Annotation of biobar/www/customize.html, revision 1.1

1.1     ! jawahar     1: <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
        !             2: <html>
        !             3: <head>
        !             4:   <meta content="text/html; charset=ISO-8859-1"
        !             5:  http-equiv="content-type">
        !             6:   <title>Customizing biobar search menus</title>
        !             7: </head>
        !             8: <body>
        !             9: <div style="text-align: center;">
        !            10: <h2><span style="font-weight: bold;">Customize your search menu</span></h2>
        !            11: <div style="text-align: justify;"><span style="font-weight: bold;"><span
        !            12:  style="font-weight: bold;"></span></span>
        !            13: <p><span style="font-weight: bold;"><span style="font-weight: bold;"><span
        !            14:  style="font-weight: bold;"></span></span></span>With version 1.3 of
        !            15: biobar it is possible to customize the search menu of the toolbar. The
        !            16: procedure involves editing an XML file and saving the file in your
        !            17: profile directory.</p>
        !            18: <br>
        !            19: There are two files which can be edited to add additional search
        !            20: terms/menu's to your searches.<br>
        !            21: <br>
        !            22: <ol>
        !            23:   <li>BiobarSearch.xml - Provides the menu listing and URLs for
        !            24: producing the standard search menu (individual databases).</li>
        !            25:   <li>BiobarGroups.xml - Provides the URLs and menu for 'Searching by
        !            26: Groups'&nbsp; option, which can be chosen from options.</li>
        !            27: </ol>
        !            28: <p>Before customizing the search menu, please copy these files to from
        !            29: the following links to your profile directory. Following these links
        !            30: will open up the XML file on your browser, please choose File-&gt; Save
        !            31: Page As to save the files. <span style="font-style: italic;">Please do
        !            32: not rename these files !!</span></p>
        !            33: <ul>
        !            34:   <li><a href="http://biobar.mozdev.org/BiobarSearch.xml">BiobarSearch.xml</a></li>
        !            35:   <li><a href="http://biobar.mozdev.org/BiobarGroups.xml">BiobarGroups.xml</a></li>
        !            36: </ul>
        !            37: Copy these files over to your Profile Directory. <br>
        !            38: <br>
        !            39: <span style="font-weight: bold;">Locating your Profile Directory: </span>From
        !            40: the main browser toolbar, choose Tools -&gt; Biobar -&gt; My Profile
        !            41: Directory.<span style="font-weight: bold;"> </span>The information
        !            42: will be displayed to you in an alert box.<br>
        !            43: <br>
        !            44: <span style="font-weight: bold;">Editing BiobarSearch.xml: </span><br>
        !            45: <br>
        !            46: Go to your profile directory using the paths above. Open the xml file
        !            47: in yoru favorite editor. This file has the following syntax:<br>
        !            48: <br>
        !            49: <span style="font-weight: bold;"><span style="font-weight: bold;"><span
        !            50:  style="font-weight: bold;"></span></span></span>
        !            51: <pre>&lt;?xml version="1.0"?&gt;<br>&lt;biobar&gt;<br>       &lt;Databases&gt;<br>---<br>---<br>               &lt;Group type="Fungal"&gt;<br>                        &lt;Database type="SGD"&gt;<br>                                &lt;Menuitem name="QuickSearch" url="Some Search URL"/&gt;<br>                            &lt;Menuitem name-"...." url="....."/&gt;<br>                        &lt;/Database&gt;<br>                &lt;/Group&gt;<br>        &lt;/Databases&gt;<br>&lt;/biobar&gt;<br><br></pre>
        !            52: The Group definition indicates the main groups of search databases in
        !            53: the search menu. EBI, NCBI, Plant, Animal, Structure etc. Please add a
        !            54: group of your own and give it a unique name like &lt;Group type="my
        !            55: menu"&gt;. Inside each group are databases each having a name. For
        !            56: example, under structure, we have databases like MSD, RCSB etc. Add
        !            57: your database under your group like &lt;Database type="MyDatabase"&gt;.
        !            58: Under each Database are a set of searchterms you would like to search
        !            59: by followed by the URL leading upto the search.<br>
        !            60: <br>
        !            61: For example if you want to search by Group (My Menu) having a database
        !            62: (MyDatabase) which has a searchitem and url, you would edit the XML
        !            63: file and add at the following:<br>
        !            64: <br>
        !            65: <pre>&lt;Group type="My Menu"&gt;<br>&lt;Database type="MyDatabase"&gt;<span
        !            66:  style="font-family: monospace;"></span><br>&lt;Menuitem name="Keyword" url="http://mydatabase.org/something.cgi?something=something&amp;amp;keyword="/&gt;<br>&lt;/Database&gt;<br>&lt;/Group&gt;<br><br></pre>
        !            67: <p>Where the the url is everything but the text you will actually
        !            68: search. Please note that each menuitem is terminated with a /. Please
        !            69: also note the format for ampersand. The items you add should be nested
        !            70: within the overall XML tree. Ideally you would add a new &lt;Group&gt;
        !            71: below a &lt;/Group&gt;.<br>
        !            72: </p>
        !            73: <p>Please save the XML file in your profile directory. Check to see
        !            74: that the XML file is valid by opening this XML file in your browser. If
        !            75: it renders properly as a tree, then you have a valid XML. Else please
        !            76: correct the errors. </p>
        !            77: <p>Once you have saved the XML file, restart
        !            78: your browser, and
        !            79: the new search menu containing the search database you added will show
        !            80: up in the Search Window. You will also be able to choose the new
        !            81: database/s as a default from the options window.<br>
        !            82: </p>
        !            83: <p><span style="font-weight: bold;">Editing BiobarGroups.xml: </span><br>
        !            84: </p>
        !            85: <p>Save BiobarGroups.xml in your profile directory as described above.
        !            86: Open this file for editing your favorite browser. This file has a
        !            87: format similar to that showb below:<br>
        !            88: </p>
        !            89: <pre>&lt;?xml version="1.0"?&gt;<br>&lt;biobarGroups&gt;<br>        &lt;Group name="Structures"&gt;<br>                &lt;Menuitems&gt;<br>                        &lt;Menuitem SearchTerm="PDB ID"&gt;<br>                                &lt;url&gt;http://www.ebi.ac.uk/msd-srv/atlas?toolbar=biobar&amp;amp;id=&lt;/url&gt;<br>                                &lt;url&gt;http://oca.ebi.ac.uk/oca-bin/ocaids?toolbar=biobar&amp;amp;id=&lt;/url&gt;<br>                                &lt;url&gt;http://www.rcsb.org/pdb/cgi/explore.cgi?toolbar=biobar&amp;amp;pdbId=&lt;/url&gt;<br>                                &lt;url&gt;http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?toolbar=biobar&amp;amp;pdbcode=&lt;/url&gt;<br>                        &lt;/Menuitem&gt;<br>             &lt;/Menuitems&gt;<br>  &lt;/Group&gt;<br>&lt;/biobarGroups&gt;<br><br></pre>
        !            90: Each Group described a search Type (Structures, Function, Taxonomy
        !            91: etc). Each search Type has a set of searchTerms associated with the
        !            92: searchType. For example, one could search all structrual databases for
        !            93: PDB code, keyword, author etc. For each searchTerm, there are a set of
        !            94: URLs which describe the full command needed for searching.<br>
        !            95: <br>
        !            96: <p>If you wanted to add your own searchType (say Sequences) containing
        !            97: searchTerms Author, Keyword etc, you would have to add a new Group with
        !            98: a tree like:</p>
        !            99: <br>
        !           100: <br>
        !           101: <pre>&lt;Group name="Sequences"&gt;<br>        &lt;Menuitems&gt;<br>           &lt;Menuitem SearchTerm="Keyword"&gt;<br>                       &lt;url&gt;SomeURL containing the whole path&lt;/url&gt;<br>                    &lt;url&gt;&lt;/url&gt;<br>             &lt;/Menuitem&gt;<br>           &lt;Menuitem SearchTerm+"Author"&gt;<br>                        &lt;url&gt;&lt;/url&gt;<br>                     &lt;url&gt;&lt;/url&gt;<br>             &lt;/Menuitem&gt;<br>   &lt;/Menuitems&gt;<br>&lt;/Group&gt;<br><br></pre>
        !           102: <p>Once you have made the changes, save the file as BiobarGroups.xml in
        !           103: your profile area. Check that the XML file is valid by opening the file
        !           104: in your browser. Restart your browser. If you chose the 'Search Groups'
        !           105: in the biobar options window, then your database will show up.</p>
        !           106: <br>
        !           107: </div>
        !           108: </div>
        !           109: </body>
        !           110: </html>

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