Merge pull request #75 from monarch-initiative/commit_mapping_tsv_files

Commit mapping tsv files
monarch-initiative · Feb 1, 2024 · d499875 · d499875
2 parents 21f85e7 + bef24ec
commit d499875
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Showing 3 changed files with 11 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -172,7 +172,10 @@ notebooks/Untitled.ipynb
 
 *.pkl
 *.tsv
+!src/oncoexporter/ncit_mapping_files/*.tsv
+!src/oncoexporter/ncit_mapping_files/*.csv
+
 .DS_Store
 src/phenopackets
 *.tar.gz
-/phenopackets/
+/phenopackets/
diff --git a/src/oncoexporter/ncit_mapping_files/cda_to_ncit_map.tsv b/src/oncoexporter/ncit_mapping_files/cda_to_ncit_map.tsv
@@ -103,4 +103,7 @@ Basaloid squamous cell carcinoma	Squamous Cell Neoplasms	Cervix uteri			-
 Basaloid squamous cell carcinoma	Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma	Cervix			-
 Serous surface papillary carcinoma	"Cystic, Mucinous and Serous Neoplasms"	Corpus uteri			-
 Serous surface papillary carcinoma	Uterine Corpus Endometrial Carcinoma	Uterus			-
-"Adenocarcinoma, NOS"	Adenomas and Adenocarcinomas	Bronchus and lung	NCIT:C3512	Lung Adenocarcinoma	
+"Adenocarcinoma, NOS"	Adenomas and Adenocarcinomas	Bronchus and lung	NCIT:C3512	Lung Adenocarcinoma	
+Adenocarcinoma	Lung Adenocarcinoma	Lung	NCIT:C3512	Lung Adenocarcinoma	
+Acantholytic squamous cell carcinoma	Lung Squamous Cell Carcinoma	Lung	NCIT:C3493	Lung Squamous Cell Carcinoma	
+Squamous Cell Carcinoma	Lung Squamous Cell Carcinoma	Lung	NCIT:C3493	Lung Squamous Cell Carcinoma	
diff --git a/src/oncoexporter/ncit_mapping_files/uberon_to_ncit_diagnosis.tsv b/src/oncoexporter/ncit_mapping_files/uberon_to_ncit_diagnosis.tsv
@@ -0,0 +1,3 @@
+uberon_label	uberon_id	NCIT_id	NCIT_label	synonyms
+uterine cervix	UBERON:0000002	NCIT:C2940	Cervical Neoplasm	Cervix uteri;Cervix
+uterus	UBERON:0000995	NCIT:C3435	Uterine Neoplasm	"Uterus, NOS;Uterus;"