# 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

| Name               | Description                                |
| ------------------ | ------------------------------------------ |
| montreal\_data.tsv | Data file containing augmented SNOMED data |

### Column descriptions

| Column name             | Column Description                                                                                        |
| ----------------------- | --------------------------------------------------------------------------------------------------------- |
| 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:

| Code                              | Description                                            |
| --------------------------------- | ------------------------------------------------------ |
| 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:

| Regex                                | SNOMED code            |
| ------------------------------------ | ---------------------- |
| 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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