Getting Started with Open Refine

Learning Objectives

• Motivate participants to clean, organize, enhance data before inserting it into a database or merging it with other data files.
• Introduce participants to Open Refine as a powerful data-cleaning tool.
• Encourage dataset exploration; look at the data with the visualization tools in Open Refine.

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Lesson

Motivations for the Open Refine Lesson

• It’s really important that you know what you did. More journals/grants/etc. are also making it important for them to know what you did. You can capture all steps done to your data in Open Refine to the raw file and share them with your publication as supplemental material.
• All steps are easily reversed in Refine.
• You must save your work to a new file; Refine does not modify your original dataset.
• Data is often very messy - and this tool saves a lot of cleaning headaches.
• Data cleaning steps often need repeating with multiple files. Refine is perfect for speeding up repetitive tasks.
• Some concepts like clustering algorithms are quite complex, but Refine makes it easy to introduce them, use them, and show their power.

Before we get started

• Check that you have Firefox browser installed. Open Refine runs in this browser. It will not run in IE.
• Download software from http://openrefine.org if you have not done this yet.
• Unzip the downloaded file into a directory. Name that directory something like Open-Refine
• Note that “double-clicking” a zipped file on a windows machine sometimes results in a correctly unzipped set of files, other times, this is not successful. Try installing 7-Zip and use 7-Zip to extract all files from the zipped file to the desired directory.
• Go to your newly created Open-Refine directory.
• Launch Open Refine
  • Windows: Click the openrefine.exe
  • Mac: Drag icon into Applications folder and double-click it
  • Linux: Run ./refine
• Note, this is a Java program that runs on your machine (not in the cloud). It runs inside the Firefox browser, but no web connection is needed.

Basics of Open Refine

You can find out a lot more about Open Refine at http://openrefine.org and check out some great introductory videos. There is also an Open Refine Google Plus community where you can find a lot of help and a lot of folks from the life sciences are members. As with other programs of this type, Open Refine libraries are available too, where you can find a script you need and copy it into your Refine instance to run it on your dataset.

• Open source.
• A large growing community, from novice to expert, ready to help.
• Works with large-ish datasets (100,000 rows). Does not scale to many millions. (yet).

Next: Working with OpenRefine