Annotation of biobar/www/Databases.html, revision 1.14

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1.13      jawahar     8: <h3>Databases currently included in biobar</h3>
                      9: <p><a href="http://biobar.mozdev.org/installation.html">biobar
1.14    ! jawahar    10: 1.3</a> provides browsing and searching access to the following
1.11      jawahar    11: biological databases.<br>
1.4       jawahar    12: </p>
1.14    ! jawahar    13: <p>The latest inclusions ar<span style="text-decoration: underline;"><span
        !            14:  style="text-decoration: underline;">e</span></span> <a
        !            15:  href="http://www.arabidopsis.org/">araCyc</a> and <a
        !            16:  href="http://www.bmrb.wisc.edu/">BMRB</a>. In addition, BioCyc now has
        !            17: a dynamic update mechanism for updating species list. Many new
        !            18: functions are now part of biobar, including customization of search
        !            19: menus, adding fixed custom links on the main menu. In the 'Group' mode,
        !            20: multiple databases can be searched simultaneously for a search term
        !            21: with results opened in individual tabs. An options menu allows
        !            22: customization of
1.13      jawahar    23: the databases (setting up defaults, choosing which group/s of
1.14    ! jawahar    24: databases to see, adding NCBI Library LinkOuts etc, choosing to see
        !            25: searches in New Tabs, Same Tab etc etc).</p>
        !            26: <br>
        !            27: <table style="text-align: left; width: 988px; height: 312px;" border="3"
        !            28:  cellpadding="2" cellspacing="2">
        !            29:   <tbody>
        !            30:     <tr>
        !            31:       <td style="vertical-align: top;"><span style="font-weight: bold;">Data
        !            32: Collections</span><br>
        !            33:       </td>
        !            34:       <td
        !            35:  style="vertical-align: top; background-color: rgb(255, 204, 204);">1.
1.5       jawahar    36: EBI Databases with SRS<br>
1.4       jawahar    37: 2. NCBI Databases<br>
                     38: 3. DNA Database of Japan(DDBj)<br>
1.14    ! jawahar    39:       </td>
        !            40:       <td style="vertical-align: top;"><span style="font-weight: bold;">Functional
        !            41: Databases</span><br>
        !            42:       </td>
        !            43:       <td
        !            44:  style="vertical-align: top; background-color: rgb(255, 204, 204);">
        !            45:       <ol>
        !            46:         <li>aMAZE</li>
        !            47:         <li>araCyc<br>
        !            48:         </li>
        !            49:         <li>BioCyc</li>
        !            50:         <li>KEGG</li>
        !            51:         <li>Gene Ontology (GO)</li>
        !            52:         <li>IntAct</li>
        !            53:         <li>Reactome Database</li>
        !            54:       </ol>
        !            55:       </td>
        !            56:     </tr>
        !            57:     <tr>
        !            58:       <td style="vertical-align: top;"><span style="font-weight: bold;">Sequence
        !            59: Databases</span><br>
        !            60:       </td>
        !            61:       <td
        !            62:  style="vertical-align: top; background-color: rgb(255, 204, 204);">
        !            63:       <ol>
        !            64:         <li>EMBL Nucleotide Database</li>
        !            65:         <li>Ensembl Genome Browser</li>
        !            66:         <li>UniProt Sequence Database</li>
        !            67:         <li>InterPro</li>
        !            68:         <li>Integr8</li>
        !            69:         <li>Expert Protein Analysis System (ExPASy)</li>
        !            70:         <li>Pfam</li>
        !            71:         <li>Alternative Splicing Database (ASD)</li>
        !            72:         <li>Glovar Genome Browser<br>
        !            73:         </li>
        !            74:       </ol>
        !            75:       </td>
        !            76:       <td style="vertical-align: top;"><span style="font-weight: bold;">Structural
        !            77: Databases</span><br>
        !            78:       </td>
        !            79:       <td
        !            80:  style="vertical-align: top; background-color: rgb(255, 204, 204);">
        !            81:       <ol>
        !            82:         <li>Macromolecular Structure Database (MSD)</li>
        !            83:         <li>Research Collaboratory for Structural Bioinformatics
1.13      jawahar    84: (RCSB)</li>
1.14    ! jawahar    85:         <li>Protein Data Bank Japan (PDBj)</li>
        !            86:         <li>BMRB</li>
        !            87:         <li>OCA<br>
        !            88:         </li>
        !            89:         <li>PDBsum<br>
        !            90:         </li>
        !            91:         <li>EM-Search</li>
        !            92:         <li>Nucleic Acid Database (NDB)</li>
        !            93:         <li>CATH</li>
        !            94:         <li>SCOP</li>
        !            95:         <li>EDS<br>
        !            96:         </li>
        !            97:       </ol>
        !            98:       </td>
        !            99:     </tr>
        !           100:     <tr>
        !           101:       <td style="vertical-align: top;"><span style="font-weight: bold;">Animal
        !           102: Databases</span><br>
        !           103:       </td>
        !           104:       <td
        !           105:  style="vertical-align: top; background-color: rgb(255, 204, 204);">
        !           106:       <ol>
        !           107:         <li>Saccharomyces Genome Database (SGD)<br>
        !           108:         </li>
        !           109:         <li>Flybase</li>
        !           110:         <li>Wormbase</li>
        !           111:         <li>Rat Genome Database (RGD)<br>
        !           112:         </li>
        !           113:         <li>Mouse Genome Informatics (MGI)</li>
        !           114:         <li>Zebrafish Information (ZFIN)</li>
        !           115:       </ol>
        !           116:       </td>
        !           117:       <td style="vertical-align: top;"><span style="font-weight: bold;">Plant
        !           118: Databases</span><br>
        !           119:       </td>
        !           120:       <td
        !           121:  style="vertical-align: top; background-color: rgb(255, 204, 204);">
        !           122:       <ol>
        !           123:         <li>Gramene</li>
        !           124:         <li>MaizeGDB<br>
        !           125:         </li>
        !           126:       </ol>
        !           127:       </td>
        !           128:     </tr>
        !           129:   </tbody>
1.4       jawahar   130: </table>
                    131: <p><br>
                    132: </p>
1.1       jawahar   133: <br>
1.4       jawahar   134: </body>
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