how to keep track of research papers

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Organizing Papers and References without Losing your Mind

In January, Ulrike Träger wrote a great PLOS ECR post describing how to stay on top of reading during graduate school. If you haven’t read it yet, go take a look, as it’s relevant for people at all career stages. As a follow up, here are a few tips on how to keep track of the papers you want to read without losing your mind.

Choose a reference manager. Sure, you can get by creating a poster or two without a reference manager, but it’s incredibly risky to cite references by hand for manuscripts and grant proposals. Choosing and using a reference manager is also a great way to track papers as you collect them, particularly because reference managers often have powerful search functions. There are many to choose from. Some are free, like Zotero and some versions of Mendeley . Others, like Papers and EndNote , are not, though some paid programs may be free through your institution. Spend some time researching which manager fits your needs, but don’t get bogged down, you can always switch later. Personally, I have transferred references from RefWorks to Zotero to Mendeley to EndNote over the past several years without much trouble.

Choose a place to keep unread papers. Whether it’s a physical folder on your desk or a virtual folder on your desktop, it’s important to have a designated place for unread papers. This folder is more than just a storage space, it should also be a reminder for you to review unread papers. It’s tempting to download papers and forget about them, falling prey to PDF alibi syndrome , wherein you fool yourself into thinking that by downloading a paper you’ve somehow read it. So, set aside some time every few weeks (on your calendar if you need to) to review papers. You won’t necessarily read each paper in detail, but you should complete a quick skim and take a few notes. Try to resist the urge to leave notes like “finish reading later.” However, if needed, consider using notes like “need to read again before citing” for papers that were skimmed particularly quickly.

Choose how to keep track of your notes. It’s a great idea to create a summary of each paper as you read it, but where do you keep this information? Some people write separate documents for each paper (e.g., using the Rhetorical Précis Format ), others write nothing at all, but tag papers (virtually or physically) with key words. The exact components of your system matter less than having a system. Right now, I keep a running document with a few sentences about each paper I read. I also note whether I read it on paper or as a PDF so that I can find notes taken on the paper itself later. If I’m doing a deep read on a specific topic, I might also start another document that has in-depth summaries. I usually keep notes in Word documents, but it’s also possible to store these notes in many reference managers.

Choose how to file read papers. Again, having a system probably matters more than which system you choose. Given the interdisciplinary nature of science, it can be complex to file by topic. Therefore, I find it easiest to file papers by last name of the first author and the publication year. It’s also useful to include a few words in the file name that summarize its content. This will help you differentiate between articles written by authors with similar last names. So, for example, using this method, you might label this blog post as Breland_2017_tracking refs. I keep articles I’ve read in a folder labeled “Articles” that includes a folder for each letter of the alphabet. Therefore, I’d file this blog post in the “B” folder for Breland.

TL;DR. The goal of creating a system to organize papers and references is to be able to easily access them later. If you follow the steps above, it’s relatively easy to keep track of and use what you’ve read – if you want to find a paper, you can search for a key word in your reference manager and/or in your running document of article summaries and then find a copy of the paper in the appropriate alphabetized folder. That said, there is no right way to organize references and I’m curious about how others manage their files. Chime in through the comments and we’ll update the post with any interesting answers!

Pat Thomson (2015) PDF alibi syndrome , Patter blog. Accessed 2/27/17.

Ulrike Träger (2017) Ten tips to stay on top of your reading during grad school , PLoS ECR Community Blog.

Sample Rhetorical Précis: http://oregonstate.edu/instruct/phl201/modules/rhetorical-precis/sample/peirce_sample_precis_click.html

Featured image available through CC0 license.

[…] Organizing Papers And References Without Losing Your Mind – Jessica Breland […]

You have a great organizing skills! I appreciate your tips!

Fantastic tips! Thank you for sharing.

Great tips! It helps me a lot while I’m doing my final diploma project. Thank you.

This is great, very helpful. Nicely written and clearly organized [like your ref lib 😉 ] C

im at the start of my phd and already feeling that i have a lot of literature. i am taking your notes onboard and going to spend some time to organise my files asap. thanks

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How to Organize Research Papers: A Cheat Sheet for Graduate Students

• August 8, 2022
• PRODUCTIVITY

It is crucial to organize research papers so that the literature survey process goes smoothly once the data has been gathered and analyzed. This is where a research organizer is useful.

It may be helpful to plan the structure of your writing before you start writing: organizing your ideas before you begin to write will help you decide what to write and how to write it.

It can be challenging to keep your research organized when writing an essay. The truth is, there’s no one “ best ” way to get organized, and there’s no one answer. Whatever system you choose, make sure it works for your learning style and writing habits.

As a graduate student, learning how to organize research papers is therefore essential.

This blog post will cover the basics of organizing research papers and the tools I use to organize my research. 

Before you start

The importance of organizing research papers.

No matter how good your paper management system is, even if you keep all your literature in places that are easy to find, you won’t be able to “create” anything unless you haven’t thought about organizing what you get from them.

The goal of the research is to publish your own work to society for the benefit of everyone in the field and, ultimately, humanity.

In your final year of your PhD, when you see all the papers you’ve stored over the years, imagine the frustration you might experience if you hadn’t gathered the information from those papers in a way that allows you to “create” something with i.

This is why organizing research papers is important when starting your research.

Research with your final product in mind

It is very important to have a clear idea of what your research’s outcome will be to collect the information you really need.

If you don’t yet have all your information, consider what “subheadings” or chunks you could write about.

Write a concept map if you need help identifying your topic chunks. As an introduction to concept mapping, it involves writing down a term or idea and then brainstorming other ideas within it.

To gather information like this, you can use a mind map.

When you find useful information.

Come up with a proper file management system.

Sort your literature with a file management system. There’s no need to come up with a very narrow filing system at this point. Try sorting your research into broader areas of your field. When you’re more familiar with your own research, you’ll be able to narrow down your filing system.

Start with these methods:

Don’t waste your time on stuff that’s interesting but not useful :  

In your own research, what’s the most important part of a particular paper? You won’t have to pay attention to other sections of that paper if you find that section first. 

What is the argument behind your research? Make notes on that information, and then throw everything else away.

Create multiple folders :

Create a file containing related topics if you’re using a computer. Bind the related articles together if you like to print out papers. In other words, keep related things together!

Color code your research papers:   

To organize notes and articles, assign different colors to each sub-topic and use highlighters, tabs, or font colors.

Organize your literature chronologically: 

Even in a short period of time, you might have missed overarching themes or arguments if you hadn’t read them previously. It’s best to organize your research papers chronologically.

If you want to do all this at once, I suggest using a reference manager like Zotero or Mendeley (more on reference managers later).

File renaming 

Make sure you rename your files on your computer according to your own renaming strategy. Taking this step will save you time and confusion as your research progresses.

My usual way of naming a pdf is to use the first author’s last name, followed by the first ten letters of the title and then the year of publication. As an example, For the paper “ Temperature-Dependent Infrared Refractive Index of Polymers from a Calibrated Attenuated Total Reflection Infrared Measurement ” by Azam et al., I renamed the file as “ Azam_Temperature-Dependent_2022.pdf “.

One thing to notice is that I don’t do this manually for all the papers I download. That wouldn’t be as productive, and I’d probably give up after some time renaming every single file. In my reference manager of choice (Zotero), I use a plugin called Zotfile to do this automatically. Zotfile automatically renames files and puts them in the folder I specify every time I add a new paper.

Organizing your research articles by the last names of the lead authors will simplify your citation and referencing process since you have to cite the names of the researchers everywhere. The articles will also be easier to find because they’ll be lined up alphabetically by any researcher’s name you can remember.

Use keywords wisely

Keywords are the most important part of sorting. It’s easy to forget to move a paper to a specific file sometimes because you’re overwhelmed. But you can tag a paper in seconds. 

When organizing research papers, don’t forget to develop a better keyword system, especially if you use a reference manager.

My reference manager, for instance, allows me to view all the keywords I have assigned in the main window, making life much easier.

Create annotations

When reading literature, it is very important to create your own annotations, as discussed in the blog post series, “ Bulletproof literature management system “.

This is the fourth post of the four-part blog series:  The Bulletproof Literature Management System . Follow the links below to read the other posts in the series:

• How to How to find Research Papers
• How to Manage Research Papers
• How to Read Research Papers
• How to Organize Research Papers (You are here)

The best thing to do is to summarize each section of the article/book you are reading that interests you. Don’t forget to include the key parts/arguments/quotes you liked.

Write your own notes

If you decide to read the whole paper, make sure you write your own summary. The reason is that 95% of the things you read will be forgotten after a certain period of time. When that happens, you may have to read the paper all over again if you do not take notes and write your own summary.

By writing your own summary, you will likely memorize the basic idea of the research paper. Additionally, you can link to other similar papers. In this way, you can benefit from the knowledge you gain from reading research papers.

After reading a paper, make sure to ask these questions:

• Why is this source helpful for your essay?  
• How does it support your thesis?  

Keep all the relevant information in one place so that you can refer to it when writing your own thesis.

Use an app like Obsidian to link your thinking if you keep all your files on a computer, making things much easier.

When you are ready to write

Write out of order .

Once you have all the necessary information, you can use your filing system, PDF renaming strategy, and keywords to draw the annotations and notes you need.

Now that you’re all set to write, don’t worry about writing the perfect paper or thesis right away.

Your introduction doesn’t have to come first.

If necessary, you can change your introduction at the end – sometimes, your essay takes a different direction. Nothing to worry about!

Write down ideas as they come to you

As you complete your research, many full-sentence paragraphs will come to your mind. Do not forget to write these down – even in your notes or annotations. Keep a notebook or your phone handy to jot down ideas as you get them. You can then find the information and revise it again to develop a better version if you’re working on the same project for a few days/weeks.

My toolbox to organize research papers

Stick with the free stuff.

Trying to be a productive grease monkey, I’ve tried many apps over the years. Here’s what I learned.

• The simplest solution is always the best solution (the Occam razor principle always wins!).
• The free solution is always the best (because they have the best communities to help you out and are more customizable).

As someone who used to believe that if something is free, you’re the product, I’ve learned that statement isn’t always true.

Ironically, open-source software tends to get better support than proprietary stuff. It’s better to have millions of enthusiasts working for free than ten paid support staff.

There are a lot of reviews out there, and EndNote usually comes out at the bottom. I used EndNote for five years – it worked fine, but other software improved faster. Now I use Zotero, which I like for its web integration. 

Obsidian, my note-taking app of choice, is also free software. Furthermore, you own your files; also, you’ve got a thriving community.

There are a lot of similarities between the software as they adopt each other’s features, and it’s just a matter of preference.

In any researcher’s toolbox, a reference manager is an essential tool.

A reference manager has two important features: the ability to get citation data into the app and the ability to use the citation data in your writing tool.

It should also work on Windows just as well as macOS or Linux, be free, and allow you to manage PDFs of papers or scanned book chapters.

Zotero , in my opinion, gives you all of this and more.

Zotero is one of the best free reference managers for collecting citation data. It includes a browser plugin that lets you save citation information on Google Scholar, journal pages, YouTube, Amazon, and many other websites, including news articles. It automatically downloads a PDF of the associated source when available for news articles, which is very convenient.

One of the things I really like about Zotero is that it has so many third-party plugins that we have almost complete control over how we use it.

With Zotero 6, you can also read and annotate PDFs, which is perfect for your needs.

My Research paper organizing workflow in Zotero :

• Get References and PDF papers into Zotero : I use Zotero’s web plugin to import PDFs directly 
• Filing and sorting : I save files from the web plugin into the file system I already have created in Zotero and assign tags as I do so.
• File renaming : When I save the file, the Zotero plugin (Zotfile) automatically renames it and stores the pdf where I specified.
• Extracting Annotations and taking notes : I use Zotero in the build pdf reader to take notes and annotate, and then I extract them and link them in Obsidian (next section).

You need to keep your notes organized and accessible once you’ve established a strong reading habit. For this purpose, I use Obsidian . I use Obsidian to manage everything related to my graduate studies, including notes, projects, and tasks. 

Using a plugin called mdnotes , Obsidian can also sync up with my reference manager of choice, Zotero. It automatically adds new papers to my Obsidian database whenever I add them to Zotero.

Obsidian may have a steep learning curve for those unfamiliar with bi-directional linking , but using similar software will make things much easier. Thus, you may be better off investing your time in devising a note-taking system that works for you.

You can also use a spreadsheet! Make a table with all the papers you read, whatever tool you choose. Include the paper’s status (e.g., whether you’ve read it) and any relevant projects. This is what mine looks like.

I keep all my notes on an associated page for each paper. In a spreadsheet, you can write your notes directly in the row or link to a Google document for each row. Zotero, for example, allows you to attach notes directly to reference files.

While it might seem like a lot of work, keeping a database of papers you’ve read helps with literature reviews, funding applications, and more. I can filter by keywords or relevant projects, so I don’t have to re-read anything.

The habit of reading papers and learning how to organize research papers has made me a better researcher. It takes me much less time to read now, and I use it to improve my experiments. I used this system a lot when putting together my PhD fellowship application and my candidacy exam. In the future, I will thank myself for having the foresight to take these steps today before starting to write my dissertation.

I am curious to know how others organize their research papers since there is no “ right ” way. Feel free to comment, and we will update the post with any interesting responses!

Images courtesy : Classified vector created by storyset – www.freepik.com

Aruna Kumarasiri

Founder at Proactive Grad, Materials Engineer, Researcher, and turned author. In 2019, he started his professional carrier as a materials engineer with the continuation of his research studies. His exposure to both academic and industrial worlds has provided many opportunities for him to give back to young professionals.

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15 Best Free Web Tools to Organize Your Research

How to stay organized when researching and writing papers

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Organizing research is important not only for your own sanity, but because when it comes time to unfold the data and put it to use, you want the process to go as smoothly as possible. This is where research organizers come in.

There are lots of free web-based organizers that you can use for any purpose. Maybe you're collecting interviews for a news story, digging up newspaper archives for a history project, or writing a research paper over a science topic. Research organizers are also helpful for staying productive and preparing for tests.

Regardless of the topic, when you have multiple sources of information and lots to comb through later, optimizing your workflow with a dedicated organizer is essential.

Patrick Tomasso / Unsplash

Many of these tools provide unique features, so you might decide to use multiple resources simultaneously in whatever way suits your particular needs.

Research and Study

You need a place to gather the information you're finding. To avoid a cluttered space when collecting and organizing data, you can use a tool dedicated to research.

• Pocket : Save web pages to your online account to reference them again later. It's much tidier than bookmarks, and it can all be retrieved from the web or the Pocket mobile app .
• Mendeley : Organize papers and references, and generate citations and bibliographies.
• Quizlet : Learn vocabulary with these free online flashcards .
• Wikipedia : Find information on millions of different topics.
• Quora : This is a question and answer website where you can ask the community for help with any question.
• SparkNotes : Free online study guides on a wide variety of subjects, anything from famous literary works of the past century to the present day. 
• Zotero : Collect, manage, and cite your research sources. Lets you organize data into collections and search through them by adding tags to every source. This is a computer program, but there's a browser extension that helps you send data to it.
• Google Scholar : A simple way to search for scholarly literature on any subject.
• Diigo : Collect, share, and interact with information from anywhere on the web. It's all accessible through the browser extension and saved to your online account.
• GoConqr : Create flashcards, mind maps, notes, quizzes, and more to bridge the gap between your research and studying.

Writing Tools

Writing is the other half of a research paper, so you need somewhere useful to go to jot down notes, record information you might use in the final paper, create drafts, track sources, and finalize the paper.

• Web Page Sticky Notes : For Chrome users, this tool lets you place sticky notes on any web page as you do your research. There are tons of settings you can customize, they're backed up to your Google Drive account, and they're visible not only on each page you created them on but also on a single page from the extension's settings.
• Google Docs or Word Online : These are online word processors where you can write the entire research paper, organize lists, paste URLs, store off-hand notes, and more.
• Google Keep : This note-taking app and website catalogs notes within labels that make sense for your research. Access them from the web on any computer or from your mobile device. It supports collaborations, custom colors, images, drawings, and reminders.
• Yahoo Notepad : If you use Yahoo Mail , the notes area of your account is a great place to store text-based snippets for easy recall when you need them.
• Notion : Workflows, notes, and more, in a space where you can collaborate with others.

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1) Plan Your Research: Keeping Track of Sources

• Research Strategy
• Developing a Research Question
• Outlining & Writing
• Proofreading & Editing

Keeping Track of Sources

Research log.

• Research log (.doc)
• Research log (.pdf)

Use this research log to keep track of your research process . Every time you find something useful, record how and where you found the item.

Available in .pdf or .doc format.

Why should I keep track of my research?

A research project may take many hours of searching. Keeping track of your search history can help you do a more thorough and systematic search  – and help you avoid duplicating your research efforts! And when it's time to write your paper, thorough research notes will save you a lot of time and energy.

What's the easiest way to keep track of my research, organize my notes, and format my bibliography?

There are several citation management programs that can help you organize your research:

• EndNote – EndNote is a feature-rich citation management program that allows you to organize your references in a searchable database.  EndNote is recommended for those heavily engaged in research .
• Import and re-format references from online databases
• Automatically enter citations
• Build reference lists in Microsoft Word (Windows and Macintosh), Pages09 (Macintosh), and OpenOffice (version 3)
• Format references according to hundreds of bibliographic citation styles, including journal-specific formats

The current version of EndNote in use at the University of Lethbridge is EndNote X4. U of L students, faculty, and staff can download the program here .

• EndNote Web   –   EndNote Web is a web-based counterpart to EndNote, the desktop application. When you save references to EndNote Web, you are saving them to servers located "in the cloud" (i.e., NOT locally at the University of Lethbridge). This makes it easy to collaborate and share your library with others. It also means you can get to your EndNote Web library from anywhere you have Internet access. EndNote Web is recommended for use by undergraduate students.

You can set up a free EndNoteWeb account by registering at: http://www.myendnoteweb.com

• Zotero – Zotero is a free Firefox addon that collects, manages, and cites research sources. It's easy to use, lives in your web browser where you do your work, and best of all it's free. Zotero allows you to attach PDFs, notes and images to your citations, organize them into collections for different projects, and create bibliographies. 
• Mendeley – Mendeley is a free reference manager and academic social network that can help you organize your research, collaborate with others online, and discover the latest research.

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Five online tools that aim to save researchers time and trouble

From investigating a lab’s publication history to scanning manuscripts for statistical errors, these apps can help streamline some of the most time-consuming tasks.

Dalmeet Singh Chawla

Credit: erhui1979/Getty Images

23 June 2021

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An expanding kit of digital tools and apps helps researchers automate certain processes and make others less burdensome.

Nature Index has selected five recently launched or revised tools that aim to make academic life easier, whether you’re thinking of relocating to a new lab, organizing your references or readying a manuscript for submission.

1) Choosing the right lab

Job-hunting can be tough, particularly if interstate or overseas relocation is on the cards. Before you commit to a new position, it’s useful to have some insight into your prospective supervisor, as well as the kind of lab culture you’d be stepping into .

A new tool called Super Researcher aims to make it easier for doctoral and postdoctoral candidates to compare lab leaders based on their productivity and impact.

Described in a bioRxiv paper published in February 2021, the app allows academics to run searches on specific researchers to see their numbers of annual publications, citation counts and details on their most frequent collaborators. The tool pulls publication data from the Scopus database.

The team behind the app, led by co-creator Sheah Lin Lee, a cancer researcher at the University of Southampton in the UK, is working to move it beyond the pilot stage. One challenge, she says, is that it’s hosted on a free (and sometimes unreliable) server, which means it’s prone to the occasional crash – something the team is hoping address in the future.

Lee says she hopes her tool will give researchers a ‘rough and ready’ indication of a lab’s publication culture, which could factor into their decision to take up a new position there. But she urges users to take other factors into consideration, too.

“We don’t think that people should judge whether you want to go to a lab solely based on publications,” says Lee.

2) A spell-checker for statistics

What if there were a way to automatically scan a manuscript for statistical errors while writing your manuscript ?

Statcheck, launched in 2015, aims to do so by recalculating p-values — a controversial but commonly used technique to measure statistical significance.

It initially received mixed reactions from academics, but has since gained more acceptance after a preprint study found that it was correct in more than 95% of its recalculations of p-values.

Statcheck has become a popular way to check manuscripts before submission to a journal, says co-creator Michèle Nuijten, who studies analytical methods at Tilburg University in the Netherlands.

It’s also being used by journals such as Psychological Science and the Journal of Experimental Social Psychology to weed out statistical mistakes during the peer-review process.

In 2020, Nuijten and her team expanded the functionality of statcheck by creating a free plugin to be used within Microsoft Word that works like a statistical spell-checker.

Nuijten cautions against using the tool as a means to imply fraud or wrongdoing, emphasizing how easy it can be, even for experienced researchers, to make mistakes in their calculations.

“We all make mistakes. It doesn’t mean we want to,” she says.

3) Spot the difference between preprint versions

Comparing different iterations of a manuscript on preprint servers such as arXiv can be a time-consuming process, says Sharvil Nanavati, a software engineer based in Mountain View, California.

After trying to find a tool to address this, Nanavati and Sergei Taguer, a software engineer in California, decided to build one themselves, which they launched in May 2021.

ArXiv Diff , which was built on top of an existing open-source tool, allows users to view manuscript updates by replacing the word “arxiv” in the URL of a paper to “arxivdiff” then clicking “Show Diff”.

So far, feedback on the new app has been mixed, Nanavati admits. Some academics have praised its usefulness, while others have pointed out that it doesn’t work on all manuscripts.

Nanavati says he’s tweaking the tool’s code to cater for cases where users flag errors. He says the tool, which is a labour of love, will continue to be available for free, but is limited to manuscripts posted to arXiv for now.

4) Find references to papers flagged on PubPeer

It’s becoming increasingly difficult to keep up with the commentary around new papers. Some of these discussions take place on Pubpeer, an online platform where researchers debate the veracity and robustness of specific papers.

While it’s possible to manually check a paper on PubPeer to see if people are talking about it, doing that for an entire reference list can be laborious.

In 2019, PubPeer launched a free plugin on Zotero, an open-source reference-management system that is popular among academics because it hosts a number of plugins with functions such as helping users find free versions of paywalled papers and flagging papers that have been retracted.

The new PubPeer plugin flags any references in a researcher’s paper shortlist — where they save studies that are potentially of interest and may be worthy of citing — that are being discussed on PubPeer, listing the number of comments.

PubPeer also has a browser extension that alerts researchers if they are citing a paper that is being discussed on the platform.

Boris Barbour, co-organizer of PubPeer and a neuroscientist at the Ecole Normale Supérieure’s Institute of Biology in France, says that while there are no immediate plans to expand the new plugin to reference management systems other than Zotero, “there are fairly significant incremental improvements and polishing that could be done”.

5) Scanning for predatory references

In May 2021, Edifix, a bibliographic referencing tool run by Boston-based publishing software firm Inera, expanded its capability to automatically flag references to papers published in predatory journals.

Inera teamed up with Cabell’s International , a scholarly-services firm headquartered in Beaumont, Texas, to access its list of predatory journals, which is usually pay-to-view .

When users check their references using Edifix, in addition to automatically formatting them and fixing any errors, the tool will flag any publications that Cabell’s has identified as predatory. Users can click on those references for an explanation of why the particular journal has been flagged as questionable .

However this new functionality will be free to use for Edifix subscribers until the end of 2021. After that, users will need to pay for a subscription to Cabell’s, says Elizabeth Blake, director of business development at Inera.

The decision to delete or retain references to flagged publications lies with the researcher, says Blake, as it’s possible for subpar journals to publish solid research, and there may be legitimate reasons to cite such work.

Edifix also highlights any references that have been retracted – which a growing number of other bots also do .

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Approaching the Literature Review

• Keeping Track
• Introduction
• Approaching the Literature Search
• Interpreting Research Results
• Advice on Writing

Why Keep Track of Your Results?

• Keeping Track of Information Created by Georgia State University Library, this guide contains recommendations and tools for keeping track of both search strategies and search results.

Tools for Analyzing Your Search Results

• Literature Search Tracking Log Adapted from the Georgia State University Library, the Literature Search Tracking Log "is where you can list the subject headings you used in your search, which databases you searched and how many results you found for each search."
• Evidence Analysis Log Adapted from the Georgia State University Library, the Evidence Analysis Log "is where you make notes about each article that is relevant to your literature review."

Citation Management Tools - Introduction

What are citation management programs?

Citation management programs are time-saving tools that allow you to:

• Create a personal database of references
• Organize and search your references
• Upload and store PDF documents with their citations
• Insert citations into word processing documents and format bibliographies in a variety of styles

What citation management program should I use?

There are several citation management programs available.  Tufts provides access to EndNote and F1000 Workspace for faculty, students and staff.  Other options are Mendeley and Zotero, free citation management programs.

See below links to additional information and help with each of these programs. 

Citation Management Tools

• EndNote EndNote is a desktop-based citation management program available to Tufts faculty, students and staff. Click the link above to learn how to get EndNote installed on your work or personal computer and start using the program.
• Sciwheel (Formerly F1000 Workspace) Sciwheel is a web-based citation manager and collaborative author program available to Tufts faculty, students and staff. Click the link above to create or access your account. You must create an account while on the Tufts network, and login from a campus network every 60 days to maintain full access.
• Mendeley Mendeley is a freely available citation management program. Click the link above to learn more about using Mendeley.
• Zotero "Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research."
• << Previous: Approaching the Literature Search
• Next: Interpreting Research Results >>
• Last Updated: Sep 7, 2023 8:35 AM
• URL: https://researchguides.library.tufts.edu/lit_review

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Keeping Track of Research Guide

• Keeping Track of Research
• Avoiding Plagiarism

Why Keep Track of your Research?

Most essays at a college level require a bibliography or reference page as well as in-text citation of some sort. It is important to gather the needed information as you work. Sometimes searches and resources are hard to find again, and it saves time at the end of the process when deadlines are looming.

There is also the added benefit of building on searches you have done to do further research. A thorough record can save time and effort in that process.

Things to keep track of:

• Search terms (including combinations and limits you may add)
• Places you search (databases, Library Search, websites)
• Information about the sources you find (author, title, date, publisher, call number, url, etc.)
• Information about the quotes or paraphrases you will be using.  (Source identification, page numbers, and context)

How to Keep Track of your Research

• Note cards are often a handy way to keep track of research and quotes as you read.
• A notebook and/or folder for each essay is also an excellent way to gather information as you find it.

Because so many sources are formatted electronically, it often easier to keep the records of research electronically as well.

• Many find a simple saved document on the desktop to be a sufficient place to keep and collect notes, URLs, and search terms.
• Email documents can also be a handy way to keep information in one place.
• Portable hard drives are also a great way to keep track of information as you research.
• Many use a third party web location to keep track of information.

Hints and Tricks

• Most databases have a marking and/or folder feature. This allows users to output the needed information about the resources in an easy way. The added benefit is that most can output information in your chosen citation format.
• Screen capture is an option if there is no readily accessible way to output the information. Pressing the [Control] and [Print Screen] buttons simultaneously will capture a "snapshot" of the desktop. This can be saved and opened in a word processing file.
• Web tagging and capturing programs like those listed, allow users to save URLs and organize them.

Electronic Spots to Keep Track of Research

• Zotero Zotero [zoh-TAIR-oh] is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources.
• Google Docs Spot to save and keep electronic files. Plus is that is can be connected to an email account.
• Next: Avoiding Plagiarism >>
• Last Updated: Mar 11, 2024 4:24 PM
• URL: https://guide.unwsp.edu/keepingtrack

How to Search and Organize Research Articles

• by Tiffany Yue Zhang
• November 01, 2021

Quick Summary

• Organizing research articles using a reference manager and other strategies will make life as a graduate student much easier.

As PhD students, reading is part of our life. There are so many new papers coming out every day, so many research blogs to follow, so many books to read. But, how would you find them and organize them? Certainly, I’ve seen people downloading everything to their desktop and piling up 100 pdfs with no labeling or grouping. To be honest, that was me at one point. When you start to write a report or research paper, it can become a nightmare to organize the reference list. If you are first year graduate student doing research, or if you are just looking for a method to organize your scientific literature, this blog can hopefully help.

Finding Articles

The best resources for starting to build your reading list are your advisor and lab mates.  This is definitely the fastest way to gain background on your research area. Simply ask around the lab about key articles in the research field. The downside of this method is that the pool of articles is limited by what’s already known by your advisor or lab mates. Starting by reading a review paper in your field, then finding and reading the most relevant references listed for the review, is also a good method.

Searching by key words is another common way to find scientific literature. I use Google Scholar, Web of Science, and Scopus, mostly.  Searches can be done by entering the key words, subject area, document type (e. g. review, articles), and sort by relevance. Start to read from the most cited papers in your field. If you are interested in a specific researcher’s publications, you can follow them on Google Scholar and you’ll get notified when they publish new articles. Lens.org is another good resource for searching, analyzing and managing patent and scholarly data.

Subscribing to RSS feeds is another good way to keep up with recent research. There are a variety of apps that can send notifications when new research papers of interest are coming out, such as Researcher, Feedly and Academia. Pick your favorite topics or journals to follow and get your daily feeds about research topics. You can even track when a paper is cited. These tools are good for scientific literature, but you can also use them for your hobbies, your favorite magazines, etc.

Following blogs can be helpful, as well. As a chemistry student, I follow some of the ACS (American Chemical Society), RSC (The Royal Society of Chemistry) blogs, as well as blogs written by researchers and professors. If you are looking for something interesting to read, follow Retraction Watch. There, you’ll find the research articles that are retracted for fraud, ethical violations, and many other reasons.  Some stories can be quite interesting.

Listening to podcasts can be a good way to broaden your knowledge. Usually, the content in podcasts is less technical and you can learn some basics for topics that you are not familiar with.

Organizing Research Papers

Different people find different ways to organize research articles. Some prefer to print everything out and put them in binders, some prefer to read the digital versions and sort them in folders. Personally, I like to read on a computer screen and sort research papers by project. I usually keep important references in a reference manager. For papers that I want to go over multiple times, I usually print them out and read them carefully. It’s easier to take notes with a printed version and, for some reason, it seems like I can memorize the content longer when I read the printed paper. The main drawback in using hard copies is that it can be difficult to find a specific paper when you have a large pile. With digital versions, it’s much easier to locate specific research articles by keywords.

There are many digital reference managers. This type of software tool can allow you to keep research articles in different folders for each research project. Within the reference manager, you can also take notes, sort by author, year, or topic. Most reference managers also help with searching for research articles. When you write a report or publication, reference managers allow for import of references from these databases directly into Microsoft Word, which is very convenient.  Here are three of the most commonly used reference managers: EndNote, Mendeley  (Figure 1)  and Zotero. All of them can sync between devices and be shared between different people. EndNote is not free, but it is very powerful. It supports many unusual or complex citation formats. Some versions of Mendeley are free. It’s good at dealing with pdfs files and can extract citations from pdfs, as well as searching from pdfs. Zotero is also free and allows for saving snapshots of web pages and annotating them in your library, which is good for web-based publications.

When I read a paper, I usually ask myself the following questions: 1) what’s the purpose of reading this article?; 2) how is the article important or relevant to my work?; and, 3) what’s the take home message?. If the paper is important, I then write down the conclusions and methods. Taking notes makes reading more efficient ( Figure 2).  Notion is a good application to keep track of reading notes and allows for creation of lists of papers for different topics. You can also assign properties to each paper and tag papers with keywords. Notion also supports markdown which makes your notes clean and easy to read. When I read a research article, I usually start with the title and abstract and try to figure out the big picture conclusions or contributions to the research field.  Then, I skim through the figures and the figure captions to get an idea of the key points. If a figure is important, I keep it in my notes. I usually skip the introduction at first if I’m familiar with the author or the research field, instead jumping directly into the results and conclusion sections. From there, I’ll decide if I want to read the paper in detail or not. Different people have different ways of reading papers; find the one that works for you.

I hope you find these methods helpful for finding and organizing research articles and happy reading!

Marcus, Adam, and Ivan Oransky. Retraction Watch , Oct 24 2021, https://retractionwatch.com/. 

“Which Reference Manager? Comparision of Endnote, Medeley and Zotero.” Library Guides , Mar 2 2021, https://aut.ac.nz.libguides.com/managingreferences.

“How to (Seriously) Read a Scientific Paper.” Science , Mar 21 2016, https://www.science.org/content/article/how-seriously-read-scientific-paper.

Primary Category

Secondary categories.

Literature Review - Finding the Resources

• The Literature
• Search Tools
• Formulating your search statement
• Buliding on what you have found

Keeping track of the resources you find

Keeping a search log, keeping a reading log, endnote - suggested citation management tool.

• Academic Reading
• Citing Sources

When you search for resources using multiple databases, keep a record of what you have done to perform the search , such as the databases you have used, the keywords you have combined and searched, and the search results retrieved using various search statements. From what you have done, you will then know what you should do next such as, to:

• Redo a previous search
• Use other terms or combination of terms
• Limit to other search fields
• Try another database

The Database Search Log below is a table for you to keep such a record.

• Database Search Log

When you find your needed resources, the next step is to read them. If you have a large number of materials to read, it is not easy to remember what you have read afterwards. Keeping a record of what you have read is essential to  effectively organize the information from each resource and to be well prepared for writing your literature review. The information to record include the theories, findings and methodologies presented in the resources, as well as the citation information of these resources. Keeping this record will also help you make connections between resources.

Make use of the Resource Reading Log below to record important information about the resources you read.

• Resource Reading Log
• << Previous: Buliding on what you have found
• Next: Evaluating Sources >>
• Last Updated: Jan 17, 2024 7:25 PM
• URL: https://libguides.library.cityu.edu.hk/litreview

© City University of Hong Kong | Copyright | Disclaimer

Keeping Track of Your Literature

Keeping track of the scientific literature in your research field without getting overwhelmed can be a struggle. But, don’t worry, we’re here to help.

We’re here to give you the inside scoop on where and how to find the relevant literature. We’ll also give you the lowdown on the main reference managers you can use to stay organized.

The Most Neglected Task Is Often the Most Important

While practical experimental work is important, it is all too easy to neglect a crucial aspect of science work—reading and keeping up with published literature.

While learning to read and understand a scientific paper thoroughly and efficiently is important, it is arguably just as important to keep up-to-date with the latest literature.

This is another frequently overlooked task but is absolutely vital to ensure you don’t miss any key advances in your field.

No one wants to get months down the line and realize someone has already published on that experiment you’ve been painstakingly performing.

Writing a literature review or grant application presents an excellent opportunity for taking a deep dive into the literature, but finding the time to keep up with the latest publications on a regular basis can be very challenging.

This task can sometimes feel impossible with the additional demands placed on scientists in terms of meetings, seminars, teaching, outreach, admin, mentoring, etc.

The dizzying number of papers published on a weekly basis also doesn’t help.

But don’t worry, we’ve got some top tips and handy hints to help you find—and manage—that literature.

Why Is Keeping Track of the Scientific Literature Important?

Well, if you don’t keep up with recent publications, you won’t know what people in your field are working on or what the current gaps in knowledge are, and you won’t be able to put your work into the proper context.

Even worse, you may end up pursuing a line of inquiry that has already been published by someone else. Moreover, newly published work often provides novel solutions to problems and/or reveals novel mechanistic insights.

Therefore, by keeping up with the literature, you may find potential solutions or alternatives to challenges you are facing in your own research.

How To Find the Latest Scientific Literature

To be able to read and take in the literature, you first need to find it. Nowadays, there are a number of tools to help you keep track of new publications, including Stork , PubCrawler , Feedly , PubMed alerts , and Google alerts .

These apps and websites allow users to set up automatic searches of online publication databases using key search terms.

You can then set daily, weekly, or monthly email alerts, which highlight all of the new and relevant papers with links to the abstracts and full text.

You can choose to make your searches as vague or specific as you wish. If you want to learn more about how to use some of these tools, read our article on How to Speed Up Your Literature Searches by Crawling .

Social media is also another very important tool for finding and keeping up with the latest science.

Twitter is becoming an increasingly valuable resource in science and it can be very useful for keeping up with the latest work in your field.

But this is true only if you follow the right people!

So, if you have a Twitter account, start by following researchers in your field, as well as journals that publish work relevant to your research.

Also, don’t feel that you have to spend hours on Twitter or other social media apps in the name of science.

If you follow the right people, you can spend as little as 10 minutes a day finding out about the latest scientific breakthroughs.

LinkedIn is another overlooked platform that, as well as being a practical tool for finding jobs, is also useful for staying informed about recent publications and the latest developments in industry and policy.

However, with the wealth of content that is available online and the rabbit hole that is the internet, it can be difficult to keep up with the latest developments on different platforms.

One very useful yet often dismissed solution to this conundrum is the good old really simple syndication (RSS) feed. An RSS feed is a simple, algorithm-free technology that enables users to receive updates from specific websites.

Subscribing to RSS feeds enables readers to stay up-to-date with specific websites in a single tailored RSS news feed that constantly monitors websites for new content.

This removes the need for users to manually search for content, leaving you free to get on with other work.

This may be the best option for you if, like me, you get easily distracted online.

Keeping Track of the Scientific Literature

You always want to have your key papers on hand for easy access, as this will make writing easier and more efficient. It will also help when trying to justify to your PI the importance of doing a particular experiment.

As soon as you start your PhD or project, try to get organized and implement a system to help you keep a handle on the literature.

Everyone is different so you might prefer an old-school filing system or you might choose one of the many online reference management systems.

Old-School Systems

I know some people who use old-school filing systems such that every time they read a physical copy of a paper, they move it into a particular folder.

For example, you might have one folder for mechanistic studies using mouse models, and another for research using human samples. You could even use the draft layout of your thesis to categorize your reading.

Another advantage of old-school systems is the ability to annotate physical copies. However, this type of old-school filing system isn’t exactly portable, nor is it environmentally friendly.

Also, cross-referencing articles that fit into multiple categories can really wreak havoc on your system!

Many researchers now use online management systems to get around these issues.

Online Reference Management Systems

Although they can seem daunting at first, online reference management systems are a great way to organize your literature.

Once you’re used to an online system, whatever topic structure you use can be easily applied to one of the online systems by setting up relevant folders.

Reference managers such as Mendeley , ReadCube Papers , Zotero , or Endnote allow you to create and organize a library of important papers, and, more importantly, in my opinion, they help to generate citations and bibliographies while writing papers, grants, and/or theses.

In addition, these tools allow users to include notes on each paper to summarize its main findings and conclusions, which comes in very handy!

Reference managers also allow you to change in-text citation styles in one click. This can be a huge time saver if you’re submitting papers to multiple journals, each with different citation and formatting requirements.

I am particularly fond of Mendeley, first because it’s user-friendly and intuitive, but, most importantly, because it’s free! In the interests of fairness, Zotero is also free!

Most, if not all, reference managers allow users to categorize papers into folders and subfolders.

And, if you have to switch computers for some reason, you will be able to access your papers if your chosen reference manager supports cloud syncing to its own servers, as Mendeley does.

To learn more about what each of these reference managers can do, click the links above and try them out to find the one that works best for you.

Make sure you also read our article for more tips on software and apps that can make your science life easier .

Annotating PDFs of Your Articles

So, you’ve got your physical or online filing system organized. You’re sorted, right? Well, if you really want to get ahead of the game, you should highlight and annotate PDF copies of your journal articles with notes and a brief summary of the paper.

Make life easier by annotating as you read and you will create a great reference point to return to any time you need to refresh your knowledge of a particular paper.

Take it from me, if you don’t do this, you’ll just end up having to reread the paper over and over again. Make sure you include the following points:

• Key authors.
• Main findings.
• Relevance to your research—does it offer a complementary or opposing view?
• How might it affect your own experimental plan?

It might seem like a lot of work but doing this really will help you keep on top of important findings in your field, so you’ll end up having more time to do your own research!

If you’re a fan of spreadsheets and if you’re looking to build your own custom paper database/annotation system, you might want to have a look at @Ste_McQuilliam’s amazing Microsoft Excel-based journal database—you can watch his YouTube tutorial on how he built his database here .

As Steve mentions in his tutorial, you could use this Excel-based annotation system in partnership with a reference management system to stay super organized!

With all these tips in mind, go forth, explore, and write! If you have any other tips for keeping on top of your reading , we’d love to hear from you in the comments.

You can learn more about the main reference managers in our reference managers series , where we highlight key features and discuss the pros and cons of each platform.

For more tips on keeping track of the scientific literature, head over to the Bitesize Bio Managing the Scientific Literature Hub .

Originally published December 4, 2013. Reviewed and updated by Zandile Nare September 2021.

To keep abreast of scientific literature, with an access to grey literature I have been using for personal research, and teaching developments in immunology https://www.scoop.it/t/immunology a curation tool called Scoop.it. Compared to other curation tools, it can be used as a specific personalized minidatabase where you can find what you or others have been collecting before

I also recommend Zotero. Mendely is another option, but, it is not as intuitive as Zotero. Zotero has plug-ins that allow cite- while- you- write as well as nearly instant biographies to be constructed! Its listing of reference formats is huge. Go ZoteRO!

I’d recommend Zotero. Stores references from many pages (for instance pubmed) using a single mouse click. Sync (for free) between devices, so you can work @home with the references you have identified @work. Plugins available for many text processors, very easy to insert citation and generate a reference list.

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9 Organizing Research: Taking and Keeping Effective Notes

Once you’ve located the right primary and secondary sources, it’s time to glean all the information you can from them. In this chapter, you’ll first get some tips on taking and organizing notes. The second part addresses how to approach the sort of intermediary assignments (such as book reviews) that are often part of a history course.

Honing your own strategy for organizing your primary and secondary research is a pathway to less stress and better paper success. Moreover, if you can find the method that helps you best organize your notes, these methods can be applied to research you do for any of your classes.

Before the personal computing revolution, most historians labored through archives and primary documents and wrote down their notes on index cards, and then found innovative ways to organize them for their purposes. When doing secondary research, historians often utilized (and many still do) pen and paper for taking notes on secondary sources. With the advent of digital photography and useful note-taking tools like OneNote, some of these older methods have been phased out – though some persist. And, most importantly, once you start using some of the newer techniques below, you may find that you are a little “old school,” and might opt to integrate some of the older techniques with newer technology.

Whether you choose to use a low-tech method of taking and organizing your notes or an app that will help you organize your research, here are a few pointers for good note-taking.

Principles of note-taking

• If you are going low-tech, choose a method that prevents a loss of any notes. Perhaps use one spiral notebook, or an accordion folder, that will keep everything for your project in one space. If you end up taking notes away from your notebook or folder, replace them—or tape them onto blank pages if you are using a notebook—as soon as possible.
• If you are going high-tech, pick one application and stick with it. Using a cloud-based app, including one that you can download to your smart phone, will allow you to keep adding to your notes even if you find yourself with time to take notes unexpectedly.
• When taking notes, whether you’re using 3X5 note cards or using an app described below, write down the author and a shortened title for the publication, along with the page number on EVERY card. We can’t emphasize this point enough; writing down the bibliographic information the first time and repeatedly will save you loads of time later when you are writing your paper and must cite all key information.
• Include keywords or “tags” that capture why you thought to take down this information in a consistent place on each note card (and when using the apps described below). If you are writing a paper about why Martin Luther King, Jr., became a successful Civil Rights movement leader, for example, you may have a few theories as you read his speeches or how those around him described his leadership. Those theories—religious beliefs, choice of lieutenants, understanding of Gandhi—might become the tags you put on each note card.
• Note-taking applications can help organize tags for you, but if you are going low tech, a good idea is to put tags on the left side of a note card, and bibliographic info on the right side.

Organizing research- applications that can help

Using images in research.

• If you are in an archive: make your first picture one that includes the formal collection name, the box number, the folder name and call numbe r and anything else that would help you relocate this information if you or someone else needed to. Do this BEFORE you start taking photos of what is in the folder.
• If you are photographing a book or something you may need to return to the library: take a picture of all the front matter (the title page, the page behind the title with all the publication information, maybe even the table of contents).

Once you have recorded where you find it, resist the urge to rename these photographs. By renaming them, they may be re-ordered and you might forget where you found them. Instead, use tags for your own purposes, and carefully name and date the folder into which the photographs were automatically sorted. There is one free, open-source program, Tropy , which is designed to help organize photos taken in archives, as well as tag, annotate, and organize them. It was developed and is supported by the Roy Rosenzweig Center for History and New Media at George Mason University. It is free to download, and you can find it here: https://tropy.org/ ; it is not, however, cloud-based, so you should back up your photos. In other cases, if an archive doesn’t allow photography (this is highly unlikely if you’ve made the trip to the archive), you might have a laptop on hand so that you can transcribe crucial documents.

Using note or project-organizing apps

When you have the time to sit down and begin taking notes on your primary sources, you can annotate your photos in Tropy. Alternatively, OneNote, which is cloud-based, can serve as a way to organize your research. OneNote allows you to create separate “Notebooks” for various projects, but this doesn’t preclude you from searching for terms or tags across projects if the need ever arises. Within each project you can start new tabs, say, for each different collection that you have documents from, or you can start new tabs for different themes that you are investigating. Just as in Tropy, as you go through taking notes on your documents you can create your own “tags” and place them wherever you want in the notes.

Another powerful, free tool to help organize research, especially secondary research though not exclusively, is Zotero found @ https://www.zotero.org/ . Once downloaded, you can begin to save sources (and their URL) that you find on the internet to Zotero. You can create main folders for each major project that you have and then subfolders for various themes if you would like. Just like the other software mentioned, you can create notes and tags about each source, and Zotero can also be used to create bibliographies in the precise format that you will be using. Obviously, this function is super useful when doing a long-term, expansive project like a thesis or dissertation.

How History is Made: A Student’s Guide to Reading, Writing, and Thinking in the Discipline Copyright © 2022 by Stephanie Cole; Kimberly Breuer; Scott W. Palmer; and Brandon Blakeslee is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License , except where otherwise noted.

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Reading Scholarly Papers

Organizing Sources

All direct quotes, paraphrasing, summarizing, statistics, and outside opinions count as outside information, and must be cited. If you have never developed a system for keeping track of your citations, the following video provides an easy to use but effective system.

View Transcript

Hi, everyone! This is Lara Hammock from the Marble Jar channel and in today's video, I'll tell you how I use Google Sheets to organize my citations and sources for papers and research projects.

I'm in my first year of graduate school and we do a lot of writing. References and citations are very important, as they are for any discipline. I supposed if I was writing a dissertation with a hundred citations, I would feel the need to pay for and learn a whole complicated citation software, but since I'm not, I prefer to use tools that I already use and know well. AND despite the fact I'm not writing a dissertation, I have written some papers that have had over 25 sources, so I do need SOME kind of system to organize and manage my citations.

I started out, as most people do, with kind of a hodge-podge system of just cutting and pasting URLs from the Internet and sticking them at the bottom of the Word document of the paper. Or, if I'm doing research, I'd just copy and paste URLs with maybe some quotes from the study or article. The problem was, if I had multiple quotes, I couldn't organize them by topic for fear of losing the reference link, or I'd have to duplicate the URL multiple times. Plus, scrolling down to check these references was annoying. I needed a better, less messy system.

Here's what I do now. For each research project or paper, I create a new Google Sheets spreadsheet for references. You could easily do this in any spreadsheet program. I name it something like Class name - Project name - Citations and Quotes. Let's use a research project that I just did for my Policy class as an example. My spreadsheet name is "Policy - Ex-Felon Voting Rights Citations and Quotes." Then -- I make 2 tabs. The first tab is called Quotes, the second is Sources. I'm going to put a sample of this Citation Spreadsheet up on my Google Drive to share with you. To use it, just follow the link that I will provide in the notes section, make a copy into your own Drive, and then use it or modify it as you see fit.

Sample Google Spreadsheet: https://docs.google.com/spreadsheets/d/1PaQbDLrTFptlZAlarTkdj_syYBxs1zUaqqXulF1e11A/edit?usp=sharing

Back to the spreadsheet -- so, now as I'm doing my research and reading a bunch of different articles -- in this case, mostly news articles and opinion pieces -- I starting finding quotes or statistics that help me to understand the issue or that I might want to use in my paper. So, I copy the quote and paste it into this first column. Okay -- the second column is a reference number. I'm going to want to remember where I got this quote from -- so go to the article and copy the URL or website address. I note some basics about the source and what the article is about -- in this case it's an Editorial from The Washington Post Editorial Board. Now I go into the Sources tab paste the URL under website address, note some basics about the article -- more for my own recall ability than anything else, and I number it -- #1. Now, I'm going to have a bunch of other articles to put in here, so I might as well go ahead and fill in these numbers, 1 to 10. Okay, back to the Quotes tab, I'm going to indicate that this quote came from article #1. Now, I can paste several quotes from the same article, I just need to indicate where they came from. So, here is my completed spreadsheet for this research project. I have 13 sources and 38 quotes. I obviously did not use all of those in my paper, but they helped to shape my understanding of the topic and served as a repository for the quotes and statistics that I DID end up using.

Just a quick note -- because of the nature of this research project, most of my sources were articles about current events, but this system also works great for scholarly research since so much is accessible on the Internet these days through your academic institution's research portal. I also use this system to capture quotes from books. Check out my video on exporting quotes from Kindle books into a spreadsheet such as this.

There are two things that I find really helpful about this system:

1) Easy to categorize - Because each quote has its own line, you can tag each quote with a theme or category. For example, in this column, I'm going to put in the main reasoning that states use to disenfranchise ex-offenders. There are a handful: safety, punishment, violation of social contract, political ideology, race etc. Not every quote is going to get a tag, but I can tag all of the ones that apply and then I can sort by this column. That way, if this is how I've decided to structure my paper, in this case -- by state rationale, I have quotes that are all nicely grouped together and ready to use for each topic. The second thing, is that this system makes it

2) Easy to cite while drafting - So, I'm writing my paper and I want to use a good statistic. Here's one: "McAuliffe's order affected 200,000 people in a state where 3.9 million people voted in the 2012 presidential election." So, I go ahead and quote this in my paper. Now, I don't want to slow down my writing process do the whole citation now (for me, that is an entirely different thinking process), so when I'm drafting, I just put the reference number in parenthesis right behind the quote. Like this (4). Then, once I've drafted and edited the paper, I go back in looking for reference numbers and replace them with proper citations. This is easy to do since I have a nice centralized place where I've gathered all of the source website information.

This system has worked well for me. Let me know what you think! Comments are always appreciated and thanks for watching!

You may also choose to organize your notes on sources in a more topical manner. For instance, you may have main points as a heading and include bullet points of quotes, information, and statistics. Be sure to include your sources!

TWITTER IN SCHOLARLY COMMUNICATION

• First conceived by Andrea Kuszewski in 2011
• “Liu notes that the hashtag was originally intended for science journalists, who typically lack access to the online library resources available to researchers at large universities; however, her research has demonstrated that academics and students use #icanhazpdf services more frequently than those in communications fields” (p. 7)
• “Such requests are evidence of users choosing social media over the library as a means of obtaining scholarly materials” (p. 11)
• https://www.altmetric.com/blog/interactions-the-numbers-behind-icanhazpdf
• “Specific tools, such as Twitter, have proved popular for frequent use by scholars to communicate with their counterparts and promote each other’s work” (Al-Aufi & Fulton, 2015, p. 228)

Now, how do you incorporate those sources into your writing? This wonderful video from ASU and Crash Course covers how you can use paraphrasing, quotations, and explanations without plagiarism.

Citing Your Sources

Most citation styles will have an  in-text citation  which is a shortened citation in the body of your paper. Some styles may use footnotes for this instead. These in-text citations or footnotes will directly correspond to a full reference  to the source you used at the end of the paper in a list. This list can be called a references list, a bibliography, or a works cited list, depending on the style.

Ask your professor which style you should use for your class. APA, MLA, and Chicago are the three mostly commonly used citation styles at Santa Fe College.

• Understanding Citation Styles This short video discusses the purpose of citation styles along with some reason why they may be different.

• APA Citation Guide [Tyree Library] Guide created by the Tyree Library with information on formatting, example citations, and tutorials.
• APA Style Blog The official blog, answering and clarifying questions about APA.
• The Basics of APA Style Official tutorial on APA.

• Chicago-Style Citation Quick Guide Quick examples from the official style guide.
• Chicago Citation Guide [Tyree Library] Guide created by the Tyree Library with information on formatting, example citations, and tutorials.

• MLA Citation Guide [Tyree Library] Guide created by the Tyree Library with information on formatting, example citations, and tutorials.
• The MLA Style Center The official website for MLA style, with more examples, guidelines, and a place to ask questions.

• Scientific Style and Format Quick Guide Quick guide provided the by the Council of Science Editors on how to cite sources using CSE.
• NLM Catalog CSE uses a journal name abbreviation in place of the the full journal title. Use this catalog to locate correct abbreviations.

Citation Clinics

The Library offers workshops for APA and MLA throughout the semester to help you learn the basics of citing. Upcoming workshops are listed here and will be available in-person in Y-240 and via Zoom.

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University of Tasmania, Australia

Systematic reviews for health: handling results & storing papers.

• Handbooks / Guidelines for Systematic Reviews
• Standards for Reporting
• Registering a Protocol
• Tools for Systematic Review
• Online Tutorials & Courses
• Books and Articles about Systematic Reviews
• Finding Systematic Reviews
• Critical Appraisal
• Library Help
• Bibliographic Databases
• Grey Literature
• Handsearching
• Citation Tracking
• 1. Formulate the Research Question
• 2. Identify the Key Concepts
• 3. Develop Search Terms - Free-Text
• 4. Develop Search Terms - Controlled Vocabulary
• 5. Search Fields
• 6. Phrase Searching, Wildcards and Proximity Operators
• 7. Boolean Operators
• 8. Search Limits
• 9. Pilot Search Strategy & Monitor Its Development
• 10. Final Search Strategy
• 11. Adapt Search Syntax
• Documenting Search Strategies
• Handling Results & Storing Papers

Storing and Keeping Track of Papers

Storing and keeping track of papers is part of the search for studies step..

When doing a systematic review it is advisable to use a reference management software ( Cochrane Handbook, 4.6.6.1 ). There are various reference management software options available. The University of Tasmania has a site license for EndNote ; all current staff and students of the university are eligible to install EndNote software on university and home computers. EndNote is supported by your Learning & Research Librarians.

We also have access to Covidence, an online systematic review tool designed to help researchers with the systematic review process, particularly the screening and data extraction process. Learn more about accessing the UTAS Covidence licence .

Using EndNote to Manage Search Results

The use of a reference managment software such as EndNote is beneficial during a systematic review process. It may help researchers store, organise, and manage the potentially large number of literature found during the search process. Here are some of the EndNote features that are worth exploring:

• Creating group sets, groups and smart groups (e.g. for databases, exclusion/inclusion criteria, reviewers)
• Exporting search results from databases
• Annotating the records (e.g. with database and date details)
• Using Research Notes field (e.g. for personal comments, reviewer comments)
• Creating and displaying customised fields (e.g. to add reviewer's comments)
• Finding and removing dublicate records
• Finding the full text of articles
• Attaching the full text of articles manually
• Viewing and annotating PDF files
• Sharing EndNote library
• Exporting the EndNote library to Covidence or Excel

Deduplicate Records with EndNote

After running your search in multiple databases, you need to deduplicate the records. You can either do this in Covidence  or EndNote.

This helpsheet steps you through the process of using EndNote to deduplicate your records for a systematic review:

• Deduplicate in EndNote

Other EndNote Resources

Double screening of literature using endnote (medical school at the university of exeter).

• How to use EndNote to double screen for a systematic review by ESMI Information Specialists [7min]
• How to use EndNote to merge two duplicate libraries together when double screening for a systematic review by ESMI Information Specialists [8min40s]

The University of Sydney has a subject guide on EndNote for managing systematic review search results with useful helpsheets on creating groups, exporting search results from databases, annotating records with database details, creating and displaying customised fields, finding full-text articles, annotating PDF files and exporting to Excel:

• EndNote for Systematic Reviews by University of Sydney Library

EndNote for UTAS Researchers

Downloading endnote.

Current staff and students of the University of Tasmania are eligible to install EndNote software on University and home computers. Download instructions can be found on the Download EndNote tab of the EndNote subject guide:

• EndNote subject guide: Download EndNote

Using EndNote

The EndNote subject guide contains introductory guides to Endnote, offers links to online tutorials and details various features of EndNotes:

• EndNote subject guide

EndNote Training

The University of Tasmania Library offers regular introductory EndNote training sessions, open to all UTAS researchers:

• EndNote workshops

Individual EndNote training can be provided on an ad-hoc basis, please contact the Learning & Research Librarians team:

• Contact a Learning & Research Librarian

Exporting Results to EndNote

For information on how to export results from a database to EndNote:

• Search the A-Z Database list for the database of your interest.
• EndNote help sheet may be available in the Notes column.

Each database has a limit on how many results can be exported to EndNote:

Other Systematic Review Tools

There are many other software options available which have been specifically designed for systematic reviews. See Systematic Review Tools .

Need More Help? Book a consultation with a  Learning and Research Librarian  or contact  [email protected] .

• << Previous: Documenting Search Strategies
• Last Updated: Apr 4, 2024 10:17 AM
• URL: https://utas.libguides.com/SystematicReviews

• Open access
• Published: 21 March 2017

LitDB - Keeping Track of Research Papers From Your Institute Made Simple

• Jörn Bethune 1 ,
• Lars Kraemer 1 ,
• Ingo Thomsen 1 ,
• Andreas Keller 2 ,
• David Ellinghaus 1 &
• Andre Franke   ORCID: orcid.org/0000-0003-1530-5811 1  

Source Code for Biology and Medicine volume  12 , Article number:  5 ( 2017 ) Cite this article

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1 Citations

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In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities.

We here describe LitDB, a novel open source literature database solution for easy maintenance of publication lists assigned to various topics. In the last 2 years more than 50 users have been using LitDB at our research institute. The LitDB system is accessed via a web browser. Publications can be uploaded through direct exports from reference manager libraries or by entering PubMed IDs. Single users or user groups can track their citation counts, h-index and impact factor statistics and gain insights into the publication records of other users. It offers various visualization functions like coauthor networks and provides ways to organize publications from dedicated projects and user groups. The latter is in particular beneficial to manage publication lists of large research groups and research initiatives through a “crowd-sourcing” effort.

Conclusions

Keeping track of papers authored and published by a research group, institute or university is an important and non-trivial task. By using a centralized web-based platform for publication management such as LitDB the compilation of project- and group-related publication lists becomes easily manageable and it is less likely that papers are forgotten along the way.

Scientific publications play an important role in research. The publication record is often used as an objective measure to benchmark productivity and excellence of a scientist within a research community. But modern scientists rarely work alone. They are part of research groups, academic departments or research initiatives. On each of these levels it is necessary to maintain current lists of publications to acquire third-party funding and to present a profile to the public.

Funding applications are usually written by senior researchers who are managing several scientists with less experience. The senior researchers not only need to keep track of their own projects and publications, but also of all the work that is done by the junior researchers which can be a lot of projects running in parallel. Given the importance of publications in academia, it is undesirable to not know about the relevant publication of a paper from your own research institution.

Here we present a software-based solution to address this problem: We developed a literature management system called LitDB (Fig.  1 ). The LitDB software is a web-based application that allows researchers to store records of their own publications on a central server. This ensures that past publications are quickly discoverable for everyone in a research organization and that publication lists for project-related grant applications can easily be constructed.

LitDB functionality overview. The figure depicts all options that are available to a super user. Normal users only see the blue menu options and staff users only see the staff menu. All entries in the LitDB that are related to the current user can be accessed under My Space. It is possible to configure LitDB so that a different logo is shown

The crucial idea behind LitDB is that all members of a research institute use the same database to keep track of their own publications and their own projects, so that other members of a research institute are aware of all publications that can be used in research grant applications.

Implementation

LitDB is implemented in Python (version 2.7 [ 1 ]) with the Django web framework (version 1.8.7 [ 2 ]). It uses the PostgreSQL database [ 3 ] for data storage (via the python package psycopg2) and the D3.js [ 4 ] library for visualization of the co-author networks. LitDB has been tested on Microsoft Windows and Linux servers for the past 2 years. LitDB can make use of the open LDAP protocol (via the django-auth-ldap python package [ 5 ]) which is a standard for user management in most university’s computer systems, but is also capable of managing users as a stand-alone tool.

We provide a Docker [ 6 ] image that facilitates the deployment of the LitDB so that it is not necessary to deal with the software’s dependencies. For further technical information see the website of the LitDB: http://www.ikmb.uni-kiel.de/litdb .

The central feature of LitDB is the management of project-related papers. Papers can be submitted manually, but LitDB assists the user in the process. For instance, it is possible to only provide the PubMed ID of a paper and LitDB will gather all the remaining metadata by itself. It is also possible to add several papers at once by providing a list of PubMed IDs. If no PubMed ID is available (e.g. for book chapters), the users can still enter their papers by providing the details themselves. Every user can list his or her own papers in LitDB (Fig.  2 ). Further papers that the user might have coauthored are also suggested. However, these papers must have been previously submitted by another LitDB user. The user can then acknowledge or reject the suggested papers. In order for the LitDB to recognize the papers of the users, every user can provide aliases for his or her name. For instance, PubMed usually only saves the first letter of the first name of a person. But sometimes the complete first name is available for the search. Therefore, it makes sense to search for “John Doe” as well as for “J Doe”. This makes it also possible to take into account that people change names due to marriage, or to account for middle names or other circumstances. The problem of uniquely identifying scientists by their name(s) is not new. One popular solution to this problem is the use of unique IDs like ORCIDs [ 7 ]. The LitDB software also supports searching for papers by ORCID. Another useful feature is the possibility to categorize papers in the form of lists. When writing a grant application, it might be helpful to have a list that focuses on a specific scientific topic that is most relevant to the application that can be shared by several users. But other types of lists can also be created: A list of the top 5 publications of a user is a popular choice and shown on our institute’s webpage (with the help of an external script which queries the database). Lists can be created for single users but it is also possible to define projects in the LitDB and then all members of a project can create shared lists.

Listing of all papers from an author in the My Space section. With the help of the search form it is possible to search for specific papers. The overview table features the publication year and the author’s position for every publication. It is possible to edit entries to change incorrect information

LitDB makes it possible to define working groups (teams), institutes and third-party projects so that all publications from a group of people can easily be obtained and employed for benchmarking, for example.

As it was demanded by the users, we implemented in LitDB the additional feature to record research prizes, third-party grants and granted patents (Fig.  3 ), all of which are important benchmarking features as well and therefore often needed in grant applications and CVs.

My Space section and paper overview. The user can create and manage grants, lists of papers, all of his papers, patents and teams in this section. In the current view, there is a table with yearly reports on the published papers. The number of papers, the number of first- and last-authorships as well as the average, minimum, maximum and total impact factors for every year are listed

LitDB also provides a table with statistics on the number of published papers and the impact factors for each year. This table can be used for writing annual reports and to compare the paper output of different years with each other.

Alternatives

We have created LitDB because it provides a solution to a problem that we could not solve with other methods and non-commercial products. Most importantly, it provides a central hub for all authored papers for a group of researchers.

Often people use Microsoft Excel sheets or reference managers for keeping track of their publications. However, these tools are not well-integrated into larger context of a scientific institution. By using a central system, the scientists directly share their knowledge about their publications with their principal investigators, which leads to more consistent and sustainable archival of such information and makes it less likely that a publication is missed when writing a research grant. To our knowledge there are no other systems available to the general public that specialize on this task like LitDB does. It should be noted that LitDB does not try to replace reference managers. Its main purpose is to create central registry of all papers from a limited group of authors. Unlike popular reference managers like Endnote, Mendeley and Zotero, LitDB has been designed from the ground up for collaborative publication management.

LitDB also supports the calculation of impact factors for the papers in the system which is also helpful for raising funding for further research.

As the LitDB is a web-based application the researchers do not need to install any software beyond a web browser and everyone is able to work together with the same database, because there are no interoperability conflicts.

Keeping track of the scientific publications of a larger group of researchers requires a lot of effort and diligence in order to not forget any publications that might be relevant for receiving further funding. The LitDB assists a research group with managing publication records based on the principle of “crowd-sourcing” to keep publication records up-to-date and complete.

These publication records are also very valuable for performing benchmarking calculations in combination with impact factors to measure and report scientific success over the years.

Availability and requirements

Project name : LitDB

Project home page : http://www.ikmb.uni-kiel.de/litdb

Operating system : GNU/Linux

Programming language : Python (version 2)

Other requirements : A mod-wsgi compatible web server like Apache. Development libraries for libldap2, libsasl2 and libpq. The python packages django-auth-ldap and psycopg2. The Django web framework version 1.8.7

Licence : BSD License 2.0

Welcome to Python.org http://www.python.org . Accessed 21 Jan 2016

The Web framework for perfectionists with deadlines https://www.djangoproject.com/ . Accessed 21 Jan 2016

PostgreSQL: The world’s most advanced open source database http://www.postgresql.org/ . Accessed 21 Jan 2016

D3.js – Data-Driven Documents http://d3js.org/ Accessed 21 Jan 2016

django-auth-ldap 1.2.7 : Python Package Index https://pypi.python.org/pypi/django-auth-ldap/1.2.7 . Accessed 21 Jan 2016

Docker - Build, Ship, and Run Any App, Anywhere https://www.docker.com/ . Accessed 21 Jan 2016

ORCID | Connecting Research and Researchers https://orcid.org/ . Accessed 12 Feb 2017

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Acknowledgements

The authors are supported by the German Ministry of Education and Research (BMBF), the Deutsche Forschungsgemeinschaft (DFG) the Cluster of Excellence “Inflammation at Interfaces” and the DFG PhD Research Training Group”Genes, Environment and Inflammation” 1743/1. Andre Franke receives an endowment professorship (Peter Hans Hofschneider Professorship) of the “Stiftung Experimentelle Biomedizin” located in Zuerich, Switzerland.

Not applicable.

The source code and the most recent version of the LitDB tool can be obtained on the website http://www.ikmb.uni-kiel.de/litdb . The web server for the installation has to meet the following minimum requirements: 300 MB RAM, 600 MB disk space plus further space for the PostgreSQL database. The web interface has been tested with the following browsers: Safari 8.0.7 (Mac OS 10.10.4), Firefox 42.0 (Ubuntu Linux 14.04 LTS, Microsoft Windows 7).

Author’s contributions

LK designed and developed the tool with support of IT. JB helped with the implementation and the release of the software package. AF initiated the project and supervised the development. JB and AF wrote the first draft of the manuscript. All authors read, edited and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests. The authors alone are responsible for the content and writing of the paper.

Consent for publication

All personal data is from the authors and they give their consent to publish it.

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Author information

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Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany

Jörn Bethune, Lars Kraemer, Ingo Thomsen, David Ellinghaus & Andre Franke

Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany

Andreas Keller

You can also search for this author in PubMed   Google Scholar

Corresponding author

Correspondence to Andre Franke .

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Bethune, J., Kraemer, L., Thomsen, I. et al. LitDB - Keeping Track of Research Papers From Your Institute Made Simple. Source Code Biol Med 12 , 5 (2017). https://doi.org/10.1186/s13029-017-0065-2

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Received : 25 April 2016

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Published : 21 March 2017

DOI : https://doi.org/10.1186/s13029-017-0065-2

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• Management of project-related publication lists
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• Impact factor
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