Summary and Setup

ATTENTION This is an experimental test of The Carpentries Workbench lesson infrastructure. It was automatically converted from the source lesson via the lesson transition script.

If anything seems off, please contact Zhian Kamvar zkamvar@carpentries.org

Before you can analyze data you need to clean it. Data cleaning identifies errors and corrects formatting to create consistent data. This step must be taken with extreme care and attention because without clean data the results of analysis may be false and non-reproducible.

OpenRefine is a powerful free and open source tool for working with messy data: cleaning it and transforming it from one format into another.

This lesson will teach you to use OpenRefine to clean and format data effectively and automatically track any changes that you make. Many people comment that this tool saves them literally months of work trying to make these edits by hand.

Getting Started

Data Carpentry’s teaching is hands-on, so participants are encouraged to use their own computers to ensure the proper setup of tools for an efficient workflow.
These lessons assume no prior knowledge of the skills or tools.

To get started, follow the directions in the Setup page to download data to your computer and follow any installation instructions.

To most effectively use these materials, please make sure to install everything before working through this lesson.

For Instructors

If you are teaching this lesson in a workshop, please see the Instructor notes.

Data

Download the data file Portal_rodents_19772002_simplified.csv, which is a csv file that will open in a new browser tab. Be sure to right click or control click in order to save the file (NOTE: In Safari, right click and select Download linked file; in Chrome and Firefox, right-click and select Save link as...). Make a note of the location (i.e. the folder, your Desktop) to which you save the file.

About the data

The data for this lesson is a part of the Data Carpentry Ecology workshop. It is a teaching version of the Portal Database. The data in this lesson is a subset of the teaching version that has been intentionally ‘messed up’ for this lesson.

The data for this lesson and the workshop are in the Portal Project Teaching Database available on FigShare, with a CC-BY license available for reuse.

Software

For this lesson you will need OpenRefine version 3.7.2 and a web browser.

Note: OpenRefine is a Java program that runs on your machine (not in the cloud). It runs inside your browser, but no web connection is needed.

Download OpenRefine version 3.7.2 from https://openrefine.org/download.

  • Do not download beta versions or the release candidates. These are only for development and testing of the software.
  • If you are on Windows and do not have Java installed, download the version Windows (including Java).
  • Unzip the downloaded file into a directory and name that directory something like OpenRefine.
  • Check below for further instructions depending on your operating system.

Windows

  1. Go to your newly created OpenRefine directory.
  2. Launch OpenRefine by double clicking on openrefine.exe (this will launch a black command prompt window first; ignore this window, and wait for OpenRefine to launch in the web browser, which is where you will interact with the program).
  • If Windows displays a blue notification titled Microsoft Defender SmartScreen prevented an unrecognized app from starting, click on More info and then click on Run anyway.
  1. If you are using a different browser, or OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to launch the program.

Mac

  1. Go to your newly created OpenRefine directory.
  2. Drag the OpenRefine icon into Applications folder, and Ctrl-click/Open… it.
  • If Mac shows a notification when you try to run the program that it cannot verify the developer, click Cancel. Then, Right-click or Ctrl-click the icon and select Open. The notification will now have an Open button. If it does not allow to open the program, repeat the process and there will be an Open button the second time. For additional details, consult the OpenRefine installation guide.
  1. If you are using a different browser, or OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to launch the program.

Linux

  1. Navigate to your newly created OpenRefine directory using the command line.
  2. Type ./refine into the terminal within the OpenRefine directory
  3. If you are using a different browser, or OpenRefine does not automatically open for you, point your browser at http://127.0.0.1:3333/ or http://localhost:3333 to launch the program.

Web Browser

OpenRefine requires one of these web browsers installed in your computer:

  • Google Chrome
  • Chromium
  • Safari
  • Opera
  • Microsoft Edge

OpenRefine has some issues with Firefox. Internet Explorer is not supported.

Note: Other versions of OpenRefine should work, but the results might be different due to changes in the software or default settings.