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.

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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.

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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:
STATUS Indicates gene set status. In the current release, all gene sets have their STATUS="public". required
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