MSigDB XML description

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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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.

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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. E.g., "public" means the set is included in the MSigDB release; "deprecated:reason" means the set is not included in the MSigDB release.