Metabolomics data files for loading include Platform file, Data file and Data mapping file. Metabolomics data is loaded from MetabolomicsDataToUpload directory.
Metabolomics Data (sample)
Data file includes several fields that are either redundant and are also included in the platform file or just ignored. Data file columns: PATHWAY_SORTORDER, BIOCHEMICAL, SUPER_PATHWAY, SUB_PATHWAY, COMP_ID, PLATFORM, RI, MASS, CAS, PUBCHEM, KEGG, HMDB, Sample ID
|PATH WAY SORT ORDER||BIOCHE MICAL||SUPER PATH WAY||SUB PATH WAY||COMP ID||PLAT FORM||RI||MASS||CAS||PUB CHEM||KEGG||HMDB||9CN||10CP|
|342||meva lonic acid||Carbo xylic acid||Meva lonic acid path way||400001||GC/MS||2310||456||96233||59925||Z036784||HMDB0||717||1396|
The last symbol in data file name (before extension) is one of following letters:
R - raw data. Values are loaded into Value column. Raw values are transformed to calculate log2 value and z-score. log2 values are loaded into Log values column
L - log2 data. Values are loaded into Log value column, raw values are not restored. The same log2 values are also loaded into Value column. z-score is calculated.
Z - z-score data. Has same meaning, value will be written to z-score without modifications if it in range of (-2.5; 2.5). It will be truncated to this range otherwise.
The platform data file defines the platform and maps metabolites (Biochemical) to metabolites’ HMDB IDs, Pathways and Super Pathways. Biochemical name is the primary identifier. Other information is optional. Only HMDB IDs are accepted at present time. Missing or any other IDs will be replaced by “PRIVATE” in the analysis results output. HMDB ID and HMDB Common Name are loaded as a dictionary. If Pathway data is loaded, it will be available in the HDD drop down filter in the Advanced Workflows. All Metabolites mapped to the selected Pathway will be used in the analysis.
#PLATFORM_TITLE: Metabolomics Platform Test 222
#SPECIES: Homo Sapiens
|mevalonic acid||Carboxylic acid||Mevalonic acid pathway||HMDB0|
|5-isopentenyl pyrophosphoric acid||Phosphoric acid||Cholesterol biosynthesis|
Some lipid metabolites have very long names that exceeds Metabolomics table limit. We recommend using Shorthand Notation for Lipid Metabolites
Mapping file is named as Study_name_Subject_Sample_Mapping_File.txt (e.g. MTBLS111_Subject_Sample_Mapping_File.txt). Mapping File has standard format.
|TRIAL NAME||SITE ID||SUBJECT ID||SAMPLE CD||PLAT FORM||TISSUE TYPE||ATTRIBUTE_1||ATTRIBUTE_2||CATEGORY CD||SOURCE CD|
|GSE37222||null||GSM918960||9CN||MET222||Blood||Visit 01||Biomarker_Data+ PLATFORM +TISSUETYPE +ATTR1||STD|