A simple digital academic workflow

[Please see digital academic workflow video at Screencast of a simple academic workflow. Scroll down just a wee bit to see the whole screen.]

The amount of lost time and lost productivity resulting from inadequate academic workflows affects not only individual researchers but their whole field. While there have not been many studies done on workflows, one survey (University of Minnesota Libraries, 2006) found that 36% of the social science faculty at the University of Minnesota used reference managers compared to only 8% in the humanities. If we can assume that even fewer faculty members are using efficient academic workflows, then the state of research is in need of an upgrade.

The same study (University of Minnesota Libraries, 2006) found that graduate students are 50% more likely than faculty to use reference managers. Thus the concept of an academic apprenticeship (McGowan, 2005) takes on a new meaning, with graduate students able to teach faculty a lesson.

Howison and Goodrun (2005, p. 3) write that the system for managing academic papers “is far from standardized and ranges from manual ‘fumbling’ through to quite sophisticated if users employ citation managers, such as Endnote or the variety of Bibtex management systems. Yet even the most sophisticated users experience difficulty in managing their files.” This, they write, is due not only to industry lagging behind in the area of integrated support for researchers, but due also to the incapacity of PDFs and most other documents to allow metadata to be included within the document itself. When we download a paper, we must download the metadata separately, whereas when we download music, the metadata is included in the music file. This kind of inefficiency, in addition to a lack of available commercial workflows for researchers, has led many of us to create our own workflows, with varied results.

This search for a simple yet effective digital academic workflow is not new. Hundreds of researchers (see e.g. Judson, 2008; Roberts, 2009) have written on the web about their attempts to set up and use a system that will:

1)    Find new articles of interest quickly and download them simply with their metadata

2)    Enable them to annotate, mark up, and take notes digitally, with no need for a paper copy of their documents

3)    Keep all their papers and other research documents in one place

4)    Provide a way to search through those documents in an efficient way

I currently use a very simple system of Google Scholar, BibDesk, Skim (all free) and Spotlight (which comes on all Macs) which is a very limited version of a much more powerful workflow called researchr (Haklev, n.p.) which was developed by Stian Haklev at OISE, University of Toronto. One day I hope to be running researchr (we have experienced some technical difficulties in running my version of researchr reliably (update October 2012 researchr is now working beautifully, thank you Stian!), but in the meantime my current very basic workflow does all of the above simply and efficiently. One advantage of my workflow is that it is so basic that I can run it by myself, with no need for computer expertise, and so can anyone else. It should be noted here that this workflow will only work on a Mac as BibDesk, Skim, and Spotlight are applications that work on Macs only, but similar workflows are possible on any computer OS.

Google Scholar

I chose Google Scholar to do my online searching for articles because it was faster and more efficient than using the University of Toronto’s (where I am a graduate student) online library (Sept. 2011 update: The U/T library system has been completely revamped and it now far faster and more efficient than it used to be). Google Scholar probably has the widest coverage of all online library search engines and provides information on the number of times an article has been cited, which most other libraries don’t (Hull, Pettifer & Kell, 2008). Google Scholar “aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature” (Scholar.google.com, n.p.). The efficiency of looking up a topic and finding the most relevant articles ranked top down is currently unmatched by other online library search engines. However, according to Jasco (2005), a big problem with Google Scholar is that millions of articles have not yet been indexed, so coverage is far from complete. Despite this, I find Google Scholar very useful and will likely use it for many years, along with the University of Toronto online library for backup.

In fact, with Google Scholar I can set my preferences (click on the cog-like spoked wheel to the right of “sign in” in the upper right hand corner of any Scholar page) for the University of Toronto’s Get It! service (any university student should be able to use their own library membership to do the same, just type in the name of your university and click search in the Library links section), which means that as soon as I am logged into the U/T library system, all articles that are available from the U/T library will be identified by a “Get it! U of Toronto” link. I just click on the link and I’m taken to the databases where the article is available. So the U/T online library is nicely synched to Google Scholar now, which is fantastic because the U/T library has access to many articles that are not available online.

BibDesk

BibDesk is a free and open-source reference manager that is under active development by a small group of volunteers (SourceForge.net, n.d.). With BibDesk, your collection of PDFs and other documents is organized by author name, document title, date of publication, etc. so that finding documents is easy. BibDesk automatically imports keywords when it imports the citation data, but you can add your own keywords as well, which is something that I have started to do with painstaking commitment. By adding my own keywords, I can find information I am looking for much faster (please see attached video for a demonstration).

BibDesk can search titles but cannot search the PDFs themselves, which would be a very useful feature, but this is easily done on a Mac using Spotlight, Apple’s powerful search tool. BibDesk also allows automatic generation of references for Latex users, and there are programs (BibDeskToWord, BibFuse) that are supposed to allow for BibDesk to Word full reference generation as well.

I am relatively happy with BibDesk as finally all my articles are in one place and bedlam has been defeated (Judson, 2008). But I could get neither the BibDeskToWord program nor BibFuse to work. So at present my workflow cannot generate instant references like a program like EndNote (over $100 for the student edition) can. As well, Zotero (free) seems very interesting and useful, so I will check out Zotero and may possibly switch from BibDesk to Zotero in the near future. This workflow is an evolving workflow… which is as it should be. There will always be new and more efficient programs appearing on the market, and I’m keeping my options open.

Image 1. BibDesk Screenshot

Skim

Skim is a PDF reader that allows highlighting and annotation. The most useful Skim tool for me is the Note tool, which allows me to write my own notes within the document. In the screenshot below, I have highlighted text referring to a topic I am very interested in – mutual aid – and I have made mutual aid the title of the note. By tagging text in this way, when I do a search using Spotlight, this reference to mutual aid will turn up (even though the words “mutual aid” do not appear in the text) and thus I can find this and other important references to mutual aid quickly and easily. This feature of Skim has ended a problem I’d had for years with not being able to tag text and search those tags.

Image 2. Skim Screenshot

Spotlight is an incredibly powerful search tool that comes installed on all Macs and allows for very efficient searching of documents, webpages, and more. The handy combination of Google Scholar, BibDesk, Skim, and Spotlight has been a huge relief for me, as my workflow used to be terribly disorganized and now it is streamlined, smooth, and highly functional, if basic. I will be developing this workflow in the coming years and I hope that it will continually be getting more efficient and powerful. Please see my basic screencast (link at the top of this page) for a demonstration of this workflow in action.

In closing, I have not yet mentioned anything about Web 2.0 and its capacity for enabling collaboration between researchers. Blogs, wikis, social bookmarking, and other Web 2.0 tools are changing the way we interact, and making international collaboration possible. Once we get our own personal workflows in order, the time saved and the efficiency gained will lead to better and more productive personal research, and international networking with researchers in our fields is leading us to Research 2.0 – networked, collaborative research on a global scale.

The future is looking good for researchers! And the first step is finding a great academic workflow.

References

Haklev, S. (2011). researchr. Available at http://reganmian.net/wiki/researchr:start

Hull, D., Pettifer, S. & Kell, D. (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web. PLoS Comput Biol 4(10): e1000204. doi:10.1371/journal.pcbi.1000204

Judson, O. (2008). Defeating bedlam. The New York Times [online version], December 16, 2008. Available at http://opinionator.blogs.nytimes.com/2008/12/16/defeating-bedlam/

Muldrow, J. & Yoder, S. (2009). Out of cite! How reference managers are taking research to the next level. PS: Political Science and Politics 42(1), pp. 167-172.

Roberts, B. (2009). Get started handling academic citations like a pro. Available at http://www.soulphysics.org/2009/12/get-started-handling-academic-citations.html

Scholar.google.com (2011). About Google Scholar. Available at http://scholar.google.com/intl/en/scholar/about.html

University of Minnesota Libraries (2006). A Multi-Dimensional Framework for Academic Support. University of Minnesota. Available at http://www.lib.umn.edu/about/mellon/docs.phtml