Inflammatory bowel disease (IBD) modified montreal data
The data uses a modified Montreal classification for ulcerative colitis disease extent based on inflammation in colonoscopy biopsies. The classification is provided for both UC patients and Crohn’s patients for the given date of colonoscopy.
This data augments the SNOMED data with 1) a modified Montreal classification of disease extent based on inflammation in colonoscopy biopsies in colon and rectum, and 2) status of inflammation in the terminal ileum. Montreal status and ileum status is assigned for all of the endoscopies sharing a date, since a single event can create multiple samples. Only samples with inflammation (morphological codes M4*, D6255, D6216) were considered for inflammation status. For samples with Snomed T code T670, location was inferred from location names in free text field. The keywords and inferred locations are detailed in the table at the end of the document.
Files
montreal_data.tsv
Data file containing augmented SNOMED data
Column descriptions
FINNGENID
Sample ID
APPROX_DATE_SNOMED
approximate date of sample
T_SNOMED_CODE
T-SNOMED code in Snomed coding system
T_SNOMED_NAME
T-SNOMED name in Snomed coding system
T_SNOMED_TEXT
T-SNOMED free written diagnosis given by pathologist, usually a combination of T and M snomed codes.
M_SNOMED_CODE
M-SNOMED code in Snomed coding system
M_SNOMED_NAME
M-SNOMED name in Snomed coding system
M_SNOMED_TEXT
M-SNOMED free written diagnosis given by pathologist, usually a combination of T and M snomed codes.
BIOBANK
biobank where sample is from
MONTREAL_STATUS
Modified Montreal classification of sample. See table below for values.
MONTREAL_STATUS_CODES
List of topographical SNOMED codes that resulted in the Montreal status.
ILEUM_STATUS
1 if ileum was found to be inflamed in this endoscopy, 0 if no inflammation, NA if no samples from ileum.
ILEUM_STATUS_CODES
List of topographical SNOMED codes that resulted in inflamed ileum status.
Valid MONTREAL_STATUS codes:
E1
Inflammation limited to rectum
E2
Inflammation limited to left side of splenic flecture
E3
Inflammation of entire or right colon
E2/3
Inflammation in colon, unable to specify whether E2/E3
Unspecified inflammation of colon
Unable to specify location of inflammation
0
No inflammation in samples in locations T67 & T68
NA
No samples in locations T67 or T68
Other
Montreal classification: doi: 10.1136/gut.2005.082909
SNOMED location data inference based on free text field
For colonoscopy samples where location was given as T670=in colon, the following regexes were used to infer the location from the free text column:
cecum|ileocecal
T671
ascending|right
T672
hepatic
T673
transverse|traverse|middle
T674
splenic|ienalis|bend of the spleen
T675
descending|left
T676
sigmoid
T677
distal
T676|T677
proximal|beginning
T671|T672|T673|T674
rectum
T68
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