198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/hgGeneGraph.html src/hg/htdocs/goldenPath/help/hgGeneGraph.html index 781e4904e96..fca4153133f 100755 --- src/hg/htdocs/goldenPath/help/hgGeneGraph.html +++ src/hg/htdocs/goldenPath/help/hgGeneGraph.html @@ -132,55 +132,55 @@ GNF2 expression and PanCancer Mutation coloring, genes will be colored on a sliding scale from light grey to black, with those items with the highest expression or the largest number of non-silent mutations being colored the darkest and those with lower expression or fewer mutations being colored grey. Genes will be colored dark blue if there is no information in the database. In this image, you can see a set of 14 genes that interact with TP53 colored by their PanCancer Mutation number:</p> <p><img class="text-center" src="../../images/hgGeneGraphAnnotateDemo.png" alt="Gene Interaction Graph 'Annotate Genes' Example" width="40%" height="40%"></p> <p> You can mouse-over items in the display to show more details about the gene such as their product. If you've chosen to annotate genes with one of the various databases, then it will display that information as well. For instance, hovering over the BAX gene in this example displays a description - of the gene product as wells as the number of Pan-Cancer mutations since that + of the gene product as well as the number of Pan-Cancer mutations since that option is selected: <p><img class="text-center" src="../../images/hgGeneGraphItemHover.png" alt="Gene Interaction Graph Item Hover Example" width="30%" height="30%"></p> <p> You can mouse-over the connecting lines between genes to see more details about the evidence that supports this connection. In this image, you can see the details that pop-up when you mouse over such a line; information displayed includes database support and text-mining support.</p> <p><img class="text-center" src="../../images/hgGeneGraphLineHover.png" alt="Gene Interaction Graph Line Hover Example" width="30%" height="30%"></p> <p> If you click on the line connecting two proteins, you can see a <a href="http://www4.ncsu.edu/~mbcusick/papers/nenkova2005impact.pdf" target="_blank">SumBasic</a>-selected snippet of text from a Pubmed abstract and, if it is a curated interaction, the supporting information from the pathway or interaction databases. This example shows the text-mined support for an interaction between CASP5 and HUNK:</p> <p><img class="text-center" src="../../images/hgGeneGraphLineClickDemo.png" alt="Gene Interaction Graph Line Click Example" width="70%" height="70%"></p> <p> - Below the graph of gene interactions and pathways, there is table of less-supported + Below the graph of gene interactions and pathways, there is a table of less-supported interactions. These are interactions which were mentioned only a few times each in the literature.</p> <p><img class="text-center" src="../../images/hgGeneGraphExtraInteractionsTable.png" alt="Gene Interaction Graph Extra Interactions" width="75%" height="75%"></p> <p> The numbers shown on mouse-over for each interaction represents the number of articles and number of databases that support this interaction. </p> <p> You can export the currently displayed gene interaction graph in a variety of formats including PDF, SVG, Cytoscape, and JSON. </p> @@ -252,31 +252,31 @@ <p> The quantitative contribution of each database in terms of number of gene-pairs is available <a href='../../cgi-bin/hgGeneGraph?page=stats' target="_blank">here</a>. </p> <p> For text mining, PubMed abstracts were downloaded from the National Library of Medicine (NLM) website. The abstracts were then <a href="https://en.wikipedia.org/wiki/Tokenization_(lexical_analysis)" target="_blank">tokenized</a> and parsed syntactically using the <a href="https://www.microsoft.com/en-us/research/project/msr-splat/" target="_blank">SPLAT toolkit</a>. Protein and Gene names were identified and normalized after which potential interactions were extracted using the Microsoft Research NLP "Protein and Pathway Extractors". The results were then mapped to the genome using their HGNC gene symbols. - Text-mining results supporting by only a single abstract are in the database tables but are + Text-mining results supported by only a single abstract are in the database tables but are not shown in the user interface. </p> <a name="dataAccess"></a> <h2>Data Access</h2> <p> The raw data for these graphs can be accessed in multiple ways. They can be explored interactively using the <a href="../../cgi-bin/hgTables">Table Browser</a>, by selecting "group" - "All Tables" and "database" - "hgFixed". Under "table", select "hgFixed.ggLink". You can then start to explore the relationships between the database tables using the "data format description" button or download tables with "get output". All database tables related to this viewer start with the prefix "gg".</p>