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subject-sample-mapping.md

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Subject Sample Mapping

This is the mapping file format:

STUDY_ID SITE_ID SUBJECT_ID SAMPLE_CD PLATFORM SAMPLE_TYPE TISSUE_TYPE TIME_POINT CATEGORY_CD SOURCE_CD
GSE8581 GSE8581GSM210005 GSM210005 GPL570_BOGUS Tumor Lung Week1 Biomarker_Data+PLATFORM+TISSUETYPE STD

The first row is skipped. It must be present, otherwise the first assay will be ignored.

  • STUDY_ID is required, but must match the STUDY_ID parameter.
  • SITE_ID is ignored.
  • SUBJECT_ID is the subject id. Must match the one provided in the clinical data set.
  • SAMPLE_CD is the name of the assay (here synonymous with "sample"). Required.
  • PLATFORM is the GPL id of the corresponding platform. Must be given; the platform must have already been loaded; must be the same for all rows. The value will be uppercased. It will be used to replace the PLATFORM placeholder in CATEGORY_CD.
  • SAMPLE_TYPE will be used to fill sample_type in de_subject_sample_mapping. It will also be used to replace the placeholder SAMPLETYPEin CATEGORY_CD. Optional.
  • TISSUE_TYPE will be used to fill tissue_type. It will also be used to replace the placeholder TISSUETYPE and ATTR1 (legacy) in CATEGORY_CD.
  • TIME_POINT will be used to fill timepoint. It will be used to replace the TIMEPOINT and ATTR2 (legacy) placeholder in CATEGORY_CD. Optional.
  • CATGEORY_CD will be used to form the concept path for the node to be created. Components of the path are separated with +. It can include several placeholders (see the descriptions of the other columns). In principle it can differ among the several assays, but that code path has never been tested.
  • SOURCE_CD is ignored (must be present as a last column).