MSigDB XML description
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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 |
