Organ Site Mapping for Metastatic Cancer

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UID: 11383

Author(s): DiNatale, Renzo G.*, Fong, Christopher* * MSK affiliated

Description: Description from GitHub:

"Cancer is a disease that can involve metastatic spread from it primary site (Ex. Lung) to another organ (Ex. Liver). However, the naming conventions used for this organs can slightly vary, or may be specified with more granularity than commonly appropriate. This is evident in free text entries, where the variability is large.

This repository contains functions that will annotate the MSK-IMPACT cohort summary table with a standardized organ site map between primary and metastatic organ sites. The annotator will either leverage various organ site names OR secondard malignant neoplasm ICD billing codes to a standard organ site ontology."

Subject of Study

Subject(s)

Access via GitHub
Access Restrictions: Free to All
Access Instructions: Available for viewing and download via GitHub
Associated Publications: Nguyen B, Fong C, Luthra A, Smith S, et al. Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients. Cell. 2022; 185(3):563-575.e11.
Software Used: pandas
open source data analysis and manipulation tool, built on top of the Python programming language.
Dataset Format(s): CSV, PY, MD, IPYNB, CYS
Dataset Size: 4.2 MB

Do you have or know of a dataset that should be added to the catalog? Let us know!