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 @@ -1,89 +1,99 @@ <h2>Description</h2> <p> The Pathways and Gene Interactions track shows a summary of gene interaction and pathway data collected from two sources: curated pathway/protein-interaction databases and interactions found through text mining of PubMed abstracts.</p> <h2>Display Conventions and Configuration</h2> <h3>Track Display</h3> <p> The track features a single item for each gene loci in the genome. On the item itself, the gene symbol for the loci is displayed followed by the top gene interactions noted by their gene symbol. Clicking an item will take you a <a href="../../goldenPath/help/hgGeneGraph.html" target="_blank">gene interaction graph</a> that includes detailed information on the support for the various interactions.</p> <p> Items are colored based on the number of documents supporting the interactions of a particular gene. Genes with >100 supporting documents are colored <strong><font color="#000000">black</font></strong>, genes with >10 but <100 supporting documents are colored <strong><font color="#000080">dark blue</font></strong>, and those with >10 supporting documents are colored <strong><font color="#add8e6">light blue</font></strong>.</p> <h3>Pathway and Gene Interaction Display</h3> <p> See the <a href="../../goldenPath/help/hgGeneGraph.html#configure" target="_blank">help documentation</a> 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 Hoifung Poon as part of <a href="https://hanover.azurewebsites.net" target="_blank">Microsoft Research, Project Hanover</a>.</p> <p> Pathway data was provided by the databases listed under "<a href="../../goldenPath/help/hgGeneGraph.html#methods" target="_blank">Data Sources and Methods</a>" section of the help page for the gene interaction graph. In particular, thank you to Ian Donaldson from IRef for his unique collection of interaction databases.</p> <p> The short gene descriptions are a merge of the <a href="http://hprd.org" target="_blank">HPRD</a> and <a href="http://pantherdb.org" target="_blank">PantherDB</a> gene/molecule classifications. Thanks to Arun Patil from HPRD for making them available as a download.</p> <p> The track display and gene interaction graph were developed at the UCSC Genome Browser by Max Haeussler.</p> <h2>References</h2> <p> Poon H, Quirk C, DeZiel C, Heckerman D. <a href="https://academic.oup.com/bioinformatics/article/30/19/2840/2422228/Literome-PubMed-scale-genomic-knowledge-base-in" target="_blank">Literome: PubMed-scale genomic knowledge base in the cloud</a> <em>Bioinformatics</em>. 2014 Oct;30(19):2840-2. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24939151" target="_blank">24939151</a></p>