Submit Data to Panorama Public

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PanoramaWeb hosts a public repository called “Panorama Public” where users may submit supplementary data associated with manuscripts that have been published or are under review. The repository provides a permanent location for data that can be referenced in publications. Users with data in their own projects on PanoramaWeb can follow the instructions below to submit the data to Panorama Public. The PanoramaWeb site administrators will get in touch with the submitter and make a copy of the data to Panorama Public. If the data is for a manuscript under review, reviewer account details will be provided and the copy on Panorama Public will be kept private until the associated manuscript is accepted for publication. Data copied to Panorama Public is read-only, ensuring its availability in the original form accepted for publication.  

 

Panorama Public: A public repository for Skyline documents (ASMS 2015 poster)

Submitting Supplementary Data to Panorama Public (A detailed tutorial that covers a broader set of Panorama features)

 

Submitting Data to Panorama Public

STEP 1: Upload Skyline documents to a folder on PanoramaWeb

Refer to the following wiki pages to create a folder in your project PanoramaWeb and upload Skyline documents. 



STEP 2: Prepare a folder for submission to Panorama Public

Folders containing supplementary data intended for submission to Panorama Public have to be annotated with a description of the experiment.  This includes information such as an abstract, experiment and sample descriptions, organism, MS instruments used etc.   To add experiment annotations to a folder, do the following:

  • Go to the home page of the folder by navigating the folder menu under the Panorama logo. 
  • Click the Gear Icon  , then Page Admin Mode.
  • Select Targeted MS Experiment from the <Select Web Part> menu at bottom-left of the page. 

  • Click the Add button. This action will add a web part titled Targeted MS Experiment at the bottom of the page that looks like this:

  • Click Exit Admin Mode.
  • Click the Create New Experiment link in the Targeted MS Experiment web part.
  • Fill out the Targeted MS Experiment form.

  • Click the Submit button at the bottom of the form.

You will be taken to the experiment details page.  All the Skyline documents that were uploaded to the folder where you added the Targeted MS Experiment webpart will get added to the experiment and will appear in the Targeted MS Runs table.  If your data is organized in subfolders under the main folder, you should click the Include Subfolders button shown in the image below.


 

STEP 3: Submit the annotated folder to Panorama Public

  • Navigate back to the folder home page by clicking on the link with the icon and folder name near the top of the page. 
  • Scroll down, if you need to, so that you can see the Targeted MS Experiment box.  
  • Click the red Submit button in the Targeted MS Experiment web part. 

You will be presented with a form that looks similar to the one in the image below: 

 

In the Submission Request to Panorama Public form do the following:

  • Select “Panorama Public” from the drop-down list next to the Publish To option, if it is not already selected
  • Enter an Access Link
  • Uncheck the Keep Private checkbox. If you were submitting data for a manuscript undergoing peer review you could keep the Keep Private box checked. This will ensure that when the data is copied to Panorama Public, it will be kept private with read-only access to the submitter. Another read-only reviewer account will be created for the data, and account details provided to the submitter. These account details can be conveyed to the journal where the manuscript is submitted
  • Click the Submit button

Access Link is the link that you will include in your manuscript to link to supplementary data on Panorama Public that can be viewed in a web browser. Initially, this link points to your folder on PanoramaWeb.  But once a copy of your data has been made to Panorama Public, it will link to the location of the copied data on Panorama Public.  This will be the permanent location of your supplementary data on Panorama Public.

The Publish Experiment form allows you to “build” these the access link.  The initial part of the link remains constant:  https://panoramaweb.org/labkey.  You can choose a string to complete the link (highlighted in yellow below).

https://panoramaweb.org/labkey/choose_a_string.url

The initial value entered in the Access Link field is a randomly generated alphanumeric string.  You can replace it with a convenient, easy to remember string.  This string has to be unique across all the experiments published to Panorama Public.  You may get an error if the link you entered is already in use for another experiment on Panorama Public.  If this happens change the text in the access link field and try again.

 

Requests to copy data are handled by Panorama Public administrators within a week of submission. Once your data has been successfully copied to Panorama Public you will receive a confirmation email. If you requested that your data on Panorama Public be kept private (e.g. for a manuscript under peer review), the confirmation email will also include reviewer account details. You can pass on the account details to the journal where you are submitting your manuscript.

Once the form is submitted successfully you can go back to the experiment details page.

In the Experiment Details box, just above the experiment title, you will see a “Copy Pending!” message.   This message will disappear once your data has been copied to Panorama Public.  Any changes that you make in the folder, such as adding/removing Skyline documents or wiki pages, or changing the layout of the page will also get copied when a copy is made to Panorama Public.   At the bottom of the page, in the Submission table, you will see the Access Link that you created for this experiment.  The Copied column will be blank until a copy has been made successfully.  Once the data has been copied this column will display the date when the data was copied.  You will also receive an email informing you that the data was successfully copied to Panorama Public.  At that point if you click on the value in the Access Link column you will be taken to the folder where your data was copied on Panorama Public and you can verify that the data, folder layout and views were copied accurately.