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720 lines
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<title>Entrez Help Document: Summary Matrices</title>
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<table border="0" width="600" cellspacing="0" cellpadding="0">
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<tr>
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<td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0"></a></td>
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<td width="360" class="head1" valign="BOTTOM"> <span class="H1">Entrez Help Document</span></td>
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<td width="100" valign="BOTTOM"></td>
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<table CLASS="TEXT" border="0" width="600" cellspacing="0" cellpadding="3" bgcolor="#000000">
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<tr CLASS="TEXT" align="CENTER">
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<td width="100"><a href="http://www.ncbi.nlm.nih.gov/PubMed/" class="BAR">PubMed</a></td>
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<td width="100"><a href="http://www.ncbi.nlm.nih.gov/Entrez/" class="BAR">Entrez</a></td>
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<td width="100"><a href="http://www.ncbi.nlm.nih.gov/BLAST/" class="BAR">BLAST</a></td>
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<td width="100"><a href="http://www.ncbi.nlm.nih.gov/omim/" class="BAR">OMIM</a></td>
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<td width="100"><a href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html" class="BAR">Taxonomy</a></td>
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<td width="100"><a href="http://www.ncbi.nlm.nih.gov/Structure/" class="BAR">Structure</a></td>
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<!--start of 2nd table -->
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<p>Last modified : July 18, 2000</p>
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<table border="0" width="460" cellspacing="0" cellpadding="0">
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<tr>
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<p><b>Summary Matrices</b><p>
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This document provides the following summary tables for the Entrez
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Nucleotide, Protein, Genome, Structure, and Popset data domains:</p>
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<blockquote>
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<a href="#Limits_Available_by_Database">Limits Available by Database</a><br>
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<a href="#Indexes_Available_by_Database">Search Fields Available by Database</a><br>
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<a href="#Search_Fields_and_Qualifiers">Search Field Desriptions and Qualifiers</a><br>
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<a href="#Display_Formats">Display Formats</a></p>
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</blockquote>
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The <a href="/corehtml/query/static/help/pmhelp.html">PubMed help document</a> contains separate information about
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the <a href="/corehtml/query/static/help/pmhelp.html#Limits">Limits</a>, <a href="/corehtml/query/static/help/pmhelp.html#SearchFieldDescriptionsandTags">Search Fields</a>, and <a href="/corehtml/query/static/help/pmhelp.html#DisplayingDocuments">Display Formats</a> available for that database.</p>
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<A HREF="helpdoc.html">Back</A> to the Entrez Help Document</p>
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<table border width="460" cellspacing="0" cellpadding="5">
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<caption align=top>
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<h2><A NAME="Limits_Available_by_Database"></A>Limits Available by Database</h2></caption>
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<tr>
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<td colspan=6 rowspan=13></td>
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<th colspan=6 align=center>Databases</th>
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</tr>
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<tr>
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<th>Limits</th>
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<th>Nucleotide</th>
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<th>Protein</th>
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<th>Genome</th>
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<th>Structure</th>
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<th>PopSet</th>
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</tr>
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<tr align=center>
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<th><A HREF="#Indexes_Available_by_Database">Search Fields</A></th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Exclude ESTs</th>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Exclude STSs</th>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Exclude GSSs</th>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Exclude Working Draft</th>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Exclude Patents</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Molecule Type</th>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Gene Location</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Segmented Sequences</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Database Source</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Modification Date</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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</td>
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</table>
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<P>
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<A HREF="helpdoc.html">Back</A> to the Entrez Help Document</p>
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<table border width="460" cellspacing="0" cellpadding="5">
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<caption align=top>
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<h2><A NAME="Indexes_Available_by_Database"></A>Search Fields Available by Database</h2></caption>
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<tr>
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<td colspan=6 rowspan=28></td>
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<th colspan=1 align=center></th>
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<th colspan=5 align=center>Databases</th>
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</tr>
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<tr>
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<th colspan=1 align=center><A HREF="#Search_Fields_and_Qualifiers">Search Field Descriptions and Qualifiers</A></th>
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<th colspan=1 align=center>Nucleotide</th>
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<th colspan=1 align=center>Protein</th>
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<th colspan=1 align=center>Genome</th>
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<th colspan=1 align=center>Structure</th>
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<th colspan=1 align=center>PopSet</th>
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</tr>
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<tr align=center>
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<th>Accession</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>All Fields</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Author Name</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>EC/RN Number</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Feature Key</th>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Filter</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Gene Name</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Issue</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Journal Name</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Keyword</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Modification Date</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Molecular Weight</th>
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<td>No</td>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Organism</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Page Number</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Primary Accession</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Properties</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Protein Name</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Publication Date</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>SeqID String</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Sequence Length</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Substance Name</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>Yes</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Text Word</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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<tr align=center>
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<th>Title Word</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>No</td>
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<td>No</td>
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</tr>
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<tr align=center>
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<th>Uid</th>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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<td>No</td>
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<tr align=center>
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<th>Volume</th>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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<td>Yes</td>
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</tr>
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</table></p>
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<A HREF="helpdoc.html">Back</A> to the Entrez Help Document</p>
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<table border width="460" cellspacing="0" cellpadding="5">
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<caption align=top>
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<h2><A NAME="Search_Fields_and_Qualifiers"></A>Search Field Descriptions and Qualifiers</h2></caption>
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<tr>
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<td colspan=3 rowspan=26></td>
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<th colspan=1>Search Field</th>
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<th colspan=1>Definition</th>
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<th colspan=1>Qualifier</th>
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</tr>
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<tr>
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<td>Accession</td>
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<td>Contains the unique accession number of the sequence or record, assigned
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to the nucleotide, protein, structure, genome record, or PopSet by a sequence
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database builder. The Structure database accession index contains the PDB IDs but
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not the MMDB IDs.</td>
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<td>[ACCN]</td>
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</tr>
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<tr>
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<td>All Fields</td>
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<td>Contains all terms from all searchable database fields in the database.</td>
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<td>[ALL]</td>
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</tr>
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<tr>
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<td>Author Name</td>
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<td>Contains all authors from all references in the
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database records. The format is last name space first initial(s),
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without punctuation (e.g., marley jf).</td>
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<td>[AUTH]</td>
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</tr>
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<tr>
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<td>EC/RN Number</td>
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<td>Number assigned by the Enzyme Commission or Chemical Abstract Service (CAS)
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to designate a particular enzyme or chemical, respectively.</td>
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<td>[ECNO]</td>
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</tr>
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<tr>
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<td>Feature Key</td>
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<td>Contains the biological features assigned or annotated to the
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nucleotide sequences and defined in the DDBJ/EMBL/GenBank Feature Table
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(http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html). Not available for
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the Protein or Structure databases.</td>
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<td>[FKEY]</td>
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</tr>
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<tr>
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<td>Filter</td>
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<td>Contains predetermined or filtered subsets of the various databases. These
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subsets or filters are created by grouping records that are commonly linked
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to other Entrez databases or within the same database.<P>
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For example, the PopSet database Filter index includes PopSet all, PopSet medline, PopSet
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nucleotide, and PopSet protein. The PopSet medline filter includes all PopSet records with
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links to PubMed; the PopSet nucleotide filter includes all PopSet records with links to the
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nucleotide database; and, the PopSet protein filter includes all PopSet records with links to
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the protein database. The PopSet all filter includes all PopSet records.<P>The Nucleotide database
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Filter index contains a great deal more filters because the database records are linked
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to numerous external links. For more information see <A HREF="helpdoc.html#Link_Out">Link Out</A></A>.</td>
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<td>[FILT]</td>
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</tr>
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<tr>
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<td>Gene Name</td>
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<td>Contains the standard and common names of genes found in the database records. This field is not
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available in Structure database.</td>
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<td>[GENE]</td>
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</tr>
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<tr>
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<td>Issue</td>
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<td>Contains the issue number of the journal in which the data were published.</td>
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<td>[ISS]</td>
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</tr>
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<tr>
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<td>Journal Name</td>
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<td>Contains the name of the journal in which the data were published. Journal
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names are indexed in the database in abbreviated form (e.g., J Biol Chem). Journals are also
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indexed by their by ISSNs. Browse the index if you do not know the ISSN or are not sure how a
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particular journal name is abbreviated.</td>
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<td>[JOUR]</td>
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</tr>
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<tr>
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<td>Keyword</td>
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<td>Contains special index terms from the
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controlled vocabularies associated with the GenBank, EMBL, DDBJ,
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SWISS-Prot, PIR, PRF, or PDB databases. Browse the Keyword indexes of the individual
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databases to become familiar with these vocabularies. A Keyword index is not available
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in the Structure database.</td>
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<td>[KYWD]</td>
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</tr>
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<tr>
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<td>Modification Date</td>
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<td>Contains the date that the most recent modification to that record is indexed in Entrez, in the format YYYY/MM/DD (e.g., 1999/08/05). A year alone, (e.g., 1999) will retrieve all records modified for that year; a year and month (e.g., 1999/03) retrieves all records modified for that month that are indexed in Entrez. </td>
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<td>[MDAT]</td>
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</tr>
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<tr>
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<td>Molecular Weight</td>
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<td>Molecular weight of a protein, in Daltons (Da), calculated by the method described in the <a href="helpdoc.html#MolecularWeight">Searching by Molecular Weight</a> section of the Entrez help document. Note that molecular weight must be entered as a fixed 6 digit field, filled with leading zeros (not letter O), e.g., 002002 [MOLWT]</td>
|
|
<td>[MOLWT]</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td>Organism</td>
|
|
<td>Contains the scientific and common names for the organisms
|
|
associated with protein and nucleotide sequences. </td>
|
|
<td>[ORGN]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Page Number</td>
|
|
<td>Contains the number of the first journal page of the article in which
|
|
the data were published.</td>
|
|
<td>[PAGE]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Primary Accession</td>
|
|
<td>Contains the primary accession number of the sequence or record, assigned
|
|
to the nucleotide, protein, structure, genome record, or PopSet by a sequence
|
|
database builder. A Primary Accession index is not available
|
|
in the Structure database.</td>
|
|
<td>[PACC]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Properties</td>
|
|
<td>Contains properties of the nucleotide or protein sequence. For
|
|
example, the Nucleotide database's Properties index includes molecule types,
|
|
publication status, molecule locations, and GenBank divisions. A
|
|
Properties index is not available in the Structure database.</td>
|
|
<td>[PROP]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Protein Name</td>
|
|
<td>Contains the standard names of proteins found in database records. Common names
|
|
may not be indexed in this field so it is best to also consider All Fields or Text Words.
|
|
A Protein Name index is not available in the Structure database. </td>
|
|
<td>[PROT]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Publication Date</td>
|
|
<td>Contains the date that records are released into
|
|
Entrez, in the format YYYY/MM/DD (e.g.,
|
|
1999/08/05). It is the date the entry first appeared in
|
|
GenBank explicitly indexed in Entrez. A year alone,
|
|
(e.g., 1999) will retrieve all records for that year; a
|
|
year and month (e.g., 1999/03) will retrieve all
|
|
records released into GenBank for that month.</td>
|
|
<td>[PDAT]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>SeqID String</td>
|
|
<td>Contains the special string identifier, similar to a FASTA identifier, for a
|
|
given sequence. A SeqID String index is not available in the Structure database.</td>
|
|
<td>[SQID]</td>
|
|
</tr>
|
|
</tr>
|
|
<tr>
|
|
<td>Sequence Length</td>
|
|
<td>Contains the total length of the sequence. Sequence Length indexes are not available in the Structure or PopSet databases.</td>
|
|
<td>[SLEN]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Substance Name</td>
|
|
<td>Contains the names of any chemicals associated with this record
|
|
from the CAS registry and the MEDLINE Name of Substance field.
|
|
Substance Name indexes are not available in the Genome or PopSet databases.</td>
|
|
<td>[SUBS]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Text Word</td>
|
|
<td>Contains all of the "free text" associated with a record.</td>
|
|
<td>[WORD]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Title Word</td>
|
|
<td>Includes only those words found in the definition line of a record. The definition
|
|
line summarizes the biology of the sequence and is carefully constructed by database staff.
|
|
A standard definition line will include the organism, product name, gene symbol,
|
|
molecule type and whether it is a partial or complete cds. Title Word indexes are not available in the Structure or PopSet databases.</td>
|
|
<td>[TITL]</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Uid</td>
|
|
<td>Contains the Medline unique identifier for records that contain published
|
|
references that are linked to PubMed. The Uid index is not browsable.</td>
|
|
<td>[UID]</td>
|
|
</tr>
|
|
</tr>
|
|
<tr>
|
|
<td>Volume</td>
|
|
<td>Contains the volume number of the journal in which the data were published.</td>
|
|
<td>[VOL]</td>
|
|
</tr>
|
|
</table><P>
|
|
|
|
<A HREF="helpdoc.html">Back</A> to the Entrez Help Document</p>
|
|
|
|
<table border width="460" cellspacing="0" cellpadding="5">
|
|
<caption align=top>
|
|
<h2><A NAME="Display_Formats"></A>Display Formats</h2></caption>
|
|
<tr>
|
|
<td colspan=4 rowspan=20></td>
|
|
<th width="100" colspan=1>Display Format</th>
|
|
<th width="200" colspan=1>Description</th>
|
|
<th width="100" colspan=1>Databases Available</th>
|
|
<th width= "60" colspan=1>Link</th>
|
|
</tr>
|
|
<tr>
|
|
<td>Summary</td>
|
|
<td>Default display, hotlinked Accession number and brief description</td>
|
|
<td>All databases</td>
|
|
<td>None</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Brief</td>
|
|
<td>Hotlinked Accession number and abbreviated description</td>
|
|
<td>All databases</td>
|
|
<td>None</td>
|
|
</tr>
|
|
<tr>
|
|
<td>GenBank/GenPept</td>
|
|
<td>Full report format</td>
|
|
<td>Nucleotide, Protein</td>
|
|
<td>None</td>
|
|
</tr>
|
|
<tr>
|
|
<td>ASN.1</td>
|
|
<td>Abstract Syntax Notation 1 form, the computer-readable form of the data</td>
|
|
<td>All databases</td>
|
|
<td>None</td>
|
|
</tr>
|
|
<tr>
|
|
<td>FASTA</td>
|
|
<td>The definition line and sequence characters</td>
|
|
<td>All databases</td>
|
|
<td>None</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Nucleotide Neighbors</td>
|
|
<td>Retrieves all similar nucleotide sequences for all documents retrieved and displays in default format</td>
|
|
<td>Nucleotide</td>
|
|
<td>Related Sequences</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Protein Neighbors</td>
|
|
<td>Retrieves all similar protein sequences for all documents retrieved and displays in default format</td>
|
|
<td>Protein</td>
|
|
<td>Related Sequences</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Genome Neighbors</td>
|
|
<td>Retrieves all similar genome sequences for all documents retrieved and displays in default format</td>
|
|
<td>Genome</td>
|
|
<td>Related Sequences</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Structure Neighbors</td>
|
|
<td>Retrieves all similar structures for all documents retrieved and displays in default format</td>
|
|
<td>Structure</td>
|
|
<td>Related Sequences</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Provider Links</td>
|
|
<td>Retrieves all external links for all documents retrieved and displays in default format
|
|
- see <A HREF="helpdoc.html#Link_Out">Link Out</A> for more information</td>
|
|
<td>All databases</td>
|
|
<td>LinkOut</td>
|
|
</tr>
|
|
<tr>
|
|
<td>PubMed Links</td>
|
|
<td>Retrieves all Medline links for all documents retrieved and displays in default format</td>
|
|
<td>All databases</td>
|
|
<td>PubMed</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Nucleotide Links</td>
|
|
<td>Retrieves all Nucleotide links for all documents retrieved and displays in default format</td>
|
|
<td>All databases, except Nucleotide</td>
|
|
<td>Nucleotide</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Protein Links</td>
|
|
<td>Retrieves all Protein links for all documents retrieved and displays in default format</td>
|
|
<td>All databases, except Protein</td>
|
|
<td>Protein</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Genome Links</td>
|
|
<td>Retrieves all Genome links for all documents retrieved and displays in default format</td>
|
|
<td>Nucleotide, Protein, and Structure</td>
|
|
<td>Genomes</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Structure Links</td>
|
|
<td>Retrieves all Structure links for all documents retrieved and displays in default format</td>
|
|
<td>Nucleotide, Protein, and Genome</td>
|
|
<td>Structure</td>
|
|
</tr>
|
|
<tr>
|
|
<td>PopSet Links</td>
|
|
<td>Retrieves all PopSet links for all documents retrieved and displays in default format</td>
|
|
<td>All databases</td>
|
|
<td>PopSet</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Graphic Summary</td>
|
|
<td>The graphical view of the sequence accessible by selecting the hotlinked Accession numbers</td>
|
|
<td>Nucleotide, Protein, and Genome</td>
|
|
<td>None</td>
|
|
</tr>
|
|
<tr>
|
|
<td>Structure Summary</td>
|
|
<td>The Structure Summary accessible by selecting the hotlinked PDB numbers</td>
|
|
<td>Structure</td>
|
|
<td>None</td>
|
|
</tr>
|
|
<tr>
|
|
<td>PopSet Summary</td>
|
|
<td>The complete set of Accession Numbers comprising the PopSet accessible by selecting the hotlinked PopSet Accession Numbers</td>
|
|
<td>PopSet</td>
|
|
<td>None</td>
|
|
</tr>
|
|
</table><P>
|
|
|
|
<A HREF="helpdoc.html">Back</A> to the Entrez Help Document
|
|
|
|
</tr>
|
|
</table>
|
|
|
|
|
|
</body>
|
|
</html>
|