1910 lines
No EOL
132 KiB
HTML
1910 lines
No EOL
132 KiB
HTML
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
<!-- PubChem template version 5.1 2012-05 -->
|
|
<!-- $Id: about.html 367034 2012-06-20 14:44:12Z jiazhang $ -->
|
|
<html xmlns="http://www.w3.org/1999/xhtml">
|
|
<head xmlns:xi="http://www.w3.org/2001/XInclude">
|
|
<meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
|
|
<meta name="description" content="Help document for FLink, a resource of the National Center for Biotechnology Information Structure Group" />
|
|
<meta name="ncbi_db" content="pubchem" />
|
|
<meta name="keywords" content="FLink, frequency-weighted links, pathways, genes, proteins, protein sequences, chemicals, biochemical, 3D, 3-D, three-dimensional structures, macromolecular structures, x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, nucleic acids, DNA, RNA, ligands, bound chemicals, drugs, medicine, Entrez, Molecular Modeling Database (MMDB), Conserved Domains Database (CDD), PubChem, BioSystems Databases, NCBI, National Center for Biotechnology Information" />
|
|
<meta name="robots" content="index,follow,noarchive" />
|
|
<title>FLink Help Document</title>
|
|
<script type="text/javascript" src="/Structure/scripts/loadbasics.min.js"></script>
|
|
<script type="text/javascript" src="/Structure/scripts/doc_tmp.min.js"></script>
|
|
<link rel="stylesheet" type="text/css" href="/Structure/stylesheets/struct_style_subset.min.css">
|
|
</head>
|
|
|
|
<body>
|
|
<A NAME="Top"></A>
|
|
<A NAME="top"></A>
|
|
|
|
<!-- ======= BEGIN_GET_PUBCHEM_HEADER_AND_NCBILOCALNAV_PULLDOWN_MENUS ========= -->
|
|
<script type="text/javascript">doc_tmp.getDocHdr('flink');</script>
|
|
<!-- ======= END_GET_PUBCHEM_HEADER_AND_NCBILOCALNAV_PULLDOWN_MENUS ========= -->
|
|
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell MiniText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ==================== END_VERTICAL SPACER ======================= -->
|
|
|
|
|
|
<!-- ##################### BEGIN_EDITABLE_CONTENT ##################### -->
|
|
<A NAME="3"></A>
|
|
|
|
<!-- ######### BEGIN_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT_AND_TOC ######## -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCell">
|
|
|
|
<!-- ===================== WARNING BANNER ====================== -->
|
|
<div style="display: block; margin-bottom: 16.003px;"><p></p><p style="padding: 0.5em 2em; font-size: 16px; text-align: center; background: #F2F281 no-repeat 5px center;">The FLink tool has been retired. Please consider using the Entrez Utility (EUtilties) to create your own scripting solution <a href="/books/NBK25501" class="btn btn-primary">/books/NBK25501</a>.</p><p></p></div>
|
|
<!-- ===================== WARNING BANNER ====================== -->
|
|
|
|
|
|
<!-- ==================== TITLE_OF_DOCUMENT =================== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
|
|
<TD class="DocTitleText" align="left"> <A HREF="../flink.cgi">FLink</A> Help</TD>
|
|
|
|
<!-- ===================== GREEN_BUTTONS ====================== -->
|
|
|
|
<TD width="350" bgcolor="#FFFFFF">
|
|
|
|
<TABLE width="350" style="margin:0px -0px 0px 0px;border-collapse:separate;" border="0" cellspacing="1" cellpadding="0" bgcolor="#FFFFFF">
|
|
|
|
<TR>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="flink_about.html"> ABOUT </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../flink.cgi"> SEARCH </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="flink_how_to.html"> HOW TO </A></TD>
|
|
|
|
<TD class="NavResourceButtonActive" align="center" valign="center" style="white-space: nowrap;"><A href="flink_help.html"> HELP </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="flink_faq.html"> FAQ </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="flink_news.html"> NEWS </A></TD>
|
|
|
|
<!-- TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="flink_tools.html"> TOOLS </A></TD -->
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="flink_publications.html"> PUBLICATIONS </A></TD>
|
|
|
|
<TD class="NavResourceButtonInactive" align="center" valign="center" style="white-space: nowrap;"><A href="../../structure_discover.html"> DISCOVER </A></TD>
|
|
|
|
<TD class="WhiteCell" width="1"> </TD>
|
|
|
|
<TR>
|
|
|
|
</TABLE>
|
|
|
|
</TD>
|
|
|
|
<!-- =================== END_GREEN_BUTTONS ==================== -->
|
|
|
|
<TD class="MiniText" width="5"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- =========== COMMENT_ABOUT_HELP_DOC_VS_HOW_TO =========== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
|
|
|
|
<TD class="WhiteCellBlueEdgeAll ThumbText2" align="center">
|
|
<SPAN class="MiniText"> <BR></SPAN>
|
|
<P class="indent20bottomspace">This help document describes how to use FLink, including detailed descriptions of input required, output displays, and the program's features and functions. The "<A HREF="flink_how_to.html"><B>How To</B></A>" page provides <A HREF="flink_how_to.html"><B>quick start guides</B></A> for some common types of searches.<!-- BR>Once records of interest are retrieved, follow Entrez's "Links" to <A HREF="../../structure_discover.html"><B>discover associations among previously disparate data</B></A --></P></TD>
|
|
|
|
<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
|
|
<TD class="WhiteCell NormalText" align="center"> </TD>
|
|
<TD class="WhiteCell NormalText" width="10" align="center"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<!-- ==================== TOC_TABLE_OF_CONTENTS ================= -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
|
|
<!-- ================= LEFT_SIDE_TOC ==================== -->
|
|
|
|
<TD class="WhiteCell TOCText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<!-- TABLE width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
|
<TR>
|
|
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">DETAILED TABLE OF CONTENTS</TD>
|
|
</TR>
|
|
</TABLE -->
|
|
|
|
<A NAME="TOCWhatIs"></A>
|
|
<UL>
|
|
<LI><A HREF="#WhatIs">What is a <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> <B>FLink</B>?</A></LI>
|
|
<UL>
|
|
<LI><!-- A HREF="#FLinkDefinition" --><A HREF="#WhatIs">frequency-weighted links across databases (e.g., proteins → biosystems)</A></LI>
|
|
<!-- LI><A HREF="#WhatIsInput"><B>Input UID list</B> from source database (e.g., proteins) and retrieve ranked list of associated records from a destination databse (e.g., biosystems)</A></LI>
|
|
<LI><A HREF="#WhatIsSubsetofInput">Identify the <B>subset of items</B> from the input list associated with each item in the output list</A></LI>
|
|
<LI><A HREF="#WhatIsSaveCSVfile"><B>Save CSV file</B> of UIDs and descriptive information from the source and/or destination databases</A></LI -->
|
|
</UL>
|
|
</UL>
|
|
|
|
<A NAME="TOCQuickStart"></A>
|
|
<UL>
|
|
<LI><A HREF="#QuickStart"><B>Quick start</B> guide</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#QuickStart">illustrated example showing the <span style="color:#d70000">1-2-3 step process</span> for using the tool</A></LI>
|
|
</UL>
|
|
</UL>
|
|
|
|
<A NAME="TOCInput"></A>
|
|
<UL>
|
|
<LI><A HREF="#Input"><B>Input Options</B></A></LI>
|
|
<UL>
|
|
|
|
<LI><A HREF="#InputUIDListDirectly"><B>Direct input of UID list into <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#InputUIDListChooseDatabase"><span style="color:#d70000">choose</span> database to start ("<span style="color:#d70000">source database</span>")</A></LI>
|
|
<LI><A HREF="#InputUIDListMethods">data input (100,000 UIDs maximum) methods:</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#InputUIDList">input ID list</A><!-- (type or copy/paste UIDs directly into <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink) --></LI>
|
|
<LI><A HREF="#UploadUIDList">upload ID list</A><!-- (browse/submit file of UIDs) --></LI>
|
|
<LI><A HREF="#InputSearchEntrez">search Entrez</A></LI>
|
|
<LI><A HREF="#InputFromEntrezHistory">input from Entrez History</A><!-- retrieve UID list from Entrez History --></LI>
|
|
</UL>
|
|
|
|
<LI><A HREF="#InputSummary"><span style="color:#d70000">review input summary</span> + select destination database</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#UIDListProcessed">UID list processed</A></LI>
|
|
<!-- UL>
|
|
<LI><A HREF="#DuplicateUIDsIgnored">duplicate UIDs ignored</A></LI>
|
|
<LI><A HREF="#InvalidUIDsReported">invalid UIDs reported</A></LI>
|
|
</UL -->
|
|
<LI><A HREF="#InputSummaryInfoDisplayed">descriptive information displayed for each input UID</A></LI>
|
|
<!-- UL>
|
|
<LI><A HREF="#UIDDescriptions">description for each input UID</A></LI>
|
|
</UL -->
|
|
<LI><A HREF="#InputSummaryFunctions">folder tab functions</A></LI>
|
|
<UL>
|
|
<!-- LI><A HREF="#InputFunctionEditUIDList">edit UID list</A></LI -->
|
|
<!-- UL>
|
|
<LI><A HREF="#InputFunctionAddUIDs">add UIDs</A></LI>
|
|
<LI><A HREF="#InputFunctionRemoveUIDs">remove UIDs</A></LI>
|
|
</UL -->
|
|
<LI><A HREF="#InputFunctionClearSelections"><!-- IMG SRC="../icons/page_white.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Clear Selections function, which clears all selections on all pages within the folder tab." -->"Clear Selections"</A></LI>
|
|
<!-- UL>
|
|
<LI><A HREF="#InputFunctionClearAllUIDs">clear all UIDs</A></LI>
|
|
<LI><A HREF="#InputFunctionUploadNewUIDList">input completely new UID list</A></LI>
|
|
</UL -->
|
|
<LI><A HREF="#InputFunctionShow"><!-- IMG SRC="../icons/page_white_stack.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Show function, which displays all (default) or selected records in the Entrez database." -->"Show" records in source database</A></LI>
|
|
<!-- UL>
|
|
<LI><A HREF="#InputFunctionShowIndividual">show individual record</A></LI>
|
|
<LI><A HREF="#InputFunctionShowAll">show all or selected records</A></LI>
|
|
</UL -->
|
|
<LI><A HREF="#InputFunctionLinkTo"><span style="color:#d70000"><IMG SRC="../icons/link_go.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the LinkTo function, which retrieves a frequency-weighted list of records, from a destination database of choice. This function acts upon all the records in the folder tab, whether or not their checkboxes are activated.">"<B>LinkTo</B>"</span> <span style="color:#d70000">destination database</span></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#FLinkJobID"><span style="color:#d70000">Job ID</span></A>
|
|
<LI><A HREF="#InputFunctionPercentCoverage"><span style="color:#d70000">Percent Coverage</span></A></LI>
|
|
<!-- LI><A HREF="#InputFunctionLinkToDestination">select destination database</A></LI>
|
|
<LI><A HREF="#InputFunctionLinkToLinkType">select link type</A></LI -->
|
|
</UL>
|
|
<LI><A HREF="#InputFunctionDownloadCSV"><!-- IMG SRC="../icons/page_excel.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Download CSV function, which saves all items in the current folder tab, whether or not they have been selected with checkboxes." -->"Download CSV" file</A></LI>
|
|
<LI><A HREF="#InputFunctionMoreDetails"><!-- IMG SRC="../icons/page_white_database.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="Icon for the Summary function, which displays additional descriptive information for all records, as available, whether or not their checkboxes are activated." -->"Summary" (display more details for each record)</A></LI>
|
|
</UL>
|
|
<LI><A HREF="#InputSummaryCloseFolderTab">Close folder tab</A></LI>
|
|
<LI><A HREF="#InputSummaryStartOver">Start over</A></LI>
|
|
</UL>
|
|
<LI><A HREF="#InputToOutput"><span style="color:#d70000">view output</span></A></LI>
|
|
</UL>
|
|
|
|
<LI><A HREF="#InputEntrezSearch"><B>Search Entrez → link to <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</B></A></LI>
|
|
<UL>
|
|
<LI><!-- A HREF="#InputEntrezSearchSourceDatabase" --><A HREF="#InputEntrezSearch">search an Entrez database of interest, then link to <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink from the search results page</A></LI>
|
|
<!-- LI><A HREF="#InputEntrezSearchLinktoFLink">[on the search results page,]link to FLink's display of associated records in a destination database via:</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#InputEntrezSearchFLinkIcon"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icon in toolbar</A></LI>
|
|
<LI><A HREF="#InputEntrezSearchSelectedRecords">"Selected Records" box</A></LI>
|
|
</UL -->
|
|
<!-- LI><A HREF="#InputEntrezSearchFLinkOutput">view output</A></LI -->
|
|
</UL>
|
|
|
|
<LI><A HREF="#InputMaximum"><B>Maximum input</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#InputMaximum">up to 100,000 UIDs</A></LI>
|
|
</UL>
|
|
|
|
</UL>
|
|
</UL>
|
|
|
|
|
|
<A NAME="TOCOutput"></A>
|
|
<UL>
|
|
<LI><A HREF="#Output"><B>Output</B></A></LI>
|
|
<UL>
|
|
|
|
<LI><A HREF="#OutputJobSummary"><B>job summary</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#OutputJobSummarySourceDatabase">source database (number of UIDs input)</A></LI>
|
|
<LI><A HREF="#OutputJobSummaryDestinationDatabase">destination database (number of UIDs retrieved)</A></LI>
|
|
<LI><A HREF="#OutputJobSummaryLinkMethod">link method</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#OutputJobSummaryLinkMethodDescription">brief description of method</A></LI>
|
|
<LI><A HREF="#OutputJobSummaryOneToOneMappings">download one-to-one mapping in csv</A></LI>
|
|
</UL>
|
|
<LI><A HREF="#OutputJobSummaryMultiStepFLink">multiple step Flink operation</A></LI>
|
|
</UL>
|
|
|
|
<LI><A HREF="#OutputRankedList"><B>ranked list of records</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#OutputRankedListItemDetails">UID and description of each retrieved record</A></LI>
|
|
<LI><A HREF="#OutputRankedListFrequency"><span style="color:#d70000"><B>Frequency</B></span> column indicates rank</A></LI>
|
|
<LI><A HREF="#OutputRankedListMaxFrequency"><span style="color:#d70000">Max Frequency</span> column</A></LI>
|
|
<LI><A HREF="#OutputRankedListPercentCoverage"><span style="color:#d70000">Percent Coverage</span> (alternative method for ranking output)</A></LI>
|
|
</UL>
|
|
|
|
<LI><A HREF="#OutputFunctions"><B>folder tab functions</B></A></LI>
|
|
<UL>
|
|
|
|
<LI><A HREF="#OutputFunctionClearSelections"><!-- IMG SRC="../icons/page_white.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Clear Selections function, which clears all selections on all pages within the folder tab." -->"Clear Selections"</A></LI>
|
|
|
|
<LI><A HREF="#OutputFunctionShow"><!-- IMG SRC="../icons/page_white_stack.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Show function, which displays all (default) or selected records in the Entrez database." -->"Show" records in source database</A></LI>
|
|
<!-- UL>
|
|
<LI><A HREF="#OutputFunctionShowIndividual">show individual record</A></LI>
|
|
<LI><A HREF="#OutputFunctionShowAll">show all or selected records</A></LI>
|
|
</UL -->
|
|
|
|
<LI><A HREF="#OutputFunctionDownloadCSV"><!-- IMG SRC="../icons/page_excel.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Download CSV function, which saves all items in the current folder tab, whether or not they have been selected with checkboxes, as a comma separated value (CSV) file." -->"Download CSV" file</A></LI>
|
|
|
|
|
|
<LI><A HREF="#OutputFunctionSummary"><!-- IMG SRC="../icons/page_white_database.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="Icon for the Summary function, which displays additional descriptive information for all records, as available, whether or not their checkboxes are activated." -->"Summary" (display more details for each record)</A></LI>
|
|
|
|
</UL>
|
|
|
|
<LI><A HREF="#OutputMaximum"><B>Maximum output</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#OutputMaximum">up to 100,000 UIDs</A></LI>
|
|
</UL>
|
|
|
|
</UL>
|
|
</UL>
|
|
|
|
|
|
<A NAME="TOCSupportedDatabases"></A>
|
|
<UL>
|
|
<LI><A HREF="#SupportedDatabases"><B>Supported Databases</B></A></LI>
|
|
|
|
<UL>
|
|
|
|
<LI><A HREF="#SupportedDatabasesSubsetOfEntrez">Subset of Entrez databases</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesLinkNames">Link names</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesFlinkIcon"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icon on Entrez search results pages</A></LI>
|
|
|
|
</UL>
|
|
|
|
|
|
<!-- UL>
|
|
|
|
<LI><A HREF="#SupportedDatabasesBioSystems">BioSystems</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesCDD">Conserved Domain Database (CDD)</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesGene">Gene</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesMESH">MESH</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesProtein">Protein</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesPCAssay">PubChem BioAssay</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesPCCompound">PubChem Compound</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesPCSubstance">PubChem Substance</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesPubMed">PubMed</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesStructure">Structure</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabasesTaxonomy">Taxonomy</A></LI>
|
|
|
|
<LI><A HREF="#SupportedDatabases________"><B>________</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
</UL>
|
|
</UL>
|
|
|
|
</UL -->
|
|
</UL>
|
|
|
|
|
|
<A NAME="TOCReferences"></A>
|
|
<UL>
|
|
<LI><A HREF="#References"><B>References</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#Citing">Citing <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A></LI>
|
|
<!-- LI><A HREF="#ReferencesSupportedDatabases">References describing the supported databases</A></LI -->
|
|
</UL>
|
|
</UL>
|
|
|
|
|
|
<!-- SECTION_HEADER:
|
|
<A NAME="TOC__anchorname___"></A>
|
|
<UL>
|
|
<LI><A HREF="#__anchorname___"><B>_____Section_Header_____</B></A></LI>
|
|
<UL>
|
|
|
|
<LI><A HREF="#________"><B>________</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
</UL>
|
|
</UL>
|
|
|
|
<LI><A HREF="#________"><B>________</B></A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
</UL>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
</UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
</UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
</UL>
|
|
<LI><A HREF="#________">________</A></LI>
|
|
</UL>
|
|
</UL>
|
|
|
|
</UL>
|
|
</UL -->
|
|
|
|
|
|
</TD>
|
|
|
|
<!-- ======= SPACER_COLUMN_TO_RIGHT_OF_TOC_LEFT_SIDE_TEXT ========= -->
|
|
|
|
<TD class="WhiteCell TOCText" width="5"> </TD>
|
|
|
|
|
|
<!-- =============== RIGHT_SIDE_THUMBNAILS ================ -->
|
|
|
|
<TD WIDTH="300" class="WhiteCell ThumbText" ALIGN="LEFT" VALIGN="TOP">
|
|
|
|
<!-- BR -->
|
|
|
|
<!-- =============== BRIEF_TABLE_OF_CONTENTS ================ -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
|
|
<TR>
|
|
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
|
<TR>
|
|
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;">BRIEF TABLE OF CONTENTS</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdgeBottomAndSides ThumbText2">
|
|
|
|
<TR>
|
|
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP" colspan="3"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD>
|
|
<TD ALIGN="Left" VALIGN="TOP" style="white-space: nowrap;" class="Yellow1Cell">
|
|
<A HREF="#WhatIs">What is <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink?</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#FLinkDefinition">frequency-weighted links</A><BR>
|
|
|
|
<A HREF="#QuickStart">Quick start guide</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#QuickStartIllustration">1-2-3 step process <I>illustration</I></A><BR>
|
|
|
|
<A HREF="#Input">Input options</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#InputUIDListDirectly">direct input of UID list into FLink</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#InputEntrezSearch">search Entrez → link to FLink</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#InputMaximum">maximum input 100,000 UIDs</A><BR>
|
|
|
|
<A HREF="#InputSummary">Review input summary + select destination</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#UIDListProcessed">UID list processed</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#InputSummaryFunctions">folder tab functions</A>, <A HREF="#InputFunctionLinkTo"><IMG SRC="../icons/link_go.png" WIDTH="13" HEIGHT="13" BORDER="0" ALT="icon for the LinkTo function, which retrieves a frequency-weighted list of records, from a destination database of choice. This function acts upon all the records in the folder tab, whether or not their checkboxes are activated."> LinkTo</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#CloseFolderTab">close folder tab</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#StartOver">start over</A><BR>
|
|
<!-- img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#______">___________</A><BR -->
|
|
|
|
|
|
<A HREF="#Output">Output</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputJobSummary">job summary</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputRankedList">ranked list of records</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputFunctions">folder tab functions</A>, <A HREF="#OutputFunctionDownloadCSV"><IMG SRC="../icons/page_excel.png" WIDTH="12" HEIGHT="12" BORDER="0" ALT="icon for the Download CSV function, which saves all items in the current folder tab, whether or not they have been selected with checkboxes.">save CSV file</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#OutputMaximum">maximum output 100,000 UIDs</A><BR>
|
|
|
|
<A HREF="#SupportedDatabases">Supported databases</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SupportedDatabasesSubsetOfEntrez">subset of Entrez</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SupportedDatabasesLinkNames">link names</A><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="40" height="1" border="0"><A HREF="#SupportedDatabasesFlinkIcon">FLink icon in Entrez search results</A><BR>
|
|
|
|
<A HREF="#References">References</A><BR>
|
|
<!-- A HREF="#___">_________</A><BR -->
|
|
</TD>
|
|
<TD ALIGN="Left" class="MiniText Yellow1Cell" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD ALIGN="Left" class="MicroText Yellow1Cell" VALIGN="TOP" colspan="3"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
<BR>
|
|
<BR>
|
|
|
|
<!-- ======= SINGLE_THUMBNAIL_YELLOW_BACKGROUND_BIOSYSTEM_RECORD ========== -->
|
|
|
|
<!-- TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
|
|
<TR>
|
|
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
|
<TR>
|
|
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#SummaryPage">BIOSYSTEM RECORD COMPONENTS & FEATURES</A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
|
|
|
|
<TR>
|
|
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
|
<A HREF="#SummaryPage"><IMG src="images/bsid82991_biosystem_record_thumbnail_callouts.png" width="280" height="500" border=0 align="center" alt="Thumbnail image showing portions of the NCBI BioSystems record bsid82991, for human arachidonic acid. Click on image to read more about biosystem record components and features in this help document."></A>
|
|
</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
<BR><BR -->
|
|
|
|
|
|
<!-- ======= SINGLE_THUMBNAIL_YELLOW_BACKGROUND_HIGHLIGHT_COMPONENTS ======== -->
|
|
|
|
<!-- TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
|
|
<TR>
|
|
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="Yellow1CellBlueEdge ThumbText2">
|
|
<TR>
|
|
<TD ALIGN="Center" VALIGN="TOP" class="Yellow1Cell" style="white-space: nowrap;"><A HREF="#BSSummaryHighightSelected">HIGHLIGHT SELECTED BIOSYSTEM COMPONENTS</A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" class="WhiteCellBlueEdgeBottomAndSides ThumbText2">
|
|
|
|
<TR>
|
|
<TD ALIGN="Left" class="MicroText WhiteCell" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD ALIGN="CENTER" VALIGN="TOP" style="white-space: nowrap;" class="WhiteCell">
|
|
<A HREF="#BSSummaryHighightSelected"><IMG src="images/bsid82991_ptgs1_highlighted_thumbnail.png" width="280" height="270" border=0 align="center" alt="Thumbnail image illustrating the highlight function. In this example, the PTGS1 gene, a component of the arachidonic acid metabolism pathway, is selected in the Genes folder tab of NCBI BioSystems record bsid82991 and then shown with a red outline in the full size image of that pathway on the web server of the source database, KEGG. Click on the image to read more about highlighting selected biosystem components."></A>
|
|
</TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
|
|
<TD class="WhiteCell ThumbText2" ALIGN="Left" VALIGN="TOP" WIDTH="10"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
<BR><BR -->
|
|
|
|
|
|
<!-- =========== ADDITIONAL_THUMBNAILS_WHITE_BACKGROUND ============== -->
|
|
|
|
<!-- BR><BR>
|
|
<A HREF="#______">Thumbnail header/key concept</A><br>
|
|
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
|
|
|
|
|
<BR><BR><BR>
|
|
<A HREF="#______">Thumbnail header/key concept</A><br>
|
|
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
|
|
|
|
|
<BR><BR><BR>
|
|
<A HREF="#______">Thumbnail header/key concept</A><br>
|
|
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
|
|
|
|
|
<BR><BR><BR>
|
|
<A HREF="#______">Thumbnail header/key concept</A><br>
|
|
<A HREF="#______"><IMG src="_________thumb.png" width="130" height="105" border=0 align="center" alt="Thumbnail image for example of ________________________. Click on image to jump to a larger, annotated version in this help document."></A>
|
|
|
|
<BR><BR -->
|
|
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- =========== PAGE_MARGIN_TO_RIGHT_OF_TABLE_OF_CONTENTS =============== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############ END_BLUE_EDGE_BOX_WITH_TITLE_OF_DOCUMENT_AND_TOC ######## -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ########### BLUE_HEADER_SECTION_1_WHAT_IS_FLink ############# -->
|
|
|
|
<A NAME="WhatIs"></A>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">What is  <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink?</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############## END_BLUE_HEADER_SECTION_1_WHAT_IS_BIOSYSTEM ############ -->
|
|
|
|
|
|
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ########### -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ================= LEVEL_1 ==================== -->
|
|
|
|
<A NAME="FLinkDefinition"></A>
|
|
<BR>
|
|
|
|
<P class="pad20">
|
|
<A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A> is a tool that enables you <!-- to start with a batch of records in one database (the "source" database) and then retrieve associated records from another database (the "destination" database) -->to traverse from a group of records in a <A HREF="#SourceDatabase"><B>source database</B></A> (e.g., Proteins) to a <A HREF="#OutputRankedList">ranked list</A> of associated records in a <A HREF="#DestinationDatabase"><B>destination database</B></A> (e.g., BioSystems).<BR><BR>
|
|
|
|
The name "FLink" is based on the German word meaning nimble, swift, agile, reflecting the tool's purpose to process large quantities of input and output (up to 100,000 UIDs in each) in an efficient and meaningful way. The name is also an abbreviation for "<A HREF="#OutputRankedListFrequency">frequency-weighted links</A>" because the records in the destination database are ranked by the number of items from the source database to which they are linked, as shown by the "frequency" column in step 3 of the <A HREF="#QuickStart">quick start guide</A> illustration, below.<BR><BR>
|
|
|
|
A list of <A HREF="#SupportedDatabases">supported databases</A> is also provided in this document.<BR><BR>
|
|
|
|
</P>
|
|
|
|
|
|
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ====== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_1_CONTENTS ############ -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ########### BLUE_HEADER_SECTION_2_QUICK_START ############# -->
|
|
|
|
<A NAME="QuickStart"></A>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Quick Start Guide</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############## END_BLUE_HEADER_SECTION_2_QUICK_START ############ -->
|
|
|
|
|
|
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ########### -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ================= LEVEL_1 ==================== -->
|
|
|
|
<A NAME="___________"></A>
|
|
<BR>
|
|
|
|
<A NAME="QuickStartPrefatoryNote"></A>
|
|
|
|
<!-- IF LIGHT GREY BACKGROUND F5F5F5 IS USED INSTEAD OF WHITE,
|
|
CHANGE TO CELLPADDING=10 AROUND IMAGE -->
|
|
|
|
<table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
|
<tr>
|
|
<td width="40"> </td>
|
|
<td>
|
|
The illustration below shows the <B>easy, 1-2-3 step</B> process for using <A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A>. It uses a <A HREF="test_input_files/protein_sample_list_417_uids.txt">sample input file</A> of 417 protein sequence unique identifiers (UIDs) and retrieves a ranked list of biosystems that contain proteins from the input list. Click on any panel of the image below to link to subsequent sections in this help document, which provide additional details about the proper formatting of the <A HREF="#Input">(1) input UID list</A> and the features of the <A HREF="#InputSummary">(2) review + select display</A> and <A HREF="#Output">(3) output display</A>.
|
|
|
|
</td>
|
|
<td width="40"> </td>
|
|
</tr>
|
|
|
|
</table>
|
|
|
|
<BR>
|
|
|
|
<!-- ================= QUICK_START_ILLUSTRATION ==================== -->
|
|
|
|
<A NAME="QuickStartIllustration"></A>
|
|
|
|
<!-- SINGLE IMAGE FILE; NOTE: IF LIGHT GREY BACKGROUND F5F5F5 IS USED INSTEAD OF
|
|
WHITE, CHANGE TO CELLPADDING=10 AROUND IMAGE -->
|
|
|
|
<!-- table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
|
<tr>
|
|
<td width="40"> </td>
|
|
<td ALIGN="center">
|
|
<IMG src="images/1_2_3_proteins_to_biosystems.png" width="800" height="605" border="0" align="center" alt="Illustration of the three steps in using FLink: (1) input UIDs for desired starting database, (2) review input list and select destination database, (3) retrieve ranked list of records from destination database.">
|
|
</td>
|
|
<td width="40"> </td>
|
|
</tr>
|
|
</table -->
|
|
|
|
<!-- SEPARATE, CLICKABLE IMAGE FILE FOR EACH PART OF GRAPHIC -->
|
|
|
|
<blockquote>
|
|
|
|
<table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
|
|
|
<tr>
|
|
<td ALIGN="center" colspan="5">
|
|
<A HREF="test_input_files/protein_sample_list_417_uids.txt"><IMG src="images/1_2_3_proteins_to_biosystems_0_banner_only.png" width="800" height="27" border="0" align="center" alt="Title banner for the Quick Start Guide illustration, which shows the three easy steps in using FLink. The featured example shows how to import a list of protein sequence GI numbers and retrieve a ranked list of BioSystems that contain those proteins. Click on this banner to open the sample input file of 417 protein GI numbers that was used to generate the step 1, 2, and 3 illustrations below. Save the file to your computer and import it into FLink to try the example yourself."></A>
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
<td ALIGN="center" VALIGN="top" colspan="5" class="MiniText"> 
|
|
<!-- img SRC="../../IMG/spacer.gif" width="25" height="1" border="0" -->
|
|
</td>
|
|
</tr>
|
|
|
|
<tr>
|
|
|
|
<td ALIGN="center" VALIGN="top" class="NormalText">
|
|
<A HREF="#Input"><IMG src="images/1_2_3_proteins_to_biosystems_1_input_panel.png" width="251" height="565" border="0" align="center" alt="Step 1 in using FLink: Select the desired starting database and input a list of UIDs. Click on this graphic to read more details about input formats and options."></A>
|
|
</td>
|
|
|
|
<td ALIGN="center" VALIGN="top" class="NormalText">
|
|
<img SRC="../../IMG/spacer.gif" width="7" height="565" border="0">
|
|
</td>
|
|
|
|
<td ALIGN="center" VALIGN="top" class="NormalText">
|
|
<A HREF="#InputSummary"><IMG src="images/1_2_3_proteins_to_biosystems_2_review_and_select_panel.png" width="259" height="565" border="0" align="center" alt="Step 2 in using FLink: Review your input list and use the LinkTo menu option to select a destination database. Click on this graphic to read more details about this display, the JobID you'll receive after using the LinkTo option, and folder tab functions."></A>
|
|
</td>
|
|
|
|
<td ALIGN="center" VALIGN="top" class="NormalText">
|
|
<img SRC="../../IMG/spacer.gif" width="7" height="565" border="0">
|
|
</td>
|
|
|
|
<td ALIGN="center" VALIGN="top" class="NormalText">
|
|
<A HREF="#Output"><IMG src="images/1_2_3_proteins_to_biosystems_3_output_panel.png" width="276" height="565" border="0" align="center" alt="Step 3 in using FLink: View the output, which displays a ranked list of records from destination database. The frequency column shows the number of items from your input list that are linked to each retrieved record. Click on this graphic to read more details about the output display, its folder tab functions, and options to save the input and/or output list as a CSV file."></A>
|
|
</td>
|
|
|
|
</tr>
|
|
|
|
</table>
|
|
|
|
</blockquote>
|
|
|
|
|
|
<!-- ================= END_QUICK_START_ILLUSTRATION ==================== -->
|
|
|
|
<!-- ================= QUICK_START_FOOTNOTE ==================== -->
|
|
|
|
<A NAME="QuickStartFootnote"></A>
|
|
|
|
<table style="margin:0px 0px 0px 0px;" width="800" border="0" bgcolor="FFFFFF" class="NormalText" cellpadding="0">
|
|
|
|
<tr>
|
|
<td width="40"> </td>
|
|
<td>
|
|
|
|
<BR>
|
|
<!-- Subsequent sections of this FLink help document provide additional details about the proper formatting of the <A HREF="#Input">input UID list</A> (part 1b of the graphic above) and the features of the <A HREF="#InputSummary">input summary display</A> (part 2a of graphic) and <A HREF="#Output">output display</A> (part 3 of graphic).<BR><BR -->
|
|
|
|
If you would like to try this example yourself, save the <A HREF="test_input_files/protein_sample_list_417_uids.txt">sample file of 417 protein sequence UIDs</A> that was used for this illustration to your computer. Then open the <A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A> home page, select "Protein" as the start database, upload the file, and follow the remaining steps illustrated above.
|
|
|
|
<I>(A corresponding textual step-by-step guide is provided in the guide on: "<A HREF="flink_how_to_proteins_to_biosystems.html">How to start with a list of proteins and find the biosystems in which they are involved</A>.")</I>
|
|
|
|
</td>
|
|
<td width="40"> </td>
|
|
</tr>
|
|
|
|
</table>
|
|
|
|
<BR><BR>
|
|
|
|
<!-- ================= END_QUICK_START_FOOTNOTE ==================== -->
|
|
|
|
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ====== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_2_CONTENTS ############ -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ########### BLUE_HEADER_SECTION_3_INPUT ############# -->
|
|
|
|
<A NAME="Input"></A>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Input Options</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############## END_BLUE_HEADER_SECTION_3_INPUT ############ -->
|
|
|
|
|
|
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ########### -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
|
|
<BR>
|
|
<BLOCKQUOTE><BLOCKQUOTE>
|
|
|
|
| <A HREF="#InputUIDListDirectly">direct input of UID list into FLink</A> | <A HREF="#InputEntrezSearch">search an Entrez database and then link to FLink</A> | <A HREF="#InputMaximum">maximum input</A> | <!-- A HREF="#_____">_________</A> | -->
|
|
|
|
</BLOCKQUOTE></BLOCKQUOTE>
|
|
|
|
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
|
|
|
<!-- ============== LEVEL_1_DIRECT_INPUT_OF_UID_LIST ================ -->
|
|
|
|
<A NAME="InputUIDListDirectly"></A>
|
|
<A NAME="ValidUIDs"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Direct input of UID list into <A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A></B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
<BR>
|
|
|
|
<!-- ================== STEP_1_INPUT_UID_LIST =============== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
|
<TR>
|
|
<TD>
|
|
|
|
<!-- ================== IMAGE_STEP_1_INPUT_UID_LIST =============== -->
|
|
|
|
<IMG SRC="../../IMG/spacer.gif" WIDTH="10" HEIGHT="500" BORDER="0" ALIGN="right">
|
|
<A HREF="#QuickStart"><IMG SRC="images/1_2_3_proteins_to_biosystems_1_input_panel.png" WIDTH="251" HEIGHT="565" BORDER="0" ALT="Example of data input into FLink, in this case, a list of protein sequence unique identifiers (UIDs). Data input is step 1 of a three step process in using the tool. Click on this image to see the complete illustration of the three steps in using FLink, featured in the Quick Start Guide." ALIGN="right"></A>
|
|
<IMG SRC="../../IMG/spacer.gif" WIDTH="10" HEIGHT="500" BORDER="0" ALIGN="right">
|
|
|
|
<!-- ================== END_IMAGE_STEP_1_INPUT_UID_LIST =============== -->
|
|
|
|
<BLOCKQUOTE>
|
|
<!-- P class="pad20" -->
|
|
One method of using <SPAN class="ThumbText"><A HREF="../flink.cgi"><B><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</B></A></SPAN> is to input a list of <span style="color:#d70000">unique identifiers (UIDs)</span> from any one of the <A HREF="#SupportedDatabases">supported databases</A> directly into the tool. <!-- To do this, open the <SPAN class="ThumbText"><A HREF="../flink.cgi"><B>FLink</B></A></SPAN> home page and select a starting database, then input your list of UIDs using one of the methods below. --> <span style="color:#d70000"><B>Valid UIDs</B></span> are <B>integers only</B>, and the current range of acceptable is <B>0 to 4294967295</B>. The input list should contain no alphanumeric combinations or other non-integer characters. For example, the <A HREF="/Sitemap/samplerecord.html#GInB">GI numbers</A> of sequence records are allowable but the <A HREF="/Sitemap/samplerecord.html#AccessionB">accession numbers</A> are not. As another example, if your input UIDs are for biosystem records, they should be formatted as digits only, e.g., 82991 not bsid82991. (Tip: the Batch Entrez tool can be used to <A HREF="#BatchEntrezTip">screen your input list</A> to identify obsolete and otherwise invalid IDs, if desired.)<BR><BR>
|
|
|
|
<!-- FLink will retrieve the records you have specified from the start database ("source database") you have selected. You can then use the "<A HREF="#InputFunctionLinkTo">LinkTo</A>" function to select the destination database and retrieve a ranked list of records from that destination. An <A HREF="#QuickStart"><span style="color:#d70000">illustrated example</span> <span style="color:#323232">shows the</span> <span style="color:#d70000">easy, 1-2-3 step process</span></A> for using the tool. -->
|
|
<!-- /P -->
|
|
</BLOCKQUOTE>
|
|
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="InputUIDListChooseDatabase"></A><P class="pad10"><B>Choose database to start ("source database")</B> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">This menu lists the <A HREF="#SupportedDatabases">supported databases</A> and allows you to indicate what type of data (proteins, genes, etc.) are represented in the UID list that you will input into FLink. Your selection will appear as the "<B>source database</B>" in the <!-- A HREF="#OutputJobSummary" -->job summary panel of FLink's <A HREF="#Output">output</A>.<BR><BR>
|
|
|
|
<I>Note: After you select an initial database and input a UID list, it is possible to continue using the "choose database to start" menu to select <B>additional source databases</B>, each of which will open in a separate folder tab on the <A HREF="#InputSummary">input summary display</A>. You can then use the <A HREF="#InputFunctionLinkTo">LinkTo</A> option in any folder tab to traverse from that data set to a ranked list of related data in a destination database. If you want to clear your input, you can either <A HREF="#InputSummaryCloseFolderTab">close an individual folder tab</A> or use the <A HREF="#InputSummaryStartOver">start over</A> button to close all the folder tabs and clear all input lists. (Although multiple folder tabs can be opened on the data input page, FLink currently displays only one folder tab on the <A HREF="#Output">output</A> display.)</I><BR><BR>
|
|
|
|
<!-- (Note: After you select a starting database and <A HREF="#InputUIDListMethods">input a UID list</A> as described below, a folder tab will appear for that database that allows you to <A HREF="#InputSummary">review the input</A>. You can then either use the "LinkTo" option to link to a destination database/data type, or you can continue using the "choose database to start" menu to select additional source databases, each of which will open in a separate folder tab. If you want to clear your input, you can either <A HREF="#InputSummaryCloseFolderTab">close an individual folder tab</A> or use the <A HREF="#InputSummaryStartOver">start over</A> button to close all the folder tabs and clear all input lists. Additionally, although multiple folder tabs can be opened on this data input page, FLink currently displays only one folder tab on the <A HREF="#Output">output</A> display.)<BR><BR -->
|
|
</LI>
|
|
</UL>
|
|
|
|
<LI><A NAME="InputUIDListMethods"></A><P class="pad10"><B>Data input (100,000 UIDs maximum) methods:</B> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P></LI><BR>
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="InputUIDList"></A><P class="pad10"><B>Input ID List</B> -- Type or copy/paste UIDs directly into the dialog box. If UIDs are input in this way, they must be separated by <B>white space or commas</B> with no carriage returns between them. The UIDs should be from a <A HREF="#SupportedDatabases">supported database</A> and should be written as integers only. Additional details about <A HREF="#InputUIDListDirectly">valid UIDs</A> are provided above, and the Batch Entrez tool can be used to <A HREF="#BatchEntrezTip">screen your input list</A> to identify obsolete and otherwise invalid IDs, if desired. <!-- (For example, the <A HREF="/Sitemap/samplerecord.html#GInB">GI numbers</A> of sequence records are allowable but the <A HREF="/Sitemap/samplerecord.html#AccessionB">accession numbers</A> are not.) --></P></LI><BR>
|
|
|
|
<LI><A NAME="UploadUIDList"></A><P class="pad10"><B>Upload ID List</B> -- Browse your computer for a file of UIDs and submit the file to FLink. If UIDs are input in this way, there must be <B>one UID per line</B>, with no commas or white space. The UIDs should be from a <A HREF="#SupportedDatabases">supported database</A>, and should be written as integers only. Additional details about <A HREF="#InputUIDListDirectly">valid UIDs</A> are provided above, and the Batch Entrez tool can be used to <A HREF="#BatchEntrezTip">screen your input list</A> to identify obsolete and otherwise invalid IDs, if desired. <!-- (For example, the <A HREF="/Sitemap/samplerecord.html#GInB">GI numbers</A> of sequence records are allowable but the <A HREF="/Sitemap/samplerecord.html#AccessionB">accession numbers</A> are not.) --></P></LI><BR>
|
|
|
|
<LI><A NAME="InputSearchEntrez"></A><P class="pad10"><B>Search Entrez</B> -- Enter an Entrez query to do a search in the <A HREF="#InputUIDListChooseDatabase">start database</A> you have selected. The records retrieved by the search will be imported automatically into FLink and will serve as the input list for your FLink operation. <I>(As an <B>example</B>, open <A HREF="../flink.cgi">FLink</A> and select <A HREF="/gene/">Entrez Gene</A> as the start database. Select "Search Entrez" as the input method and enter a query string such as: <B>human[organism] AND colon cancer</B><!-- AND alive[PROP] -->. Once the retrieved genes are displayed in FLink, select "LinkTo: gene_biosystems" to see a list of biosystems, ranked by the number of genes they contain from the input list. While viewing the biosystem list, click on any value in the "frequency" column to see which subset of genes is associated with the corresponding biosystem.)</I> The <A HREF="/books/NBK3837/">Entrez help document</A> provides general information on searching in that system, and database-specific help documents (e.g., <A HREF="/books/NBK3827/">PubMed</A>, <A HREF="../../cdd/cdd_help.shtml">CDD</A>, <A HREF="../../biosystems/docs/biosystems_help.html">BioSystems</A>, <A HREF="https://pubchem.ncbi.nlm.nih.gov/help.html">PubChem</A>, <A HREF="../../MMDB/docs/mmdb_help.html">Structure</A>, <A HREF="/books/NBK3839/">Gene</A>, <A HREF="/books/NBK44864/">Protein</A>) provide additional tips on searching those particular databases.
|
|
</P></LI><BR>
|
|
|
|
<LI><A NAME="InputFromEntrezHistory"></A><P class="pad10"><B>Input from Entrez History</B> -- If you have done an Entrez search in one of the <A HREF="#SupportedDatabases">supported databases</A> within the <B>last 8 hours</B>, the Entrez system has saved the UID list from your search results in Entrez History, and you can use the "input from Entrez History" option in FLink to import the UID list from a search. (More technically, the searches you have done in a given Entrez database are saved in Entrez History for 8 hours after the last activity you've had in that database.)</P></LI>
|
|
|
|
</UL>
|
|
</UL>
|
|
|
|
<!-- A NAME="InvalidUIDs"></A>
|
|
<BLOCKQUOTE><BLOCKQUOTE>
|
|
<I>NOTE:  If your input list contains any integers beyond the current acceptable range of 0 to 4294967295, or if it contains any non-integer characters, FLink will display an error message reporting that the input file contains <B>invalid UIDs</B> (e.g., "Failed to Get List. <B>ERROR</B>:The input file contains invalid UID(s), which cannot be processed by FLink..."). In such a case, remove the invalid UIDs from the input list and submit the job again. Additional details about <A HREF="#InputUIDListDirectly"><B>valid UIDs</B></A> are provided above.</I>
|
|
</BLOCKQUOTE></BLOCKQUOTE -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ========== BATCH_ENTREZ_TIP ========= -->
|
|
|
|
<A NAME="UIDListBatchEntrezTip"></A>
|
|
<A NAME="BatchEntrezTip"></A>
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" class="WhiteCell">
|
|
|
|
<TR>
|
|
<TD class="WhiteCell" ALIGN="Center" VALIGN="TOP">
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="10" class="WhiteCell NormalText3">
|
|
<TR>
|
|
<TD class="WhiteCell" WIDTH="70" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
<TD class="WhiteCellBlueEdgeAll" ALIGN="Left" VALIGN="TOP">
|
|
<P class="indent20bottomspace NormalText3"><P class="pad10"><B>Tip</B>: You can use <A HREF="/sites/batchentrez?db=Protein"><B>Batch Entrez</B></A>, if desired, to screen a UID list and identify obsolete or otherwise invalid UIDs. Be sure to <B>select the appropriate database</B> from the pull-down menu at the top of the page, then "Browse" to find the file of UIDs you'd like to upload, and press "Retrieve." Batch Entrez will then display a report summarizing the data it found in your input file, such as: (1) number of lines that were present in the file (there should be one UID per line); (2) rejected lines (indicating how many invalid UIDs were detected); (3) removed duplicates (indicating how many duplicate UIDs were detected/removed); (4) passed to Entrez (indicating how many of the UIDs from your list are valid and will therefore be acted upon). The latter may include obsolete UIDs that have been superceded by newer UIDs. The <B>obsolete UIDs</B>, as well as any <B>invalid UIDs</B> that were present in your file, are explicitly reported at the top of the Batch Entrez report. You can revise your UID list file on your computer based on that report, if needed, before importing into FLink.</P>
|
|
</TD>
|
|
<TD class="WhiteCell" WIDTH="70" ALIGN="Center" VALIGN="TOP"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
</TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
<BR>
|
|
|
|
<!-- ========== END_BATCH_ENTREZ_TIP ========= -->
|
|
|
|
<!-- ================== END_STEP_1_INPUT_UID_LIST =============== -->
|
|
|
|
|
|
<!-- ================== STEP_2_REVIEW_AND_SELECT =============== -->
|
|
|
|
<A NAME="InputSummary"></A>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
|
<TR>
|
|
<TD>
|
|
|
|
<!-- ================== IMAGE_STEP_2_REVIEW_SELECT =============== -->
|
|
|
|
<IMG SRC="../../IMG/spacer.gif" WIDTH="10" HEIGHT="500" BORDER="0" ALIGN="right">
|
|
<A HREF="#QuickStart"><IMG SRC="images/1_2_3_proteins_to_biosystems_2_review_and_select_panel.png" WIDTH="259" HEIGHT="565" BORDER="0" ALT="Example of the FLink display that allows you to review your input and select a destination database. This is step 2 of a three step process in using the tool. Click on this image to see the complete illustration of the three steps in using FLink, featured in the Quick Start Guide." ALIGN="right"></A>
|
|
<IMG SRC="../../IMG/spacer.gif" WIDTH="10" HEIGHT="500" BORDER="0" ALIGN="right">
|
|
|
|
<!-- ================== END_IMAGE_STEP_2_INPUT_UID_LIST =============== -->
|
|
|
|
<UL>
|
|
|
|
<LI><P class="pad10"><B>Input summary display:  REVIEW input + SELECT destination database <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></B></P>
|
|
<P class="pad10">After you <A HREF="#InputUIDListDirectly">input a UID list directly</A> into FLink, you will see an intermediate display such as the one illustrated here that summarizes your input and allows you to <A HREF="#InputFunctionLinkTo">LinkTo</A> a destination database. <I>(If you access FLink by <A HREF="#InputEntrezSearch">starting with an Entrez Search</A> instead of inputting a UID list directly, you will not see this intermediate display. Any <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icons that appear on the Entrez search results page will take you directly to FLink's <A HREF="#Output">output display</A>.)</I></P>
|
|
</LI><BR>
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="UIDListProcessed"></A><P class="pad10"><B>UID list processed</B> -- <!-- After you have <A HREF="#InputUIDListChooseDatabase">chosen a database to start</A> and have <A HREF="#InputUIDListMethods">input your UI list</A-->After you <A HREF="#InputUIDListMethods">input a UID list</A> into FLink, the tool checks your list to ensure all the <A HREF="#InputUIDListDirectly"><B>UIDs are valid</B></A>.</P></LI>
|
|
|
|
<UL>
|
|
<LI>If all the UIDs are <B>valid</B>, FLink will ignore duplicate UIDs and will open an input summary page such as the one shown in the illustration to the right. Note that it lists the items in order of <B>increasing UID</B>, regardless of the order in which they were input into the system.</LI><BR><BR>
|
|
|
|
<LI>If the input list contains any <B>invalid UIDs</B>, FLink will display an error message (e.g., "Failed to Get List. ERROR:The input file contains invalid UID(s), which cannot be processed by FLink..."). In such a case, remove the invalid UIDs from the input list and submit the job again. (See the <A HREF="#BatchEntrezTip">tip on using Batch Entrez</A> to check the UIDs in your list.)</LI>
|
|
</UL>
|
|
<BR>
|
|
|
|
|
|
<LI><A NAME="InputSummaryInfoDisplayed"></A><P class="pad10"><B>Descriptive information displayed</B> -- FLink retrieves descriptive information from Entrez about each valid UID in your list and presents it on the summary page for your review. <B>Note</B>: If your input list contains any UIDs that fall within the acceptable range of integers, 0 to 4294967295, but do not correspond to available database records, these UIDs will appear in the input summary folder tab but no descriptive information will be displayed for them.</P></LI><BR>
|
|
|
|
<LI><A NAME="InputSummaryFunctions"></A><P class="pad10"><B>Folder tab functions</B><img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></LI><BR>
|
|
|
|
As noted in the section on <A HREF="#InputUIDListChooseDatabase">choosing a start database</A>, it is possible to have multiple folder tabs open in the <!-- A HREF="#InputSummary" -->input summary display<!-- /A -->, one for each starting database. Each folder tab will have the following options:
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="#InputFunctionClearSelections"></A><P class="pad10"><IMG SRC="../icons/page_white.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Clear Selections function, which clears all selections on all pages within the folder tab."> <B>Clear Selections</B> -- Clear of the all checkboxes that have been selected on all pages within the folder tab. (<I>Note: It is possible to select items on multiple pages (1 of 10, 4 of 10, 9 of 10, etc.) within a folder tab, and the "clear selections" function will clear the checkboxes on all the pages.</I>)</P></LI><BR>
|
|
|
|
<LI><A NAME="InputFunctionShow"></A><P class="pad10"><IMG SRC="../icons/page_white_stack.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Show function, which displays all (default) or selected records in the Entrez database."> <B>Show</B> records in source database -- Retrieve all (default) or selected items from the corresponding Entrez database. This function will temporarily take you out of FLink and into that Entrez database, but you can use the browser's back button to return to the FLink display.</P></LI><BR>
|
|
|
|
<LI><A NAME="InputFunctionLinkTo"></A><A NAME="LinkTo"></A><P class="pad10"><IMG SRC="../icons/link_go.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the LinkTo function, which retrieves a frequency-weighted list of records, from a destination database of choice. This function acts upon all the records in the folder tab, whether or not their checkboxes are activated."> <span style="color:#d70000"><B>LinkTo</B></span> -- This is the main function of the FLink tool, and it acts upon all the records in the folder tab, whether or not their checkboxes are activated. It allows you to select your desired <A HREF="#SupportedDatabases"><B>destination database</B></A> and data type, represented as a <A NAME="InputFunctionLinkToLinkName"></A>"<A HREF="#SupportedDatabasesLinkNames"><B>link name</B></A>." For example, if you are starting in the Protein database, the "Link Name" menu will include choices such as "protein_biosystems," "protein_cdd," "protein_gene," "protein_structure," etc., where the second part of each term indicates the destination database. Some destination databases might have several options, for example, "protein_structure" and "protein_structure_related." To learn the difference, just select an option to read its description in the "LinkTo Options" dialog box. You can continue browsing the various LinkNames in that way, then press the "submit" button in the dialog box once you've selected the LinkName of interest to you.</P></LI><BR>
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="FLinkJobID"></A><P class="pad10"><span style="color:#d70000"><B>Job ID</B></span>: After you select a "LinkTo" option and press the "Submit" button, a randomly generated job ID will be displayed in the URL (e.g., /Structure/flink/flink.cgi?cmd=getjob&&jobid=237915522). That job ID, and hence the URL, will remain valid for <span style="color:#d70000"><B>24 hours</B></span> and can therefore be used to retrieve the results of a job during that time period.<BR><BR>
|
|
|
|
A <B>separate job ID</B> is assigned to each LinkTo operation. For example, if you import the <A HREF="test_input_files/protein_sample_list_417_uids.txt">sample list of 417 protein UIDs</A> into <A HREF="../flink.cgi">FLink</A> and select "LinkTo: <A HREF="#protein_biosystems">protein_biosystems</A>," the URL that appears on the output page of ranked biosystems will include a randomly generated job ID. <B>Save the URL</B> if you want to retrieve those results within the next 24 hours. If you then want to select another LinkTo option for the same input list, use the browser's back button to return to input summary page and select a new destination option such as "LinkTo: <A HREF="#protein_gene">protein_gene</A>." A new job ID for that "LinkTo" operation will appear on the output page, which can also be saved and used over the next 24 hours.</P></LI><BR>
|
|
|
|
<LI><A NAME="InputFunctionPercentCoverage"></A><P class="pad10"><IMG SRC="images/percent_coverage_checkbox.png" WIDTH="255" HEIGHT="155" BORDER="0" ALIGN="RIGHT" ALT="checkbox for the option to rank output by percent coverage"><span style="color:#d70000"><B>Percent Coverage</B></span>: Some "LinkTo" options, such as links from the Gene, Protein, and PubChem databases to BioSystems, display a checkbox for "<A HREF="#OutputRankedListPercentCoverage">Percent Coverage</A>." If you select the checkbox, the FLink output will rank output by that value rather than by "<A HREF="#OutputRankedListFrequency">Frequency</A>." The "Frequency" column will still be present in the output and can still be used to re-sort the data by that value, if desired. Details about both sorting methods are provided in the section on "<A HREF="#OutputRankedList">ranked list of records</A>."<BR>
|
|
<I>(<span style="color:#d70000">Illustrated examples</span> of <A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems.html#FlinkOutputIllustration">pathways ranked by percent coverage</A> vs. <A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems2.html#FlinkOutputIllustration">pathways ranked by frequency</A> are provided in the "How To" file on "Start with a gene expression study and retrieve a ranked list of pathways (biosystems) in which the up- or down-regulated genes are involved.")</I>
|
|
|
|
|
|
<!-- An <A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems.html#FlinkOutputRankBy"><span style="color:#d70000">illustrated example</span></A> of each type of output is provided in the "How To" file on "<A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems.html">Start with a gene expression study and retrieve a ranked list of biosystems in which the up- or down-regulated genes are involved.</A>". -->
|
|
|
|
</P></LI>
|
|
|
|
</UL><BR>
|
|
|
|
<LI><A NAME="InputFunctionDownloadCSV"></A><P class="pad10"><IMG SRC="../icons/page_excel.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Download CSV function, which saves all items in the current folder tab, whether or not they have been selected with checkboxes."> <B>Download CSV</B> file -- Download the data displayed in the folder tab as a comma separated value (CSV) file. This function acts upon all the records in the display, whether or not their checkboxes are activated.</P></LI>
|
|
|
|
<UL>
|
|
<LI><P class="pad10"><B>Tip:</B> The csv file is in <B>Unicode (UTF-8) format</B>. If you plan to import the file into a <B>spreadsheet program</B>, you might need to specify the Unicode (UTF-8) format during the import process.</P></LI>
|
|
<LI><P class="pad10">For <B>example</B>, if you plan to import the file into <B>Excel</B>, follow the instructions at <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help (https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/)</A>, starting with step 4, in order to import Unicode properly.<!-- For convenience, those steps are also included here: --></P></LI>
|
|
<!-- UL>
|
|
<LI><P class="pad10">Start Microsoft <B>Excel</B></P></LI>
|
|
<LI><P class="pad10">In Excel, click the <B>Data</B> tab, and in the <B>Get External Data</B> ribbon/panel, click <B>From Text</B> (as shown in the screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">In the <B>Import Text File</B> dialog box, in the lower-right corner (to the right of the File name box), select <B>Text Files (*.prn;*.txt;*.csv)</B> as the file type, <B>browse</B> to the location where you exported/downloaded the <B>CSV file</B>, and then click <B>Open</B> (or <B>Import</B>) (as shown in the following screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">In the <B>Text Import Wizard - Step 1 of 3</B> dialog box, select <B>Delimited</B>, and from the <B>File</B> origin drop-down list, select <B>65001: Unicode (UTF-8)</B> (or the appropriate language character identifier for your particular environment). In the <B>Preview</B> box below, make sure that your unicode text displays properly, and then click Next (as shown in the screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">In the <B>Text Import Wizard - Step 2 of 3</B> dialog box, in the <B>Delimiters</B> section, make sure that only <B>Comma</B> is checked, and then click <B>Finish</B> (as shown in the screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">In the <B>Import Data</B> dialog box, select <B>New worksheet</B> (or Existing worksheet if you have one), and then click <B>OK</B> (as shown in the screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">You now have a <B>properly formatted (and unicode-friendly)</B> Excel worksheet</P></LI>
|
|
</UL -->
|
|
<LI><P class="pad10"><B>Note:</B> If the <B>Unicode (UTF-8) format</B> is not specified during the process of importing the CSV file into the spreadsheet program, certain <B>ASCII characters</B> such as the <B>umlaut</B> (<B>ö</B>), <B>e-acute</B> (<B>é</B>), etc. might not appear correctly.</P></LI>
|
|
</UL>
|
|
|
|
<LI><A NAME="InputFunctionMoreDetails"></A><P class="pad10"><IMG SRC="../icons/page_white_database.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="Icon for the Summary function, which displays additional descriptive information for all records, as available, whether or not their checkboxes are activated."> <B>Summary</B> -- Display additional descriptive information for all records, as available, whether or not their checkboxes are activated.</P></LI>
|
|
|
|
</UL>
|
|
<BR>
|
|
|
|
<LI><A NAME="InputSummaryCloseFolderTab"></A><A NAME="CloseFolderTab"></A><P class="pad10"><B>Close folder tab</B> -- The "X" in the upper right hand corner of a folder tab on the <A HREF="#InputSummary">input summary display</A> will close that tab and will delete from the server the UID list it currently contains. The database tab can be opened again later, if desired, by selecting it from the start menu. A new UID list can then be imported.</P></LI><BR>
|
|
|
|
<LI><A NAME="InputSummaryStartOver"></A><A NAME="StartOver"></A><P class="pad10"><B>Start Over</B> -- Pressing the "Start Over" button at the bottom of the <A HREF="#InputSummary">input summary display</A> will close all of the folder tabs and will delete from the server the UID lists they currently contain. If you prefer to close only one of the "start" databases and delete its UID list, simply close the appropriate folder tab. </P></LI>
|
|
|
|
</UL>
|
|
<BR>
|
|
|
|
<LI><A NAME="InputToOutput"></A><P class="pad10"><B>View output</B> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">After you have used the "<A HREF="#InputFunctionLinkTo">LinkTo</A>" function to select a destination database, an output display will appear that shows a <A HREF="#OutputRankedList">ranked list</A> of records from the destination database you chose. More details about that display are provided in the <A HREF="#Output">output</A> section below.</P></LI>
|
|
</UL>
|
|
<BR>
|
|
|
|
<!-- LI><A NAME="_____"></A><P class="pad10"><B>______________________</B></P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL>
|
|
<BR -->
|
|
|
|
</UL>
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_STEP_2_REVIEW_SELECT =============== -->
|
|
|
|
<!-- =========== LEVEL_1_SEARCH_ENTREZ_THEN_LINK_TO_FLink ============== -->
|
|
|
|
<A NAME="InputEntrezSearch"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Search Entrez → link to <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
A second way to use FLink is to start by searching an <A HREF="/gquery/">Entrez</A> database of interest (from the list of <A HREF="#SupportedDatabases">supported databases</A>) and then link to FLink from the search results page. The name an appearance of the link might vary. For example:<BR><BR>
|
|
|
|
If you start a search in the <A HREF="/geoprofiles/">GEO Profiles</A> database, the search results will display a "<B>Find Pathways</B>" button in the right-hand margin of the page. That button performs a <A HREF="#OutputJobSummaryMultiStepFLink">multiple-step FLink operation</A> which retrieves a ranked list of pathways associated with the gene expression studies. (A detailed example is provided in the "How To" file on "<A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems.html">Start with a gene expression study and retrieve a ranked list of biosystems in which the up- or down-regulated genes are involved.</A>"<BR><BR>
|
|
|
|
If you start a search in <!-- the <A HREF="/biosystems/">BioSystems</A> database --> some other databases, the link to FLink will appear on the search results page as an <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> <B>icon</B><!-- A HREF="#InputEntrezSearchNotes"><B>*</B></A --> and will retrieve the related data from the destination database as a <A HREF="#OutputRankedList">ranked list</A>. <!-- More details about that display are provided in the <A HREF="#Output">output</A> section below. --> <!-- An <A HREF="../../biosystems/docs/biosystems_help.html#SelectedRecords"><span style="color:#d70000">illustrated example</span></A> and additional details are provided in the BioSystems help document. --><BR><BR>
|
|
|
|
<A NAME="InputEntrezSearchNotes"></A>
|
|
<P class="indent20">
|
|
Important notes about displays that use the <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink <B>icon</B>:
|
|
</P>
|
|
|
|
<UL>
|
|
<LI>clicking on the <B>link name</B> (e.g., "BioSystems") that appears beside the icon will open the records directly in the destination database, where records will be listed in the default sort order for that database. <B>In contrast</B>, clicking on the <B>FLink icon</B> (<IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon">) will display the records as a <A HREF="#OutputRankedListFrequency">frequency-weighted</A> list in the FLink tool.</LI><BR><BR>
|
|
|
|
<!-- LI>If a FLink icon appears in the <B>Find Related Data</B> box in the right margin of a search results page, it will act upon <B>all</B> (default) of the records in your search results or upon those selected with checkboxes. In contrast, if the icon appears in a "<B>Refine your results</B>" box in the right margin of a search results page, it will act upon the relevant <B>subset</B> of the search results. (For an example of a "Refine your results" box, see the PubChem Compound search results for "<A HREF="/pccompound?cmd=search&term=prostaglandin%5BAll+Fields%5D">prostaglandin</A>.")</LI><BR><BR -->
|
|
|
|
<LI>Only a <B>subset of supported databases currently contain <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icons</B> on their search results page at the time of FLink's initial release. If you do an Entrez search in a <A HREF="#SupportedDatabases">supported database</A> and the search results page does <B>not</B> display any FLink icons, <B>you can still access</B> frequency-weighted lists of related data for your search results. This is because your search results are temporarily stored in Entrez History (for up to 8 hours after your last activity in a given Entrez database) and they can be imported as a UID list directly into FLink. To do this, open the <A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A> home page, choose the database you just searched as the starting point, then select "<A HREF="#InputFromEntrezHistory"><B>Input from Entrez History</B></A>" in the dialog box. Your search results will be imported into FLink and you can then use the "<A HREF="#InputFunctionLinkTo">LinkTo</A>" menu to select the desired destination database and data type, as described above.</LI>
|
|
|
|
</UL>
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<!-- UL>
|
|
|
|
<LI><A NAME="InputEntrezSearch"></A><P class="pad10"><B>open an <A HREF="/gquery/">Entrez</A> database of interest and do a search</B></P></LI>
|
|
<UL>
|
|
<LI><A NAME="InputEntrezSearchLinktoFLink"></A><P class="pad10">link to FLink's display of associated records in a destination database via:</P></LI>
|
|
<UL>
|
|
<LI><A NAME="InputEntrezSearchFLinkIcon"></A><P class="pad10"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icon in toolbar</P></LI>
|
|
<LI><A NAME="InputEntrezSearchSelectedRecords"></A><P class="pad10">"Selected Records" box</P></LI>
|
|
</UL>
|
|
</UL>
|
|
<BR>
|
|
|
|
<LI><A NAME="InputEntrezSearchFLinkOutput"></A><P class="pad10"><B>view output</B></P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL>
|
|
<BR>
|
|
|
|
<LI><A NAME="_____"></A><P class="pad10"><B>______________________</B></P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL>
|
|
<BR>
|
|
|
|
</UL>
|
|
<BR -->
|
|
|
|
|
|
|
|
<!-- ================= LEVEL_1_MAXIMUM_INPUT ==================== -->
|
|
|
|
<A NAME="InputMaximum"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Maximum input</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
<A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A> can accept up to 100,000 UIDs as <A HREF="#Input">input</A> (and can display up to 100,000 associated UIDs from the destination database on the <A HREF="#Output">output</A> page). <!-- This maximum is applied after duplicate UIDs from the input list have been removed. -->
|
|
</P>
|
|
|
|
<!-- UL>
|
|
|
|
<LI><A NAME="_____"></A><P class="pad10"><B>______________________</B></P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL>
|
|
<BR>
|
|
|
|
</UL -->
|
|
<BR>
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
|
|
|
|
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ====== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_3_CONTENTS ############ -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ########### BLUE_HEADER_SECTION_4_OUTPUT ############# -->
|
|
|
|
<A NAME="Output"></A>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Output</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############## END_BLUE_HEADER_SECTION_4_OUTPUT ############ -->
|
|
|
|
|
|
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_4_CONTENTS ########### -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
|
|
<BR>
|
|
<BLOCKQUOTE><BLOCKQUOTE>
|
|
|
|
| <A HREF="#OutputJobSummary">job summary</A> | <A HREF="#OutputRankedList">ranked list of records</A> | <A HREF="#OutputFunctions">folder tab functions</A> | <A HREF="#OutputMaximum">maximum output</A> |
|
|
|
|
</BLOCKQUOTE></BLOCKQUOTE>
|
|
|
|
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
|
|
|
|
|
<P class="indent20">
|
|
Regardless of the input method you have used (<A HREF="#InputUIDListDirectly">direct input of UID list into FLink </A>  or  <A HREF="#InputEntrezSearch">search an Entrez database and then link to FLink</A>), the output display will include the described components below.<BR><BR>
|
|
|
|
FLink currently displays a single folder tab on the output page, representing the destination database you have most recently selected. The URL for the display includes a randomly assigned <A HREF="#FLinkJobID"><B><span style="color:#d70000">Job ID</span></B></A>. You can save that URL to a file and use it anytime over the next 24 hours to view the display again. If you would like to retrieve records from a different destination database than the one currently being displayed, use the browser's back button to return to your <A HREF="#InputSummary">input summary display</A> (or to your <A HREF="#InputEntrezSearch">Entrez search results page</A>, if that's how you entered FLink), then use the <A HREF="#InputFunctionLinkTo">LinkTo</A> function (or the FLink icon on your Entrez search results page) to select a new destination database/data type. A new Job ID will be assigned to each LinkTo operation you do. The URLs for those output displays can also be saved and used over the next 24 hours.
|
|
</P>
|
|
<BR>
|
|
|
|
<!-- ================= LEVEL_1_JOB_SUMMARY ==================== -->
|
|
|
|
<A NAME="OutputJobSummary"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Job summary</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<!-- ================== IMAGE_STEP_3_OUTPUT =============== -->
|
|
|
|
<IMG SRC="../../IMG/spacer.gif" WIDTH="10" HEIGHT="500" BORDER="0" ALIGN="right">
|
|
<A HREF="#QuickStart"><IMG SRC="images/1_2_3_proteins_to_biosystems_3_output_panel.png" WIDTH="276" HEIGHT="565" BORDER="0" ALT="Example of the FLink output display, showing a frequency-weighted list of biosystems that contain proteins from your input list. The output display is the last step of a three step process in using the tool. Click on this image to see the complete illustration of the three steps in using FLink, featured in the Quick Start Guide." ALIGN="right"></A>
|
|
<IMG SRC="../../IMG/spacer.gif" WIDTH="10" HEIGHT="500" BORDER="0" ALIGN="right">
|
|
|
|
<!-- ================== END_IMAGE_STEP_3_OUTPUT =============== -->
|
|
|
|
<BLOCKQUOTE>
|
|
The top of the output display shows a blue header bar that says:
|
|
<BR>
|
|
<IMG SRC="../icons/table.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="Icon from the job summary panel title bar displayed on a FLink output page."> <B>Links from [source database name] to [destination database name] records weighted by frequency.</B>
|
|
<BR>
|
|
Click on the triangle <IMG SRC="images/expand_job_summary_panel.png" WIDTH="15" HEIGHT="15" BORDER="0" ALT="image of triangle button used to expand the job summary panel on the FLink output display"> at end of that header bar to expand the job summary panel (which is minimized by default) and view the job details, such as:
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="OutputJobSummarySourceDatabase"></A><A NAME="SourceDatabase"></A><P class="pad10"><B>source database</B> -- the name of the <A HREF="#SupportedDatabases">database</A> in which you <A HREF="#InputUIDListChooseDatabase">started</A> and the number of UIDs that were <A HREF="#UIDListProcessed">processed</A> by FLink. <I>(The "download csv" option can be used to download a comma-separated value file of the UIDs in your input list, along with the <A HREF="#InputSummaryInfoDisplayed">descriptive information</A> about each UID that was retrieved from the source database.)</I></P></LI>
|
|
<!-- UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL -->
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputJobSummaryDestinationDatabase"></A><A NAME="DestinationDatabase"></A><P class="pad10"><B>destination database</B> -- the name of the <A HREF="#SupportedDatabases">database</A> to which you chose to link <!-- (when you used the "<A HREF="#InputFunctionLinkTo">LinkTo</A>" option on the FLink <A HREF="#InputSummary">input summary page</A>, or when you clicked on a <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icon in an <A HREF="#InputEntrezSearch">Entrez search results</A> page) --> and the number of records (UIDs) that were retrieved. <I>(The "download csv" option can be used to download a comma-separated value file of the UIDs that were retrieved by FLink from the destination database. The file will also include the information about each UID that is displayed in the corresponding folder tab for that destination database.)</I></P></LI>
|
|
<!-- UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL -->
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputJobSummaryLinkMethod"></A><P class="pad10"><B>link method</B> -- indicates the relationship between the data in your <A HREF="#Input">input</A> list and the data that were retrieved from the destination database. It includes: </P></LI><BR>
|
|
|
|
<UL>
|
|
<LI><P class="pad10"><A NAME="OutputJobSummaryLinkMethodDescription"><B>brief description</B></A> of the method that was used to create links between items from your input list and items in the destination database, and cross-references to documents that provide additional detail, as available.<!-- brief description of how the links between the input and output data were calculated in the Entrez system, and cross-references to documents that provide additional detail, as available. --></P></LI><BR>
|
|
|
|
<LI><P class="pad10"><A NAME="OutputJobSummaryOneToOneMappings"><B>download one-to-one mapping in csv</B></A> -- This function downloads a comma-separated value (csv) file that lists the one-to-one correspondences between unique identifiers (UIDs) in the source and destination databases. This is an alternative output format that allows you to download the underlying link data in raw form, grouped by the UID of input items rather than sorted as a <A HREF="#OutputRankedListFrequency">frequency</A>-weighted list.<BR><BR>
|
|
|
|
<I>An an <B>example</B>, open FLink and input a list of <B>proteins</B>, then <B>link to</B> the associated list of <B>genes</B>. On the output display, expand the job summary panel to view its details, then click on "download one-to-one mapping in csv" to generate a file that lists each protein UID and the specific gene ID(s) to which it is linked.</I><BR><BR>
|
|
|
|
<B>Note</B> that some items from your input list might not have any links to items in the destination database. The csv file will <B>only</B> include UIDs from your input list that have links to at least one item in the selected destination database. If an item from your input list has links to <B>multiple items</B> in the destination database, each pairwise linkage will be listed on a separate row of the csv file.</P></LI>
|
|
|
|
<!-- LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI -->
|
|
</UL>
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputJobSummaryMultiStepFLink"></A><A NAME="MultiStepFLink"></A><P class="pad10"><B>multiple step Flink operation</B> -- Some FLink operations can traverse across several databases. In that case, the job summary panel will display the details for each step of the operation and allow you to download, if desired, the list of input and output items for each step.</I></P></LI>
|
|
|
|
<UL>
|
|
<LI><P class="pad10">For example, the "Find Pathways" link in the right-hand margin of a <A HREF="/geoprofiles/">GEO Profiles</A> search results page performs a FLink operation that traverses across three databases: <B>GEO Profiles → Genes → BioSystems</B>. That operation is done in two steps:</P>
|
|
<OL>
|
|
<LI><P class="indent20"><B>Step 1</B>: GEO Profiles → Genes</P></LI>
|
|
<LI><P class="indent20"><B>Step 2</B>: Genes → BioSystems</P></LI>
|
|
</OL>
|
|
<!-- P class="indent10">The job summary panel will report the number of items in the input and output list from each step and allow you to download a comma-separated value file of each list, if desired.</P -->
|
|
<P class="indent10">The output list (destination database) from one step serves as the input list (source database) for the next step.</P>
|
|
</LI><BR>
|
|
|
|
<LI><P class="pad10">The bottom of the FLink display will contain a folder tab with the results from the destination database of each step. In this example, the results of Step 1 will be shown in a <B>"Genes" folder tab</B>, and the results of Step 2 will be shown in a <B>"BioSystems" folder tab</B>. <!-- Each folder tab will rank its content by the number of items from that step's input list that are linked to each record that was retrieved from the destination database. --> Note that the "<A HREF="#OutputRankedListFrequency"><span style="color:#d70000"><B>Frequency</B></span></A>" column in each folder tab indicates the number of items <I>from that step's input list</I> that are linked to each record retrieved from the destination database.</P></LI>
|
|
|
|
<LI><P class="pad10">This example<!-- A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems.html#IllustrationFinalOutput"><span style="color:#d70000">illustrated example</span></A --> is discussed in more detail in the "How To" file on "<A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems.html">Start with a gene expression study and retrieve a ranked list of biosystems in which the up- or down-regulated genes are involved</A>."</P></LI>
|
|
|
|
</UL>
|
|
<BR>
|
|
|
|
</UL>
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<!-- =============== LEVEL_1_RANKED_LIST_OF_RECORDS =================== -->
|
|
|
|
<A NAME="OutputRankedList"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Ranked list of records</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
The <B>folder tab</B> in the output display shows the name of the <B>destination database</B> to which you have linked and the items found to be associated with your initial set of records (that were specified in your <A HREF="#InputUIDListDirectly">input UID list</A> or found by your <A HREF="#InputEntrezSearch">Entrez search</A>). The following information is provided for each record retrieved from the destination database. By default, <B>output is ranked</B> by <A HREF="#OutputRankedListFrequency"><span style="color:#d70000"><B>Frequency</B></span></A>, and can also be ranked by <A HREF="#OutputRankedListPercentCoverage"><span style="color:#d70000"><B>Percent (%) Coverage</B></span></A>, if that option is available for a particular destination database.
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="OutputRankedListItemDetails"></A><P class="pad10"><B>UID and description of each retrieved record</B> -- the unique identifier (UID) of each record in the destination database that is associated with any records from your input list, along with descriptive information.</P></LI>
|
|
<!-- UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL -->
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputRankedListFrequency"></A><P class="pad10"><B><span style="color:#d70000"><B>Frequency</B></span> column indicates rank</B> -- The Frequency column shows the number of items from your <A HREF="#Input">input</A> list that are linked to each retrieved record. Click on the value in that column to see which subset of items from your input list are linked to the retrieved record.</P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">For example, if your input list contains 20 GeneIDs, and 12 of those are involved in a given biosystem, the frequency column will display a value of 12. Clicking on the number "12" will open a list of the 12 genes in the Entrez Gene database.</P></LI>
|
|
<LI><P class="pad10">Note: In the case of a <A HREF="#OutputJobSummaryMultiStepFLink">multiple step FLink operation</A> (e.g., GEO Profiles → Genes → BioSystems), the FLink output will display one folder tab with the results of each step (Step 1: GEO Profiles → Genes; Step 2: Genes → BioSystems). The "Frequency" column in each folder tab indicates the number of items <I>from that step's input list</I> that are linked to each record retrieved from the destination database.</P></LI>
|
|
<!-- LI><P class="pad10">_______________________</P></LI -->
|
|
</UL>
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputRankedListMaxFrequency"></A><P class="pad10"><B><span style="color:#d70000"><B>Max Frequency</B></span> column indicates relative size of a record in the destination database</B> -- The Max Frequency column is available for select destination databases such as BioSystems. It is an indicator of the relative size of a record in the destination database in that it shows the total number of items (of the same type as your input list) that are linked to the record. It also <B>represents the maximum value that can appear in the frequency column</B> and is <B>used to calculate the <A HREF="#OutputRankedListPercentCoverage">percent (%) coverage</A></B>. Note that the "Max Frequency" column is displayed only if you select the <A HREF="#InputFunctionPercentCoverage">option to view the "percent coverage"</A> after you input your data file and select your "<A HREF="#InputFunctionLinkTo">LinkTo</A>" destination.</P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">For example, if a biosystem record has links to a total of total of 48 Entrez <B>Gene</B> records, 100 Entrez <B>Protein</B> sequence records, and 35 <B>PubChem</B> (small molecule) records, the "Max Frequency" column will display a value of 48 if your input file contained a list of GeneIDs, a value of 100 if your input file contained a list of protein sequence IDs, or a value of 35 if your input file contained a list of CIDs (PubChem Compound IDs). Those values represent the maximum number of genes, proteins, or small molecules from any input list that can have links to this biosystem.</P></LI>
|
|
</UL>
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputRankedListPercentCoverage"></A><P class="pad10"><B><span style="color:#d70000"><B>Percent (%) Coverage</B></span> column indicates the degree to which your input list covers the scope of each retrieved record<!-- indicates percent coverage of the destination database record by your input list --></B> -- This column is available for select destination databases such as BioSystems, and is calculated as:<BR>
|
|
<img SRC="../../IMG/spacer.gif" width="100" height="1" border="0">
|
|
<B>(Frequency ÷ MaxFrequency) × 100 = % Coverage <!-- P% --></B><BR>
|
|
Note that this column is displayed only if you select the <A HREF="#InputFunctionPercentCoverage">option to view the "percent coverage"</A> after you input your data file and select your "<A HREF="#InputFunctionLinkTo">LinkTo</A>" destination. It is used as an <B>alternative method for ranking output</B>.</P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">For example, if 12 GeneIDs from your input list are linked to a particular biosystem record, and if the biosystem record has links to a total of 48 GeneIDs in the Entrez <B>Gene</B> database, then the percent coverage of that biosystem record by your input list will be:<BR>
|
|
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0">
|
|
<B>(Frequency ÷ MaxFrequency) × 100 = % Coverage <!-- P% --></B><BR>
|
|
<img SRC="../../IMG/spacer.gif" width="60" height="1" border="0">
|
|
<B>(12 ÷ 48) × 100 = 25%</B><BR>
|
|
</P></LI>
|
|
<!-- LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI -->
|
|
</UL>
|
|
<BR>
|
|
|
|
<!-- LI><A NAME="_____"></A><P class="pad10"><B>______________________</B></P></LI>
|
|
<UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL>
|
|
<BR -->
|
|
|
|
</UL>
|
|
|
|
<span style="color:#d70000"><B>Illustrated examples</B></span> of pathways ranked by frequency vs. percent coverage are provided in the "How To" file on "<A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems.html">Start with a gene expression study and retrieve a ranked list of pathways (biosystems) in which the up- or down-regulated genes are involved</A>":
|
|
<UL>
|
|
<LI><P class="pad10"><A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems2.html#FlinkOutputIllustration">pathways ranked by <span style="color:#d70000">frequency</span></A></P></LI>
|
|
<LI><P class="pad10"><A HREF="flink_how_to_geoprofiles_to_genes_to_biosystems.html#FlinkOutputIllustration">pathways ranked by <span style="color:#d70000">percent coverage</span></A></P></LI>
|
|
</UL>
|
|
<BR>
|
|
|
|
<!-- I>Note:</I> Although multiple folder tabs can be opened on the <A HREF="#InputSummary">input summary display</A> (one for each <A HREF="#InputUIDListChooseDatabase">start database</A>), FLink currently displays only one folder tab on the output display. You can save the output display's URL, which includes a <A HREF="#FLinkJobID">Job ID</A>, to view it again anytime over the next 24 hours. If you would like to retrieve records from a different destination database than the one currently being displayed, use the browser's back button to return to your <A HREF="#InputSummary">input summary display</A>, where you can use the LinkTo function to select a new destination database/data type. A new Job ID will be assigned to each LinkTo operation you do. The URLs for those output displays can also be saved and used over the next 24 hours. -->
|
|
|
|
</BLOCKQUOTE>
|
|
<BR>
|
|
|
|
<!-- ================= LEVEL_1_FOLDER_TAB_FUNCTIONS ==================== -->
|
|
|
|
<A NAME="OutputFunctions"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Folder tab functions</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
<!-- Text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text.<BR><BR>
|
|
|
|
Text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text text. -->
|
|
|
|
<UL>
|
|
|
|
<LI><A NAME="OutputFunctionClearSelections"></A><P class="pad10"><IMG SRC="../icons/page_white.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Clear Selections function, which clears all selections on all pages within the folder tab."> <B>Clear Selections</B> -- Clear of the all checkboxes that have been selected on all pages within the folder tab. (<I>Note: It is possible to select items on multiple pages (1 of 10, 1 of 10, 9 of 10, etc.) within a folder tab, and the "clear selections" function will clear the checkboxes on all the pages.</I>)</P></LI>
|
|
<!-- UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL -->
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputFunctionShow"></A><P class="pad10"><IMG SRC="../icons/page_white_stack.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Show function, which displays all (default) or selected records in the Entrez database."> <B>Show</B> records in source database -- Retrieve all (default) or selected items from the corresponding Entrez database. This function will temporarily take you out of FLink and into that Entrez database, but you can use the browser's back button to return to the FLink display.</P></LI>
|
|
<!-- UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL -->
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputFunctionDownloadCSV"></A><P class="pad10"><IMG SRC="../icons/page_excel.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="icon for the Download CSV function, which saves all items in the current folder tab, whether or not they have been selected with checkboxes."> <B>Download CSV</B> -- Download the data displayed in the folder tab as a comma separated value (CSV) file. This function acts upon all the records in the display, whether or not their checkboxes are activated. This function is also available from the <A HREF="#OutputJobSummary">job summary panel</A>.</P></LI>
|
|
|
|
<UL>
|
|
<LI><P class="pad10"><B>Tip:</B> The CSV file is in <B>Unicode (UTF-8) format</B>. If you plan to import the file into a <B>spreadsheet program</B>, you might need to specify the Unicode (UTF-8) format during the import process.</P></LI>
|
|
<LI><P class="pad10">For <B>example</B>, if you plan to import the file into <B>Excel</B>, follow the instructions at <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help (https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/)</A>, starting with step 4, in order to import Unicode properly.<!-- For convenience, those steps are also included here: --></P></LI>
|
|
<!-- UL>
|
|
<LI><P class="pad10">Start Microsoft <B>Excel</B></P></LI>
|
|
<LI><P class="pad10">In Excel, click the <B>Data</B> tab, and in the <B>Get External Data</B> ribbon/panel, click <B>From Text</B> (as shown in the screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">In the <B>Import Text File</B> dialog box, in the lower-right corner (to the right of the File name box), select <B>Text Files (*.prn;*.txt;*.csv)</B> as the file type, <B>browse</B> to the location where you exported/downloaded the <B>CSV file</B>, and then click <B>Open</B> (or <B>Import</B>) (as shown in the following screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">In the <B>Text Import Wizard - Step 1 of 3</B> dialog box, select <B>Delimited</B>, and from the <B>File</B> origin drop-down list, select <B>65001: Unicode (UTF-8)</B> (or the appropriate language character identifier for your particular environment). In the <B>Preview</B> box below, make sure that your unicode text displays properly, and then click Next (as shown in the screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">In the <B>Text Import Wizard - Step 2 of 3</B> dialog box, in the <B>Delimiters</B> section, make sure that only <B>Comma</B> is checked, and then click <B>Finish</B> (as shown in the screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">In the <B>Import Data</B> dialog box, select <B>New worksheet</B> (or Existing worksheet if you have one), and then click <B>OK</B> (as shown in the screenshot on the <A HREF="https://help.tune.com/marketing-console/how-to-import-a-unicode-csv-to-excel/">Tune Help</A> page).</P></LI>
|
|
<LI><P class="pad10">You now have a <B>properly formatted (and unicode-friendly)</B> Excel worksheet</P></LI>
|
|
</UL -->
|
|
<LI><P class="pad10"><B>Note:</B> If the <B>Unicode (UTF-8) format</B> is not specified during the process of importing the CSV file into the spreadsheet program, certain <B>ASCII characters</B> such as the <B>umlaut</B> (<B>ö</B>), <B>e-acute</B> (<B>é</B>), etc. might not appear correctly.</P></LI>
|
|
</UL>
|
|
<BR>
|
|
|
|
<LI><A NAME="OutputFunctionSummary"></A><P class="pad10"><IMG SRC="../icons/page_white_database.png" WIDTH="16" HEIGHT="16" BORDER="0" ALT="Icon for the Summary function, which displays additional descriptive information for all records, as available, whether or not their checkboxes are activated."> <B>Summary</B> -- Display additional descriptive information for all records, as available, whether or not their checkboxes are activated.</P></LI>
|
|
<!-- UL>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
<LI><P class="pad10">_______________________</P></LI>
|
|
</UL -->
|
|
<BR>
|
|
|
|
</UL>
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<!-- ================= LEVEL_1_MAXIMUM_OUTPUT ==================== -->
|
|
|
|
<A NAME="OutputMaximum"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Maximum output</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
<A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A> can display up to 100,000 associated UIDs from the destination database on the <A HREF="#Output">output</A> page (and can accept up to 100,000 UIDs as <A HREF="#Input">input</A>).
|
|
</BLOCKQUOTE>
|
|
|
|
<BR>
|
|
|
|
|
|
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_4_CONTENTS ====== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_4_CONTENTS ############ -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ########### BLUE_HEADER_SECTION_5_SUPPORTED_DATABASES ############# -->
|
|
|
|
<A NAME="SupportedDatabases"></A>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">Supported Databases</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############## END_BLUE_HEADER_SECTION_5_XXXXXX ############ -->
|
|
|
|
|
|
<!-- ########## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_5_CONTENTS ########### -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ============== LEVEL_1_SUPPORTED_DATABASES_SUBSET_OF_ENTREZ =============== -->
|
|
|
|
<A NAME="SupportedDatabasesSubsetOfEntrez"></A>
|
|
|
|
<BR>
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>A subset of <A HREF="/gquery/">Entrez</A> databases is supported in FLink</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" border="0">
|
|
|
|
<TR>
|
|
<TD ALIGN="left" VALIGN="top">
|
|
|
|
<A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A> can be used to find associations among data in the following subset of <A HREF="/gquery/">Entrez</A> databases:
|
|
|
|
<BLOCKQUOTE>
|
|
|
|
<A HREF="/biosystems"><IMG SRC="../icons/biosystems.gif" WIDTH="17" HEIGHT="17" BORDER="0" ALT="BioSystems database icon"> BioSystems</A><BR>
|
|
|
|
<A HREF="/cdd"><IMG SRC="../icons/CDD.gif" WIDTH="16" HEIGHT="17" BORDER="0" ALT="Conserved Domain Database (CDD) icon"> Conserved Domain Database (CDD)</A><BR>
|
|
|
|
<A HREF="/gene"><IMG SRC="../icons/Gene.gif" WIDTH="17" HEIGHT="17" BORDER="0" ALT="Gene database icon"> Gene</A><BR>
|
|
|
|
<A HREF="/protein"><IMG SRC="../icons/Protein.gif" WIDTH="17" HEIGHT="17" BORDER="0" ALT="Protein database icon"> Protein</A><BR>
|
|
|
|
<A HREF="/pcassay"><IMG SRC="../icons/pcbioassay.gif" WIDTH="17" HEIGHT="17" BORDER="0" ALT="PubChem BioAssay database icon"> PubChem BioAssay</A><BR>
|
|
|
|
<A HREF="/pccompound"><IMG SRC="../icons/pccompound.gif" WIDTH="17" HEIGHT="17" BORDER="0" ALT="PubChem Compound database icon"> PubChem Compound</A><BR>
|
|
|
|
<A HREF="/pcsubstance"><IMG SRC="../icons/pcsubstance.gif" WIDTH="17" HEIGHT="17" BORDER="0" ALT="PubChem Substance database icon"> PubChem Substance</A><BR>
|
|
|
|
<A HREF="/pubmed"><IMG SRC="../icons/PubMed.gif" WIDTH="17" HEIGHT="17" BORDER="0" ALT="PubMed database icon"> PubMed</A><BR>
|
|
|
|
<A HREF="/structure"><IMG SRC="../icons/Structure.gif" WIDTH="17" HEIGHT="16" BORDER="0" ALT="Structure (Molecular Modeling Database, MMDB) icon"> Structure (Molecular Modeling Database, MMDB)</A><BR>
|
|
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
Any one of them can be used as a <A HREF="#OutputJobSummarySourceDatabase">source database</A> or <A HREF="#OutputJobSummaryDestinationDatabase">destination database</A> if you start on the <A HREF="../flink.cgi"><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink</A> home page and <A HREF="#InputUIDListDirectly">input a UID list directly</A> into the tool.
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<!-- ============== END_SUPPORTED_DATABASES_SUBSET_OF_ENTREZ =============== -->
|
|
|
|
<!-- ============== LEVEL_1_SUPPORTED_DATABASES_LINK_NAMES =============== -->
|
|
|
|
<A NAME="SupportedDatabasesLinkNames"></A>
|
|
<A NAME="LinkNames"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Link Names represent the available data types</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
|
<TR>
|
|
|
|
<TD ALIGN="left" VALIGN="top">
|
|
|
|
The types of data you can retrieve (as frequency-weighted lists) via FLink depend on which <A HREF="#InputUIDListChooseDatabase">database you started in</A>. The options available for any given database are listed in the "<A HREF="#InputFunctionLinkTo"><B>LinkTo</B></A>" dialog box on FLink's <A HREF="#InputSummary">input summary display (<span style="color:#d70000">illustrated example</span>)</A>, which appears after you <A HREF="#InputUIDListDirectly">input a UID list directly</A> into FLink. The data types are represented as
|
|
|
|
<BLOCKQUOTE>
|
|
|
|
"<B>Link Names</B>" in the format:<BR><BR>
|
|
|
|
<B>sourcedatabase_destinationdatabase</B> (e.g., "protein_biosystems," "protein_cdd," "protein_gene," "protein_structure")<BR><BR>
|
|
|
|
or<BR><BR>
|
|
|
|
<B>sourcedatabase_destinationdatabase_linkmethod</B> (e.g., "biosystems_pcassay_active," "biosystems_pcassay_target"), if multiple link types are available in a given destination database.
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
You can select a link name from the menu to read its description in the "LinkTo Options" dialog box and continue browsing the various link names in that way. Once you've found a link of interest, press the "Submit" button to retrieve that data type.<BR><BR>
|
|
|
|
</TD>
|
|
|
|
<!-- TD width="10" ALIGN="right" VALIGN="top"> </TD>
|
|
|
|
<TD width="450" class="WhiteCellBlueEdgeAll" ALIGN="right" VALIGN="center">
|
|
<IMG src="images/____________" height="90" width="430" border="0" align="left" alt="Image of concept being discussed.">
|
|
</TD -->
|
|
|
|
</TR>
|
|
</TABLE>
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<!-- ============== END_SUPPORTED_DATABASES_LINK_NAMES =============== -->
|
|
|
|
<!-- ============== LEVEL_1_SUPPORTED_DATABASES_FLink_ICON =============== -->
|
|
|
|
<A NAME="SupportedDatabasesFlinkIcon"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B><IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icon on Entrez search results pages</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<BLOCKQUOTE>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText">
|
|
<TR>
|
|
|
|
<TD ALIGN="left" VALIGN="top">
|
|
|
|
If you prefer to <A HREF="#InputEntrezSearch">start with an Entrez search</A> rather than upload a UID list directly into FLink, you can click on <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icons, when present, on the Entrez search results page to access the tool. Please note that only a subset of supported databases currently contain <IMG SRC="images/flinkicon.png" WIDTH="10" HEIGHT="11" BORDER="0" ALT="FLink icon"> FLink icons/links on their search results page at the time of FLink's initial release. If you do an Entrez search in a supported database and the search results page does not display any FLink icons, you can still access frequency-weighted lists of related data for your search results. To do that, just open the <A HREF="../flink.cgi">FLink</A> home page, select the database you searched from the "choose database to start" menu, and select "<A HREF="#InputFromEntrezHistory">Input from Entrez History</A>" as the <A HREF="#InputUIDListMethods">input method</A>. Your search results will be imported into FLink and you can then use the "<A HREF="#InputFunctionLinkTo">LinkTo</A>" menu to select the desired destination database and data type, as described above.<BR><BR>
|
|
|
|
</TD>
|
|
|
|
<!-- TD width="10" ALIGN="right" VALIGN="top"> </TD>
|
|
|
|
<TD width="450" class="WhiteCellBlueEdgeAll" ALIGN="right" VALIGN="center">
|
|
<IMG src="images/____________" height="90" width="430" border="0" align="left" alt="Image of concept being discussed.">
|
|
</TD -->
|
|
|
|
</TR>
|
|
</TABLE>
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<!-- ============== END_SUPPORTED_DATABASES_FLink_ICON =============== -->
|
|
|
|
|
|
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_5_CONTENTS ====== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############# END_BLUE_EDGE_BOX_WITH_SECTION_5_CONTENTS ############ -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ==================== VERTICAL SPACER ======================= -->
|
|
|
|
<TABLE width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD class="WhiteCell NormalText"> </TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ================== END_VERTICAL SPACER ===================== -->
|
|
|
|
<!-- ################## BLUE_HEADER_SECTION_7 ######################## -->
|
|
|
|
<A NAME="References"></A>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#F0F8FF">
|
|
<TR>
|
|
<TD class="SteelBlueCell"><SPAN class="HeaderText1">References</SPAN></TD>
|
|
<TD class="SteelBlueCell" WIDTH="15" ALIGN="left" VALIGN="center"><A HREF="#Top"><img SRC="/Structure/IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ################## END_BLUE_HEADER_SECTION_7 ######################## -->
|
|
|
|
|
|
<!-- ############## BEGIN_BLUE_EDGE_BOX_WITH_SECTION_7_CONTENTS ########### -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" class="NormalText" width="100%" border="0" cellspacing="0" cellpadding="0" bgcolor="#FFFFFF">
|
|
<TR>
|
|
<TD class="WhiteCellBlueEdgeAll">
|
|
|
|
<!-- ============ MINI_TOC_FOR_THIS_SECTION ============== -->
|
|
<!-- BR>
|
|
<BLOCKQUOTE><BLOCKQUOTE>
|
|
|
|
| <A HREF="#_____">_________</A> | <A HREF="#_____">_________</A> | <A HREF="#_____">_________</A> | <A HREF="#_____">_________</A> |
|
|
|
|
</BLOCKQUOTE></BLOCKQUOTE -->
|
|
|
|
<!-- ========== END_MINI_TOC_FOR_THIS_SECTION ============ -->
|
|
|
|
<!-- ================= LEVEL_1_REFERENCES_CITING ==================== -->
|
|
|
|
<A NAME="Citing"></A>
|
|
<BR><BR>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Citing FLink:</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P>
|
|
|
|
<!-- =========== LEVEL_2_TABLE_CITING_ONLY_FLink ============== -->
|
|
|
|
<A NAME="CitingFLink"></A>
|
|
|
|
|
|
<!-- BLOCKQUOTE>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="4" class="ReferenceText">
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="BioSystems_201001_NAR"></A><A HREF="/pubmed/19854944?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/19854944?dopt=AbstractPlus">Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH. The NCBI BioSystems database. <B><I>Nucleic Acids Res.</I> 2010</B> Jan; 38(Database issue):D492-6.</A> <I>(Epub 2009 Oct 23)</I> [<A HREF="/pubmed/19854944?dopt=AbstractPlus">PubMed</A>] [<A HREF="http://nar.oxfordjournals.org/cgi/content/full/38/suppl_1/D492">Full Text</A>] [<A HREF="http://nar.oxfordjournals.org/cgi/reprint/38/suppl_1/D492?ijkey=fviGQqrfUu5Nvhs&keytype=ref">PDF</A>]</TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
<BR -->
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<BLOCKQUOTE>
|
|
To cite FLink, please use the following format, based on <I><A HREF="/books/NBK7256/">Citing Medicine</A>: The NLM Style Guide for Authors, Editors, and Publishers</I> (2nd ed., 2007), <A HREF="/books/NBK7273/">Chapter 24</A>: Databases/Retrieval Systems on the Internet.<BR><BR>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="4" class="ReferenceText">
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="CitingFLinkWebSite"></A><A HREF="../flink.cgi"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="../flink.cgi">FLink: Frequency weighted links [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information. 2010 - [cited YYYY MMM DD]. Available from: /Structure/flink/flink.cgi</A></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
<BR>
|
|
|
|
</BLOCKQUOTE>
|
|
|
|
<!-- ======== LEVEL_1_REFERENCES_CITING_SPECIFIC_BIOSYSTEMS_RECORD ========= -->
|
|
|
|
<!-- A NAME="CitingBiosystemsRecord"></A>
|
|
|
|
<P class="indent20">
|
|
<SPAN class="HeaderText3"><B>Citing an individual BioSystems Database record:</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P -->
|
|
|
|
<!-- ======= LEVEL_2_TABLE_CITING_SPECIFIC_BIOSYSTEMS_RECORD_EXAMPLE ========= -->
|
|
|
|
<!-- A NAME="CitingBiosystemsRecordExample"></A>
|
|
|
|
<BLOCKQUOTE>
|
|
If you are citing a particular record from the BioSystems database, it is appropriate to cite both that database and the source database (using the citation suggested on the web site of the source database). For example, the BioSystems record for human arachidonic acid metabolism (<A HREF="/biosystems/82991">bsid82991</A>) could be cited in the following way:<BR><BR>
|
|
|
|
...The list of human genes involved in arachidonic acid metabolism was obtained from the NCBI BioSystems Database record BSID82991 (1), based on the KEGG record hsa00590 (2)...
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="4" class="ReferenceText">
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="CitingBSID82991">(1)</TD>
|
|
<TD valign="top" align="left"><A HREF="/biosystems/82991">NCBI BioSystems Database [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information. 2009 - Record No. 82991, Arachidonic acid metabolism; [cited 2009 Mar 11]; [about 1 screen]. Available from: /biosystems/82991</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="CitingKEGGhsa00590">(2)</TD>
|
|
<TD valign="top" align="left"><A HREF="http://www.genome.jp/dbget-bin/show_pathway?hsa00590">KEGG: Kyoto Encyclopedia of Genes and Genomes. Kyoto, Japan: Kyoto University, Institute for Chemical Research, Bioinformatics Center, Kanehisa Laboratory. 1995 - Record No. hsa00590, Arachidonic acid metabolism; [cited 2009 Mar 11]; [about 1 screen]. Available from: http://www.genome.jp/dbget-bin/show_pathway?hsa00590</A></TD>
|
|
</TR>
|
|
|
|
</TABLE>
|
|
<BR>
|
|
|
|
</BLOCKQUOTE -->
|
|
|
|
<!-- =============== LEVEL_1_REFERENCES_SUPPORTED_DATABASES ================== -->
|
|
|
|
<A NAME="ReferencesSupportedDatabases"></A>
|
|
|
|
<!-- P class="indent20">
|
|
<SPAN class="HeaderText3"><B>References Describing the Supported Databases:</B></SPAN> <img SRC="../../IMG/spacer.gif" width="25" height="1" border="0"><A HREF="#Top"><img SRC="../../IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A>
|
|
</P -->
|
|
|
|
<!-- ============ LEVEL_2_TABLE_OF_REFERENCES_SUPPORTED_DATABASES ============= -->
|
|
|
|
<A NAME="____"></A>
|
|
|
|
<!-- BLOCKQUOTE>
|
|
|
|
The references below are provided for your convenience if you would like more information on any <A HREF="#SupportedDatabases">supported database</A>. <B>Please consult the web site of a source database for information on how to cite it</B> and for additional references, as available.<BR><BR>
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" border="0" cellpadding="4" class="ReferenceText">
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="PubMed_NCBIHandbook"></A><A HREF="/books/NBK______/"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/books/NBK______/">Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. Chapter N IN The <I><B>NCBI Handbook</B></I> [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, <B>YYYY</B> Mmm. DD [revised YYYY Mmm. DD]. [cited YYYY Mmm DD]. Available from /books/NBK______/ in Entrez Books (/books)</A>.</TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>PubMed --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>Conserved Domain Database (CDD) --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>BioSystems --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>PubChem Compound --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>PubChem Substance --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>PubChem BioAssay --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>Structure --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>Gene --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>Protein --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR -->
|
|
|
|
<!-- ============ TEMPLATE_FOR_JOURNAL_ARTICLE ================ -->
|
|
|
|
<!-- TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>___DATABASENAME___ --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR>
|
|
|
|
<TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NAR_YYYY"></A><A HREF="/pubmed/________?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/pubmed/________?dopt=AbstractPlus"><B>___DATABASENAME___ --</B> Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. <B><I>JournalName</I> YYYY</B> Mmm; Vol(Issue): PPP-PPP. [PubMed]</A> <A HREF="__________">[Full Text]</A> <A HREF="/pmc/articles/_______/">[Free Author Manuscript in PubMedCentral]</A></TD>
|
|
</TR -->
|
|
|
|
<!-- ============ TEMPLATE_FOR_NCBI_HANDBOOK_CHAPTER ================ -->
|
|
|
|
<!-- TR>
|
|
<TD width="18" valign="top" align="left"><A NAME="DBNAME_NCBIHandbook"></A><A HREF="/books/NBK______/"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="../../IMG/PubMed.gif"></A></TD>
|
|
<TD valign="top" align="left"><A HREF="/books/NBK______/">Author AB, Author AB, Author AB, Author AB, Author AB, Author AB. Title title title title title title. Chapter N IN The <I><B>NCBI Handbook</B></I> [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, <B>YYYY</B> Mmm. DD [revised YYYY Mmm. DD]. [cited YYYY Mmm DD]. Available from /books/NBK______/ in Entrez Books (/books)</A>.</TD>
|
|
</TR -->
|
|
|
|
<!-- /TABLE -->
|
|
<!-- BR -->
|
|
|
|
<!-- /BLOCKQUOTE -->
|
|
|
|
|
|
<!-- ====== PAGE_MARGIN_TO_RIGHT_OF_BLUE_EDGE_BOX_WITH_SECTION_CONTENTS ====== -->
|
|
|
|
</TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- ############### END_BLUE_EDGE_BOX_WITH_SECTION_7_CONTENTS ############ -->
|
|
|
|
<!-- =================== PAGE_FOOTER_AND_DATE_REVISED ================== -->
|
|
|
|
<TABLE style="margin:0px 0px 0px 0px;" width="100%" border="0" cellspacing="0" cellpadding="0">
|
|
<TR>
|
|
<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 7 December 2021</SPAN></TD>
|
|
<TD width="25"><IMG SRC="/coreweb/template1/pix/pixel.gif" width="1" height="1" alt="" border=0></TD>
|
|
</TR>
|
|
</TABLE>
|
|
|
|
<!-- =================== END_PAGE_FOOTER_AND_DATE_REVISED ================== -->
|
|
|
|
|
|
<!-- ##################### END_EDITABLE_CONTENT ##################### -->
|
|
|
|
<script type="text/javascript">doc_tmp.getDocFtr('<A HREF="/research/">Computational Biology Branch</A> > <A HREF="/Structure/index.shtml">Structure Group</A> > <A HREF="/biosystems">Biosystems</A> > <A HREF="../flink.cgi">FLink</A> > Help','other');</script>
|
|
|
|
<!-- script type="text/javascript">doc_tmp.getDocFtr(' > <A HREF="______">__________</A> > <A HREF="______">__________</A> > <A HREF="______">__________</A> > ___currentpage_____', 'other');</script -->
|
|
|
|
</body>
|
|
</html> |