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metabolomics.md

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Metabolomics

Annotation

The parameters file should be named metabolomics_annotation.params.

The annotations file has 4 columns. These can be in any order, but their names need to be correct. The recommended order is BIOCHEMICAL, SUPER_PATHWAY, SUB_PATHWAY and HMDB_ID. Constraints:

  • The only mandatory column is BIOCHEMICAL.
  • The column SUB_PATHWAY is required if SUPER_PATHWAY is provided.
  • If a super-pathway is included in more than one row, the corresponding sub-pathways can only map to that particular super-pathway. This cannot be a one to many mapping.
  • The columns BIOCHEMICAL and HMDB_ID must be independently unique. (Note: the database schema supports associating one biochemical with multiple sub-pathways; this is currently not supported in the job).

Example file:

BIOCHEMICAL SUPER_PATHWAY SUB_PATHWAY HMDB_ID
mevalonic acid Carboxylic acid Mevalonic acid pathway HMDB0TEST
5-isopentenyl pyrophosphoric acid Phosphoric acid Cholesterol biosynthesis
3,3-dimethyl allyl pyrophosphoric acid Phosphoric acid Cholesterol biosynthesis
xylitol Carbohydrate Nucleotide sugars; pentose metabolism HMDB00568
farnesyl pyrophosphate Phosphoric acid Cholesterol biosynthesis; Squalene synthesis
presqualene diphosphate Phosphoric acid Cholesterol biosynthesis; Squalene synthesis
bogus no super Sub pathway without super
bogus no sub/super

Refer to the general annotations documentation for general information about annotation loading jobs, including their parameters.

Data

The parameters file should be named metabolomics.params. For the content of this file see the HD data parameters and the study-specific parameters.

How HD data are processed. How to upload zscores