Difference between revisions of "MSigDB XML description"
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| Line 11: | Line 11: | ||
<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>Date the XML file was built</td> |
<td>required</td> | <td>required</td> | ||
</tr> | </tr> | ||
| Line 143: | Line 143: | ||
MEMBERS, MEMBERS_SYMBOLIZED, MEMBERS_EZID |</td> | MEMBERS, MEMBERS_SYMBOLIZED, MEMBERS_EZID |</td> | ||
<td>required</td> | <td>required</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>FOUNDER_NAMES</td> | ||
| + | <td>Pipe-separated list of v4.0 MSigDB founder gene sets for the hallmark signatures</td> | ||
| + | <td>applies to hallmarks only</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
| + | <td>REFINEMENT_DATASETS</td> | ||
| + | <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> | ||
| + | <td>applies to hallmarks only</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td>VALIDATION_DATASETS</td> | ||
| + | <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> | ||
| + | <td>applies to hallmarks only</td> | ||
| + | </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> | <td>Indicates gene set status. In the current release, all gene sets have their STATUS="public". </td> | ||
Revision as of 22:31, 16 March 2015
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 |
