Interval: Exam 1
51 VTE 274392 phv00274392.v1.p10 pht006006.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:23:17+00:00 2018-08-09 15:23:17+00:00 g3a231 Have you ever had a pulmonary embolus (blood clot in lungs)
51 VTE 257557 phv00257557.v1.p10 pht005150.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:24:10+00:00 2018-08-09 15:24:10+00:00 j803 Ankle Brachial Blood Pressure Measurements: Had any problems with blood clots in legs?
51 VTE 71923 phv00071923.v2.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:26:48+00:00 2018-08-09 15:26:48+00:00 PE024 PE FINAL DIAGNOSTIC SUMMARY: SOE 110 Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 71924 phv00071924.v2.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:27:16+00:00 2018-08-09 15:27:16+00:00 PE025 PE FINAL DIAGNOSTIC SUMMARY: SOE 111 Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 71925 phv00071925.v2.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:27:36+00:00 2018-08-09 15:27:36+00:00 PE026 PE FINAL DIAGNOSTIC SUMMARY: SOE 112 Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 71926 phv00071926.v2.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:28:00+00:00 2018-08-09 15:28:00+00:00 PE027 PE FINAL DIAGNOSTIC SUMMARY: SOE 113 Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 71927 phv00071927.v2.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:28:22+00:00 2018-08-09 15:28:22+00:00 PE028 PE FINAL DIAGNOSTIC SUMMARY: Other PE 1 Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 71930 phv00071930.v2.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:29:17+00:00 2018-08-09 15:29:17+00:00 PE031 DVT FINAL DIAGNOSTIC SUMMARY: SOE 114 Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 71931 phv00071931.v2.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:30:12+00:00 2018-08-09 15:30:12+00:00 PE032 DVT FINAL DIAGNOSTIC SUMMARY: Other DVT 1 Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 10478 phv00010478.v5.p10 pht000036.v8.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-08-09 15:34:22+00:00 2018-08-09 15:34:22+00:00 G404 CDI: DEEP VEIN THROMBOSIS
51 VTE 193695 phv00193695.v3.p3 pht003414.v3.p3 phs000200.v11.p3 Women's Health Initiative (WHI) 200 11 2018-08-21 00:15:48+00:00 2018-08-21 00:15:48+00:00 F33VTEHOSP F33 Hospitalized Blood Clot (DVT or PE)
51 VTE 193696 phv00193696.v3.p3 pht003414.v3.p3 phs000200.v11.p3 Women's Health Initiative (WHI) 200 11 2018-08-21 00:15:48+00:00 2018-08-21 00:15:48+00:00 F33VTEHOSPDY Days enrollment to F33 Hospitalized Blood Clot
51 VTE 193697 phv00193697.v3.p3 pht003414.v3.p3 phs000200.v11.p3 Women's Health Initiative (WHI) 200 11 2018-08-21 00:15:48+00:00 2018-08-21 00:15:48+00:00 F33VTEOP F33 Outpatient DVT or PE
51 VTE 193698 phv00193698.v3.p3 pht003414.v3.p3 phs000200.v11.p3 Women's Health Initiative (WHI) 200 11 2018-08-21 00:15:48+00:00 2018-08-21 00:15:48+00:00 F33VTEOPDY Days enrollment to F33 Outpatient DVT or PE
51 VTE 121342 phv00121342.v2.p2 pht001869.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-08-30 00:30:43+00:00 2018-08-30 00:30:43+00:00 Y01DVTDG DIAGNOSIS FOR DEEP VEIN THROMBOSIS
51 VTE 121349 phv00121349.v2.p2 pht001869.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-08-30 00:31:38+00:00 2018-08-30 00:31:38+00:00 Y01PEDG DIAGNOSIS FOR PULMONARY EMBOLISM
51 VTE 121486 phv00121486.v2.p2 pht001871.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-08-30 19:43:49+00:00 2018-08-30 19:43:49+00:00 Y01VTDEP ENDPT - DEEP VEIN THROMB/PULMONARY EMBOL
51 VTE 121270 phv00121270.v2.p2 pht001869.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-08-30 19:43:57+00:00 2018-08-30 19:43:57+00:00 Y01VTDEP ENDPT - DEEP VEIN THROMB/PULMONARY EMBOL
51 VTE 121561 phv00121561.v2.p2 pht001871.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-08-30 19:52:40+00:00 2018-08-30 19:52:40+00:00 Y01DVTDG DIAGNOSIS FOR DEEP VEIN THROMBOSIS
51 VTE 121568 phv00121568.v2.p2 pht001871.v2.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-08-30 19:53:25+00:00 2018-08-30 19:53:25+00:00 Y01PEDG DIAGNOSIS FOR PULMONARY EMBOLISM
51 VTE 121735 phv00121735.v1.p2 pht001874.v1.p2 phs000285.v3.p2 Coronary Artery Risk Development in Young Adults (CARDIA) Study - Cohort 285 3 2018-08-30 20:12:00+00:00 2018-08-30 20:12:00+00:00 Z33EPE PULMONARY EMOBOLUS
51 VTE 121860 phv00121860.v2.p1 pht001886.v2.p1 phs000289.v2.p1 GENEVA GWAS of VTE 289 2 2018-09-07 15:50:48+00:00 2018-09-07 15:50:48+00:00 VTE Ever had a blood clot in your vein
51 VTE 71936 phv00071936.v3.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-09-28 14:56:53+00:00 2018-09-28 14:56:53+00:00 pe004 PULMONARY EMBOLUS: Date of clinical occurrence Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 71942 phv00071942.v3.p10 pht000744.v5.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-09-28 14:57:08+00:00 2018-09-28 14:57:08+00:00 pe011 DEEP VENOUS THROMBOSIS: Date of clinical occurrence Collection Interval: Cases reviewed from 1994 to 2012 (data collection began in 1994)
51 VTE 277005 phv00277005.v1.p10 pht006025.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-09-28 14:57:52+00:00 2018-09-28 14:57:52+00:00 EDATE1 First event date Collection Interval: 1975 through 2014
51 VTE 277006 phv00277006.v1.p10 pht006025.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-09-28 14:58:07+00:00 2018-09-28 14:58:07+00:00 EDATE2 Second event date Collection Interval: 1975 through 2014
51 VTE 277007 phv00277007.v1.p10 pht006025.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-09-28 14:58:24+00:00 2018-09-28 14:58:24+00:00 EDATE3 Third event date Collection Interval: 1975 through 2014
51 VTE 277008 phv00277008.v1.p10 pht006025.v1.p10 phs000007.v29.p10 Framingham Heart Study 7 29 2018-09-28 14:58:38+00:00 2018-09-28 14:58:38+00:00 EDATE4 Fourth event date Collection Interval: 1975 through 2014
51 VTE 259384 phv00259384.v1.p2 pht005311.v1.p2 phs001013.v2.p2 Heart and Vascular Health Study (HVH) 1013 2 2018-12-20 19:14:09+00:00 2018-12-20 19:14:09+00:00 priorvt Prior VT
51 VTE 259388 phv00259388.v1.p2 pht005311.v1.p2 phs001013.v2.p2 Heart and Vascular Health Study (HVH) 1013 2 2018-12-20 19:14:20+00:00 2018-12-20 19:14:20+00:00 vttype VT type
5 changes: 4 additions & 1 deletion tests/integration/test_parsers.py
Original file line number Diff line number Diff line change
@@ -11,6 +11,9 @@ def test_db_gap_parser():

def test_topmed_tag_parser():
parser = TOPMedTagParser()
parse_file = str(TEST_DATA_DIR / "test_variables_v1.0.csv")
parse_file = str(TEST_DATA_DIR / "test_variables_v2.0.csv")
elements = parser(parse_file)
assert len(elements) == 62
for element in elements:
assert element.name != element.id
assert element.description != element.id