9a9e2112afc062638a5d9e83345a650fb7486719 max Tue Jun 25 05:09:04 2019 -0700 making data access section of gene interactions better, refs #17960 diff --git src/hg/makeDb/trackDb/interactions.html src/hg/makeDb/trackDb/interactions.html index 7e519b5..390c51d 100644 --- src/hg/makeDb/trackDb/interactions.html +++ src/hg/makeDb/trackDb/interactions.html @@ -28,34 +28,44 @@ accompanying this gene interaction graph for more information on its configuration.</p> <h2>Methods</h2> <p> The pathways and gene interactions were imported from a number of databases and mined from millions of PubMed abstracts. More information can be found in the "<a href="../../goldenPath/help/hgGeneGraph.html#methods" target="_blank">Data Sources and Methods</a>" section of the help page for the gene interaction graph.</p> <h2>Data Access</h2> <p> The underlying data for this track can be accessed interactively through the <a href="hgTables" target="_blank">Table Browser</a> or <a href="hgIntegrator" target="_blank">Data Integrator</a>. -For automated analysis, the genome annotation is stored in a bigBed file that can be obtained +The data for this track is spread across a number of relational tables. The best way to +export or analyze the data is using our <a href="../goldenPath/help/mysql.html">public MySQL server</a>. +The list of tables and how they are linked together are described in the +<a href="../goldenPath/help/hgGeneGraph.html#dataAccess">documentation</a> +linked at the bottom of the <a href="hgGeneGraph">gene interaction viewer</a>. +</p> + +<p> +The genome annotation is just a summary of the actual interactions database and therefore often not +of interest to most users. It is stored in a bigBed file that can be obtained from the <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/" target="_blank">download server</a>. -The data for this track is spread across a number of files and tables. The data underlying the + +The data underlying the graphical display is in <a href="../../goldenPath/help/bigBed.html" target="_blank">bigBed</a> formatted file named <tt>interactions.bb</tt>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>. Instructions for downloading source code and precompiled binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>. The tool can also be used to obtain only features within a given range, for example: <p> <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/bbi/interactions.bb -chrom=chr6 -start=0 -end=1000000 stdout</tt> </p> <h2>Credits</h2> <p> The text-mined data for the gene interactions and pathways were generated by Chris Quirk and