Difference between revisions of "MSigDB XML description"
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<p>Database tags and attributes: apply to all genes in the file.</p> | <p>Database tags and attributes: apply to all genes in the file.</p> | ||
| − | <table width=75% border=2> | + | <table width=75% border=2 cellpadding=5 cellspacing=2> |
| − | <tr><th> | + | |
| − | <tr><td>MSIGDB NAME</td><td>name of the database</td></tr> | + | <tr><th>XML TAG </th><th>DESCRIPTION </th><th></th></tr> |
| − | <tr><td> | + | <tr><td> MSIGDB NAME</td><td>name of the database </td><td>required</td></tr> |
| − | <tr><td>BUILD_DATE</td><td>date the XML file has been built</td></tr> | + | <tr><td>VERSION </td><td>version of the database </td><td>required</td></tr> |
| + | <tr><td>BUILD_DATE </td><td>date the XML file has been built</td><td>required</td></tr> | ||
| + | |||
</table> | </table> | ||
| + | |||
| + | <br> | ||
| + | <br> | ||
<p>Gene set tags and attributes: apply to individual gene sets in the file.</p> | <p>Gene set tags and attributes: apply to individual gene sets in the file.</p> | ||
| − | <table width=75% border=2> | + | <table width=75% border=2 cellpadding=5 cellspacing=2> |
| − | <tr><th> | + | |
| + | <tr><th>XML TAG </th><th>DESCRIPTION </th><th></th></tr> | ||
| + | |||
| + | <tr><td>GENE_SET_STANDARD_NAME </td><td>gene set name </td><td>required</td></tr> | ||
| + | <tr><td>SYSTEMATIC_NAME </td><td>gene set name for internal indexing purposes </td><td>required</td></tr> | ||
| + | <tr><td>HISTORICAL_NAMES </td><td>comma separated list of older gene set names, starting from VERSION="V.2.5" of MSigDB</td><td>optional</td></tr> | ||
| + | <tr><td>ORGANISM </td><td>organism name </td><td>required</td></tr> | ||
| + | <tr><td>PMID </td><td>PubMed ID for the source publication </td><td>optional</td></tr> | ||
| + | <tr><td>AUTHORS </td><td>Authors of the gene set source publication, according to PubMed ID </td><td>optional</td></tr> | ||
| + | <tr><td>GENE_SET_LISTING_URL </td><td>URL to the original source listing gene set members </td><td>optional</td></tr> | ||
| + | <tr><td>EXTERNAL_DETAILS_URL </td><td>URL to the original source page of the gene set </td><td>optional</td></tr> | ||
| + | <tr><td>CHIP </td><td>Indicates type of original gene set members, equivalent to the CHIP file, e.g., "HG-U133A" </td><td>required</td></tr> | ||
| + | <tr><td>CATEGORY_CODE </td><td>Gene set collection code, e.g. C2 </td><td>required</td></tr> | ||
| + | <tr><td>CONTRIBUTOR </td><td>Name of person or institution that contributed the gene set to MSigDB </td><td>required</td></tr> | ||
| + | <tr><td>CONTRIBUTOR_ORG </td><td>Name of organization associated with the gene set contributor </td><td>required</td></tr> | ||
| + | <tr><td>DESCRIPTION_BRIEF </td><td>Brief description of the gene set </td><td>required</td></tr> | ||
| + | <tr><td>DESCRIPTION_FULL </td><td>Full description of the gene set or abstract of the source publication </td><td>optional</td></tr> | ||
| + | <tr><td>TAGS </td><td>Optional tags to enhance gene set annotations; currently not in use </td><td>optional</td></tr> | ||
| + | <tr><td>MEMBERS </td><td>Comma separated list of gene set members as they have originally appeared in the source </td><td>required</td></tr> | ||
| + | <tr><td>MEMBERS_SYMBOLIZED </td><td>Comma separated list of gene set members in the form of human gene symbols </td><td>required</td></tr> | ||
| + | <tr><td>MEMBERS_EZID </td><td>Comma separated list of gene set members in the form of human Entrez Gene IDs </td><td>required</td></tr> | ||
</table> | </table> | ||
| − | |||
Revision as of 16:16, 30 July 2010
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 |
