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Session Title: SEASR Analytics for Zotero

Importance of the Topic

Leveraging the extensive capabilities of the Meandre engine is not limited to the Workbench and Community Hub. Zotero is a very popular Firefox extension among humanities researchers, allowing them to collect, manage, and cite their research sources. This session will show how to leverage the capabilities of the Meandre engine from Zotero, allowing researchers to bring the power of analytics to their Zotero collections. Researchers at Tufts University who created VUE (Visual Understanding Environment) have also leveraged SEASR services for automatically extracting some information for concept mapping. This session will provide information on expanding the analytical capabilities provided by the Zotero extension. Being able to create and run custom analytical algorithms on their Zotero collections is important for researchers to be able to address meaningful research questions regarding their data.

Focus of the Topic

Upon completion of this session, participants will:

  • Be able to install and use the SEASR Analytics for Zotero
  • Understand what happens behind the scene - what information is pulled from Zotero and transmitted to a Meandre flow for analysis
  • Be able to use the VUE Firefox plugin which also works from within Zotero and calls SEASR services
  • Be able to adapt an existing flow (or create a new flow) that will perform some analysis on the items in a collection
  • Understand how the configuration mechanism for enabling flows in the SEASR Analytics extension works

Format of the Session

  • Presentation
  • Demonstration
  • Learning Exercise
  • Discussion Questions
  • Summary and Review

Presentation

Demonstration

  • We will be demonstrating the use of the SEASR Analytics for Zotero
  • We will also showcase Tufts' Visual Understanding Environment (VUE) for Zotero and its integration with SEASR
  • We will go through an example of what a Zotero-enabled flow looks like and what's special about it
  • We will show how to modify an existing Zotero-enabled flow and how to "deploy" it so that it can be leveraged within Zotero

Learning Exercises

  • Have participants run some of the Zotero-enabled flows on some collection
    1. If you already have a Zotero collection you want to use, skip to the next step
      1. Create a collection by right-clicking on "My Library" and selecting "New Collection"
        1. Give the collection a name (such as "DocSouth")
      2. Select this collection
      3. Use Firefox to navigate to http://docsouth.unc.edu/neh/aaron/aaron.html
      4. Open Zotero by clicking the Zotero icon in Firefox (bottom-right corner)
      5. Capture the current webpage as a Zotero item by clicking the "Create new item from current page" button (fifth from the left on the Zotero toolbar)
      6. Navigate to http://docsouth.unc.edu/neh/adams/adams.html and repeat the previous step
      7. You should now have two documents in your "DocSouth" collection
    2. Select one or more items in Zotero and then right-click on one of the selected items and choose SEASR Analytics -> SEASR -> Tag Cloud Viewer to create a tag cloud from text extracted from your Zotero item(s)
    3. Do the same thing but select SEASR Analytics -> SEASR -> Hits Summarizer instead, to view a list of top tokens and sentences extracted from your item(s)
    4. Repeat the same procedure one more time, but this time select SEASR Analytics -> SEASR -> Date Entities to Simile Timeline to view a timeline containing dates extracted from your item(s)
  • Run an analysis on a Zotero collection through VUE. These steps will create nodes in VUE and extract the words from these documents and connect them with a link. By doing this for multiple documents, you will see what words (concepts) are mentioned in  multiple documents. Note that we could change from words to an extracted entity, like Person and automatically build a social network around the documents that are selected.
    1. Note: This exercise requires the existence of a Zotero collection; you can create one by following step 1 in the previous exercise, if necessary
    2. Open Zotero by clicking on the Zotero icon in Firefox (bottom-right corner)
    3. Click the Settings button on the Zotero toolbar (third from left) and select "Start VUE"
      1. Confirm the security prompt, if one is presented
    4. Right-click the collection (ex: "DocSouth") and select "Send to VUE and Add to Map"
    5. Select one of the boxes (documents) in the VUE workspace and then choose Analysis -> SEASR from the VUE menu
    6. In the new window that is displayed, select "Create new nodes" in step 2, and the "Resource Word Count" analysis in step 3 and press Analyze
    7. Repeat this for additional nodes in your graph to build a more complex network of words. You can now use the functionality of VUE to rearrange your graph to tell a story.
  • Create a new flow (or adapt an existing flow) using the Meandre Workbench that performs some simple analysis and "deploy" it for access by Zotero; in the following steps we will adapt the Tag Cloud Viewer flow for Zotero to add the ability for users to specify additional words to be filtered out from the tag cloud
    1. Log in to Meandre Workbench and open the flow "Zotero Tag Cloud Viewer"
    2. Use the "Save As..." button in the Workbench to save a copy of this flow as "Zotero Tag Cloud Viewer Custom"
    3. From the list of components, find "Concatenate Text" and "Push Text" and add each one in turn to the custom flow
    4. Connect the output of Push Text to one of the inputs of the Concatenate Text we just added; next we will be placing this Concatenate Text between the other Concatenate Text and Tokenizer
    5. Connect the output of this Concatenate Text to the input port of Tokenizer (where the other Concatenate Text is also connected)
    6. Now connect the output of the old Concatenate Text to the remaining input of the new Concatenate Text we just added
    7. Finally, change the "message" property of the Push Text added earlier to include a whitespace-separated list of words you want to filter out from the tag cloud
    8. Save the flow and execute it, noting the "Service location:" address displayed during the initial stages of execution; we need this address to "tell" Zotero where to access the flow
  • Create a local configuration file and load it in the SEASR Firefox addon
    1. Point your browser to http://repository.seasr.org/Zotero/config/seasr.xml
    2. Use File -> Save As... to save a copy of this file on your computer with the name "SEASRcustom.xml"
    3. Edit "SEASRcustom.xml" with any text editor and replace the url attribute of Tag Cloud Viewer (http://services.seasr.org:10004/service/post) with the "service location" address obtained in the last step of the previous exercise, then save and close the file
    4. In Firefox open the menu Tools -> Addons and click the Preferences button for "SEASR Analytics for Zotero"
    5. In the window that opened click the SEASR logo (if not already selected) to display the preferences page
    6. Click Add and then type "Custom" in the "Provider" field
    7. Next, click Browse and select the file we edited earlier ("SEASRcustom.xml")
    8. Check the "Enable" checkbox and click OK
    9. Test the new capability
      1. Select one or more items in Zotero, then right-click on one of the selected items and choose SEASR -> Custom -> Tag Cloud Viewer

Attendee Project Plan

  • Review project plan
  • Modify and develop the project plan over the week

Discussion Questions

  • What kinds of data assets would you be creating in Zotero?
  • What other analysis would you like to use against this data?
  • What improvements would you like to see in the SEASR-Zotero integration, both in terms of functionality and user interaction experience?

Optional: Installing Zotero, SEASR Analytics, and VUE

  • Zotero
    1. Use Firefox to navigate to http://www.zotero.org
    2. Click the Download button (top-right) and then select "Allow" to install the Zotero addon for Firefox
  • SEASR Analytics
    1. Use Firefox to navigate to http://addons.mozilla.org/en-US/firefox/addon/10020
    2. Check the "Let me install this experimental addon" checkbox and then click on the "Add to Firefox" button
    3. Click the "Accept and Install" button to install the SEASR Analytics for Zotero addon
  • VUE
    1. Use Firefox to navigate to http://releases.atech.tufts.edu/vue/
    2. Click the "Firefox Plugin..." link and save the file somewhere on your computer
    3. In Firefox, open the File menu and select "Open File..." and open the previously saved file to install the VUE addon for Zotero

Summary and Review

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