Difference between revisions of "MSigDB XML description"

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MSigDB database in XML format captures both the content  (i.e., gene members) and annotation about the gene sets in MSigDB. Here we describe the tags and attributes of the XML file.
+
MSigDB database in XML format captures both the content  (i.e., gene members) and annotation about the gene sets in MSigDB. This page describes the tags and attributes of the XML file.
−
 
 
 
<p>Database tags and attributes: apply to all genes in the file.</p>
 
<p>Database tags and attributes: apply to all genes in the file.</p>
−
 
+
<table width="75%" cellspacing="2" cellpadding="5" border="2">
−
<table width=75% border=2 cellpadding=5 cellspacing=2>
+
    <tbody>
−
 
+
        <tr>
−
<tr><th>XML TAG          </th><th>DESCRIPTION                                </th><th></th></tr>
+
            <th>XML TAG          </th>
−
<tr><td> MSIGDB NAME</td><td>name of the database                </td><td>required</td></tr>
+
            <th>DESCRIPTION                                </th>
−
<tr><td>VERSION          </td><td>version of the database              </td><td>required</td></tr>
+
            <th>&nbsp;</th>
−
<tr><td>BUILD_DATE    </td><td>date the XML file has been built</td><td>required</td></tr>
+
        </tr>
−
 
+
        <tr>
 +
            <td> MSIGDB NAME</td>
 +
            <td>Name of the database                </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>VERSION          </td>
 +
            <td>Version of the database              </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>BUILD_DATE    </td>
 +
            <td>Date the XML file was built</td>
 +
            <td>required</td>
 +
        </tr>
 +
    </tbody>
 
</table>
 
</table>
−
 
+
<br />
−
<br>
+
<br />
−
<br>
 
−
 
 
 
<p>Gene set tags and attributes: apply to individual gene sets in the file.</p>
 
<p>Gene set tags and attributes: apply to individual gene sets in the file.</p>
−
 
+
<table width="75%" cellspacing="2" cellpadding="5" border="2">
−
<table width=75% border=2 cellpadding=5 cellspacing=2>
+
    <tbody>
−
 
+
        <tr>
−
<tr><th>XML TAG          </th><th>DESCRIPTION                                </th><th></th></tr>
+
            <th>XML TAG          </th>
−
 
+
            <th>DESCRIPTION                                </th>
−
<tr><td>GENE_SET_STANDARD_NAME </td><td>gene set name                                                                                                                                    </td><td>required</td></tr>
+
            <th>&nbsp;</th>
−
<tr><td>SYSTEMATIC_NAME                  </td><td>gene set name for internal indexing purposes                                                                              </td><td>required</td></tr>
+
        </tr>
−
<tr><td>HISTORICAL_NAMES                </td><td>comma separated list of older gene set names, starting from VERSION="V.2.5" of MSigDB</td><td>optional</td></tr>
+
        <tr>
−
<tr><td>ORGANISM                                </td><td>organism name                                                                                                                                    </td><td>required</td></tr>
+
            <td>GENE_SET_STANDARD_NAME </td>
−
<tr><td>PMID                                            </td><td>PubMed ID for the source publication                                                                                            </td><td>optional</td></tr>
+
            <td>Gene set name                                                                                                                                    </td>
−
<tr><td>AUTHORS                                  </td><td>Authors of the gene set source publication, according to PubMed ID                                      </td><td>optional</td></tr>
+
            <td>required</td>
−
<tr><td>GENE_SET_LISTING_URL          </td><td>URL to the original source listing gene set members                                                                    </td><td>optional</td></tr>
+
        </tr>
−
<tr><td>EXTERNAL_DETAILS_URL        </td><td>URL to the original source page of the gene set                                                                              </td><td>optional</td></tr>
+
        <tr>
−
<tr><td>CHIP                                            </td><td>Indicates type of original gene set members, equivalent to the CHIP file, e.g., "HG-U133A"   </td><td>required</td></tr>
+
            <td>SYSTEMATIC_NAME                  </td>
−
<tr><td>CATEGORY_CODE                    </td><td>Gene set collection code, e.g. C2                                                                                                        </td><td>required</td></tr>
+
            <td>Gene set name for internal indexing purposes                                                                              </td>
−
<tr><td>CONTRIBUTOR                          </td><td>Name of person or institution that contributed the gene set to MSigDB                                    </td><td>required</td></tr>
+
            <td>required</td>
−
<tr><td>CONTRIBUTOR_ORG                </td><td>Name of organization associated with the gene set contributor                                                  </td><td>required</td></tr>
+
        </tr>
−
<tr><td>DESCRIPTION_BRIEF                  </td><td>Brief description of the gene set                                                                                                        </td><td>required</td></tr>
+
        <tr>
−
<tr><td>DESCRIPTION_FULL                  </td><td>Full description of the gene set or abstract of the source publication                                        </td><td>optional</td></tr>
+
            <td>HISTORICAL_NAMES                </td>
−
<tr><td>TAGS                                          </td><td>Optional tags to enhance gene set annotations; currently not in use                                          </td><td>optional</td></tr>
+
            <td>Comma-separated list of older gene set names, starting from VERSION=&quot;V.2.5&quot; of MSigDB</td>
−
<tr><td>MEMBERS                                    </td><td>Comma separated list of gene set members as they have originally appeared in the source  </td><td>required</td></tr>
+
            <td>optional</td>
−
<tr><td>MEMBERS_SYMBOLIZED            </td><td>Comma separated list of gene set members in the form of human gene symbols                      </td><td>required</td></tr>
+
        </tr>
−
<tr><td>MEMBERS_EZID                          </td><td>Comma separated list of gene set members in the form of human Entrez Gene IDs                  </td><td>required</td></tr>
+
        <tr>
 +
            <td>ORGANISM                                </td>
 +
            <td>Organism name                                                                                                                                    </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>PMID                                            </td>
 +
            <td>PubMed ID for the source publication                                                                                            </td>
 +
            <td>optional</td>
 +
        </tr>
 +
        <tr>
 +
            <td>AUTHORS                                  </td>
 +
            <td>Authors of the gene set source publication, according to PubMed ID                                      </td>
 +
            <td>optional</td>
 +
        </tr>
 +
        <tr>
 +
            <td>GENE_SET_LISTING_URL          </td>
 +
            <td>URL of the original source that listed the gene set members                                                                    </td>
 +
            <td>optional</td>
 +
        </tr>
 +
        <tr>
 +
            <td>EXTERNAL_DETAILS_URL        </td>
 +
            <td>URL of the original source page of the gene set                                                                              </td>
 +
            <td>optional</td>
 +
        </tr>
 +
        <tr>
 +
            <td>CHIP                                            </td>
 +
            <td>Indicates the type of the original gene set members, equivalent to the CHIP file, e.g., &quot;HG-U133A&quot;   </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>CATEGORY_CODE                    </td>
 +
            <td>Gene set collection code, e.g., C2                                                                                                        </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>CONTRIBUTOR                          </td>
 +
            <td>Name of the person or institution that contributed the gene set to MSigDB                                    </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>CONTRIBUTOR_ORG                </td>
 +
            <td>Name of the organization associated with the gene set contributor                                                  </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>DESCRIPTION_BRIEF                  </td>
 +
            <td>Brief description of the gene set                                                                                                        </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>DESCRIPTION_FULL                  </td>
 +
            <td>Full description of the gene set or abstract of the source publication                                        </td>
 +
            <td>optional</td>
 +
        </tr>
 +
        <tr>
 +
            <td>TAGS                                          </td>
 +
            <td>Optional tags to enhance gene set annotations; currently not in use                                          </td>
 +
            <td>optional</td>
 +
        </tr>
 +
        <tr>
 +
            <td>MEMBERS                                    </td>
 +
            <td>Comma-separated list of gene set members as they originally appeared in the source  </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>MEMBERS_SYMBOLIZED            </td>
 +
            <td>Comma-separated list of gene set members in the form of human gene symbols                      </td>
 +
            <td>required</td>
 +
        </tr>
 +
        <tr>
 +
            <td>MEMBERS_EZID                          </td>
 +
            <td>Comma-separated list of gene set members in the form of human Entrez Gene IDs                  </td>
 +
            <td>required</td>
 +
        </tr>
 +
    </tbody>
 
</table>
 
</table>

Revision as of 13:07, 2 August 2010

MSigDB database in XML format captures both the content (i.e., gene members) and annotation about the gene sets in MSigDB. This page describes the tags and attributes of the XML file.

Database tags and attributes: apply to all genes in the file.

<tbody> </tbody>
XML TAG DESCRIPTION  
MSIGDB NAME Name of the database required
VERSION Version of the database required
BUILD_DATE Date the XML file was built required



Gene set tags and attributes: apply to individual gene sets in the file.

<tbody> </tbody>
XML TAG DESCRIPTION  
GENE_SET_STANDARD_NAME Gene set name required
SYSTEMATIC_NAME Gene set name for internal indexing purposes required
HISTORICAL_NAMES Comma-separated list of older gene set names, starting from VERSION="V.2.5" of MSigDB optional
ORGANISM Organism name required
PMID PubMed ID for the source publication optional
AUTHORS Authors of the gene set source publication, according to PubMed ID optional
GENE_SET_LISTING_URL URL of the original source that listed the gene set members optional
EXTERNAL_DETAILS_URL URL of the original source page of the gene set optional
CHIP Indicates the type of the original gene set members, equivalent to the CHIP file, e.g., "HG-U133A" required
CATEGORY_CODE Gene set collection code, e.g., C2 required
CONTRIBUTOR Name of the person or institution that contributed the gene set to MSigDB required
CONTRIBUTOR_ORG Name of the organization associated with the gene set contributor required
DESCRIPTION_BRIEF Brief description of the gene set required
DESCRIPTION_FULL Full description of the gene set or abstract of the source publication optional
TAGS Optional tags to enhance gene set annotations; currently not in use optional
MEMBERS Comma-separated list of gene set members as they originally appeared in the source required
MEMBERS_SYMBOLIZED Comma-separated list of gene set members in the form of human gene symbols required
MEMBERS_EZID Comma-separated list of gene set members in the form of human Entrez Gene IDs required
Retrieved from "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=MSigDB_XML_description&oldid=3106"