Tag Archives: Research

Spatially Enabled Zotero Database

As a geographer, I’m a visual person.  I like to see distributions on a map and where things are matters to me.  A few years ago, while I was writing a paper I became overwhelmed with trying to remember the locations for the studies I had read (for coastal plants, latitude matters), so I started marking the locations of studies on a map and eventually turned it into a printed map.


But adding new studies and sharing the results is a cumbersome and the spatial data is largely separate from the citation information.  So I set out to find a way to store spatial information in my citation database and access the spatial information for mapping purposes.  The end result (which is still a work in progress at press time) is a web map of coastal vegetation literature that updates when new citations are added to my Zotero database online.


How I Did It:

Key ingredients: Zotero, QGIS, Spatialite, Zotero Online Account

I started working with the Zotero database I already have populated with literature relevant to my research on coastal vegetation.  I moved citations that I wanted to map into a separate folder just to make the API queries easier later.  I made a point in a shapefile for the location of each study using QGIS.  I gave the attribute table fields for the in-text citation and a text description of the location for human-readability, but the most important field is the ZoteroKey.  This is the item key that uniquely identifies each record in the Zotero database.  To find the key for each citation, in your local version of Zotero, right click on the record and pick “generate report”.  The text for the key is after the underscore in the URL for the report.  In the online version, click the citation in your list.  The key is at the end of the URL in the page that opens.


My map only has point geometries right now, but that will change in the coming weeks.

The spatial information was then to be added to the Zotero database (specific queries can be found on GitHub) in Spatialite.  The Zotero schema is quite large but not impossible to navigate.  Currently, there is no option to add your own fields to Zotero (I tried… I failed… they tell me the option is coming soon) so I put my geometries into the “Extra” field.  Using Spatialite, I opened the Zotero database and imported my shapefile of citation locations (having new tables doesn’t break the database, thank goodness).  Then I removed any existing information in the “Extra” field and filled it in with geometry information in the style of geoJSON.  The string looks like this:

{"type": "Point", "coordinates": [-123.069403678033, 38.3159528822055]}

After updating the citation records to house the geometries, I synced the changes to my online Zotero repository from my desktop program.  Now it’s ready to go into a web map using the Zotero API.  My webmap code can be found in my GitHub Repository.

What’s Next?

I would like to develop a plug-in for QGIS that makes adding the geometries to the Zotero database easier because not everyone wants to run SQL queries on their active citation database that has been years in the making (I backed mine up first!).  The interface would show the citations you want to map, then users would pick a citation, then click the location on their QGIS project where the citations should be located.  The plug-in would insert the corresponding geometry for them.

Call for Guest Bloggers

Home-made kite tail for kite aerial photography

Home-made kite tail for kite aerial photography

One of the fascinating things I find about doing biological and geographical research is the tools that scientists make for themselves to help them in their research.  For example, I designed and my dad constructed a set of quadrat frames for me.  I’ve also constructed two low altitude remote sensing platforms and the accessories that go with them like a fuzzy tail and camera housing for my air photo kite.

Now it’s your turn!  What tools have you made or re-purposed to help you collect or process data?  Do you have a creative use for straws?  Have you constructed a tool you couldn’t buy anywhere?  I’m looking for researchers of all kinds who have made their own tools to write a blog post about their creation.  The text can be as short as a paragraph or as long as a page and should describe what the tool is and how you use it.  It can also include instructions for how to make it, if you would like.  All submissions should include at least one photograph of the tool.  Submissions should be emailed to micheletobias [at] yahoo [dot] com.

Business Cards

Business cards!  Yay!  I’m really excited about having new business cards printed.  One side will have my blog information and the other will have my research contact information (please note: the phone number is obscured and the email address has been replaced with the one I use for my blog, not for research).   Unfortunately, my old pile of business cards from my days as a graduate student (of which I have about 450 remaining) are about to expire so I needed new ones.  These are so much more expressive of what I do and what I would like to be doing than the stuffy university ones.  I designed these myself with inspiration from cards I liked on the internet.

This brings me to the question: what can I do with a huge stack of old business cards that are blank on one side?

Research Logo

I made this graphic over a year ago to help brand my research.  The idea is that it will be placed on research equipment, like the camera housing for my kite aerial photography rig, and on t-shirts to make field work look more official.  It’s remarkably hard to get people to take research on a beach seriously, not that they have to, but it might be nice since it really is important and might some day save their homes if they live in coastal areas.  I haven’t actually used the logo yet on anything, but maybe that’s something I can fix this summer.

I think it’s pretty obvious that it was inspired by the National Parks’ iconography and it has a lot in common with the Robert Tobias Photography Logo I made for my dad.

You’re probably wondering what the four squares mean or why they have the images that they have.  Well, I study plants (seedling square) that live on beaches (dune square) using kite aerial photography (kite and camera squares).  There ya go!

DIY KAP Trash Can Rig in Action | publiclaboratory.org

I’ve been doing some work over at the Public Laboratory site again.  This is a quick video of one of my aerial photography rigs in action.

The YouTube video:


The original post to Public Lab:  Trash Can Rig in Action | publiclaboratory.org.

Beach Plant Competition Diagram

Nothing’s better than a diagram for an explanation, as far as I’m concerned.  This is a diagram I drew for a talk about beach plants (shocking, I know!) for the BEACH Ecology Coalition meeting last year.  It explains where we expect plants to compete with each other.  Again, this was made with Inkscape, my favorite vector illustration software.

Comic: Ye Olde Story of Science

“A flip & thoroughly anachronistic retelling of what science has been through.”

This is a comic I drew for the final for a class on the history of the scientific method.  All quarter we read historical documents on the scientific method, including essays by Plato, Aristotle, and the like.  The final project requirements were very open – it could have been an essay, art project, or really anything demonstrating that we learned something.  This is what I decided to do.  I think this is much better than my original plan to analyze how the Mythbusters used or misused the scientific method.

Please accept my apologies that this image might be difficult to read on some browsers.  I recommend zooming in on your browser window (ctrl + + on Firefox) to help make it easier to read.