594e3295e115d96e05b3f5b67150704cc30ded0e lrnassar Thu Feb 23 14:36:50 2023 -0800 Updating docs since changing the table schema button to be more general data format description, refs #30491 diff --git src/hg/htdocs/goldenPath/help/hgGeneGraph.html src/hg/htdocs/goldenPath/help/hgGeneGraph.html index 0596632..300d1ee 100755 --- src/hg/htdocs/goldenPath/help/hgGeneGraph.html +++ src/hg/htdocs/goldenPath/help/hgGeneGraph.html @@ -264,31 +264,31 @@ 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 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 "describe table schema" button or + 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> <p> The database tables can also be accessed programmatically through our <a href="../../goldenPath/help/mysql.html">public MariaDB server</a> or downloaded from our <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hgFixed/database/">downloads server</a> for local processing. The database tables are: <ul> <li><tt>ggLink</tt> - one row per gene/gene interaction. The field "minResCount" is the minimum number of interactions obtained from the same supporting article. E.g. if it is 10, then out of all supporting articles, there is one with 10 interactions curated from it and maybe others with more interactions. A cutoff of 50 should remove high-throughput data from the table. Note that while most databases are in the format source -> target, in this table, the target comes first and the source second. Gene names are