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<TD class="DocTitleText" align="left"> Protein Domains and Macromolecular Structures:<BR>
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<SPAN class="TOCText2">  Tools for discovery of sequence/function/structure associations</SPAN></TD>
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<!-- TR>
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">Tools for Discovery: traverse from literature to gene and protein sequence, function, 3D structures, and more...</TD>
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<FONT class="MiniText"> <BR></FONT>
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<B>Tools for Discovery</B>:</TD>
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Various data types, such as literature, nucleotide and protein sequences, and three-dimensional structures, are often submitted to public databases independently of each other by different research groups. Yet these data are related through their coverage of the same topic via different research methods, and the sum of the information they contain is greater than any one part.<BR><BR>
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To address this, the NCBI Protein Classification and Structure Group contributes to the broader NCBI effort to provide <A HREF="#DataIntegration"><B>integrated access to previously disparate data</B></A> through the <A HREF="/gquery/"><B>Entrez</B></A> retrieval system, which uses computational methods to identify related data and makes it possible to traverse from <B>literature</B> about diseases → <B>gene</B> locations and sequences → <B>protein</B> sequences → <B>conserved domains</B> & protein functions, <B>3D structures</B>, <B>small molecules</B> & their biological activities → and more.<BR><BR>
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The illustration below provides an <B>example</B>, starting with a <B>PubMed</B> article about the human <B>CLCN1 gene</B> and Becker-type myotonia, then linking to the <B>protein</B> sequence, its <B>conserved domains</B>, and a <B>related 3D structure</B>. <!-- Open the live PubMed record (<A HREF="/pubmed/7951242?dopt=AbstractPlus"><B>PMID 7951242</B></A>) to try the links! -->
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If you would like to explore these paths interactively, open the PubMed record for <A HREF="/pubmed/7951242?dopt=AbstractPlus"><B>PMID 7951242</B></A> shown below (or any other record of interest in <A HREF="/pubmed/"><B>PubMed</B></A> or other <A HREF="/gquery/"><B>Entrez</B></A> databases), then use the "<B>Related information</B>" menu in the right margin of the display to select related data of interest and begin traversing through the Entrez system. <!-- Note that <B>PubMed</B> records associated with <B>protein</B> sequences ultimately link to <B>conserved domains</B>, <B>biosystems</B>, and <B>related structures</B>, shedding light on the possible function and 3D shape of the proteins. --><BR><BR>
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The exact appearance and position of links to related data in the live Entrez system may vary from the image below due to ongoing enhancements in the Entrez user interface. They can appear as "<B>Links</B>" pull down menus near the top of a display or as <B>ads</B> in the right margin of displays (for example, the "<B>Find Related Data</B>" pull down menu in the right margin of search results pages, or the "<B>Related information</B>" ad in the right margin of database record displays).
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<IMG src="IMG/discovery_path_clcn1_cd03683.png" width="800" height="1085" border=0 align="center" alt="Example of data integration in Entrez through its Links feature. Starting with a single record in any Entrez database, you can use the Links menu to traverse to related data in other Entrez databases. This can facilitate biological discovery through identifying associations among previously disparate data.">
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<!-- ===================== BOX2_RESEARCH ======================== -->
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<A NAME="DataIntegration"></A>
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">Integrated access to previously disparate data</TD>
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<TD class="SteelBlueCell" WIDTH="20" ALIGN="LEFT" VALIGN="center"><A HREF="#Top"><img SRC="IMG/arrowup_blue.gif" width="12" height="12" border="0" alt="back to top"></A></TD>
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<P class="indent10 NormalText">The NCBI Protein Classification and Structure Group contributes to the broader NCBI effort to provide integrated access to previously disparate data through the <A HREF="/gquery/"><B>Entrez</B></A> retrieval system. Identification of relationships among those data in turn can lead to new discoveries.<BR><BR>
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This system was developed because the study of a biological question, such as the molecular mechanism underlying a human disease, is often approached from many angles by many different laboratories -- some might focus on gene identification and sequencing, while others might focus on analyzing protein function and three-dimensional structure, and yet others might study associated genetic variations, gene expression profiles, or phenotypes. Because each group submits its data independently of the others to a public database, the resultant distinct but related data sets may be scattered across a variety of databases.<BR><BR>
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Recognizing that the sum of the total knowledge is greater than any one part, Entrez brings a wide range of data types from varying sources into a single search system and identifies relationships among records within an individual database and across databases. These associations are presented as <B>Links</B> in Entrez search results displays and in individual database records. Therefore, once you retrieve one data element in Entrez, such as a PubMed record for an article that reports the sequencing of a disease gene, the corresponding sequence data and much more are one click away, as shown in the illustration above.
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<P class="indent10 NormalText">Further reading:
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<!-- =========== REFERENCES ============= -->
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<TD width="10" align="center"><b> </b></TD>
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<TD width="18" align="center"><b>PubMed</b></TD>
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<TD align="center"><b>Table Header 2</b></TD>
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<TD width="10" align="center"><b> </b></TD>
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<TD width="18" valign="top" align="left"><A NAME="NCBIHandbookEntrezChapter"></A><A HREF="/books/NBK21081"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="IMG/PubMed.gif"></A></TD>
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<TD valign="top" align="left"><A HREF="/books/NBK21081">Ostell, J. The Entrez Search and Retrieval System. In <A HREF="/books/NBK21101">The NCBI Handbook</A> [Internet], National Library of Medicine (US), National Center for Biotechnology Information, Bethesda, MD, Chapter 15, 2002 Oct. 9 [revised 2003 Aug. 13]. [cited 2008 Oct 02]. Available from <A HREF="/books/NBK21081">/books/NBK21081</A> in the Entrez Bookshelf (<A HREF="/sites/entrez?db=books">/sites/entrez?db=books</A>)</TD>
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<TD width="10" align="center"><b> </b></TD>
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<TD width="18" valign="top" align="left"><A NAME="EntrezPower2003"></A><A HREF="/pubmed/12846398?dopt=AbstractPlus"><img border=0 align=left height=15 width=15 style="margin-right:0.2em" src="IMG/PubMed.gif"></A></TD>
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<TD valign="top" align="left"><A HREF="/pubmed/12846398?dopt=AbstractPlus">Geer RC, Sayers EW. Entrez: making use of its power. Brief Bioinform.:4(2):179-84, 2003 Jun.</A> <!-- (summary and full text also accessible from <A HREF="/Entrez/tutor.html">/Entrez/tutor.html</A>; also available at <A HREF="/entrez/query/static/help/entrez_tutorial_BIB.pdf">/entrez/query/static/help/entrez_tutorial_BIB.pdf</A>) --></TD>
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<TD class="SteelBlueCell HeaderText2B" ALIGN="LEFT" VALIGN="TOP">Tools for Discovery</TD>
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<A HREF="______"><B>Discover associations<BR>among previously disparate data</B></A></TD>
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<A HREF="______"><IMG src="IMG/discovery_path_thumbnail_v04o.png" width="190" height="480" 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>
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<P class="pad20">Legend briefly summarizing what is shown in graphic and containing a <A HREF="#______">link to full size graphic and detailed description</A> in help document.</P>
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<TD VALIGN="top" ALIGN="RIGHT"><SPAN CLASS="HELPBAR1" STYLE="color="#646464"">Revised 25 August 2021</SPAN></TD>
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