176 lines
8.4 KiB
HTML
176 lines
8.4 KiB
HTML
<html>
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<head>
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<title>XML at NCBI</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
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<META NAME="keywords" CONTENT="NCBI, GenBank, BLAST, PubMed, MEDLINE, Bioinformatics, toolkit, software">
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<META NAME="description" CONTENT="The National Center for Biotechnology Information (NCBI) provides an integrated approach to the use of gene and protein sequence information, the scientific literature (MEDLINE), molecular structures, and related resources, in biomedicine.">
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<link rel="stylesheet" href="http://www.ncbi.nlm.nih.gov/corehtml/ncbi.css">
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</head>
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<body bgcolor="#FFFFFF" background="http://www.ncbi.nlm.nih.gov/corehtml/bkgd.gif" text="#000000" link="#000099" vlink="#6666CC">
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<!-- the header -->
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<table border="0" width="600" cellspacing="0" cellpadding="0">
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<tr>
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<td width="140"><a href="http://www.ncbi.nlm.nih.gov">
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<img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0" ALT="NCBI logo"></a></td>
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<td width="460" valign="TOP">
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<img src="/IEB/GreenIEB.gif" ALIGN=BOTTOM width="456" height="60" ALT="IEB banner">
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</td>
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</tr>
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</table>
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<H1 ALIGN="center">XML at NCBI</H1>
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<table border="0" width="600" cellspacing="0" cellpadding="0">
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<tr valign="TOP">
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<td width="125">
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<!-----edit this.....left column----->
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<table border="0" width="125" cellspacing="0" cellpadding="0">
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<tr valign="bottom">
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<td width="120"> <A
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href="/IEB/ToolBox/"
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class="GUTTER3"><FONT COLOR="#FFFFFF">IEB ToolBox Page</FONT></a><br>
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<img src="http://www.ncbi.nlm.nih.gov/PMGifs/query/corehtml/transparent.gif" width="1" height="4"></td>
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<td width="8" align="right">
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<img src="http://www.ncbi.nlm.nih.gov/PMGifs/query/corehtml/GoUp1.gif" width="8" height="19"></td>
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</tr>
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<tr align="right">
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<td colspan="2">
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<img src="http://www.ncbi.nlm.nih.gov/PMGifs/query/corehtml/GoUp2.gif" width="125" height="12"></td>
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</tr>
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</table>
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<BR>
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<SPAN class="GUTTER1"><a href="/IEB/MainPage/AboutIEB.html" class="GUTTER1"><FONT COLOR="#ffcc66">About IEB</FONT><BR></SPAN>
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<SPAN class="GUTTER2"><FONT COLOR="#FFFFFF" SIZE="-1">general and contact information</FONT></a><BR><BR></SPAN>
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<SPAN class="GUTTER1"><a href="/IEB/ToolBox/index.cgi" class="GUTTER1"><FONT COLOR="#ffcc66">NCBI ToolBox</FONT><BR></SPAN>
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<SPAN class="GUTTER2"><FONT COLOR="#FFFFFF" SIZE="-1">Supported software tools from IEB</FONT></a><BR><BR></SPAN>
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<SPAN class="GUTTER1"><a href="/IEB/Research/index.cgi" class="GUTTER1"><FONT COLOR="#ffcc66">Research within IEB</FONT><BR></SPAN>
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<SPAN class="GUTTER2"><FONT COLOR="#FFFFFF" SIZE="-1">Research and Development Projects</FONT></a><BR><BR></SPAN>
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<SPAN class="GUTTER1"><a href="ftp://ftp.ncbi.nih.gov/toolbox" class="GUTTER1"><FONT COLOR="#ffcc66">ToolBox FTP site</FONT><BR></SPAN>
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<SPAN class="GUTTER2"><FONT COLOR="#FFFFFF" SIZE="-1">download data and software</FONT></a><BR><BR></SPAN>
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</td>
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<td width="15"> </td>
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<td width="320" CLASS="TEXT">
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<BR>
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<table border="0" width="320" cellspacing="0" cellpadding="0">
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<tr>
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<td width="320" bgcolor="#CCCCFF" class="H4"><img src="http://www.ncbi.nlm.nih.gov/corehtml/bluebullet.gif" width="16" height="14" border="0" ALT="blue bullet">What is the NCBI ToolBox?</td>
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</tr>
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</table>
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<!-----XML Intro---->
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<P>Internally NCBI stores data in a variety of ways most appropriate to the flow of the data
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and its semantics. These may include normalized relational databases (eg. for ESTs), ASN.1
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(eg. for other types of sequences), or XML (eg. for journal articles). NCBI also distributes
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the same data in a number of formats such as GenBank, FASTA, ASN.1, and XML, no matter how
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they are natively stored.
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For a particular nucleotide sequence of the human beta globin locus, options are:
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<UL>
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<LI>
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<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=455025&dopt=GenBank">GenBank format</a></LI>
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<LI>
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<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=455025&dopt=Fasta">FASTA format</a></LI>
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<LI><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=455025&dopt=asn1">ASN.1 format</a></LI>
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<LI>Data Encoding - A formal specification and encoding rules. The
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telecommunications standard, ASN.1, has been used for this.
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This has also been mapped to XML.</LI>
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<LI>Programming Libraries - Originally written in a portable dialect of
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C. This has also been written in C++.</LI>
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</UL>
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The ToolBox model and code is used extensively within NCBI for the internal pipelines
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and tools such as GenBank, Entrez, BLAST, Sequin, OMIM, RefSeq, and others. We make
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the same tools available to the public domain for whatever purposes the community
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may desire. These tools are supported in the sense that they are designed to work in
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many environments outside NCBI, and as such we feel we can fix any bugs or answer
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questions about using them. Unfortunately they are not supported in the sense of
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a turnkey system with extensive documentation. However, there are applications set up
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in the distribution with standard makefiles, such as Sequin, BLAST, a program to convert
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ASN.1 data to XML, and others. But this distribution is primarily for serious
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programmers.
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</P>
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<!-----Highlights ----->
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<table border="0" width="300" bgcolor="#ffffcc" cellspacing="0" cellpadding="5">
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<tr>
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<td valign="top" align="center" CLASS="TEXT"><B>NCBI Data in XML</B></td></tr>
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<tr><td valign="TOP">NCBI software tools can now automatically produce data as either ASN.1, as before,
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or as XML. This provides developers access to the full internal NCBI data set
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using a variety of open source tools. In addition, a number of specifications
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have been developed to present simpler views of the data in XML, specifically
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for use by applications developers outside NCBI. Entrez can display and download
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data in XML, and a standalone tool, asn2xml, can convert ASN.1 daily update files
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into XML on your site. <A HREF="ncbixml.txt" >More..</A></td></tr>
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</table>
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<BR>
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<TABLE border="0" width="320" cellspacing="0" cellpadding="0">
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<TR>
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<TD width="320" bgcolor="#CCCCFF" class="H4"><IMG src="http://www.ncbi.nlm.nih.gov/corehtml/bluebullet.gif" width="16" height="14" border="0" ALT="blue bullet">Contacting Us</TD>
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</TR>
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</TABLE>
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<P>Information is made available on this page to ToolBox programmers. In addition, you
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may ask questions by email to <A HREF="mailto:toolbox@ncbi.nlm.nih.gov">toolbox@ncbi.nlm.nih.gov
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</A>.
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<P><A HREF="/About/disclaimer.html" class="SMALL1">Disclaimer</A>
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<A HREF="/About/privacy.html" class="SMALL1">Privacy statement</A></P>
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<P class="SMALL1">Revised May 8, 2003</P>
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<!-- extra column to force things over the gif border -->
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<td width="15"> </td>
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<TD class="TEXT" width="125">
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<BR>
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<TABLE WIDTH="125" BORDER="0" CELLSPACING="0" CELLPADDING="0">
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<TR><TD ALIGN="CENTER" BGCOLOR="#003366" CLASS="TEXT" height="17.8"><FONT COLOR="#FFFFFF">Hot Spots</FONT></TD></TR>
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<TR><TD><BR><A HREF="/IEB/ToolBox/SDKDOCS/INDEX.HTML" class="HELPBAR"><IMG SRC="http://www.ncbi.nlm.nih.gov/Gifs/head.gif" WIDTH="8" HEIGHT="13" BORDER="0" ALIGN="TOP" ALT="arrowhead"> DataModel and C Toolkit Docs</A></span></TD>
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</TR>
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<TR><TD><BR><A HREF="/dtd/" class="HELPBAR"><IMG SRC="http://www.ncbi.nlm.nih.gov/Gifs/head.gif" WIDTH="8" HEIGHT="13" BORDER="0" ALIGN="TOP" ALT="arrowhead"> XML DTDs</A></span></TD>
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</TR>
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<TR><TD><BR><A HREF="http://www.ncbi.nlm.nih.gov/books/NBK7160/" class="HELPBAR"><IMG SRC="http://www.ncbi.nlm.nih.gov/Gifs/head.gif" WIDTH="8" HEIGHT="13" BORDER="0" ALIGN="TOP" ALT="arrowhead"> NCBI C++ Toolkit Docs</A></span></TD>
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</TR>
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<TR><TD><BR><A HREF="/IEB/ToolBox/SB/hbr.html" class="HELPBAR"><IMG SRC="http://www.ncbi.nlm.nih.gov/Gifs/head.gif" WIDTH="8" HEIGHT="13" BORDER="0" ALIGN="TOP" ALT="arrowhead"> NCBI Toolkit Source Browser</A></span></TD>
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</TR>
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</TABLE>
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</TD>
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</TR>
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</TABLE>
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</TD>
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</TR>
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</TABLE>
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<map name="NCBIbanner.gif">
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<area shape="rect" coords="56,33,204,48" href="http://www.nlm.nih.gov">
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<area shape="rect" coords="257,32,405,48" href="http://www.nih.gov">
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</map>
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</BODY>
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</HTML>
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