edits

docs/ensembl-help/using-ensembl/ensembl-apps/entity-viewer/gene-homology.md

@@ -10,7 +10,11 @@ related_articles:
 
 Homologous genes share a common ancestor, being separated 'split' by a speciation event or a gene duplication event.
 
+<<<<<<< Updated upstream
 A list of homologous genes for a given gene are found in the homology table.
+=======
+A list of homologous genes for a given gene is found in the homology table.
+>>>>>>> Stashed changes
 
 The homology table for a gene is the first tab in the gene relationship panel found in the detailed view of a gene in the Entity viewer.
 
@@ -21,13 +25,13 @@ The homology table for a gene is the first tab in the gene relationship panel fo
   </figcaption>
 </figure>
 
-For each homologous gene found in another species genome the following information is provided:
+For each homologous gene found in another species' genome the following information is provided:
 
 * __Common name__: Domestic guinea pig
 * __Scientific name__: _Cavia porcellus_
 * __% Protein similarity__: The percentage of identical amino acid residues aligned against each other.
 * __% Coverage__: The percent of query which is in local alignment with the respective reference.
-* __Gene symbol__: Gene symbol for homologues in each species - these may vary between species .
+* __Gene symbol__: Gene symbol for homologues in each species - these may vary between species.
 * __Gene ID__: the Ensembl ID - ENSG eg ENSCPOG00000005153.4.
 * __Hit type__: The type of homology: RBBH: reciprocal best blast hit, BBH: best blast hit.
 * __Assembly__: Genome assembly.

docs/ensembl-help/using-ensembl/ensembl-apps/entity-viewer/variant-entity-viewer.md

@@ -11,7 +11,7 @@ related_articles:
 
 # How to view variants in the Entity viewer?
 
-The Entity viewer reveals detailed information about a variant, such as its transcript consequences, allele frequencies and phenotypes.
+The Entity viewer reveals detailed information about a variant, such as its predicted molecular consequences, population allele frequencies and phenotype associations.
 
 The view of variants in the Entity viewer consists of a navigation bar, the main display, the right-hand panel and an action bar.
 
@@ -29,40 +29,38 @@ Key information about a variant is summarised on the navigation bar and in the r
 ### Variant summary on the navigation bar 
 
 The key information listed on the navigation bar, for each variant, is the  
-* variant id eg rs1663519126
-* variant type eg insertion
-* most severe consequences of the variant eg non_coding_transcript_exon_variant
+* id eg rs1663519126
+* type eg insertion
+* most severe predicted consequence eg missense_variant
 * reference allele eg G
-* variant allele eg GC
-* genomic coordinates of the variant eg 1:230,709,875.
+* alternative allele eg GC
+* genomic coordinates on the specific genome assembly eg 1:230,709,875.
 
 ### Variant information on the right-hand panel 
 
-The key information listed on the right-hand panel for each variant, includes all the information displayed in the navigation bar (see above),
+The information listed on the right-hand panel for each variant, includes all the information displayed in the navigation bar (see above),
 along with additional information about the variant’s:
 
-* data source eg dbSNP
-* release number (of data source)
-* link to the Sequence ontology (SO) terms for variant types
-* biotype of the variant eg protein altering variant
+* source and version eg dbSNP release 156
+* link to the Sequence ontology (SO) terms for the most severe predicted molecular consequence
 * all variant alleles 
-* change tolerance scores for  (CADD and GERP) 
-* strand (forward or reverse) on which the variant is found
-* Variant call format (VCF).
+* change tolerance scores (CADD and GERP) 
+* location and strand (forward or reverse) on which the variant is reported
+* representation in Variant Call Format (VCF).
 
 ## How do I find detailed information about a variant? 
 
-Detailed data about a variant is (are?) presented in the nine panels in the main body of the Entity viewer.
+Detailed information about a variant is presented within the nine panels found in the main body of the Entity viewer.
 
 Currently only three panels contain data 
 
-* Variant ID 
+* Variant summary panel (default panel)
 * Transcript consequences
 * Allele frequency.
 
-### What's in the variant ID panel?
+### What's in the variant summary panel (default)?
 
-The variant ID tab displays a zoomed in view of the reference sequence showing the location of the reference allele on the forward strand and the alternative allele(s) directly below. 
+The variant summary panel (default) displays a zoomed in view of the reference sequence showing the location of the reference allele on the forward strand and the alternative allele(s) directly below. 
 
 #### Variant types
 
@@ -92,10 +90,9 @@ The transcript consequence panel shows all the Ensembl transcripts that overlap
 The main view of transcript consequence panel shows the: 
 * variant ID eg rs699
 * variant type eg SNV
-* transcript strand allele eg C
-* reference strand allele eg G
-* gene containing the variant eg AGT
-* gene id eg ENSG 00000135744.9
+* transcript strand allele eg C  (this will differ from the allele on the genomic forward strand for genes on the reverse strand)
+* genomic reference strand allele eg G
+* name and identifier of gene the transcript belongs to containing the variant eg BRCA2, ENSG00000139618
 * number of transcripts eg 12 
 
 This information is followed by a list of the Ensembl transcripts overlapping the variant, displaying each transcript’s:

docs/ensembl-help/using-ensembl/ensembl-apps/genome-browser/variant-track.md

@@ -13,11 +13,11 @@ related_articles:
 
 ## How do I find the variants within a gene?
 
-Search for your gene of interest, using Find a gene. 
+Search for your gene of interest using Find a gene. 
 
-Select your gene of interest and pick the DNA symbol to view the gene in the genome browser.
+Select your gene of interest and pick the DNA symbol to view the gene in the Genome browser.
 
-Your gene of interest is the focus of the view in the Genome browser. 
+Your gene of interest is now the focus of the view in the Genome browser. 
 
 The gene boundaries are highlighted in the browser by red dotted lines.
 
@@ -33,7 +33,7 @@ The variant track is displayed toward the bottom of the view as a green line.
 
 Currently the variant track only displays short variants. 
 
-Use your mouse or keypad to zoom into the variant track to reveal individual variants in the region, their variant types and their variant consequences.
+Use your mouse or keypad to zoom into the variant track to reveal individual variants in the region, their types (eg insertion, SNV) and their predicted molecular consequences (eg missense variant, frameshift variant).
 
 
 
@@ -49,13 +49,13 @@ Different types of variants have specific visual representations in the variant
 
 ### Short variant groups:
 
-The types of variant consequence have been organised into five groups based on the effect the short variants have on the proteins, splicing, transcripts, regulatory and intergenic regions, as shown in the right-hand panel under short variant groups.
+Variant have been organised into five groups based on the molecular effect they are predicted to have as shown in the right-hand panel under short variant groups.
 
-The individual variant consequences found in each group are listed in the right-hand drawer which   can be accessed by selecting the three dots to the right of each group.
+The specific consequences types in each group are listed in the right-hand drawer which   can be accessed by selecting the three dots to the right of each group.
 
-eg A list of individual variant consequences in the Protein altering variant group
+eg A list of more specific consequences in the Protein altering variant group
 
-The variants in each short variant group are represented by different colours:
+The variants in each group are represented by different colours:
 
 * Protein altering variants are red
 * Splicing variants are orange
@@ -77,12 +77,12 @@ If you see a variant you would like to focus on select the variant on the track.
 A menu will pop up that lists the variant’s:
 
 * name 
-* most severe consequences
+* most severe predicted consequences
 * type
 * location
 * alleles
 
-and the option to see view the variant in the genome browser or entity viewer.
+and the option to view the variant in the genome browser or entity viewer.
 
 If you select the genome browser the variant track will move to the top of the genome browser and the variant of interest will become the central focus of the view.
 
@@ -95,10 +95,10 @@ Key information about the variant is summarised on the navigation bar and in the
 The key information on the navigation bar and right-hand panel lists the variant’s:
 * id eg rs1663519126
 * type eg insertion
-* most severe consequences of the variant eg non_coding_transcript_exon_variant
+* most severe predicted consequences eg non_coding_transcript_exon_variant
 * reference allele eg G
-* variant allele(s) eg GC
-* genomic coordinates eg 1:230,709,875.
+* alternative allele(s) eg GC
+* genomic coordinates for the assembly you are viewing eg 1:230,709,875.