MSigDB XML description

MSigDB database in XML format captures both the content (i.e., gene members) and annotation about the gene sets in MSigDB. Here we describe the tags and attributes of the XML file.

Database tags and attributes: apply to all genes in the file.

XML TAG	DESCRIPTION
MSIGDB NAME	name of the database	required
VERSION	version of the database	required
BUILD_DATE	date the XML file has been built	required

Gene set tags and attributes: apply to individual gene sets in the file.

XML TAG	DESCRIPTION
GENE_SET_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
GENE_SET_LISTING_URL	URL to the original source listing gene set members	optional
EXTERNAL_DETAILS_URL	URL to the original source page of the gene set	optional
CHIP	Indicates type of original gene set members, equivalent to the CHIP file, e.g., "HG-U133A"	required
CATEGORY_CODE	Gene set collection code, e.g. C2	required
CONTRIBUTOR	Name of person or institution that contributed the gene set to MSigDB	required
CONTRIBUTOR_ORG	Name of 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 have 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