Fixed links

docs/Data/File_Formats/MAF_Format.md

@@ -135,7 +135,7 @@ The table below describes the columns in a protected MAF and their definitions.
 |82 - EAS_MAF | Non-reference allele and frequency of existing variant in 1000 Genomes combined East Asian population |
 |83 - EUR_MAF | Non-reference allele and frequency of existing variant in 1000 Genomes combined European population |
 |84 - SAS_MAF | Non-reference allele and frequency of existing variant in 1000 Genomes combined South Asian population |
-|85 - AA_MAF | Non-reference allele and frequency of existing variant in [NHLBI-ESP](https://esp.gs.washington.edu/drupal/) African American population |
+|85 - AA_MAF | Non-reference allele and frequency of existing variant in [NHLBI-ESP](https://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=evsEsp6500&hgta_table=evsEsp6500&hgta_doSchema=describe+table+schema) African American population |
 |86 - EA_MAF | Non-reference allele and frequency of existing variant in NHLBI-ESP European American population|
 |87 - CLIN_SIG | Clinical significance of variant from dbSNP as annotated in ClinVar |
 |88 - SOMATIC |Somatic status of each ID reported under Existing_variation (0, 1, or null) |
@@ -194,7 +194,7 @@ The table below describes the columns in a protected MAF and their definitions.
 
 ### FILTER Value Definitions (column 111)
 
-* __oxog :__ Signifies that this variant was determined to be an OxoG artifact. This was calculated with [D-ToxoG](https://software.broadinstitute.org/cancer/cga/dtoxog)
+* __oxog :__ Signifies that this variant was determined to be an OxoG artifact. This was calculated with D-ToxoG.
 * __bPcr :__ Signifies that this variant was determined to be an artifact of bias on the PCR template strand.  This was calculated with the [DKFZ Bias Filter](https://github.com/eilslabs/DKFZBiasFilter).
 * __bSeq :__ Signifies that this variant was determined to be an artifact of bias on the forward/reverse strand. This was also calculated with the [DKFZ Bias Filter](https://github.com/eilslabs/DKFZBiasFilter).
 

docs/Data_Dictionary/gdcmvs.md

@@ -41,7 +41,7 @@
       </div>
       <div class="ref-box">
         <a href="https://ncit.nci.nih.gov/" class="ref-box__link" target="_blank">Search in NCIt</a>
-        <a href="https://cdebrowser.nci.nih.gov/cdebrowserClient/cdeBrowser.html#/search?programArea=0&contextId=2C8BAF10-7E19-B797-E050-BB89AD43619C"
+        <a href="https://cadsr.cancer.gov/onedata/Home.jsp"
           class="ref-box__link" target="_blank">Search in caDSR</a>
       </div>
     </div>

docs/Data_Portal/Users_Guide/mutation_frequency.md

@@ -53,11 +53,11 @@ The summary section of the gene page contains the following information:
 * __Description:__ A description of gene function and downstream consequences of gene alteration
 * __Annotation:__ A notation/link that states whether the gene is part of [The Cancer Gene Census](http://cancer.sanger.ac.uk/census/)
 
-__External References__ 
+__External References__
 
 A list with links that lead to external databases with additional information about each gene is displayed here. These external databases include: [Entrez](https://www.ncbi.nlm.nih.gov/gquery/), [Uniprot](http://www.uniprot.org/), [Hugo Gene Nomenclature Committee](http://www.genenames.org/), [Online Mendelian Inheritance in Man](https://www.omim.org/), [Ensembl](http://may2015.archive.ensembl.org/index.html), and [CIViC](https://civicdb.org/home).
 
-__Cancer Distribution__ 
+__Cancer Distribution__
 
 A table and two bar graphs (one for mutations, one for CNV events) show how many cases are affected by mutations and CNV events within the gene as a ratio and percentage. Each row/bar represents the number of cases for each project.  The final column in the table lists the number of unique mutations observed on the gene for each project.
 
@@ -77,7 +77,7 @@ A table is displayed below that lists information about each mutation including:
 * __Consequences:__ The effects the mutation has on the gene coding for a protein (i.e. synonymous, missense, non-coding transcript)
 * __# Affected Cases in Gene:__ The number of affected cases, expressed as number across all mutations within the Gene
 * __# Affected Cases Across GDC:__ The number of affected cases, expressed as number across all projects. Choosing the arrow next to the percentage will expand the selection with a breakdown of each affected project.
-* __Impact:__ A subjective classification of the severity of the variant consequence. This is determined using [Ensembl VEP](http://www.ensembl.org/info/genome/variation/predicted_data.html), [PolyPhen](http://genetics.bwh.harvard.edu/pph/), and [SIFT](http://sift.jcvi.org/). The categories are outlined [here](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/#impact-categories).
+* __Impact:__ A subjective classification of the severity of the variant consequence. This is determined using [Ensembl VEP](https://useast.ensembl.org/info/docs/tools/vep/index.html), [PolyPhen](http://genetics.bwh.harvard.edu/wiki/!pph2/about), and [SIFT](http://sift.jcvi.org/). The categories are outlined [here](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/#impact-categories).
 
 *Note: The Mutation UUID can be displayed in this table by selecting it from the Customize Columns button, represented by three parallel lines*
 
@@ -112,7 +112,7 @@ The fields that describe each consequence are listed below:
   * __Coding DNA Change:__ The specific nucleotide change and position of the mutation within the gene
   * __Impact:__ VEP, SIFT, and/or PolyPhen Impact ratings
   * __Gene Strand:__ If the gene is located on the forward (+) or reverse (-) strand
-  * __Transcript:__ The transcript(s) affected by the mutation. Each contains a link to the [Ensembl](https://www.ensembl.org) entry for the transcript 
+  * __Transcript:__ The transcript(s) affected by the mutation. Each contains a link to the [Ensembl](https://www.ensembl.org) entry for the transcript
 
 __Cancer Distribution__
 

docs/Encyclopedia/pages/Annotations.md

@@ -7,7 +7,7 @@ Annotations are automatically downloaded in TSV format with impacted files when
 
 For information on Annotation structure and content please review the [GDC Data Dictionary](/Data_Dictionary/viewer/#?view=table-definition-view&id=annotation)
 
-For information about TCGA conventions for annotations please see the [TCGA Introduction to Annotations](Annotations_TCGA/).  
+For information about TCGA conventions for annotations please see the [TCGA Introduction to Annotations](/Encyclopedia/pages/Annotations_TCGA).  
 
 If a submitter would like to create an annotation, please contact the GDC Support Team ([email protected]).