Registering Datafiles and Samples#
PART1: Registering/Uploading datafiles#
Step1: Download the datafiles provided in the IBISBA_WorkShop_Material :
1.MassSpec_Results.xls
2.ProteinModelReannotation.doc
Step2: Assuming you are already logged in click the “Create” button from the top-navigation bar and from the drop-down menu select “datafile” and a new page will open up:
Upload datafile(1.MassSpec_Results.xls)
You can also register a Data file by registering a URL to either another page or remote file
Step3: Fill in the sections using the following information:
Title: Proteins detected by high-throughput mass spectrometry of secretome Aspergillus Niger
Description: Secretome enriched fractions of A. niger N402 cultured under controlled conditions in defined synthetic media were analysed by high-throughput mass spectrometry
Projects: Assign this datafile to the project to which it belongs
Project : An inventory of Aspergillus niger secrotome*
Tags: Add some tag to the datafile which will help to describe it, For e.g. *Mass Spec Data
Click “Next”
Step4: License and Permissions
License: From the list choose “Creative Common License”
Sharing Policy: Choose “No access” if you wish to keep the datafile private
Click “Next”
Associated Assays:
Associated this datafile to the ASSAY :“Liquid Chromatography and Mass Spectrometry” from the list You can also select an existing Experimental assay or Modelling analysis to associate with this Data file.
Click “Next”
On this page you add additional properties to the datafile such as:
Associate it with other datafiles
Add associated publications
Events related to this datafile
Hit the “Create” button.
Optional Steps:
Once the datafile is created, using the “Actions” drop down menu you can
edit this file
manage the file
delete the file or
upload a new version
Using the “Explore” button you can:
view the contents of the file
plot the data
add annotation
PART2: Sample Registration#
To register Samples we have to create Sample Types. Sample Types are templates that detail the key information that needs to be included to describe a given sample correctly.
A Sample Type can be made in two ways:
By manually defining the attributes using a form
Uploading a spreadsheet that contains a Sample Template
Using the FAIR Data Station
In this section we will be creating Samples using a spreadsheet containing the Sample Type Template
Step1:
Download the file “3.Samples_A.Niger.xlsx” from the IBISBA_WorkShop_Material
Step2:
Assuming you are already logged in click the Create button from the top-navigation bar and from the drop-down menu select “Sample Types” and a new page New Sample Type will open up:
Choose the tab Use spreadsheet template
Step3:
Fill in the sections using the following information:
Title: Samples used for the Aspergillus Niger experiments
Description: Secretome enriched fractions of A. niger cultured under controlled conditions in defined synthetic media and analysed by high-throughput mass spectrometry
Projects: Assign to the project to which it belongs:
Project: An inventory of Aspergillus niger secrotome*
Step4: Permissions and template Upload
Optional Steps:#
Once the datafile is created, using the “Actions” drop down menu you can
Edit Sample Type
Manage Sample Type
Delete Sample Type
Step6:
From here you can now create your samples using the
“Create sample” button in the top menu
You’ll be directed to a New Sample page. Where you can add the following information:
Sample Name: Strain: Type:
Projects: Assign the Sample to the project to which it belongs:
Project: An inventory of Aspergillus niger secrotome*
Permissions and template Upload
Sharing Policy: Choose “No access” if you wish to keep the datafile private
Creators:
Observation Unit:
Hit the “Create” button
Creating Samples from a template#
You can bulk-create samples by populating a template and uploading as a Datafile. Once uploaded it should be recognised as having originated from a sample type template, and an option to extract samples will be displayed as a button.
Step1:
Download the file “3.Samples_A.Niger.xlsx” from the IBISBA_WorkShop_Material
Step2: Assuming you are already logged in click the Create button from the top-navigation bar and from the drop-down menu select “datafile” and a new page will open up: Upload datafile(3.Samples_A.Niger.xlsx)
Step3:
Fill in the sections using the following information:
Title: Samples used for the Aspergillus Niger experiments
Description: Secretome enriched fractions of A. niger cultured under controlled conditions in defined synthetic media and analysed by high-throughput mass spectrometry
Projects: Assign this datafile to the project to which it belongs:
Project: An inventory of Aspergillus niger secrotome*
Click “Next”
Step4: License and Permissions
License: From the list choose “Creative Common License”
Sharing Policy: Choose “No access” if you wish to keep the datafile private
Click “Next”
Associated Assays: Choose the existing assay to which the Sample belongs
Click “Next”
On this page you can add additional properties to the datafile such as
Associate it with Discussion Channels
Add associated publications
Events related to this datafile
Associated Observations Units
Hit the “Create” button
Step5: From the top panel of options click “Extract Samples” and you will be directed to a new page
Step6: Select “Sample Type” from the list and click “Continue”. It will take a few moments to extract the Samples
Step7:
Click on the “Review Extracted Samples” and check whether the data looks right to you
Step8:
Click “Confirm” button and the samples will be assigned to your Project
Using the “Explore” button you can:
view the contents of the file
plot the data
add annotation
Optional Steps#
Once the datafile is created, using the “Actions” drop down menu you can
edit this file
manage the file
delete the file or
Register new version