From e26927ab1aa0e15ac40f3776d493f1d8be85e3b5 Mon Sep 17 00:00:00 2001
From: Nezar Abdennur <nabdennur@gmail.com>
Date: Mon, 20 Jan 2025 15:43:56 -0500
Subject: [PATCH] Update readme

---
 README.md | 51 +++++++++++++++++++++++++++++----------------------
 1 file changed, 29 insertions(+), 22 deletions(-)

diff --git a/README.md b/README.md
index 924b03d..3655a86 100644
--- a/README.md
+++ b/README.md
@@ -1,32 +1,37 @@
-# GDC metadata
+# tcga-db
+
+Create a local database of TCGA metadata from the GDC API.
 
 ## Resources
 
-https://gdc.cancer.gov/about-data/gdc-data-processing/resources-tcga-users
-https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables
-https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/#reading-barcodes
+Useful links
+* TCGA Resources: https://gdc.cancer.gov/about-data/gdc-data-processing/resources-tcga-users
+* Code tables: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables
+* About barcodes: https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/#reading-barcodes
+* Encyclopedia: https://docs.gdc.cancer.gov/Encyclopedia/
 
-https://docs.gdc.cancer.gov/Encyclopedia/
-https://docs.gdc.cancer.gov/Encyclopedia/pages/GDC_API/
+Data Model
+* https://docs.gdc.cancer.gov/Data/Data_Model/GDC_Data_Model/
+* https://docs.gdc.cancer.gov/Data_Dictionary/
+* https://docs.gdc.cancer.gov/Data_Dictionary/viewer/
+* https://github.com/NCI-GDC/gdcdictionary/tree/develop/src/gdcdictionary/schemas
 
-https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/
-https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval
-https://docs.gdc.cancer.gov/API/Users_Guide/Python_Examples/
-https://docs.gdc.cancer.gov/API/Users_Guide/GraphQL_Examples/
-https://docs.gdc.cancer.gov/API/Users_Guide/Additional_Examples/
-https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_A_Available_Fields/
-https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_B_Key_Terms/
-https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_C_Format_of_Submission_Requests_and_Responses/
+API
+* https://docs.gdc.cancer.gov/Encyclopedia/pages/GDC_API/
+* https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/
+* https://docs.gdc.cancer.gov/API/Users_Guide/Search_and_Retrieval
+* https://docs.gdc.cancer.gov/API/Users_Guide/Python_Examples/
+* https://docs.gdc.cancer.gov/API/Users_Guide/GraphQL_Examples/
+* https://docs.gdc.cancer.gov/API/Users_Guide/Additional_Examples/
+* https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_A_Available_Fields/
+* https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_B_Key_Terms/
+* https://docs.gdc.cancer.gov/API/Users_Guide/Appendix_C_Format_of_Submission_Requests_and_Responses/
+* https://gdc.cancer.gov/developers/gdc-application-programming-interface-api
+* https://github.com/NCI-GDC/gdc-frontend-framework/blob/3aeb60a6/packages/core/src/features/gdcapi/gdcapi.ts#L96
 
-https://docs.gdc.cancer.gov/Data/Data_Model/GDC_Data_Model/
-https://docs.gdc.cancer.gov/Data_Dictionary/
-https://docs.gdc.cancer.gov/Data_Dictionary/viewer/
-https://github.com/NCI-GDC/gdcdictionary/tree/develop/src/gdcdictionary/schemas
 
-https://gdc.cancer.gov/developers/gdc-application-programming-interface-api
-https://github.com/NCI-GDC/gdc-frontend-framework/blob/3aeb60a6/packages/core/src/features/gdcapi/gdcapi.ts#L96
 
-## Endpoints
+### API Endpoints
 
 * `projects`: Information about projects
 * `cases`: Information related to cases, or sample donors
@@ -40,10 +45,12 @@ https://github.com/NCI-GDC/gdc-frontend-framework/blob/3aeb60a6/packages/core/sr
 https://api.gdc.cancer.gov/v0/all?query=TCGA&size=5
 ```
 
-## Information about available fields
+### Information about available fields
 
 ```
 https://api.gdc.cancer.gov/{endpoint}/_mapping
 ```
 
+## Other info
+
 BCR = "Biospecimen Core Resource"