Date of liver biopsy
Item
1. Date of liver biopsy
date
C0586689 (UMLS CUI [1,1])
C0011008 (UMLS CUI [1,2])
Biopsy size
Item
2. Approximate size of liver biopsy
integer
C1299482 (UMLS CUI [1])
Biopsy size unit
Item
3. Biopsy size unit
text
Item
4. Final Diagnosis
text
C0332144 (UMLS CUI [1])
Code List
4. Final Diagnosis
CL Item
Check all that apply (AAA)
Acute hepatitis
Item
[A1] Acute hepatitis
boolean
C0267797 (UMLS CUI [1])
Chronic hepatitis
Item
[A2] Chronic hepatitis
boolean
C0019189 (UMLS CUI [1])
Cholestatic hepatitis
Item
[A3] Cholestatic hepatitis
boolean
C0149904 (UMLS CUI [1])
Drug-induced cholestasis
Item
[A4] Drug-induced cholestasis
boolean
C2062350 (UMLS CUI [1])
Acute viral hepatitis
Item
[A5] Acute viral hepatitis
boolean
C0276622 (UMLS CUI [1])
Chronic viral hepatitis
Item
[A6] Chronic viral hepatitis
boolean
C0276623 (UMLS CUI [1])
Drug-induced hepatitis
Item
[A7] Drug-induced hepatitis
boolean
C1262760 (UMLS CUI [1])
Autoimmune hepatitis
Item
[A8] Autoimmune hepatitis
boolean
C0241910 (UMLS CUI [1])
Bridging necrosis
Item
[A9] Bridging necrosis
boolean
C0027540 (UMLS CUI [1])
Submassive hepatic necrosis
Item
[A10] Submassive hepatic necrosis
boolean
C0151798 (UMLS CUI [1])
Massive hepatic necrosis
Item
[A11] Massive hepatic necrosis
boolean
C0151798 (UMLS CUI [1])
Steatosis - microvesicular
Item
[A12] Steatosis - microvesicular
boolean
C1850415 (UMLS CUI [1])
Steatosis - macrovesicular
Item
[A13] Steatosis - macrovesicular
boolean
C1837256 (UMLS CUI [1])
Steatosis - mixed
Item
[A14] Steatosis - mixed
boolean
C2711227 (UMLS CUI [1])
Non-alcoholic steatohepatitis
Item
[A15] Non-alcoholic steatohepatitis
boolean
C3241937 (UMLS CUI [1])
Alcoholic hepatitis
Item
[A16] Alcoholic hepatitis
boolean
C0019187 (UMLS CUI [1])
Hepatic granulomas
Item
[A17] Hepatic granulomas
boolean
C0745754 (UMLS CUI [1])
Sarcoidosis
Item
[A18] Sarcoidosis
boolean
C0036202 (UMLS CUI [1])
Fibrosis
Item
[A19] Fibrosis
boolean
C0016059 (UMLS CUI [1])
Cirrhosis
Item
[A20] Cirrhosis
boolean
C0023890 (UMLS CUI [1])
Primary biliary cirrhosis
Item
[A21] Primary biliary cirrhosis
boolean
C0008312 (UMLS CUI [1])
Primary sclerosing cholangitis
Item
[A22] Primary sclerosing cholangitis
boolean
C0008311 (UMLS CUI [1])
Autoimmune overlap syndrome
Item
[A23] Autoimmune overlap syndrome
boolean
C2702837 (UMLS CUI [1])
Hemochromatosis
Item
[A24] Hemochromatosis
boolean
C0018995 (UMLS CUI [1])
Alpha-1-antitrypsin deficiency
Item
[A25] Alpha-1-antitrypsin deficiency
boolean
C0221757 (UMLS CUI [1])
Wilson's disease
Item
[A26] Wilson's disease
boolean
C0019202 (UMLS CUI [1])
Veno-occlusive disease
Item
[A27] Veno-occlusive disease
boolean
C0948441 (UMLS CUI [1])
Budd-Chiari syndrome
Item
[A28] Budd-Chiari syndrome
boolean
C0856761 (UMLS CUI [1])
Neoplasia
Item
[A29] Neoplasia
boolean
C1882062 (UMLS CUI [1])
Other Final Diagnosis
Item
[A99] Other
boolean
C1546485 (UMLS CUI [1])
Other Final Diagnosis specification
Item
Other, specify:
text
C0011900 (UMLS CUI [1,1])
C2348235 (UMLS CUI [1,2])
Item
5. Liver Architecture
text
C0935919 (UMLS CUI [1,1])
C0023884 (UMLS CUI [1,2])
Code List
5. Liver Architecture
CL Item
Check all that apply (BBB)
Bridging fibrosis
Item
[B2] Bridging fibrosis
boolean
C0016059 (UMLS CUI [1])
Diffuse fibrosis
Item
[B3] Diffuse fibrosis
boolean
C0205219 (UMLS CUI [1,1])
C0016059 (UMLS CUI [1,2])
Nodular regenerative hyperplasia
Item
[B4] Nodular regenerative hyperplasia
boolean
C0020510 (UMLS CUI [1])
Congenital hepatic fibrosis
Item
[B5] Congenital hepatic fibrosis
boolean
C0009714 (UMLS CUI [1])
Cirrhosis
Item
[B6] Cirrhosis
boolean
C0023890 (UMLS CUI [1])
Centrilobular congestion
Item
[B7] Centrilobular congestion
boolean
C0700148 (UMLS CUI [1])
Endophlebitis
Item
[B8] Endophlebitis
boolean
C0014234 (UMLS CUI [1])
Veno-occlusive disease
Item
[B9] Veno-occlusive disease
boolean
C0007465 (UMLS CUI [1,1])
C0948441 (UMLS CUI [1,2])
Canalicular cholestasis
Item
[B10] Canalicular cholestasis
boolean
C0008370 (UMLS CUI [1])
Apoptosis
Item
[B11] Apoptosis
boolean
C0162638 (UMLS CUI [1])
Focal (or spotty or mild) hepatocellular necrosis
Item
[B12] Focal (or spotty or mild) hepatocellular necrosis
boolean
C1855038 (UMLS CUI [1])
Interface hepatitis
Item
[B13] Interface hepatitis (periportal hepatitis or piecemeal necrosis)
boolean
C0333515 (UMLS CUI [1])
Ischaemic necrosis
Item
[B14] Ischaemic necrosis
boolean
C3887513 (UMLS CUI [1])
Centrolobular necrosis
Item
[B15] Centrolobular (Zone 3) necrosis
boolean
C0027540 (UMLS CUI [1])
Focal coagulative necrosis
Item
[B16] Focal coagulative necrosis
boolean
C1522058 (UMLS CUI [1])
Centrolobular coagulative necrosis
Item
[B17] Centrolobular (Zone 3) coagulative necrosis
boolean
C1522058 (UMLS CUI [1,1])
C0682619 (UMLS CUI [1,2])
Bridging hepatocellular necrosis
Item
[B18] Bridging hepatocellular necrosis
boolean
C1855038 (UMLS CUI [1,1])
C0333511 (UMLS CUI [1,2])
Massive or panlobular hepatocellular necrosis
Item
[B19] Massive or panlobular hepatocellular necrosis
boolean
C1855038 (UMLS CUI [1,1])
C0442131 (UMLS CUI [1,2])
Dysplasia
Item
[B20] Dysplasia
boolean
C0334044 (UMLS CUI [1])
Neoplasia
Item
[B21] Neoplasia
boolean
C1882062 (UMLS CUI [1])
Other Liver Architecture
Item
[B99] Other
boolean
C0935919 (UMLS CUI [1,1])
C0426686 (UMLS CUI [1,2])
Other Liver Architecture specification
Item
Other, specify:
text
C0935919 (UMLS CUI [1,1])
C0426686 (UMLS CUI [1,2])
C2348235 (UMLS CUI [1,3])
C0205394 (UMLS CUI [1,4])
Item
6. Description of Liver Cells or Hepatocytes
text
C0227525 (UMLS CUI [1])
Code List
6. Description of Liver Cells or Hepatocytes
CL Item
Check all that apply (CCC)
Ballooning Liver Cells or Hepatocytes
Item
[C1] Ballooning
boolean
C0333445 (UMLS CUI [1,1])
C0227525 (UMLS CUI [1,2])
Acidophilic Liver Cells or Hepatocytes
Item
[C2] Acidophilic
boolean
C0227525 (UMLS CUI [1,1])
C0333931 (UMLS CUI [1,2])
Pseudoxanthomatous Liver Cells or Hepatocytes
Item
[C3] Pseudoxanthomatous
boolean
C0227525 (UMLS CUI [1,1])
C3277905 (UMLS CUI [1,2])
Multinucleated giant hepatocytes
Item
[C4] Multinucleated giant hepatocytes
boolean
C3550474 (UMLS CUI [1])
Other Liver Cells or Hepatocytes
Item
[C99] Other
boolean
C0227525 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
Other Liver Cells or Hepatocytes specification
Item
Other, specify:
text
C0227525 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
C0227525 (UMLS CUI [1,3])
C0205394 (UMLS CUI [1,4])
Item
7. Liver Cell or Hepatocyte Inclusions or Vacuoles
text
C0042219 (UMLS CUI [1,1])
C0227525 (UMLS CUI [1,2])
C1512693 (UMLS CUI [1,3])
Code List
7. Liver Cell or Hepatocyte Inclusions or Vacuoles
CL Item
No inclusions (D0)
CL Item
Check all that apply (DDD)
Macrovesicular steatosis
Item
[D1] Macrovesicular steatosis
boolean
C1837256 (UMLS CUI [1])
Microvesicular steatosis
Item
D2] Microvesicular steatosis
boolean
C1850415 (UMLS CUI [1])
Bile accumulation
Item
[D3] Bile accumulation
boolean
C3686784 (UMLS CUI [1])
Diastase-resistant, PAS-positive cytoplasmic inclusions
Item
[D4] Diastase-resistant, PAS-positive cytoplasmic inclusions
boolean
C0205708 (UMLS CUI [1])
Alpha-1-antitrypsin inclusions
Item
[D5] Alpha-1-antitrypsin inclusions
boolean
C0002191 (UMLS CUI [1])
Megamitochondria
Item
[D6] Megamitochondria
boolean
C0026237 (UMLS CUI [1])
Mallory bodies
Item
[D7] Mallory bodies
boolean
C0333744 (UMLS CUI [1])
Ground Glass inclusions
Item
[D8] "Ground Glass" inclusions
boolean
C0598786 (UMLS CUI [1])
Lipofuscin pigment
Item
[D9] Lipofuscin pigment
boolean
C0023789 (UMLS CUI [1])
Hemosiderin granules
Item
[D10] Hemosiderin granules
boolean
C0019113 (UMLS CUI [1])
Orcein-positive cytoplasmin granules
Item
[D11] Orcein-positive cytoplasmin granules
boolean
C0069596 (UMLS CUI [1])
Protoporphyrin crystals
Item
[D12] Protoporphyrin crystals (birefringent under polarised light)
boolean
C0033733 (UMLS CUI [1])
Uroporphyrin crystals
Item
[D13] Uroporphyrin crystals (red fluorescence under ultraviolet light)
boolean
C0042093 (UMLS CUI [1])
Other Liver Cell or Hepatocyte Inclusions or Vacuoles
Item
[D99] Other
boolean
C0227525 (UMLS CUI [1])
Other Liver Cell or Hepatocyte Inclusions or Vacuoles specification
Item
Other, specify:
text
C0227525 (UMLS CUI [1,1])
C1521902 (UMLS CUI [1,2])
Item
8. Hepatocyte or Liver Cell Nuclear Abnormalities
text
C0227525 (UMLS CUI [1,1])
C1849376 (UMLS CUI [1,2])
Code List
8. Hepatocyte or Liver Cell Nuclear Abnormalities
CL Item
Check all that apply (EEE)
Hepatocellular mitosis
Item
[E1] Hepatocellular mitosis
boolean
C2697585 (UMLS CUI [1,1])
C0026255 (UMLS CUI [1,2])
Binucleated or multinucleated hepatocytes
Item
[E2] Binucleated or multinucleated hepatocytes
boolean
C0227525 (UMLS CUI [1,1])
C0333909 (UMLS CUI [1,2])
C4054455 (UMLS CUI [2])
CMV inclusion bodies
Item
[E3] CMV inclusion bodies
boolean
C0582172 (UMLS CUI [1])
HSV inclusions
Item
[E4] HSV inclusions
boolean
C0319232 (UMLS CUI [1])
Varicella inclusions
Item
[E5] Varicella inclusions
boolean
C0740380 (UMLS CUI [1])
Other Hepatocyte or Liver Cell Nuclear Abnormalities
Item
[E99] Other
boolean
C0227525 (UMLS CUI [1,1])
C0333717 (UMLS CUI [1,2])
Other Hepatocyte or Liver Cell Nuclear Abnormalities specification
Item
Other, specify:
text
C0227525 (UMLS CUI [1,1])
C0333717 (UMLS CUI [1,2])
C1521902 (UMLS CUI [1,3])
Item
9. Liver or Lobular Infiltrates
text
C0205417 (UMLS CUI [1,1])
C0023884 (UMLS CUI [1,2])
Code List
9. Liver or Lobular Infiltrates
CL Item
Check all that apply (FFF)
Liver or Lobular Infiltrates Eosinophils
Item
[F1] Eosinophils
boolean
C0205417 (UMLS CUI [1,1])
C0023884 (UMLS CUI [1,2])
C0014467 (UMLS CUI [1,3])
Liver or Lobular Infiltrates Lymphocytes
Item
[F2] Lymphocytes
boolean
C0023884 (UMLS CUI [1,1])
C0024264 (UMLS CUI [1,2])
Liver or Lobular Infiltrates Plasma cells
Item
[F3] Plasma cells
boolean
C0023884 (UMLS CUI [1,1])
C0032112 (UMLS CUI [1,2])
Liver or Lobular Infiltrates Neutrophils
Item
[F4] Neutrophils
boolean
C0023884 (UMLS CUI [1,1])
C0027950 (UMLS CUI [1,2])
Liver or Lobular Infiltrates Macrophages and proliferating Kupffer cells
Item
[F5] Macrophages and proliferating Kupffer cells
boolean
C0023884 (UMLS CUI [1,1])
C0022801 (UMLS CUI [1,2])
Liver or Lobular Infiltrates Granulomas
Item
[F6] Granulomas
boolean
C0023884 (UMLS CUI [1,1])
C0745754 (UMLS CUI [1,2])
Other Liver or Lobular Infiltrates
Item
[F99] Other
boolean
C0023884 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
Other Liver or Lobular Infiltrates specification
Item
Other, specify:
text
C0023884 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
C1521902 (UMLS CUI [1,3])
Item
10. Portal Tract Inflammation
text
C3854488 (UMLS CUI [1])
Code List
10. Portal Tract Inflammation
CL Item
Check all that apply (GGG)
Portal Tract Inflammation Eosinophils
Item
[G1] Eosinophils
boolean
C0014467 (UMLS CUI [1,1])
C3854488 (UMLS CUI [1,2])
Portal Tract Inflammation Lymphoid aggregates and/or follicles
Item
[G2] Lymphoid aggregates and/or follicles
boolean
C3854488 (UMLS CUI [1,1])
C0229653 (UMLS CUI [1,2])
Portal Tract Inflammation Plasma cells
Item
[G3] Plasma cells
boolean
C3854488 (UMLS CUI [1,1])
C0032112 (UMLS CUI [1,2])
Portal Tract Inflammation Neutrophils
Item
[G4] Neutrophils
boolean
C3854488 (UMLS CUI [1,1])
C0027950 (UMLS CUI [1,2])
Portal Tract Inflammation Histocytes and macrophages
Item
[G5] Histocytes and macrophages
boolean
C3854488 (UMLS CUI [1,1])
C0024432 (UMLS CUI [1,2])
Other Portal Tract Inflammation
Item
[G99] Other
boolean
C3854488 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
Other Portal Tract Inflammation specification
Item
Other, specify:
text
C3854488 (UMLS CUI [1,1])
C3845569 (UMLS CUI [1,2])
Item
11. Bile Ducts
text
C0005400 (UMLS CUI [1])
CL Item
Check all that apply (HHH)
Proliferation of bile ducts
Item
[H1] Proliferation of bile ducts (bile ductular reaction)
boolean
C0005400 (UMLS CUI [1,1])
C0334094 (UMLS CUI [1,2])
Dilation, degeneration or disruption of portal bile ducts
Item
[H2] Dilation, degeneration or disruption of portal bile ducts
boolean
C0005400 (UMLS CUI [1,1])
C0011164 (UMLS CUI [1,2])
Paucity of bile ducts
Item
[H3] Paucity of bile ducts
boolean
C4273160 (UMLS CUI [1])
Periductal fibrosis
Item
[H4] Periductal fibrosis
boolean
C0016059 (UMLS CUI [1])
Bile ducts Other
Item
[H99] Other
boolean
C0205394 (UMLS CUI [1,1])
C0005400 (UMLS CUI [1,2])
Bile ducts Other specification
Item
Other, specify
text
C0205394 (UMLS CUI [1,1])
C0005400 (UMLS CUI [1,2])
C2348235 (UMLS CUI [1,3])
Item
12. Portal Veins
text
C0032718 (UMLS CUI [1])
Code List
12. Portal Veins
CL Item
Check all that apply (III)
Pyelophlebitis
Item
[I1] Pyelophlebitis
boolean
C1405883 (UMLS CUI [1])
Thrombosis, sclerosis or occlusion of portal vein
Item
[I2] Thrombosis, sclerosis or occlusion of portal vein
boolean
C0155773 (UMLS CUI [1])
C0400960 (UMLS CUI [2,1])
|C0265029 (UMLS CUI [2,2])
Neoplastic invasion of portal vein
Item
[I3] Neoplastic invasion of portal vein
boolean
C1709160 (UMLS CUI [1,1])
C0032718 (UMLS CUI [1,2])
Granulomatous compression of portal vein
Item
[I4] Granulomatous compression of portal vein
boolean
C0032718 (UMLS CUI [1,1])
C0439667 (UMLS CUI [1,2])
Portal veins Other
Item
[I99] Other
boolean
C0032718 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
Portal veins Other specification
Item
Other, specify:
text
C0032718 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
C2348235 (UMLS CUI [1,3])
Item
13. Liver Infections
text
C1112211 (UMLS CUI [1])
Code List
13. Liver Infections
CL Item
Check all that apply (JJJ)
Leishmaniasis donovani
Item
[J1] Leishmaniasis donovani
boolean
C0023281 (UMLS CUI [1])
Plasmodium falciparum
Item
[J2] Plasmodium falciparum
boolean
C0032150 (UMLS CUI [1])
Toxoplasmosis
Item
[J3] Toxoplasmosis
boolean
C0040558 (UMLS CUI [1])
Cryptococcus neoformans
Item
[J4] Cryptococcus neoformans
boolean
C0010416 (UMLS CUI [1])
Histoplasma capsulatum
Item
[J5] Histoplasma capsulatum
boolean
C0319941 (UMLS CUI [1])
Mycobacterium tuberculois
Item
[J6] Mycobacterium tuberculois
boolean
C0026926 (UMLS CUI [1])
Other mycobacterial species
Item
[J7] Other mycobacterial species
boolean
C0026918 (UMLS CUI [1])
Other Liver Infections
Item
[J99] Other
boolean
C1112211 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
Other Liver Infections specification
Item
Other, specify:
text
C1112211 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
C2348235 (UMLS CUI [1,3])
Item
14. Parasites or Ova
text
C0030498 (UMLS CUI [1])
C0555117 (UMLS CUI [2])
Code List
14. Parasites or Ova
CL Item
Check all that apply (KKK)
Schistosome and/or ova
Item
[K1] Schistosome and/or ova
boolean
C0555117 (UMLS CUI [1])
C0036315 (UMLS CUI [2])
Ascaris and/or ova
Item
[K2] Ascaris and/or ova
boolean
C0555117 (UMLS CUI [1])
C0003954 (UMLS CUI [2])
Toxocara and/or ova
Item
[K3] Toxocara and/or ova
boolean
C0555117 (UMLS CUI [1])
C0040550 (UMLS CUI [2])
Echinococcus cysts
Item
[K4] Echinococcus cysts
boolean
C0013502 (UMLS CUI [1])
Hepatic capillariasis worms and/or ova
Item
[K5] Hepatic capillariasis worms and/or ova
boolean
C0555117 (UMLS CUI [1,1])
C0277202 (UMLS CUI [1,2])
C0018889 (UMLS CUI [1,3])
Other Parasites or Ova
Item
[K99] Other
boolean
C0555117 (UMLS CUI [1,1])
C0030498 (UMLS CUI [1,2])
C0205394 (UMLS CUI [1,3])
Other Parasites or Ova specification
Item
Other, specify:
text
C0555117 (UMLS CUI [1,1])
C2348235 (UMLS CUI [1,2])
C0030498 (UMLS CUI [1,3])
C0205394 (UMLS CUI [1,4])
Haematoxylin and eosin
Item
[L1] Haematoxylin and eosin (or H & E)
boolean
C0523207 (UMLS CUI [1])
Masson
Item
[L2] Masson
boolean
C0221936 (UMLS CUI [1])
Toluidine blue or Giemsa
Item
[L3] Toluidine blue or Giemsa
boolean
C0523203 (UMLS CUI [1])
Prussian blue
Item
[L4] Prussian blue
boolean
C0060234 (UMLS CUI [1])
Periodic Acidic Schiff with or without diastase
Item
[L5] Periodic Acidic Schiff (PAS), with or without diastase
boolean
C0030125 (UMLS CUI [1])
Oil red O
Item
[L6] Oil red O
boolean
C1294000 (UMLS CUI [1])
Congo red
Item
[L7] Congo red
boolean
C0009742 (UMLS CUI [1])
Hall's stain
Item
[L8] Hall's stain
boolean
C1720394 (UMLS CUI [1])
Gridley's stain
Item
[L9] Gridley's stain
boolean
C1293978 (UMLS CUI [1])
Rhodanine
Item
[L10] Rhodanine (copper)
boolean
C0035486 (UMLS CUI [1])
Rubeanic acid
Item
[L11] Rubeanic acid (copper)
boolean
C0073680 (UMLS CUI [1])
Orcein, aldehyde fuchsin or Victoria blue
Item
[L12] Orcein, aldehyde fuchsin or Victoria blue
boolean
C0491984 (UMLS CUI [1])
C0078232 (UMLS CUI [2])
Electron microscopy
Item
[L13] Electron microscopy
boolean
C0026019 (UMLS CUI [1])
Hepatitis A immunostains positive
Item
[L14] Hepatitis A immunostains positive
boolean
C0560226 (UMLS CUI [1])
Hepatitis B core antigen or hepatitis B surface antibody immunostains positive
Item
[L15] Hepatitis B core antigen or hepatitis B surface antibody immunostains positive
boolean
C0201477 (UMLS CUI [1,1])
C0201480 (UMLS CUI [1,2])
Hepatitis D immunostains
Item
[L16] Hepatitis D immunostains
boolean
C0011226 (UMLS CUI [1])
Other immunostains
Item
[L17] Other immunostains
boolean
C1846082 (UMLS CUI [1])
Other Histologic Staining or Additional Studies Obtained
Item
[L99] Other
boolean
C0487602 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
Other Histologic Staining or Additional Studies Obtained specification
Item
Other, specify:
text
C0487602 (UMLS CUI [1,1])
C0205394 (UMLS CUI [1,2])
C2348235 (UMLS CUI [1,3])