Difference between revisions of "MSigDB XML description"
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| − | MSigDB database in XML format captures both the content (i.e., gene members) and annotation about the gene sets in MSigDB. This page describes the tags and attributes of the XML file. | + | 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. |
| − | <p> | + | <p>Attributes of the MSIGDB tag document the whole database in the file.</p> |
<table width="75%" cellspacing="2" cellpadding="5" border="2"> | <table width="75%" cellspacing="2" cellpadding="5" border="2"> | ||
<tbody> | <tbody> | ||
<tr> | <tr> | ||
| − | <th>XML | + | <th>XML ATTRIBUTE </th> |
<th>DESCRIPTION </th> | <th>DESCRIPTION </th> | ||
<th> </th> | <th> </th> | ||
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<br /> | <br /> | ||
| − | <p> | + | <p>Attributes of the GENESET tags document individual gene sets in the file.</p> |
<table width="75%" cellspacing="2" cellpadding="5" border="2"> | <table width="75%" cellspacing="2" cellpadding="5" border="2"> | ||
<tbody> | <tbody> | ||
<tr> | <tr> | ||
| − | <th>XML | + | <th>XML ATTRIBUTE </th> |
<th>DESCRIPTION </th> | <th>DESCRIPTION </th> | ||
<th> </th> | <th> </th> | ||
Revision as of 10:55, 4 August 2010
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 |
| 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 |
| GEOID |
