Difference between revisions of "MSigDB XML description"
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| Line 38: | Line 38: | ||
<tbody> | <tbody> | ||
<tr> | <tr> | ||
| − | <th>XML ATTRIBUTE | + | <th>XML ATTRIBUTE</th> |
| − | <th>DESCRIPTION | + | <th>DESCRIPTION</th> |
<th> </th> | <th> </th> | ||
</tr> | </tr> | ||
<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>SYSTEMATIC_NAME</td> |
| − | <td>Gene set name for internal indexing purposes | + | <td>Gene set name for internal indexing purposes</td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td>HISTORICAL_NAMES | + | <td>HISTORICAL_NAMES</td> |
| − | <td>Comma-separated list of older gene set names, starting from VERSION="V.2.5" of MSigDB | + | <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>ORGANISM</td> |
| − | <td>Organism name | + | <td>Organism name</td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td>PMID | + | <td>PMID</td> |
| − | <td>PubMed ID for the source publication | + | <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>Authors of the gene set source publication, according to PubMed ID</td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>GEOID</td> | <td>GEOID</td> | ||
| − | <td>A GEO or ArrayExpress ID for the raw microarray data in GEO or ArrayExpress repository | + | <td>A GEO or ArrayExpress ID for the raw microarray data in GEO or ArrayExpress repository</td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td>GENESET_LISTING_URL | + | <td>GENESET_LISTING_URL</td> |
| − | <td>URL of the original source that listed the gene set members | + | <td>URL of the original source that listed the gene set members</td> |
<td>optional</td> | <td>optional</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td>EXTERNAL_DETAILS_URL | + | <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>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>CATEGORY_CODE</td> |
| − | <td>Gene set collection code, e.g., C2 | + | <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>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>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>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>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>DESCRIPTION_FULL</td> |
| − | <td>Full description of the gene set or abstract of the source publication | + | <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>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>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>MEMBERS_SYMBOLIZED</td> |
| − | <td>Comma-separated list of gene set members in the form of human gene symbols | + | <td>Comma-separated list of gene set members in the form of human gene symbols</td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| − | <td>MEMBERS_EZID | + | <td>MEMBERS_EZID</td> |
| − | <td>Comma-separated list of gene set members in the form of human Entrez Gene IDs | + | <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> | ||
| Line 146: | Line 146: | ||
<tr> | <tr> | ||
<td>MEMBERS_MAPPING</td> | <td>MEMBERS_MAPPING</td> | ||
| − | <td>Pipe-separated list of mappings between gene set members in the form of: <br | + | <td>Pipe-separated list of mappings between gene set members in the form of: <br> |
MEMBERS, MEMBERS_SYMBOLIZED, MEMBERS_EZID</td> | MEMBERS, MEMBERS_SYMBOLIZED, MEMBERS_EZID</td> | ||
<td>required</td> | <td>required</td> | ||
| Line 157: | Line 157: | ||
<tr> | <tr> | ||
<td>REFINEMENT_DATASETS</td> | <td>REFINEMENT_DATASETS</td> | ||
| − | <td>Pipe-separated list of GEO or ArrayExpress identifiers of microarray data used to refine hallmark signatures<br | + | <td>Pipe-separated list of GEO or ArrayExpress identifiers of microarray data used to refine hallmark signatures<br> |
GEO or ArrayExpress ID, comparison details</td> | GEO or ArrayExpress ID, comparison details</td> | ||
<td>applies to hallmarks only</td> | <td>applies to hallmarks only</td> | ||
| Line 163: | Line 163: | ||
<tr> | <tr> | ||
<td>VALIDATION_DATASETS</td> | <td>VALIDATION_DATASETS</td> | ||
| − | <td>Pipe-separated list of GEO or ArrayExpress identifiers of microarray data used to validate hallmark signatures<br | + | <td>Pipe-separated list of GEO or ArrayExpress identifiers of microarray data used to validate hallmark signatures<br> |
GEO or ArrayExpress ID, comparison details |</td> | GEO or ArrayExpress ID, comparison details |</td> | ||
<td>applies to hallmarks only</td> | <td>applies to hallmarks only</td> | ||
| Line 169: | Line 169: | ||
<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>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
</tbody> | </tbody> | ||
</table> | </table> | ||
Revision as of 09:29, 17 March 2015
<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> |
<a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> |
<a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular Signatures Database</a> |
<a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page">Documentation</a> |
<a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>
The 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 |
| GENESET_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 list of mappings between gene set members in the form of: MEMBERS, MEMBERS_SYMBOLIZED, MEMBERS_EZID |
required |
| FOUNDER_NAMES | Pipe-separated list of v4.0 MSigDB founder gene sets for the hallmark signatures | applies to hallmarks only |
| REFINEMENT_DATASETS | Pipe-separated list of GEO or ArrayExpress identifiers of microarray data used to refine hallmark signatures GEO or ArrayExpress ID, comparison details |
applies to hallmarks only |
| VALIDATION_DATASETS | Pipe-separated list of GEO or ArrayExpress identifiers of microarray data used to validate hallmark signatures GEO or ArrayExpress ID, comparison details | |
applies to hallmarks only |
| STATUS | Indicates gene set status. In the current release, all gene sets have their STATUS="public" | required |
