5357f43c35e9cfb7bb2fae897eab6286954865c1 ccpowell Wed Jul 10 11:33:53 2019 -0700 Switching MySQL to MariaDB where appropriate in the documentation, refs #23597 diff --git src/hg/htdocs/goldenPath/help/hgGeneGraph.html src/hg/htdocs/goldenPath/help/hgGeneGraph.html index 33cdf5e..5d52f2e 100644 --- src/hg/htdocs/goldenPath/help/hgGeneGraph.html +++ src/hg/htdocs/goldenPath/help/hgGeneGraph.html @@ -258,31 +258,31 @@ <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 "describe table schema" 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 MySQL server</a> or downloaded from 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 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 @@ -522,31 +522,31 @@ <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 "describe table schema" 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 MySQL server</a> or downloaded from 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 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