/api/cacheendpoint with a
-uwith local cBioPortal and
-htmlwith preferred location for html report):
stable id(MsigDB calls this "standard name"), e.g. GO_POTASSIUM_ION_TRANSPORT, not longer than 100 characters. The second column contains the REF_LINK. This is an optional URL linking to external information about this gene set. Column 3 to N contain the Entrez gene IDs that belong to this gene set.
stable id, the long name (max 100 characters) and description of the gene set (max 300 characters).
--new-versionargument with a
<Version>parameter is used for loading new gene set definitions. It is not possible to add new gene sets or change the genes of current gene sets, without removing the old gene sets first. This is to prevent the user from having gene sets from different definitions and data from older definitions. The user can choose the name or number of the
<Version>as he likes, e.g.
Oncogenic_2017. Running the script with
--new-versionremoves all previous gene sets, gene set hierarchy and gene set genetic profiles. A prompt is given to make sure the user wants to do this. Note that it is possible enter the same version as the previous version, but previous data is removed nevertheless.
--update infocan be used only to update only the long name, description and reference URL.
:. Every branch can contain new branches (which can be considered subcategories) or gene sets (which are designated by the
Gene sets:statement). The gene set names are the
stable idsimported by
ImportGenesetData.javaand should start with
metaImport.py. cBioPortal supports GSVA Scores and p-values (from bootstrapping) calculated using Gene Set Variation Analysis (GSVA, Hänzelmann, 2013). A description of GSVA study data can be found in the cBioPortal File Formats documentation.