Tag Archives: google refine

A Librarian’s Guide to OpenRefine

This originally appeared on the ACRL TechConnect blog.

Academic librarians working in technical roles may rarely see stacks of books, but they doubtless see messy digital data on a daily basis. OpenRefine is an extremely useful tool for dealing with this data without sophisticated scripting skills and with a very low learning curve. Once you learn a few tricks with it, you may never need to force a student worker to copy and paste items onto Excel spreadsheets.

As this comparison by the creator of OpenRefine shows, the best use for the tool is to explore and transform data, and it allows you to make edits to many cells and rows at once while still seeing your data. This allows you to experiment and undo mistakes easily, which is a great advantage over databases or scripting where you can’t always see what’s happening or undo the typo you made. It’s also a lot faster than editing cell by cell like you would do with a spreadsheet.

Here’s an example of a project that I did in a spreadsheet and took hours, but then I redid in Google Refine and took a lot less time. One of the quickest things to do with OpenRefine is spot words or phrases that are almost the same, and possibly are the same thing. Recently I needed to turn a large export of data from the catalog into data that I could load into my institutional repository. There were only certain allowed values that could be used in the controlled vocabulary in the repository, so I had to modify the bibliographic data from the catalog (which was of course in more or less proper AACR2 style) to match the vocabularies available in the repository. The problem was that the data I had wasn’t consistent–there were multiple types of abbreviations, extra spaces, extra punctuation, and outright misspellings. An example is the History Department. I can look at “Department of History”, “Dep. of History”, “Dep of Hist.” and tell these are probably all referring to the same thing, but it’s difficult to predict those potential spellings. While I could deal with much of this with regular expressions in a text editor and find and replace in Excel, I kept running into additional problems that I couldn’t spot until I got an error. It took several attempts of loading the data until I cleared out all the errors.

In OpenRefine this is a much simpler task, since you can use it to find everything that probably is the same thing despite the slight differences in spelling, punctuation and spelling. So rather than trying to write a regular expression that accounts for all the differences between “Department of History”, “Dep. of History”, “Dep of Hist.”, you can find all the clusters of text that include those elements and change them all in one shot to “History”. I will have more detailed instructions on how to do this below.

Installation and Basics

OpenRefine was called, until last October, Google Refine, and while the content from the Google Refine page is being moved to the Open Refine page you should plan to look at both sites. Documentation and video tutorials refer interchangeably to Google Refine and OpenRefine. The official and current documentation is on the OpenRefine GitHub wiki. For specific questions you will probably want to use the OpenRefine Custom Search Engine, which brings together all the mix of documentation and tutorials on the web. OpenRefine is a web app that runs on your computer, so you don’t need an internet connection to run it. You can get the installation instructions on this page.

While you can jump in right away and get started playing around, it is well worth your time to watch the tutorial videos, which will cover the basic actions you need to take to start working with data. As I said, the learning curve is low, but not all of the commands will make sense until you see them in action. These videos will also give you an idea of what you might be able to do with a data set you have lying around. You may also want to browse the “recipes” on the OpenRefine site, as well search online for additional interesting things people have done. You will probably think of more ideas about what to try. The most important thing to know about OpenRefine is that you can undo anything, and go back to the beginning of the project before you messed up.

A basic understanding of the Google Refine Expression Language, or GREL will improve your ability to work with data. There isn’t a whole lot of detailed documentation, so you should feel free to experiment and see what happens when you try different functions. You will see from the tutorial videos the basics you need to know. Another essential tool is regular expressions. So much of the data you will be starting with is structured data (even if it’s not perfectly structured) that you will need to turn into something else. Regular expressions help you find patterns which you can use to break apart strings into something else. Spending a few minutes understanding regular expression syntax will save hours of inefficient find and replace. There are many tutorials–my go-to source is this one. The good news for librarians is that if you can construct a Dewey Decimal call number, you can construct a regular expression!

Some ideas for librarians

 

(A) Typos

Above I described how you would use OpenRefine to clean up messy and inconsistent catalog data. Here’s how to do it. Load in the data, and select “Text Facet” on the column in question. OpenRefine will show clusters of text that is similar and probably the same thing.

AcademicDept Text Facet

AcademicDept Text Facet

 

Click on Cluster to get a menu for working with multiple values. You can click on the “Merge” check box and then edit the text to whatever you need it to be. You can also edit each text cluster to be the correct text.

Cluster and Edit

Cluster and Edit

You can merge and re-cluster until you have fixed all the typos. Back on the first Text Facet, you can hover over any value to edit it. That way even if the automatic clustering misses some you can edit the errors, or change anything that is the same but you need to look different–for instance, change “Dept. of English” to just “English”.

(B) Bibliographies

The main thing that I have used OpenRefine for in my daily work is to change a bibliography in plain text into columns in a spreadsheet that I can run against an API. This was inspired by this article in the Code4Lib Journal: “Using XSLT and Google Scripts to Streamline Populating an Institutional Repository” by Stephen X. Flynn, Catalina Oyler, and Marsha Miles. I wanted to find a way to turn a text CV into something that would work with the SHERPA/RoMEO API, so that I could find out which past faculty publications could be posted in the institutional repository. Since CVs are lists of data presented in a structured format but with some inconsistencies, OpenRefine makes it very easy to present the data in a certain way as well as remove the inconsistencies, and then to extend the data with a web service. This is a very basic set of instructions for how to accomplish this.

The main thing to accomplish is to put the journal title in its own column. Here’s an example citation in APA format, in which I’ve colored all the “separator” punctuation in red:

Heller, M. (2011). A Review of “Strategic Planning for Social Media in Libraries”. Journal of Electronic Resources Librarianship, 24 (4), 339-240)

From the drop-down menu at the top of the column click on “Split into several columns…” from the “Edit Column” menu. You will get a menu like the one below. This example finds the opening parenthesis and removes that in creating a new column. The author’s name is its own column, and the rest of the text is in another column.

Spit into columns

 

The rest of the column works the same way–find the next text, punctuation, or spacing that indicates a separation. You can then rename the column to be something that makes sense. In the end, you will end up with something like this:

Split columns

When you have the journal titles separate, you may want to cluster the text and make sure that the journals have consistent titles or anything else to clean up the titles. Now you are a ready to build on this data with fetching data from a web service. The third video tutorial posted above will explain the basic idea, and this tutorial is also helpful. Use the pull-down menu at the top of the journal column to select “Edit column” and then “Add column by fetching URLs…”. You will get a box that will help you construct the right URL. You need to format your URL in the way required by SHERPA/RoMEO, and will need a free API key. For the purposes of this example, you can use 'http://www.sherpa.ac.uk/romeo/api29.php?ak=[YOUR API KEY HERE]&qtype=starts&jtitle=' + escape(value,'url'). Note that it will give you a preview to see if the URL is formatted in the way you expect. Give your column a name, and set the Throttle delay, which will keep the service from rejecting too many requests in a short time. I found 1000 worked fine.

refine7

After this runs, you will get a new column with the XML returned by SHERPA/RoMEO. You can use this to pull out anything you need, but for this example I want to get pre-archiving and post-archiving policies, as well as the conditions. A quick way to to this is to use the Googe Refine Expression Language parseHtml function. To use this, click on “Add column based on this column” from the “Edit Column” menu, and you will get a menu to fill in an expression.

refine91

In this example I use the code value.parseHtml().select("prearchiving")[0].htmlText(), which selects just the text from within the prearchving element. Conditions are a little different, since there are multiple conditions for each journal. In that case, you would use the following syntax (after join you can put whatever separator you want): forEach(value.parseHtml().select("condition"),v,v.htmlText()).join(". ")"

So in the end, you will end up with a neatly structured spreadsheet from your original CV with all the bibliographic information in its own column and the publisher conditions listed. You can imagine the possibilities for additional APIs to use–for instance, the WorldCat API could help you determine which faculty published books the library owns.

Once you find a set of actions that gets your desired result, you can save them for the future or to share with others. Click on Undo/Redo and then the Extract option. You will get a description of the actions you took, plus those actions represented in JSON.

refine13

Unselect the checkboxes next to any mistakes you made, and then copy and paste the text somewhere you can find it again. I have the full JSON for the example above in a Gist here. Make sure that if you save your JSON publicly you remove your personal API key! When you want to run the same recipe in the future, click on the Undo/Redo tab and then choose Apply. It will run through the steps for you. Note that if you have a mistake in your data you won’t catch it until it’s all finished, so make sure that you check the formatting of the data before running this script.

Learning More and Giving Back

Hopefully this quick tutorial got you excited about OpenRefine and thinking about what you can do. I encourage you to read through the list of External Resources to get additional ideas, some of which are library related. There is lots more to learn and lots of recipes you can create to share with the library community.

Have you used OpenRefine? Share how you’ve used it, and post your recipes.

 

Analyzing CVs for publisher copyrights and self-archiving with OpenRefine

This originally appeared on the ACRL TechConnect blog.

I started working on this project yesterday, but I wanted to write it up as quickly as possible so that I could see how others are approaching this issue. First of all, I should say that this approach was inspired by this article in the Code4Lib Journal: “Using XSLT and Google Scripts to Streamline Populating an Institutional Repository” by Stephen X. Flynn, Catalina Oyler, Marsha Miles.

The problem I had was a faculty member who sent a CV to a liaison for adding the items to the repository, but whose citations were not showing up in the citation databases–and I now work at an institution with all of the resources I need for this. So I wanted to go the other way, and start with the CV and turn that into something that I could use to query SHERPA/RoMEO.

It occurred to me that the best tool for this might be Google Refine (now OpenRefine, I guess), which I’ve always wanted to play around with. I am sure there are lots of other ways to do this, but I found this pretty easy to get set up. Here’s the approach I’m taking, with a version of my own CV.

  1. Start with a CV, and identify the information you want–you could copy the whole thing or use screen scraping or what have you, but most people’s CVs are about 20 pages long and you only care about 1 or 2 pages of journal articles.cv
  2. Copy this into a text editor to remove weird formatting or spacing. You want to have each citation in its own line, so if you had a CV with hanging indents or similar you would have to remove those.text
  3. Now (assuming you’ve installed and opened Google Refine), either import this text file, or copy in the text. Import it as line based text file, and don’t select anything else.
    importtorefine
  4. Click on Create Project>>, and it will bring it into Google Refine. Note that each line from the text file has become a row in the set of data, but now you have to turn it into something useful.refine1
  5. My tactic was to separate the author, date, title, journal title, and other bibliographic information into their own columns. The journal title is the only one that really matters for these purposes, but of course you want to hang on to all the information. There are probably any number of ways to accomplish this, but since citations all have a standard structure, it’s really easy to exploit that to make columns. The citations above are in APA style, and since I started with social work faculty to test this out, that’s what I am starting with, but I will adjust for Chicago or MLA in the future. Taking a look at one citation as example we see the following:

    Heller, M. (2011). A Review of “Strategic Planning for Social Media in Libraries”. Journal of Electronic Resources Librarianship, 24 (4), 339-240)

    Note that we always have a space after the name, an open parentheses, the date, a closed parentheses, and a period followed by a space (I’ve colored all the punctuation we want blue). So I can use this information to split the columns. To do so, select “Split into several columns” from the Edit Column menu.
    refine2
    Then in the menu, type in the separator you want to use, which in this case is space open parentheses. Split into two columns, and leave the rest alone. Note that you can also put a regular expression in here if necessary. Since dates are always the same length you could get away with field lengths, but this way works fine.
    refine3
    After this, you will end up with the following change to your data:
    refine4
    Now the author is in the first column, and the opening parenthesis is gone.

  6. Following along with the same rationale for each additional field and renaming the columns we end up with (cooking show style) the following:
    refine5Each piece of information is in its own column so we can really start to do something with it.
  7. I am sure there’s a better way to do this, but my next step was to use the journal title as the query term to the SHERPA/RoMEO API call. This was super easy once I watched the data augmentation screencast; there is documentation here as well. Open up the following option from the edit column menu:
    refine6
    You get a box to fill in the information about your API call. You have all kinds of options, but all you really need to do for this is format your URL in the way required by SHERPA/RoMEO. You should get an API key, and can read all about this in the article I linked to above. There are probably several ways to do this, but I found that what I have below works really well. Note that it will give you a preview to see if the URL is formatted in the way you expect. Give your column a name, and set the Throttle delay. I found 1000 worked fine.
    refine7In a copy and pastable format, here’s what I have in the box:'http://www.sherpa.ac.uk/romeo/api29.php?ak=[YOUR API KEY HERE]&qtype=starts&jtitle=' + escape(value,'url')
  8. Now it will run the query and send back a column of XML that looks like this:
    refine8
  9. From this you can extract anything you want, but in my case I want to quickly get the pre and post-archiving allowances, plus any conditions. This took me awhile to figure out, but you can use the Googe Refine Expression Language parseHtml function to work on this. Click on Add column based on this column from the Edit Column menu, and you will get a menu to fill in an expression to do something to your data. After a bit of trial and error, I decided the following makes the most sense. This grabs the text out between the <prearchiving> element in the XML and shows you the text. You can see from the preview that you are getting the right information. Do the same thing for post-archiving or any other columns you want to isolate. The code you want is value.parseHtml().select("elementname")
    refine9
    Conditions are a little different, since there are multiple conditions for each journal. In that case, you would use the following syntax (after join you can put whatever separator you want): forEach(value.parseHtml().select("condition"),v,v.htmlText()).join(". ")"
  10. Now you have your data neatly structured and know the conditions for archiving, hooray! Again, cooking show style, here’s what you end up with. You can certainly remove the SHERPA/RoMEO column at this point, and export the data as Excel or whatever format you want it in.
    refine11
  11. BUT WAIT, IT GETS BETTER. So that was a lot of work to do all that moving and renaming. Now you can save this for the future. Click on Undo/Redo and then the Extract option.
    refine12
    Make sure to unclick any mistakes you made! I entered the information wrong the first time for the API call, so that added an unnecessary step. Copy and paste the JSON into a text editor and save for later. refine13
  12. From now on when you have your CV data, you can click on the Undo/Redo tab and then choose Apply. It will run through the steps for you and automatically spit out your nicely formatted and researched publications. Well… realistically the first time it will spit out something with multiple errors, and you will see all the typos that are messing up your plan. But since the entire program is built to clean up messy data, you’re all set on that end. Here’s the APA format I described above for you to copy and paste if you like–make sure to fill in your API key: cvomatic

I hope this is useful to some people. I know even in this protean form this procedure will save me a ton of time and allow library liaisons to concentrate on outreach to faculty rather than look up a ton of things in a database. Let me know if you are doing something similar and the way you are doing it.