The Academic Browser

Subtitle: Your Librarian in the Cloud

In an earlier post, A Research Rubric, we showed how to do online journal article searches, based on Aaron Tay’s blog. This post extends the basic idea and provides a structured method for performing a search.

Library image from Francesca Grima, Unsplash Sept. 30, 2019.


The search process

The first step is to select and install a reference manager (Zotero, Mendeley, Qiqqa, Docear).

The search begins with understanding the terms used by researchers in the field, followed by a high-level look at review articles. Next, do a more focused search for articles related to the topic you’re interested in, and find other articles cited by, or referencing these papers.

Download or bookmark interesting articles, read, summarize, and make sure you understand the relevant papers.

An outline of the process is:

Organizing the tools

I wanted a way to organize the various online tools useful for researchers. My first thought was to do what I’m about to show you, but then I started thinking about making some fancy GUI, maybe in Qt, and making a dedicated browser for the purpose.

The advantage of a dedicated browser is that I wouldn’t get distracted by checking the latest news on CNN and then feeling the need to find a video of monkeys jumping into a pool to make up for the bad karma.

Jan and I talked about this concept, possibly with buttons to automatically open a new tab in the browser linked to the appropriate tool. Jan was rightfully dubious about all of this, pointing out that everyone dives right into building the fanciest widget without fully considering the purpose.

So, back to my first thought, why not just organize links to the online tools in bookmarks? Browsers are already nice GUIs, everyone understands bookmarks, and they’re very flexible. You can add or delete bookmarks, or drag them around inside the bookmark folder to put them in any order you like.

I started by making a dedicated folder called Academic Journal Search. Inside that folder, I created new folders for each step of the search process, plus a few extra folders for links to databases, browser extensions, reference managers, and miscellaneous others.

bookmarks-folders

Another advantage to this method of organizing bookmarks is that you can put the same bookmark into more than one folder. For instance, Google Scholar appears in “Meta search” and “Journal articles”. Aaron Tay wrote about a new feature in Google Scholar that searches for review articles. Type in your search term and hit Enter to request review articles.

google-scholar-review-articles

Other literature databases have similar tools to do meta searches, or you can add “review”, “meta-analysis”, or “systematic reviews” to the search term. You might decide to combine the “Meta search” and “Journal articles” folders into a single folder and use one search engine for each type of search.

A look inside

Dictionaries and Thesauri

To learn about a new topic, you need to understand the definitions and have synonyms handy. The top links in these folders are to Merriam-Webster, but you might have other favorites.

Encyclopedias

The first link is to Wikipedia, but Scholarpedia might be better if your topic is covered. Scholarpedia is written by subject experts and the articles are peer-reviewed. The scope is mostly physics and math, but if that’s your interest, this is a good resource. Another interesting resource is Leonardo, an AI system designed to answer queries. Be aware that it’s still in beta, and may not give completely accurate answers.

leonardo

Search for basic terms in Google, Bing, or one of several other search engines.

These tools provide much greater capabilities than a simple Google search. 2DSearch lets you graphically build a query, and suggests synonyms. Use Boolean operators to combine terms, and select the literature database to search for papers about your topic.

2Dsearch

Inciteful discovers papers linked to a given article through references, and the Literature Connector tool finds the citation links from one paper to another.

The litserachr package for R lets you apply advanced search techniques programmatically. It’s also available online with slightly reduced functionality.

Journal articles

In the Journal articles folder, you’ll find search engines specifically designed to look for papers of interest. Google Scholar is a good start, but Semantic Scholar, Dimensions, and BASE (Bielefeld Academic Search Engine) are other sources linking to millions of published papers.

Science.gov searches federally funded science, and ERIC looks for education-related research. eThOS (e-theses online service) is a website provided by The British Library where you can search for UK doctoral theses, giving free full access.

The Zenodo search engine and database let researchers upload papers, software, and data. Papers on any subject are accepted so long as they abide by Open Science requirements.

Citation mapping

Connected Papers generates a visual representation of papers similar to another article. You can find derivative work, and build a bibliography from the connections.

connected-papers

Citation Gecko begins searching from a few relevant papers. It suggests others that might be useful, and with these “seed” papers, Citation Gecko builds a tree of connections.

citation-gecko-recommended-papers

VOSviewer constructs bibliometric networks of journals, researchers, institutions, and publications based on Open Alex, Web of Science, Scopus, Dimensions, Lens, and PubMed.

Summarizers

Summarizers aren’t a substitute for reading the paper but can be a starting point for finding important points made in the article. Many require a subscription, but Resoomer, SpinBot, Summarizer, Sassbook AI Text Summarizer, and the Quillbot Paraphrasing Tool are free (sometimes with reduced capability). Scholarcy is a paid service but has a free extension for Chrome and Edge browsers.

The Summarize the Internet and TLDR This - Auto text summary summarizer extensions for Firefox are listed in the Extensions folder.

Download tools

You can often download a paper directly from the search engine found in the Journal articles folder, but if you get stuck, try the Unpaywall, Open Access Button, or CORE Discovery extensions. Library Genesis is a shadow repository for undigitized or paywalled articles but has been accused by Elsevier of internet piracy. Sci-hub is a similar repository where you’re likely to find any article you want.

Note taking

If you want to take notes on the papers you’re reading, Obsidian or Zettlr are excellent alternatives to simple text editors. They allow both internal and external links, use LaTeX in Markdown for writing formulas, and can include images.

Publishing

Depending on your intended audience, you could try Obsidian or Zettlr. LyX is a good editor if your document contains LaTeX, but to get to full control you might need a dedicated LaTeX editor like TeXStudio or TeXnicCenter.

For simple Markdown editing, try ghostwriter or typora. Typora isn’t free but is only $14.99 for installation on three computers.

Firefox lets you open (or hide) the bookmarks view in a sidebar by typing Ctrl-b. Chrome doesn’t have a sidebar built-in, but you can add the Bookmarks Sidebar extension. Showing bookmarks in the sidebar makes an organized search convenient.

You will probably want several extensions which can clutter the toolbar if you’ve installed a lot of them. In Firefox, there’s an overflow menu where you can drag and drop extension icons if you don’t need to access them routinely. They’re still easily accessible. Just click on the >> at the end of the toolbar to open a drop-down menu of the extensions in the overflow area.

overflow-menu

Some extensions, like Unpaywall, Open Access, Core Discovery, and Bypass Paywalls could go into the overflow area and be accessed as needed. The Google Scholar button or Zotero connector might be something you want to have more immediately available.

Loading the bookmarks

To get you started, I’ve created a bookmarks HTML file containing the folders shown above, populated with helpful links. You can download the file and import it into your favorite browser.

If you use Chrome, click on the three vertical dots in the upper right corner just below the ‘X’ that closes the window. This will open a menu, and you should select “Bookmarks”. Now, select “Import bookmarks and settings …” and in the drop-down box, choose “Bookmarks HTML file”.

Click “Import”, choose the file you downloaded, and open it. After a few seconds, a message box will open showing that you’ve successfully imported the bookmarks.

import-bookmarks-to-chrome

Open your bookmark manager and scroll to the bottom to find a folder called “Imported”. Below that, you’ll see the folder “Academic Journal Search”. Drag that folder to a more convenient location, and then delete the “Imported” folder.

You will still need to add any extensions you like from the links in the “Browser extensions” folder.

Your journal search tools should now be ready to help you discover the world of online academic literature.


Software

Zotero

A free, easy-to-use tool to help you collect, organize, annotate, cite, and share research.

Posts using Zotero

Mendeley

Mendeley Reference Manager simplifies your workflow, so you can focus on achieving your goals.

Posts using Mendeley

Qiqqa

The essential free research and reference manager.

Posts using Qiqqa

Docear

Docear is a unique solution to academic literature management, i.e. it helps you organizing, creating, and discovering academic literature.

Posts using Docear

RStudio

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Posts using RStudio

Zettlr

Your one-stop publication workbench. From idea to publication in one app: Zettlr accompanies you while writing your blog post, newspaper article, term paper, thesis, or entire book.

Lyx

LyX is a document processor that encourages an approach to writing based on the structure of your documents (WYSIWYM) and not simply their appearance (WYSIWYG).

Posts using Lyx

Ghostwriter

Enjoy a distraction-free writing experience, including a full screen mode and a clean interface. With Markdown, you can write now, and format later.

Typora

Simple markdown editor. Used to generate this document.

See all software used on wildpeaches →