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/ENCODE/FAQ/index.html src/hg/htdocs/ENCODE/FAQ/index.html index 7711ea6..18e4212 100755 --- src/hg/htdocs/ENCODE/FAQ/index.html +++ src/hg/htdocs/ENCODE/FAQ/index.html @@ -286,31 +286,31 @@ <td align="right"><a href="#FAQ"><img src="../../images/top.gif" alt="" align="right" border="0"></a> <div class="bar"><h4 class="title">ENCODE METADATA AND FILENAMES</h4></div> <div class="content"> <p> <b><font color="#006666">Question: </font></b><br> How do I extract information about an ENCODE experiment from the filename? <p> <b><font color="#006666">Response:</font></b><br> This is not recommended. While ENCODE filenames have some metadata embedded, the information there is not complete nor easily extracted. Rather, use the file's metadata, for example in "files.txt", or access metadata in the following places: <ol>By opening "files.txt" - the metadata file located in each track's corresponding download directory. <br/>By clicking the blue down-arrow next to each subtrack listed on a track's Track Settings page. <br/>By using <a href="/ENCODE/search.html" target="_blank">Track Search or File Search</a> to filter files by metadata. <br/>By using the <a href="../../cgi-bin/hgTables" target="_blank">Table Browser tool</a> and setting "Group" to "All Tables" and selecting the "metaDb" table. Click - the "describe table schema" button to learn more about the metaDb table. + the "data format description" button to learn more about the metaDb table. <br/>By using the <a href="../../goldenPath/help/mysql.html" target="_blank">public MariaDB database</a> to query the metaDb table for each database. </ol> The metadata uses controlled vocabulary (cv.ra), which can be downloaded as a text file <a href="http://hgdownload.soe.ucsc.edu/goldenPath/encodeDCC/cv.ra" target="_blank">here</a>. </div><!--end content--> </div><!--end wrapper--> <!--Content Tables-------------------------------------------------------> <a name="release7"></a> <!--outer table is for border purposes--> <div class="wrapper"> <td align="right"><a href="#FAQ"><img src="../../images/top.gif" alt="" align="right" border="0"></a> <div class="bar"><h4 class="title">ENCODE FILE FORMATS</h4></div> <div class="content"> @@ -623,31 +623,31 @@ <p> <b><font color="#006666">Response:</font></b><br> The <a href="../../FAQ/FAQformat.html">File Format FAQ</a> provides explanations about various file formats. Also a file's related Track Description page may include important information, such as the <a href="../../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwHistone">UW Histone</a> "Methods section", which describes how data were processed to produce peaks. In the "Credits" section there is also a lab contact. To request further information for UW Histone data, for example, you could contact the lab to learn more about the peak calling algorithm or other methods involved. </p> <p> When using the <a href="../../cgi-bin/hgTables">Table Browser</a> there is a "describe table schema" button that gives information similar to that located in the File Format FAQ, plus the related Track Description. </p> <p> For example with settings "group: Regulation", "track: UW Histone", and - "table: wgEncode...PkRep#", if you click the "describe table schema" button you will + "table: wgEncode...PkRep#", if you click the "data format description" button you will find definitions for signalValue and peak. Scrolling down you will find the related Track Description for UW Histone with the explanation for peak calling under "Methods" and the laboratory contact under "Credits". </div><!--end content--> </div><!--end wrapper--> <!--Content Tables-------------------------------------------------------> <a name="release19"></a> <!--outer table is for border purposes--> <div class="wrapper"> <td align="right"><a href="#FAQ"><img src="../../images/top.gif" alt="" align="right" border="0"></a> <div class="bar"><h4 class="title">ENCODE SOFTWARE TOOLS</h4></div> <div class="content"> <p> <b><font color="#006666">Question: </font></b><br>