From 9a3a1167b8c111961f7de67fca4baa1e187d8cb6 Mon Sep 17 00:00:00 2001 From: Shirley Shu Date: Fri, 24 Nov 2023 12:48:40 -0800 Subject: [PATCH 1/2] update ncit header to match the latest version --- src/ncit/README.md | 10 ++++++---- src/ncit/index.js | 1 + 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/src/ncit/README.md b/src/ncit/README.md index bc747a81..034d0153 100644 --- a/src/ncit/README.md +++ b/src/ncit/README.md @@ -3,8 +3,9 @@ First download the latest version of the plain text tab delimited files. This should include both the main thesaurus file and the cross mapping file -- [Load the Main Flat File](#load-the-main-flat-file) -- [FDA Cross Mapping File](#fda-cross-mapping-file) +- [NCI Thesaurus](#nci-thesaurus) + - [Load the Main Flat File](#load-the-main-flat-file) + - [FDA Cross Mapping File](#fda-cross-mapping-file) ## Load the Main Flat File @@ -27,11 +28,12 @@ This is a headerless tab delimited file with the following - display name - concept status - semantic type +- concept in subset Next use the general file loader to load the NCIt terms ```bash -node bin/loadFile ncit Thesaurus.txt +node bin/load.js file ncit Thesaurus.txt ``` ## FDA Cross Mapping File @@ -46,5 +48,5 @@ Then, after you have loaded the [FDA-SRS](../fdaSrs) data (if you are planning t load the cross-reference mapping data ```bash -node bin/loadFile ncitFdaXref FDA-UNII_NCIt_Subsets.txt +node bin/load.js file ncitFdaXref FDA-UNII_NCIt_Subsets.txt ``` diff --git a/src/ncit/index.js b/src/ncit/index.js index 562ee06f..9ffe897e 100644 --- a/src/ncit/index.js +++ b/src/ncit/index.js @@ -211,6 +211,7 @@ const uploadFile = async ({ 'name', 'conceptStatus', 'semanticType', + 'conceptInSubset', ], }); // determine unresolvable records From 3f8d20f7034033dbab362ff33a5e342f381db02c Mon Sep 17 00:00:00 2001 From: Shirley Shu Date: Fri, 24 Nov 2023 14:40:07 -0800 Subject: [PATCH 2/2] update ncit README to new format header --- src/ncit/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ncit/README.md b/src/ncit/README.md index 034d0153..e137b2d5 100644 --- a/src/ncit/README.md +++ b/src/ncit/README.md @@ -21,7 +21,7 @@ This is a headerless tab delimited file with the following [format](https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/ReadMe.txt) - code -- concept name +- concept IRI - parents - synonyms - definition