Parameters for Procedure: Gross Pathology and Tissue Collection IMPC_PAT_001

Procedure carried out on Week 16

Version Type Req. Upload Req. Analysis Annotation Increment Option Ontology Options Derived Unit Data Type
Brain IMPC_PAT_001_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0002152] abnormal brain morphology [MP:0001891] hydroencephaly [MP:0000774] decreased brain size [MP:0005238] increased brain size         TEXT
Eye with optic nerve IMPC_PAT_002_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0002092] abnormal eye morphology [MP:0001293] anophthalmia [MP:0006249] phthisis bulbi [MP:0001296] macrophthalmia [MP:0001297] microphthalmia [MP:0001330] abnormal optic nerve morphology         TEXT
Spinal cord IMPC_PAT_003_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000955] abnormal spinal cord morphology         TEXT
Thymus IMPC_PAT_004_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000703] abnormal thymus morphology [MP:0000705] athymia [MP:0000706] small thymus [MP:0000709] enlarged thymus [MP:0003007] ectopic thymus         TEXT
Thyroid IMPC_PAT_005_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000681] abnormal thyroid glands         TEXT
Heart IMPC_PAT_006_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000266] abnormal heart morphology [MP:0006065] abnormal heart position or orientation [MP:0003140] dilated heart atrium [MP:0008725] enlarged heart atrium [MP:0010409] cor triatriatum [MP:0000644] dextrocardia [MP:0000650] mesocardia [MP:0010431] atrial situs inversus [MP:0000277] abnormal heart shape [MP:0000274] enlarged heart [MP:0002188] small heart         TEXT
Trachea IMPC_PAT_007_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0002282] abnormal trachea morphology [MP:0004550] short trachea [MP:0004549] small trachea [MP:0003321] tracheoesophageal fistula [MP:0012672] enlarged trachea         TEXT
Esophagus IMPC_PAT_008_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000467] abnormal esophagus morphology [MP:0004548] dilated esophagus [MP:0004545] enlarged esophagus [MP:0003276] esophageal atresia         TEXT
Lung IMPC_PAT_009_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0001175] abnormal lung morphology [MP:0004882] enlarged lung [MP:0003641] small lung [MP:0000531] right pulmonary isomerism [MP:0003178] left pulmonary isomerism [MP:0004880] lung cysts [MP:0006050] pulmonary fibrosis         TEXT
Liver IMPC_PAT_010_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000598] abnormal liver morphology [MP:0003333] liver fibrosis [MP:0000599] enlarged liver [MP:0000601] small liver [MP:0003332] liver abscess [MP:0003046] liver cirrhosis         TEXT
Gall bladder IMPC_PAT_011_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0005084] abnormal gallbladder morphology [MP:0003250] absent gallbladder [MP:0009343] dilated gallbladder [MP:0009342] enlarged gallbladder [MP:0005675] small gallbladder         TEXT
Stomach IMPC_PAT_012_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000470] abnormal stomach morphology [MP:0009511] distended stomach [MP:0003883] enlarged stomach [MP:0003299] gastric polyps [MP:0003282] gastric ulcer [MP:0003323] gastrocolic fistula         TEXT
Small intestine IMPC_PAT_013_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0003271] abnormal duodenum morphology [MP:0003294] intussusception [MP:0003272] duodenal atresia [MP:0002580] duodenal lesions [MP:0008012] duodenum polyps [MP:0004002] abnormal jejunum morphology [MP:0000498] absent jejunum [MP:0002581] abnormal ileum morphology [MP:0003294] intussusception [MP:0009485] distended ileum [MP:0009483] enlarged ileum         TEXT
Large intestine IMPC_PAT_014_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000489] abnormal large intestine morphology [MP:0003294] intussusception [MP:0000494] abnormal cecum morphology [MP:0009000] absent cecum [MP:0009510] cecal atresia [MP:0008013] cecum polyps [MP:0009478] coiled cecum [MP:0009480] distended cecum [MP:0009476] enlarged cecum [MP:0009477] small cecum [MP:0000495] abnormal colon morphology [MP:0003269] colon polyps [MP:0001652] colonic necrosis [MP:0003323] gastrocolic fistula [MP:0002731] megacolon [MP:0003296] microcolon [MP:0000492] abnormal rectum morphology [MP:0000493] rectal prolapse [MP:0003302] perirectal abscess [MP:0003318] rectoperineal fistula [MP:0009487] rectourethral fusion [MP:0003320] rectovaginal fistula [MP:0009486] rectovaginal fusion [MP:0003305] proctitis         TEXT
Pancreas IMPC_PAT_015_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0001944] abnormal pancreas morphology [MP:0003450] enlarged pancreas [MP:0004247] small pancreas [MP:0003336] pancreas cysts [MP:0003334] pancreas fibrosis         TEXT
Spleen IMPC_PAT_016_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000689] abnormal spleen morphology [MP:0000690] absent spleen [MP:0000691] enlarged spleen [MP:0000692] small spleen [MP:0003342] accessory spleen [MP:0009246] pale spleen [MP:0000690] absent spleen         TEXT
Kidney IMPC_PAT_017_001 1.1 ontologyParameter Tick         Tick                 [PATO:0001323] area [PATO:0001334] diameter [PATO:0000918] volume [PATO:0000411] round [PATO:0001891] oval [PATO:0000407] flat [PATO:0000330] irregular [PATO:0001369] raised [PATO:0002416] sunken [PATO:0001199] linear [PATO:0000387] soft [PATO:0000386] hard [PATO:0002406] friable [PATO:0002376] air-filled [PATO:0002409] fluid-filled [PATO:0002408] watery [PATO:0000322] red [PATO:0000317] black [PATO:0000952] brown [PATO:0000954] pink [PATO:0000950] grey [PATO:0000323] white [PATO:0002410] beige [PATO:0000318] blue [PATO:0000320] green [PATO:0000329] mottled [PATO:0000417] absolute number value [PATO:0002118] multiple [PATO:0000366] left [PATO:0000367] right [PATO:0000324] yellow [PATO:0000953] orange [MP:0002169] normal [MP:0002135] abnormal kidney morphology [MP:0003604] single kidney [MP:0002989] small kidney [MP:0003068] enlarged kidney [MP:0008528] polycystic kidney         TEXT
Adrenal gland IMPC_PAT_018_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000639] abnormal adrenal gland morphology [MP:0005313] absent adrenal gland [MP:0002768] small adrenal glands [MP:0000642] enlarged adrenal glands         TEXT
Mammary gland IMPC_PAT_019_001 1.1 ontologyParameter                 Tick                 [MP:0002169] normal [MP:0000627] abnormal mammary gland morphology [MP:0000629] absent mammary gland [MP:0009721] supernumerary mammary glands [MP:0009741] ectopic mammary gland         TEXT
Lymph node IMPC_PAT_020_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0002339] abnormal lymph node morphology [MP:0008024] absent lymph nodes [MP:0002217] small lymph nodes [MP:0002219] decreased lymph node number [MP:0000702] enlarged lymph nodes [MP:0002218] increased lymph node number         TEXT
Skin IMPC_PAT_021_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0002060] abnormal skin morphology [MP:0003653] decreased skin turgor [MP:0003414] epidermal cyst [MP:0001193] psoriasis [MP:0001786] skin edema         TEXT
Skeletal muscle IMPC_PAT_022_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000759] abnormal skeletal muscle morphology [MP:0009415] skeletal muscle degeneration [MP:0010240] decreased skeletal muscle size [MP:0003398] increased skeletal muscle size         TEXT
Urinary bladder IMPC_PAT_023_001 1.1 ontologyParameter Tick         Tick                 [MP:0002169] normal [MP:0000538] abnormal urinary bladder morphology [MP:0009252] absent urinary bladder [MP:0009552] urinary bladder obstruction [MP:0003614] urinary bladder prolapse [MP:0003615] urinary bladder diverticulum [MP:0000539] distended urinary bladder         TEXT
Testes IMPC_PAT_024_001 1.1 ontologyParameter                 Tick                 [MP:0002169] normal [MP:0001146] abnormal testis morphology [MP:0001148] enlarged testes [MP:0001147] small testis [MP:0006415] absent testes [MP:0002286] cryptorchism [MP:0003623] hydrocele         TEXT
Epididymis IMPC_PAT_025_001 1.1 ontologyParameter                 Tick                 [MP:0002169] normal [MP:0002631] abnormal epididymis morphology [MP:0004727] absent epididymus [MP:0004930] small epididymus [MP:0004931] enlarged epididymus         TEXT
Prostate IMPC_PAT_026_001 1.1 ontologyParameter                 Tick                 [MP:0002169] normal [MP:0001159] absence of prostate gland         TEXT
Seminal vesicle IMPC_PAT_027_001 1.2 ontologyParameter                 Tick                 [MP:0002169] normal [MP:0002059] abnormal seminal vesicle morphology [MP:0003642] absent seminal vesicle [MP:0002997] enlarged seminal vesicle [MP:0001157] small seminal vesicle         TEXT
Ovary IMPC_PAT_028_001 1.1 ontologyParameter                 Tick                 [MP:0002169] normal [MP:0001126] abnormal ovary morphology [MP:0004832] enlarged ovary [MP:0001127] small ovary [MP:0002016] ovary cysts [MP:0003578] absent ovary         TEXT
Uterus IMPC_PAT_029_001 1.1 ontologyParameter                 Tick                 [MP:0002169] normal [MP:0009085] abnormal uterine horn morphology [MP:0009087] dilated uterine horn [MP:0009084] blind uterus [MP:0001123] dilated uterus [MP:0009709] hydrometra [MP:0009081] thin uterus [MP:0003568] uterus atresia [MP:0009082] uterus cysts [MP:0005577] uterus prolapse [MP:0003571] uterus rupture         TEXT
Body Weight IMPC_PAT_049_001 1.2 simpleParameter Tick                                         g FLOAT
Experimenter ID IMPC_PAT_052_001 1.1 procedureMetadata Tick                                         TEXT
Method of sacrifice IMPC_PAT_054_001 1.1 procedureMetadata Tick                         Isoflurane overdoseExsanguinationCarbon dioxideAvertinKetamine (100mg/kg)/Xylazine (10mg/kg)Ketamine(100mg/kg)/ Xylazine (10mg/kg )/ Antisedan (1mg/kg)Ketamine (110mg/kg)/Xylazine (11mg/kg)Ketamine (110mg/kg)/Xylazine (11mg/kg)/ Antisedan (1mg/kg)Pentobarb (0.1ml)NoneCervical dislocation         TEXT
Method of Blood Collection IMPC_PAT_055_001 1.1 procedureMetadata                                 Cardiac puncture1ml EDTA tubes, Braun-Melsungen, GERRetro-orbital puncture         TEXT
Equipment ID IMPC_PAT_056_001 1.0 procedureMetadata Tick                                         TEXT
Images IMPC_PAT_057_001 1.4 seriesMediaParameter                                                 IMAGE
Fixative IMPC_PAT_058_001 1.1 procedureMetadata Tick                         10% buffered formalin phosphate4% NBF-24hrsNeutral buffered formalin4% PFA/PBS10% neutral buffer formalin, RT, O/NFormolBouin         TEXT
Date equipment last calibrated IMPC_PAT_059_001 1.2 procedureMetadata                                                 DATE
Equipment manufacturer IMPC_PAT_060_001 1.1 procedureMetadata Tick                         OhausLeicaKeyence Co., LtdOlympus         TEXT
Equipment model IMPC_PAT_061_001 1.1 procedureMetadata Tick                         AV2101ASP200SVHX-100AV213CSC100Z6 ApoEM651         TEXT
Date of sacrifice IMPC_PAT_030_001 1.0 procedureMetadata Tick                                         DATETIME
ID for sample banking protocol IMPC_PAT_031_001 1.3 procedureMetadata Tick                                         TEXT
Comments (in English) IMPC_PAT_032_001 1.1 simpleParameter                                                 TEXT