Transmart Loader

How To

1. Download/Create clinical data, put data file and map file on a server location where you can find.
2. Change and save clinical.params file. (Parameters definition list in Params List section)
3. Load clinical data.

./load_clinical.sh clinical.params

4. Check if gpl is already in tranSMART

./check_gpl.sh

5. If gpl already in the list, skip next 3 steps.
6. (Optional) Download annotation file from transmart dataset
7. (Optional) Change and save annoataion.params file.
8. (Optional) Load annotation data.

./load_annotation.sh annotation.params

9. Change and save expression.params file
10. Load expression data.

./load_expression.sh expression.params

Done!

Running Scripts

• load_clinial.sh
• load_expression.sh
• load_annotation.sh

Params Files

• clinical.params
• expression.params
• annotation.params

Params List

clinical.params

# data  
DATA_LOCATION="/home/transmart/datasets/RanchoGSE4698/clinical"  
COLUMN_MAP_FILE="Acute_Lymphoblastic_Leukemia_Kirschner_Schwabe_GSE4698_Mapping_File.txt"  

# info  
STUDY_ID="GSE4698"  
TOP_NODE="\\Public Studies\\Acute Lymphoblastic Leukemia_Kirschner_Schwabe_GSE4698"  

# security  
SECURITY_REQUIRED="N"  

# not using  
WORD_MAP_FILE=x  
RECORD_EXCLUSION_FILE=x  

Field Name	Meaning
DATA_LOCATION	Location of clinical data folder.
COLUMN_MAP_FILE	Map file.
STUDY_ID	Study id.
TOP_NODE	Top node. (TOP_NODE=\\TOP_NODE_PREFIX\\STUDY_NAME)
SECURITY_REQUIRED	Is private?
WORD_MAP_FILE	Word map file.
RECORD_EXCLUSION_FILE	Record exclusion file.

expression.params

# data
DATA_LOCATION="/home/transmart/datasets/RanchoGSE4698/expression"
DATA_FILE_PREFIX="Acute_Lymphoblastic_Leukemia_Kirschner_Schwabe_GSE4698_Gene_Expression_Data"
MAP_FILENAME=\
"Acute_Lymphoblastic_Leukemia_"\
"Kirschner_Schwabe_GSE4698_"\
"Subject_Sample_Mapping_File.txt"\

# info
STUDY_ID="GSE4698"
TOP_NODE="\\Public Studies\\Acute Lymphoblastic Leukemia_Kirschner_Schwabe_GSE4698"
SOURCE_CD=""

# security
SECURITY_REQUIRED="N"

Field Name	Meaning
DATA_LOCATION	Location of clinical data folder.
DATA_FILE_PREFIX	Prefix of data file.
MAP_FILENAME	Map file name.
STUDY_ID	Study id.
TOP_NODE	Top node. (TOP_NODE=\\TOP_NODE_PREFIX\\STUDY_NAME)
SOURCE_CD	Source to include. Corresponding to SOURCE_CD filed in map file. Default value: STD
SECURITY_REQUIRED	Is private?

annotation.params

# data
DATA_LOCATION="/home/transmart/datasets/EtriksGSE43696/annotation"
SOURCE_FILENAME="GPL6480.txt"

# info
ANNOTATION_TITLE="Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name Version)"
GPL_ID="GPL6480"

# col numbers
PROBE_COL=2
GENE_SYMBOL_COL=3
GENE_ID_COL=4
ORGANISM_COL=5

# header?
SKIP_ROWS=0

Field Name	Meaning
DATA_LOCATION	Location of annotation data folder.
SOURCE_FILENAME	Data file name.
ANNOTATION_TITLE	Title. (copy from xz)
GPL_ID	GPL id.
PROBE_COL	Column index of the probe ID.
GENE_SYMBOL_COL	Column index of the gene symbol.
GENE_ID_COL	Column index of the gene ID.
ORGANISM_COL	Column index of the organism.
SKIP_ROWS	Number of rows to skip. Note: This script does not assume a header row is present. If a header row exists, this should be set to one.

UI Explain

• TOP_NODE_PREFIX
  
• STUDY_NAME
  
• TOP_NODE (TOP_NODE=\\TOP_NODE_PREFIX\\STUDY_NAME)
  
• CATEGORY_CD