Paper exploration

The Exploration platform of Qresp | Explorer is a GUI to explore and make available data on a per-publication basis. It provides a portal for the scientific community to access data sets, tools and workflows of a published scientific paper, enabling the reproducibility and validation of the paper results.

Connect to a mongo database instance

This step allows the administrator to establish a connection to a running instance of MongoDB. The Qresp database configuration is accessible through /admin page of Qresp. To establish a connection between the Qresp | Explorer and a local or private instance of MongoDB the MongoDB instance information must be provided on the Qresp admin page. The passcode to access the admin page is the KEY variable set during installation.

_images/Explorer_Connect.png

Example key-values for configuring a connection to an instance of MongoDB are provided below:

hostName=fire.uchicago.edu
port=27017
dbName=datahub
dbUsername={database user name}
dbPwd={database password}
dbCollection=paper
isSSL=No

Note

Details of the installation of a mongo database can be found at mongo database.

Access a Qresp Server Instance

This step allows the user to choose one/all Qresp instances to explore the curated papers.

_images/Explorer_Home.png

Search/Filtered Search View

This step allows the user to filter their search results by entering any of the following:

  • General keyword search
  • Collection names
  • DOI of paper
  • Tags to the paper
  • Title of paper
  • Authors of the paper
  • Publication source

Alternatively, the user can click the search button to view all papers without applying any filter.

_images/Explorer_Search.png

All publications/Filtered View

This step allows the user to view all/filtered paper content.

_images/Explorer_Search_1.png

View Paper Information & Charts

This step allows the user to view and download files that generated the figure/table.

  • The Data Tree button shows all the files in a tree format.
  • The Download button redirects to Globus (if available) to download the files of figure/table using GridFTP.
  • The Workflow button shows the workflow which represents how the figure/table was created.
_images/Explorer_Figures_Info.png _images/Explorer_Figures.png

View Datasets

This step defines all datasets used in the paper.

_images/Explorer_Datasets.png

Workflow

This step defines a workflow for the entire paper content. It represents how the content of the paper was created. Specific workflows for reproducibility of a figure/table can also be viewed by clicking the workflow button.

_images/Explorer_Workflow.png _images/Explorer_Chart_Workflow.png

Download

This step allows the user to redirect to Globus (if available) to download the entire paper content using GridFTP.

_images/Explorer_Globus.png

Notebook

This step loads a notebook viewer where the user can view or download the notebook that generated the figure/table.

_images/Explorer_Notebook_Viewer.png

Publication

This step redirects to the publishers page where the journal publication can be found.

Mint

This step allows the user to mint a DOI for the paper.

_images/DataHub_Mint1.png _images/DataHub_Mint2.png
  • After signing up, the user may click on create application and add Application name, Description & Callback URL. The Callback URL must contain mint.jsp page of the Explorer.
_images/DataHub_Mint3.png _images/DataHub_Mint4.png
  • This action will reveal a Consumer ID, which can then be copied and pasted in the Qresp mint page as shown in the example below.
_images/DataHub_Mint5.png _images/Explorer_Paper.png