Scenario 'Eugene'

Import study-level information of toxocologic studies from NTC into GSCF using the simple import wizard.

Background

The Netherlands Toxicogenomics Centre (NTC) will perform toxicological experiments for different toxicological endpoints (liver, carcino, repro, immuno etc.) using different model systems (different organisms, different cell systems, in vitro-in vivo-ex vivo) using different omics approaches (transcriptomics, miRNA, (phospho-)proteomics, metabolomics, imaging). NTC wants to use GSCF for full metadata capture and use it in combination with Array Track for data storage/visualization/analysis. Currently, NTC uses a website, called NTC Sharing, to collect information at study-level of all NTC experiments and store it in a simple Excel sheet. For GSCF, it should be possible to import this study-level information from NTC Sharing using the simple import wizard and a dedicated NTC Study template.

Description of Scenario

We want to test the scenario of importing study-level information for NTC. To this end, we have created three mock NTC experiment descriptions in an Excel sheet which has the exact same columns as used for NTC (see attachment "NTC_Experiment_test3.xls"):

• ​https://trac.nbic.nl/gscf/attachment/wiki/ScenarioEugene/NTC_Experiment_test3.xls

This scenario should be implemented with the following milestones:

• gscf 0.6
• sam 0.1.1

NTC Experiment_test3.xls

This Excel sheet contains the study-only information of three mock NTC experiments.
It contains three rows and columns from A-Y.
Below are three screenshots from left to right:

Scenario execution

Below is a description of the exact steps to execute this scenario

Step 1:

Login as user "user"

Step 2:

=> Studies => Import study data => Simple Wizard

Step 3:

This is Simple Import Wizard Step 1:
"Choose your Excel file to import" = "NTC_Experiment_test3.xls"
"Choose type of data" = "Study"
"Choose type of data template" = "NTC Study 2"
Keep rest of fields default and press "Next" (see screenshot below):

Step 4:

This is Simple Import Wizard Step 2:
"Timestamp" = "Submission Date"
"Experiment ID" = "code (IDENTIFIER)"
"Primary Contact" = "Primary Contact"
"Species of Origin" = "Main Species in Study"
"Source" = "SourceOfSample?"
"Title" = "title"
"Description" = "Description"
"Bioinformatics Date" = "startDate"
Keep rest of fields default and press "Next" (see the two screenshots below):

Step 5:

This is "Simple Import Wizard Step 2a: ontologies which could not be determined":
"Source" = "peripheral blood mononuclear cell" (obtained by searching PBMC and selecting BRENDA version)
"Source" = "C2C12 cell" (obtained by searching C2C12 and selecting BRENDA version)
"[Species of Origin, Source]" = "Rattus Norvegicus" (obtained by searching rattus norvegicus and selecting NCBI)
NOTE: SOMETHING WENT WRONG IN THIS LAST ITEM (Species and source are seen as one???!!!)