bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/hgGeneGraph.html src/hg/htdocs/goldenPath/help/hgGeneGraph.html index 3ddaf7d54c9..781e4904e96 100755 --- src/hg/htdocs/goldenPath/help/hgGeneGraph.html +++ src/hg/htdocs/goldenPath/help/hgGeneGraph.html @@ -205,52 +205,52 @@ <li><a href="http://irefindex.org/" target="_blank">iRefIndex 13</a> which includes <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165503/" target="_blank">BIND</a>, <a href="https://thebiogrid.org/" target="_blank">BioGRID</a>, <a href="http://mips.helmholtz-muenchen.de/corum/" target="_blank">CORUM</a>, <a href="http://dip.doe-mbi.ucla.edu/" target="_blank">DIP</a>, <a href="http://www.hprd.org/" target="_blank">HPRD</a>, <a href="http://www.innatedb.com/" target="_blank">InnateDB</a>, <a href="http://www.ebi.ac.uk/intact/" target="_blank">IntAct</a>, <a href="http://matrixdb.univ-lyon1.fr/" target="_blank">MatrixDB</a>, <a href="http://mint.bio.uniroma2.it/" target="_blank">MINT</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/16381906" target="_blank">MPact</a>, <a href="https://www.ncbi.nlm.nih.gov/pubmed/18556668" target="_blank">MPIDB</a> and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8218707/" target="_blank">MPPI</a></li> <li><a href="https://www.ncbi.nlm.nih.gov/pubmed/19762544" target="_blank">Androgen Responsive Gene Database</a>. This database is not available anymore on the internet, but we kept - <a href="http://hgdownload.soe.ucsc.edu/goldenPath/external/geneGraph/">a copy</a>.</li> + <a href="http://hgdownload.gi.ucsc.edu/goldenPath/external/geneGraph/">a copy</a>.</li> <li><a href="http://string-db.org/" target="_blank">String 9.1</a></li> <li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965096/" target="_blank">Negatome 2.0</a></li> <li><a href="http://mips.helmholtz-muenchen.de/corum/" target="_blank">Corum Protein Complexes</a></li> <li><a href="http://www.geneontology.org" target="_blank">Gene Ontology Protein Complexes</a></li> </ul> <li>Pathways</li> <ul> <li><a href="http://www.genome.jp/kegg/pathway.html" target="_blank">KEGG</a>, Version from April 2011. This is a version of the database before the switch to a <a href="http://www.kegg.jp/kegg/legal.html">non-commercial license</a>.</li> <li><a href="https://pid.nci.nih.gov/" target="_blank">NCI Pathway Interaction Database</a>. This database is not available anymore on the internet in its original format, - but we kept <a href="http://hgdownload.soe.ucsc.edu/goldenPath/external/geneGraph/">a + but we kept <a href="http://hgdownload.gi.ucsc.edu/goldenPath/external/geneGraph/">a copy</a>.</li> <li><a href="https://cgap.nci.nih.gov/Pathways/BioCarta_Pathways" target="_blank">BioCarta</a>. This database is not directly available in a machine readable format. We use a version from 2009 that was included in the original NCI-PID. As the original file is not available - anymore, we provide <a href="http://hgdownload.soe.ucsc.edu/goldenPath/external/geneGraph/">a + anymore, we provide <a href="http://hgdownload.gi.ucsc.edu/goldenPath/external/geneGraph/">a copy</a>.</li> <li><a href="http://www.reactome.org/" target="_blank">Reactome 2014</a></li> <li><a href="http://www.wikipathways.org" target="_blank">WikiPathways</a>, version 20170510</li> <li><a href="https://github.com/OpenBEL/openbel-framework-resources/tree/latest/knowledge" target="_blank">OpenBEL large corpus</a>, version 20150611 (commit 5515fcf, Jan 2016). This database is Copyright 2011-2015, Selventa and under a non-commercial license.</li> <li><a href="http://fastforward.sys-bio.net/" target="_blank">FastForward</a></li> </ul> </ul> <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> @@ -271,31 +271,31 @@ <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> <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 + <a href="http://hgdownload.gi.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 separated by the "|"-symbol.</li> <li><tt>ggLinkEvent</tt> - connections between a ggLink and one of the ggEvent tables. The prefix of the eventId indicates the table: ppi/pwy links to ggEventDb, msr links to ggEventText.</li> <li><tt>ggEventDb</tt> - information about gene/gene interactions imported from protein interaction or pathway databases. The structure is modeled after the NCI PID interactions data schema and distinguishes genes, complexes and compounds on each side of the reaction, @@ -303,31 +303,31 @@ are part of the table but not shown in our user interface.</li> <li><tt>ggEventText</tt> - information about gene/gene interactions obtained from text mining.</li> <li><tt>ggDocEvent</tt> - connections between documents and events.</li> <li><tt>ggDoc</tt> - information about documents referenced from ggEventText and ggDocEvent.</li> <li><tt>ggGeneClass</tt> - the HPRD/Panther class, one for each gene symbol.</li> <li><tt>ggGeneName</tt> - the HGNC name, one for each gene symbol.</li> </ul> <p>For more details about the tables and their fields, use the Table Browser's "describe schema" button.</p> <p> The annotations (GNF2 average expression, DrugBank, etc.) for genes are accessed as text files for performance reasons and can be downloaded from our - <a href="http://hgdownload.soe.ucsc.edu/gbdb/hgFixed/geneGraph/">downloads server</a>. + <a href="http://hgdownload.gi.ucsc.edu/gbdb/hgFixed/geneGraph/">downloads server</a>. <p> <a name="credits"></a> <h2>Credits</h2> <ul> <li>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>. <li>Pathway data was provided by the databases listed under methods. <li>Thanks to Ian Donaldson for IRefIndex, the biggest and free collection of protein interaction databases. <li>Arjun Rao (UCSC) provided the ArgDB converter. <li>Thanks to Dexter Pratt for help with OpenBEL and to Charles Tepley Hoyt for the <a href="https://github.com/pybel/pybel" target="_blank">pybel</a> converter. <li>Thanks to Alexander Pico for help with the WikiPathways data format GPML <li>The short gene descriptions are a merge of the <a href="http://hprd.org"