Metadata Generation

Qresp | Curator tool accesses the folder that contains your research data and collects information about:

  • Data location & access
  • Data content
  • Paper details
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Start

This step allows the user to resume a previously interrupted curation process, by uploading the JSON metadata file or to leave it blank and click continue.

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Enter Your Details

This step defines the identity of the person that is using Qresp to generate metadata.

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Connect to Server

This step defines the location of the remote server where the paper content is organized and stored. The paper will be accessed by establishing an SSH connection using the credentials inserted below. Username and password will not be saved.

  • Server Name: Enter the name of the remote server where the paper content is organized and stored. e.g. midway.rcc.uchicago.edu
  • Username: Enter the username used to establish a SSH connection to the remote server.
  • Password: Enter password associated to the username.
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Access Paper Content

This step allows the user to navigate the server data tree and to select the folder with the paper content.

  • Path to paper content: Enter the path locating the paper content. If you do not know the full path, the data tree below helps you locate the paper content, and when you click on a folder the path field is automatically updated. If your paper path is not under your home directory, type the root of the path tree and click the Search button.

It also identifies whether the following services are running on the remote server.

  • Http: It is required only by Qresp Exploration. If an HTTP service is running on the server, a URL may be associated to the paper content. This URL is only required by Qresp | Exploration to view images & download files using a web browser.
  • Git: It is not required but recommended for version control.If a Git service is running on the server, the user may version control the paper content.
  • Globus: It is not required but recommended for download of large files. The Globus (add link to globus) service allows to download the paper content using gridFTP.
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Tag Paper Content

This step tags the paper content. The tagging procedure is divided in sections. Each section may require the interaction with the paper content widget (on the left). The paper content widget allows the user to navigate the content of the paper and enter file names during the tagging operation.

Note

Continue button re-verifies with the user if the user has filled all mandatory fields.

Note

Save button enables only if the user has filled all mandatory fields.

Note

Multiple charts, tools, scripts or datasets are saved as buttons on top of each section.

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Add Information

This section collects general information about your paper.

  • PIs: First Name, Middle Name and Last Names of all co-PI of the paper. Use plus to add additional PIs.
  • Paper Stack: Enter name(s) defining group of papers (e.g. according to source of fundings).
  • Keywords: Enter keyword(s) (e.g: ‘DFT’, ‘organic materials’, ‘charge transfer’): they facilitate paper searches using Qresp | Exploration.
  • Main Notebook File: Enter name of a notebook file, this file may serve as a table of contents and may contain links to all datasets, charts, scripts, tools and documentation. Use the Paper Content widget (on the left) to fill this field.
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Add Charts

This section collects information about the Charts of the paper.

  • Kind: Select Figure or Table.
  • Caption: Enter chart caption.
  • Number: Enter chart number.
  • Files: Enter file name(s) containing the data displayed in the chart (e.g. a file in CSV format). Use the Paper Content widget (on the left) to fill this field.
  • Image File: Enter file name containing a snapshot of the chart. Use the Paper Content widget (on the left) to fill this field. Allowed formats are: jpg, jpeg, gif, png.
  • Notebook File: Enter name of the notebook file used to generate the chart. Use the Paper Content widget(on the left) to fill this field. Allowed format is ipynb.
  • Keywords: Enter keyword(s) for the content displayed in the chart (e.g. ‘potential energy surface’, ‘band gap’).
  • Save As: Enter a name to identify the chart.
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Add Tools

This section collects information about the Tools used in the paper. The tool represents the use of an instrument (either software or experimental set up).

  • Kind: Select Software or Experiment.
  • Package Name: Enter name of the package (e.g. ‘WEST’).
  • URLs: Enter link(s) to package official website (e.g. ‘www.west-code.org’).
  • Version: Enter version number of the package (e.g. ‘3.0.0’) .
  • Executable Name: Enter name of the package executable (e.g. ‘wstat.x’).
  • Patches: Enter file name(s) containing the patches of publicly available or versioned software, customized by the user to generate some of the datasets. Use the Paper Content widget (on the left) to fill this field (e.g. enter ‘Tools/modified_wstat.txt’).
  • Description: Enter a summary of the modifications, if any, made to the executable(s) using the patches.
  • Save As: Enter a name to identify the Software tool.
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If an Experiment,

  • Facility name: Enter name of the facility where the experiment was conducted (e.g. ‘Argonne Advanced Photon Source’).
  • Measurement: Enter type of measurement (e.g. ‘soft X-ray Photoemission’).
  • URLs: Enter link(s) to facility website (e.g. ‘https://www.aps.anl.gov’).
  • Save As: Enter a name to identify the Experiment.
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Add Datasets

This section collects information about the datasets generated in the paper. A dataset is a file or folder or a combination of the two which contains raw data generated in the scientific paper. Datasets are created by an instrument or by a versioned software.

  • Files: Enter file name(s) to identify the dataset. Use the Paper Content widget (on the left) to fill this field (e.g. enter ‘Data/dataset.dat’). If you list a folder name, all documents of the folder belong to the dataset.
  • Description: Enter a summary about the content of the dataset.
  • URLs: Enter link(s) to the URL of the dataset, if available.
  • Save As: Enter a name to identify the dataset.
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Add Scripts

This section collects information about the scripts. Scripts are source codes not available publicly used to manipulate datasets and generate the data files of charts, or other data discussed in the scientific paper.

  • Files: Enter file names to identify the script. Use the Paper Content widget (on the left) to fill this field (e.g. ‘Script/scriptA.py’). If you list a folder name, all documents of the folder belong to the script.
  • Description: Enter a summary about the content of the script.
  • URLs: Enter link(s) to the URL of the script, if available.
  • Save as: Enter a name to identify the script.
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Add Paper

This section collects information about the publication associated to the paper. The DOI number may aid in auto filling certain fields.

  • Kind: Choose type of publication. Preprint , Journal, Dissertation

If Journal,

  • DOI: Enter the Digital Object Identifier of the publication.
  • Title: Enter title.
  • JournalFull: Enter name (in full) of journal.
  • JournalAbbr:Enter name (abbreviated) of journal.
  • Volume: Enter volume number.
  • Page: Enter page number.
  • Year: Enter year.
  • Abstract: Enter abstract.
  • URLs: Enter link(s) of the paper.

If Dissertation,

  • Advisors: Enter name(s) of advisor(s).
  • School: Enter name of school where dissertation was presented.
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Define Workflow

This step defines the workflow of the paper. A workflow represents how the content of the paper was created.

  • Use the Edit Button in the canvas to add: Add External Node , or to Add Node Connection. The type of nodes are listed on the right. (Hover over the node for hints).
  • Use the Rearrange Button to animate the workflow.
  • External: The external node represents content that was used within the paper, but not generated within the paper. A reference/link is not required but recommended.
  • Chart: The chart node represents a figure or a table, and is typically considered an end-point within the workflow.
  • Tools: The tool node represents an instrument (either software or experimental set up) utilized in the paper.
  • Dataset: The dataset node represents data generated by either a Tool or Script node.
  • Script: The script node represents user-defined procedures utilized in the paper (e.g. to analyze or post-process data belonging to datasets).

Note

The Continue button enables only after connecting atleast two nodes with an edge.

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Download & Publish Metadata

This step defines the location of the remote server where MongoDB is installed.

  • Database Hostname: Enter the address of the database. Qresp automatically inserts the metadata file in the database. The hostname may be inserted manually or selected from a list of established database names (available from the drop down menu. Safari users need to double click the field).
  • Port: Enter port number of the database.
  • Username: Enter username to login to the database.
  • Password: Enter password associated to the username.
  • Database Name: Enter name of the database.
  • Collection: Enter collection of the database where the metadata file will be inserted.
  • Is the Database SSL protected?: SSL (Secure Sockets Layer) is the standard security technology for establishing an encrypted link between a web server and a browser.
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Finish

Qresp | Curator has generated the metadata file. A copy of the metadata file was downloaded in your local system.

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