Difference between revisions of "MSigDB XML description"
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| Line 7: | Line 7: | ||
<tr> | <tr> | ||
<th>XML ATTRIBUTE </th> | <th>XML ATTRIBUTE </th> | ||
| − | <th>DESCRIPTION | + | <th>DESCRIPTION</th> |
<th> </th> | <th> </th> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td> MSIGDB NAME</td> | <td> MSIGDB NAME</td> | ||
| − | <td>Name of the database | + | <td>Name of the database.</td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>VERSION </td> | <td>VERSION </td> | ||
| − | <td>Version of the database | + | <td>Version of the database.</td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>BUILD_DATE </td> | <td>BUILD_DATE </td> | ||
| − | <td>Date the XML file was built</td> | + | <td>Date the XML file was built.</td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
| Line 39: | Line 39: | ||
<tr> | <tr> | ||
<td>STANDARD_NAME </td> | <td>STANDARD_NAME </td> | ||
| − | <td>Gene set name | + | <td>Gene set name. </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>SYSTEMATIC_NAME </td> | <td>SYSTEMATIC_NAME </td> | ||
| − | <td>Gene set name for internal indexing purposes </td> | + | <td>Gene set name for internal indexing purposes. </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>HISTORICAL_NAMES </td> | <td>HISTORICAL_NAMES </td> | ||
| − | <td>Comma-separated list of older gene set names, starting from VERSION="V.2.5" of MSigDB</td> | + | <td>Comma-separated list of older gene set names, starting from VERSION="V.2.5" of MSigDB.</td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>ORGANISM </td> | <td>ORGANISM </td> | ||
| − | <td>Organism name </td> | + | <td>Organism name. </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>PMID </td> | <td>PMID </td> | ||
| − | <td>PubMed ID for the source publication </td> | + | <td>PubMed ID for the source publication. </td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>AUTHORS </td> | <td>AUTHORS </td> | ||
| − | <td>Authors of the gene set source publication, according to PubMed ID </td> | + | <td>Authors of the gene set source publication, according to PubMed ID. </td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
| Line 79: | Line 79: | ||
<tr> | <tr> | ||
<td>EXTERNAL_DETAILS_URL </td> | <td>EXTERNAL_DETAILS_URL </td> | ||
| − | <td>URL of the original source page of the gene set | + | <td>URL of the original source page of the gene set. </td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>CHIP </td> | <td>CHIP </td> | ||
| − | <td>Indicates the type of the original gene set members, equivalent to the CHIP file, e.g., "HG-U133A" </td> | + | <td>Indicates the type of the original gene set members, equivalent to the CHIP file, e.g., "HG-U133A". </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>CATEGORY_CODE </td> | <td>CATEGORY_CODE </td> | ||
| − | <td>Gene set collection code, e.g., C2 </td> | + | <td>Gene set collection code, e.g., C2. </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>SUB_CATEGORY_CODE</td> | <td>SUB_CATEGORY_CODE</td> | ||
| − | <td>Gene set subcategory code, e.g., CGP</td> | + | <td>Gene set subcategory code, e.g., CGP.</td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>CONTRIBUTOR </td> | <td>CONTRIBUTOR </td> | ||
| − | <td>Name of the person or institution that contributed the gene set to MSigDB </td> | + | <td>Name of the person or institution that contributed the gene set to MSigDB. </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>CONTRIBUTOR_ORG </td> | <td>CONTRIBUTOR_ORG </td> | ||
| − | <td>Name of the organization associated with the gene set contributor </td> | + | <td>Name of the organization associated with the gene set contributor. </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>DESCRIPTION_BRIEF </td> | <td>DESCRIPTION_BRIEF </td> | ||
| − | <td>Brief description of the gene set | + | <td>Brief description of the gene set. </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>DESCRIPTION_FULL </td> | <td>DESCRIPTION_FULL </td> | ||
| − | <td>Full description of the gene set or abstract of the source publication </td> | + | <td>Full description of the gene set or abstract of the source publication. </td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>TAGS </td> | <td>TAGS </td> | ||
| − | <td>Optional tags to enhance gene set annotations; currently not in use | + | <td>Optional tags to enhance gene set annotations; currently not in use. </td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>MEMBERS </td> | <td>MEMBERS </td> | ||
| − | <td>Comma-separated list of gene set members as they originally appeared in the source | + | <td>Comma-separated list of gene set members as they originally appeared in the source.</td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>MEMBERS_SYMBOLIZED </td> | <td>MEMBERS_SYMBOLIZED </td> | ||
| − | <td>Comma-separated list of gene set members in the form of human gene symbols </td> | + | <td>Comma-separated list of gene set members in the form of human gene symbols. </td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
| Line 135: | Line 135: | ||
<td>MEMBERS_EZID </td> | <td>MEMBERS_EZID </td> | ||
<td>Comma-separated list of gene set members in the form of human Entrez Gene IDs </td> | <td>Comma-separated list of gene set members in the form of human Entrez Gene IDs </td> | ||
| − | <td>required</td> | + | <td>required.</td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 145: | Line 145: | ||
</tr> | </tr> | ||
<td>STATUS</td> | <td>STATUS</td> | ||
| − | <td>Indicates gene set status. In the current release, all gene sets have their STATUS="public | + | <td>Indicates gene set status. In the current release, all gene sets have their STATUS="public. |
</td> | </td> | ||
<td></td> | <td></td> | ||
Revision as of 12:19, 4 August 2010
MSigDB database in XML format captures both the content (i.e., gene members) and annotation about the gene sets in a given release of MSigDB. This page describes the tags and attributes of the XML file.
Attributes of the MSIGDB tag document the whole database in the file.
<tbody> </tbody>| XML ATTRIBUTE | DESCRIPTION | |
|---|---|---|
| MSIGDB NAME | Name of the database. | required |
| VERSION | Version of the database. | required |
| BUILD_DATE | Date the XML file was built. | required |
Attributes of the GENESET tags document individual gene sets in the file.
<tbody> </tbody>| XML ATTRIBUTE | DESCRIPTION | |
|---|---|---|
| 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 |
| GEOID | A GEO or ArrayExpress ID for the raw microarray data in GEO or ArrayExpress repository. | 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 |
| SUB_CATEGORY_CODE | Gene set subcategory code, e.g., CGP. | optional |
| 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. |
| MEMBERS_MAPPING | Pipe-separated ist of mappings between gene set members in the form of: MEMBERS, MEMBERS_SYMBOLIZED, MEMBERS_EZID | |
required |
| STATUS | Indicates gene set status. In the current release, all gene sets have their STATUS="public. |
