[PGDC-3150] update website links to gdc.cancer.gov (#183)

CONVENTIONS.md

@@ -1,6 +1,6 @@
 This page identifies web site conventions and is intended for content editors.
 
-It is copied from [GDC Website](https://gdc.nci.nih.gov/conventions-page)
+It is copied from [GDC Website](https://gdc.cancer.gov/conventions-page)
 
 ## Web Site Grammar
 

README.md

@@ -1,4 +1,4 @@
-![](https://gdc.nci.nih.gov/sites/all/themes/gdc_bootstrap/logo.png)
+![](https://gdc.cancer.gov/sites/all/themes/gdc_bootstrap/logo.png)
 
 # GDC Open Source code
 
@@ -13,7 +13,7 @@ GDC is Open Source, Github Repositories containing source code of GDC Applicatio
 
 # Support
 
-Please direct technical questions to [GDC Support](https://gdc.nci.nih.gov/support).
+Please direct technical questions to [GDC Support](https://gdc.cancer.gov/support).
 
 # GDC Documentation Site
 
@@ -59,7 +59,7 @@ example:
 
 ### Documentation Conventions
 
-A detailed list of all conventions is available on [GDC Website](https://gdc.nci.nih.gov/conventions-page)
+A detailed list of all conventions is available on [GDC Website](https://gdc.cancer.gov/conventions-page)
 
 
 ### Build PDF

docs/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline.md

@@ -32,7 +32,7 @@ Quality control metrics for each file endpoint can be accessed through the API u
 
 #### Reference Genome
 
-All alignments are performed using the human reference genome GRCh38.d1.vd1. Decoy viral sequences are included in the reference genome to prevent erroneous read alignments and attract reads from viruses known to be present in human samples. Ten types of human viral genomes are included: human cytomegalovirus (CMV), Epstein-Barr virus (EBV), hepatitis B (HBV), hepatitis C (HCV), human immunodeficiency virus (HIV), human herpes virus 8 (HHV-8), human T-lymphotropic virus 1 (HTLV-1), Merkel cell polyomavirus (MCV), Simian vacuolating virus 40 (SV40), and human papillomavirus (HPV). Reference sequences can be downloaded [here](https://gdc.nci.nih.gov/download-gdc-reference-files).
+All alignments are performed using the human reference genome GRCh38.d1.vd1. Decoy viral sequences are included in the reference genome to prevent erroneous read alignments and attract reads from viruses known to be present in human samples. Ten types of human viral genomes are included: human cytomegalovirus (CMV), Epstein-Barr virus (EBV), hepatitis B (HBV), hepatitis C (HCV), human immunodeficiency virus (HIV), human herpes virus 8 (HHV-8), human T-lymphotropic virus 1 (HTLV-1), Merkel cell polyomavirus (MCV), Simian vacuolating virus 40 (SV40), and human papillomavirus (HPV). Reference sequences can be downloaded [here](https://gdc.cancer.gov/download-gdc-reference-files).
 
 
 | I/O | Entity | Format |
@@ -190,13 +190,13 @@ Variant calls are reported by each pipeline in a VCF formatted file. See the GDC
 #### Pipeline Descriptions
 Four separate variant calling pipelines are implemented for GDC data harmonization. There is currently no scientific consensus on the best variant calling pipeline so the investigator is responsible for choosing the pipeline(s) most appropriate for the data. Some details about the pipelines are indicated below.
 
-The [MuTect2 pipeline](https://gdc.nci.nih.gov/files/public/image/Broad_MuTect_0.png) employs a "Panel of Normals" to identify additional germline mutations. This panel is generated using genomes from TCGA blood normal samples from thousands of individuals that were curated and confidently assessed to be cancer-free. This method allows for a higher level of confidence to be assigned to somatic variants that were called by the MuTect2 pipeline.
+The [MuTect2 pipeline](https://gdc.cancer.gov/files/public/image/Broad_MuTect_0.png) employs a "Panel of Normals" to identify additional germline mutations. This panel is generated using genomes from TCGA blood normal samples from thousands of individuals that were curated and confidently assessed to be cancer-free. This method allows for a higher level of confidence to be assigned to somatic variants that were called by the MuTect2 pipeline.
 
 Basic outlines for the other three pipelines can be found here:
 
-- [VarScan2 pipeline](https://gdc.nci.nih.gov/files/public/image/varscan-somatic-variant-calling-pipeline.png)
-- [MuSE pipeline](https://gdc.nci.nih.gov/files/public/image/muse-somatic-variant-calling-pipeline.png)  
-- [SomaticSniper pipeline](https://gdc.nci.nih.gov/files/public/image/somaticsniper-variant-calling-pipeline.png).
+- [VarScan2 pipeline](https://gdc.cancer.gov/files/public/image/varscan-somatic-variant-calling-pipeline.png)
+- [MuSE pipeline](https://gdc.cancer.gov/files/public/image/muse-somatic-variant-calling-pipeline.png)  
+- [SomaticSniper pipeline](https://gdc.cancer.gov/files/public/image/somaticsniper-variant-calling-pipeline.png).
 
 #### Indels
 Indel mutations that were generated with the MuTect2 pipeline are detected and reported in GDC VCF files. Indels detected with the VarScan pipeline are currently removed from the VCF output.

docs/Data/Data_Model/GDC_Data_Model.md

@@ -2,7 +2,7 @@
 
 ## Introduction
 
-The GDC Data Model is the central method of organization of all data artifacts in the GDC. An overview of the data model, including a visual representation of its components, is provided [on the GDC website](https://gdc.nci.nih.gov/developers/gdc-data-model). This section provides technical details about its implementation for data users, submitters, and developers.
+The GDC Data Model is the central method of organization of all data artifacts in the GDC. An overview of the data model, including a visual representation of its components, is provided [on the GDC website](https://gdc.cancer.gov/developers/gdc-data-model). This section provides technical details about its implementation for data users, submitters, and developers.
 
 ## Entities, Properties, and Links
 
@@ -47,8 +47,8 @@ In addition to UUIDs stored in the `id` property, many entities also have a `sub
 
 ### Data Users
 
-Users can access information stored in the GDC Data Model using the [GDC Data Portal](https://gdc.nci.nih.gov/access-data/gdc-data-portal), the [GDC API](https://gdc.nci.nih.gov/developers/gdc-application-programming-interface-api), and the [GDC Data Transfer Tool](https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool). For more information see [Data Access Processes and Tools](https://gdc.nci.nih.gov/access-data/data-access-processes-and-tools).
+Users can access information stored in the GDC Data Model using the [GDC Data Portal](https://gdc.cancer.gov/access-data/gdc-data-portal), the [GDC API](https://gdc.cancer.gov/developers/gdc-application-programming-interface-api), and the [GDC Data Transfer Tool](https://gdc.cancer.gov/access-data/gdc-data-transfer-tool). For more information see [Data Access Processes and Tools](https://gdc.cancer.gov/access-data/data-access-processes-and-tools).
 
 ### Data Submitters
 
-Data submitters can create and update submittable entities in the GDC Data Model and upload data files registered in the model using the [GDC Data Submission Portal](https://gdc.nci.nih.gov/submit-data/gdc-data-submission-portal), the [GDC API](https://gdc.nci.nih.gov/developers/gdc-application-programming-interface-api), and the [GDC Data Transfer Tool](https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool). For more information see [Data Submission Processes and Tools](https://gdc.nci.nih.gov/submit-data/data-submission-processes-and-tools).
+Data submitters can create and update submittable entities in the GDC Data Model and upload data files registered in the model using the [GDC Data Submission Portal](https://gdc.cancer.gov/submit-data/gdc-data-submission-portal), the [GDC API](https://gdc.cancer.gov/developers/gdc-application-programming-interface-api), and the [GDC Data Transfer Tool](https://gdc.cancer.gov/access-data/gdc-data-transfer-tool). For more information see [Data Submission Processes and Tools](https://gdc.cancer.gov/submit-data/data-submission-processes-and-tools).

docs/Data/Data_Security/Data_Security.md

@@ -11,7 +11,7 @@ To perform these functions, GDC users must first obtain appropriate authorizatio
 
 ## Authorization via dbGaP
 
-Instructions for obtaining authorization via dbGaP are provided in [Obtaining Access to Controlled Data](https://gdc.nci.nih.gov/access-data/obtaining-access-controlled-data) and [Obtaining Access to Submit Data](https://gdc.nci.nih.gov/submit-data/obtaining-access-submit-data).
+Instructions for obtaining authorization via dbGaP are provided in [Obtaining Access to Controlled Data](https://gdc.cancer.gov/access-data/obtaining-access-controlled-data) and [Obtaining Access to Submit Data](https://gdc.cancer.gov/submit-data/obtaining-access-submit-data).
 
 ## Authentication via eRA Commons
 

docs/Data_Portal/Release_Notes/Data_Portal_Release_Notes.md

@@ -45,7 +45,7 @@ Example
 *   Cart
     *   Counts displayed in the top right of the screen, next to the Cart icon, may become inconsistent if files are removed from the server. <!-- PGDC-2403 / PRTL-133 -->
 *   Web Browsers
-    *   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.nci.nih.gov/about-gdc/gdc-faqs).
+    *   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.cancer.gov/about-gdc/gdc-faqs).
     *   Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets <!-- PGDC-2467 / PRTL-109 -->
     *   The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode. <!-- PGDC-2480 -->    
 
@@ -99,7 +99,7 @@ Example
 *   Cart
     *   Counts displayed in the top right of the screen, next to the Cart icon, may become inconsistent if files are removed from the server. <!-- PGDC-2403 / PRTL-133 -->
 *   Web Browsers
-    *   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.nci.nih.gov/about-gdc/gdc-faqs).
+    *   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.cancer.gov/about-gdc/gdc-faqs).
     *   Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets <!-- PGDC-2467 / PRTL-109 -->
     *   The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibility mode. <!-- PGDC-2480 -->    
 
@@ -144,7 +144,7 @@ Release details are maintained in the [GDC Data Portal Change Log](https://githu
     *   Annotations notes do not wrap to the next line at the beginning or the end of a word, some words might be split in two lines <!-- PGDC-2474 -->
     *   Sorting annotations by Case UUID causes error <!-- PRTL-95 -->
 *   Web Browsers
-    *   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.nci.nih.gov/about-gdc/gdc-faqs).
+    *   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.cancer.gov/about-gdc/gdc-faqs).
     *   Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets <!-- PGDC-2467 -->
     *   The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibilty mode <!-- PGDC-2480 -->    
 
@@ -200,7 +200,7 @@ Release details are maintained in the [GDC Data Portal Change Log](https://githu
 *   Annotations
     *   Annotations notes do not wrap to the next line at the beginning or the end of a word, some words might be split in two lines <!-- PGDC-2474 -->
 *   Web Browsers
-    *   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.nci.nih.gov/about-gdc/gdc-faqs).
+    *   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.cancer.gov/about-gdc/gdc-faqs).
     *   Internet Explorer users are not able to use the "Only show fields with no values" when adding custom facets <!-- PGDC-2467 -->
     *   The GDC Portals are not compatible with Internet Explorer running in compatibility mode. Workaround is to disable compatibilty mode <!-- PGDC-2480 -->    
 
@@ -244,6 +244,6 @@ Release details are maintained in the [GDC Data Portal Change Log](https://githu
     *   Sorting File Submitter ID option on the file tab result in a Data Portal Error <!-- PGDC-2430 -->
 *   Tables and Export
     *   Table sorting icon does not include numbers <!-- PGDC-35 -->    
-*   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.nci.nih.gov/about-gdc/gdc-faqs).
+*   Browsers limit the number of concurrent downloads, it is generally recommended to add files to the cart and download large number of files through the GDC Data Transfer Tool, more details can be found on [GDC Website](https://gdc.cancer.gov/about-gdc/gdc-faqs).
 
 Release details are maintained in the [GDC Data Portal Change Log](https://github.com/NCI-GDC/portal-ui/blob/master/CHANGELOG.md).

docs/Data_Submission_Portal/Users_Guide/Submission_Workflow.md

@@ -16,13 +16,13 @@ To upload submittable data files, such as sequence data in BAM or FASTQ format,
 
 ### Review and Submit Data
 
-When all necessary data and files have been uploaded, the submitter reviews the dataset and submits it to the GDC for processing through the [GDC Data Harmonization Pipeline](https://gdc.nci.nih.gov/submit-data/gdc-data-harmonization).
+When all necessary data and files have been uploaded, the submitter reviews the dataset and submits it to the GDC for processing through the [GDC Data Harmonization Pipeline](https://gdc.cancer.gov/submit-data/gdc-data-harmonization).
 
 ### Release Data
 
 The GDC will release data according to [GDC data sharing policies](https://gdc.cancer.gov/submit-data/data-submission-policies). A project may be released after six months from the date of upload or the submitter may request earlier release using the "Release Project" function.  
 
-Harmonized data will be released to GDC users through the [GDC Data Portal](https://gdc-portal.nci.nih.gov/) and other [GDC Data Access Tools](https://gdc.nci.nih.gov/access-data/data-access-processes-and-tools). Once a project is released, all additional submitted data will automatically be released after harmonization.
+Harmonized data will be released to GDC users through the [GDC Data Portal](https://gdc-portal.nci.nih.gov/) and other [GDC Data Access Tools](https://gdc.cancer.gov/access-data/data-access-processes-and-tools). Once a project is released, all additional submitted data will automatically be released after harmonization.
 
 ## Project Lifecycle
 
@@ -36,6 +36,6 @@ The diagram below demonstrates the transition of a project through the various s
 
 ## File Status Lifecycle
 
-This section describes states pertaining to submittable data files throughout the data submission process. A submittable data file could contain data such as genomic sequences (such as a BAM or FASTQ) or pathology slide images. The file lifecycle starts when a submitter uploads metadata for a file to the GDC Data Submission Portal. Upload of file metadata, as a GDC Data Model entity, registers a description of the file in the GDC. The submitter can then use the [GDC Data Transfer Tool](https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool) to upload the actual file. Throughout the lifecycle, the file status transitions through various states from when the file is initially registered through file submission and processing. The diagram below details these status transitions.   
+This section describes states pertaining to submittable data files throughout the data submission process. A submittable data file could contain data such as genomic sequences (such as a BAM or FASTQ) or pathology slide images. The file lifecycle starts when a submitter uploads metadata for a file to the GDC Data Submission Portal. Upload of file metadata, as a GDC Data Model entity, registers a description of the file in the GDC. The submitter can then use the [GDC Data Transfer Tool](https://gdc.cancer.gov/access-data/gdc-data-transfer-tool) to upload the actual file. Throughout the lifecycle, the file status transitions through various states from when the file is initially registered through file submission and processing. The diagram below details these status transitions.   
 
 [![GDC Data Submission Portal File Status](images/gdc-submission-portal-file-state-vs-state.png)](images/gdc-submission-portal-file-state-vs-state.png "Click to see the full image.")

docs/Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md

@@ -100,7 +100,7 @@ Users may see the following error message when attempting to download a file fro
 		  }
 
 
-This error message indicates that the user does not have dbGaP access to the project to which the file belongs. Instructions for requesting access from dbGaP can be found [here](https://gdc.nci.nih.gov/access-data/obtaining-access-controlled-data/registering-and-working-era-commons-and-dbgap).
+This error message indicates that the user does not have dbGaP access to the project to which the file belongs. Instructions for requesting access from dbGaP can be found [here](https://gdc.cancer.gov/access-data/obtaining-access-controlled-data/registering-and-working-era-commons-and-dbgap).
 
 ### File Availability Error
 

docs/Data_Transfer_Tool/Users_Guide/Getting_Started.md

@@ -19,7 +19,7 @@ The system recommendations for using the GDC Data Transfer Tool are as foll
 
 ### Binary Distributions
 
-Binary distributions are available on the [GDC Transfer Tool page](https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool). To install the GDC Data Transfer Tool, download the respective binary distribution and unzip the distribution's archive to a location on the target system.
+Binary distributions are available on the [GDC Transfer Tool page](https://gdc.cancer.gov/access-data/gdc-data-transfer-tool). To install the GDC Data Transfer Tool, download the respective binary distribution and unzip the distribution's archive to a location on the target system.
 
 ### Release Notes
 

docs/index.md

@@ -1,6 +1,6 @@
 # Welcome
 
-This is the official project documentation site of the NCI [Genomic Data Commons (GDC)](https://gdc.nci.nih.gov).
+This is the official project documentation site of the NCI [Genomic Data Commons (GDC)](https://gdc.cancer.gov).
 
 ## Contents
 
@@ -15,4 +15,4 @@ The GDC documentation is divided into the following top-level sections:
 
 ## Learn More
 
-To learn more about GDC, please visit our official [GDC Website](https://gdc.nci.nih.gov).
+To learn more about GDC, please visit our official [GDC Website](https://gdc.cancer.gov).