what is annotation in article

Understanding Annotation: A Comprehensive Guide

What is annotation, the purpose of annotation, types of annotation, how to annotate effectively, annotation tools, annotation examples, annotation in different disciplines, annotation vs. abstract, annotation in digital learning, the future of annotation.

Let's take a journey into the world of annotation, a concept that often makes students cringe and researchers sigh. But, don't worry — this guide will help you understand annotation in a simple, friendly, and clear way. Whether you're a newbie or someone who just needs a refresher, this comprehensive guide will provide a clear definition of annotation and its many uses.

So, what exactly is the definition of annotation? In its simplest form, annotation refers to adding notes or comments to a text or a diagram. It's like having a personal conversation with the author, or making sense of a complex graph. It doesn't stop there, though. The process of annotation is much more than just dropping notes — it's about understanding, interpreting, and engaging with the material. Let's break it down:

• Understanding: Annotations help you to grasp the ideas and concepts presented in the text or diagram. You might underline key phrases or highlight important data points, all in the service of better understanding what you're reading or viewing.
• Interpreting: By providing your own insights or explanations, you're not merely reading or looking at the material, but actively interpreting it. This could be as simple as jotting down "This means..." or "The author is saying..." next to a paragraph.
• Engaging: When you annotate, you're not just a passive reader anymore. You're actively engaging with the material, questioning it, agreeing or disagreeing, even arguing with the author! This active engagement helps to deepen your understanding and retention of the material.

To sum it up, the definition of annotation isn't just about making notes — it's a method to read, understand, interpret, and engage with any piece of content more effectively. And guess what? There's more to annotation than you might think! Stick around as we delve deeper into the purpose, types, and tools of annotation in the following sections.

Now that we've nailed down the definition of annotation, let's talk about why it's so important. Why do teachers, professors, and researchers keep insisting on it? Well, there are several reasons:

• Improves comprehension: Annotating helps you understand the text or diagram better. It's like having a personal guide walking you through a dense forest of words or a complex maze of data. By highlighting and commenting, you can make sense of the material more easily.
• Enhances retention: We've all been there. You read a page, flip it, and — poof! — everything's gone. But with annotation, you can remember more. When you actively engage with the material, you're more likely to remember it. It's like the difference between watching a movie and participating in it.
• Facilitates analysis: Annotation is not just about understanding, but also about analyzing. By adding your own thoughts, insights, and interpretations, you can dig deeper into the material, uncovering layers of meaning that might not be immediately apparent.
• Promotes critical thinking: When you annotate, you're not just accepting information passively — you're actively questioning, evaluating, and critiquing it. This cultivates critical thinking skills, which are crucial in today's information-saturated world.

Remember, the purpose of annotation is not to make your book look like a rainbow or to fill the margins with a clutter of notes. It's about making the material work for you, helping you to understand, remember, analyze, and think critically. So next time someone mentions annotation, don't cringe. Embrace it. It's your secret weapon in the world of learning!

Now that we've got a grip on the definition of annotation and its purpose, it's time to dive into the different types of annotation. You might be thinking, "Wait a minute, there's more than one type?" Yes, indeed! And picking the right one can make a world of difference. So, let's explore:

• Descriptive Annotation: This kind of annotation is like a sneak peek of a movie. It gives an overview of the main points, themes, or arguments without revealing too much. It's like a book cover — enticing enough to draw you in, but not revealing all the secrets.
• Critical Annotation: This type goes a step further. It not only describes the content but also evaluates it. It's like a movie review, discussing the strengths and weaknesses, the relevance of the content, and the author's credibility. It helps you decide whether the material is worth your time.
• Informative Annotation: This annotation is like an all-you-can-eat buffet. It provides a summary of the material, including all the significant findings and conclusions. It's ideal when you need a detailed understanding of the content without having to read the whole thing.
• Reflective Annotation: This type of annotation is a bit more personal. It includes your thoughts, reactions, and reflections on the material. It's like a diary entry, capturing your intellectual journey as you engage with the material.

So, next time you're tasked with annotating, consider the type of annotation that best suits your needs. Remember, the goal is not to make your work harder, but to make it easier and more effective. Happy annotating!

Here you are, equipped with the definition of annotation and an overview of its types. But, how do you do it effectively? Let's break it down:

• Get clear on your purpose: Why are you annotating? Is it to understand better, remember, or critique? Your purpose will guide your annotation process.
• Take a quick preview: Before you start annotating, skim through the material. Get a feel for its structure and main ideas. This way, you'll know what to pay special attention to.
• Be selective: Resist the urge to highlight or underline everything. Limit your annotations to crucial points, unfamiliar concepts, and interesting ideas. The goal is to create signposts that can guide you back to key information when needed.
• Make it meaningful: Don’t just underline or highlight. Write brief notes that summarize, question, or react to the content. This makes your annotations a tool for active learning.
• Use symbols or codes: Develop your own system of symbols or codes to denote different types of information. For example, a question mark could indicate parts you don’t understand, while an exclamation mark could point to surprising or important insights.

Remember, effective annotation is not about how much you mark, but about how well you understand and engage with the material. Keep practicing and refining your approach, and soon you'll become an annotation pro!

So, now that we know how to annotate effectively, let's talk about some tools that can make this process even smoother. These are especially handy if you're dealing with digital content, or if you want to share your annotations with others. Here are some noteworthy ones:

• Pencil and Paper: Sometimes, the old ways are the best ways. Nothing beats the flexibility and simplicity of annotating with a good old-fashioned pencil. You can underline, highlight, make notes in the margin — the possibilities are endless!
• Highlighters: These are great for emphasizing key points in your text. Just remember not to go overboard and turn your page into a rainbow!
• Post-it Notes: If you don't want to write directly on your material, or if you need more space for your thoughts, these little sticky notes can be a lifesaver.
• PDF Annotation Tools: If you're working with digital documents, tools like Adobe Reader, Preview, and others offer built-in annotation features. These can include highlighting, underlining, and adding comments.
• Online Annotation Tools: Websites like Hypothesis and Genius let you annotate web pages and share your annotations with others. They're like social media for readers!

These tools are just the tip of the iceberg. There are many other annotation tools out there, each with its own strengths and weaknesses. So, don't be afraid to experiment and find the ones that work best for you!

Let's put the definition of annotation into real-world scenarios. Here are some examples to help you get a better sense of how annotation works.

• Novels: You're reading a gripping mystery novel and you come across a clue. You underline it and jot down your theories in the margin. That's annotation!
• Textbooks: Remember the last time you studied for an exam? You probably highlighted important information and made notes to help you remember key points. That's annotation too!
• Articles: When reading a long article online, you might use a tool to underline key sections and add your own thoughts. This not only helps you understand the content better but also lets you share your insights with others. Yep, that's annotation.
• Research Papers: If you're conducting research, annotation is your best friend. Underlining important data, writing summaries of complex sections, and noting down your ideas can make the whole process much easier.
• Social Media: Ever added a funny caption to a photo before sharing it with your friends? Guess what? That's annotation too!

As you can see, annotations can be as simple or as complex as you need them to be. They're all about adding extra information to make the original content more useful or meaningful for you. So, next time you're reading something, why not give annotation a try? Who knows, you might discover some fascinating insights!

Now that we've nailed down the definition of annotation, let's see how it's applied across different disciplines. You might be surprised to know that annotation isn't just for the world of literature or academia. Here's how different fields use annotation:

• Sciences: Scientists use annotations to note down observations during experiments. They can also annotate diagrams to explain complex processes.
• Arts: Artists often annotate their sketches with notes about colors, textures, or ideas for future works. Art historians may also use annotations to provide deeper insight into famous paintings or sculptures.
• Computer Science: In the world of coding, annotations can provide extra details about how a piece of code functions. They're like a roadmap for other programmers who might need to understand or modify the code later.
• Geography: Geographers use annotations on maps to highlight specific features or explain certain phenomena. For example, they might annotate a map to show the path of a storm or the spread of a forest fire.
• Business: Business professionals annotate reports and presentations to highlight key points. This helps everyone stay on the same page and understand the main takeaways.

As you can see, no matter the discipline, the power of annotation is universal. It's all about enhancing understanding and fostering communication! So, the next time you're working on a project, why not consider how annotation could help you?

Dealing with academic or professional texts, you've probably come across both annotations and abstracts. But do you know the difference? Many people get confused between the two, but they serve unique roles. Let's clear the air by exploring the definition of annotation versus an abstract:

Annotation: An annotation adds extra information to a text. It could be a comment, explanation, or even a question. Imagine you're reading a complex scientific paper. You might annotate it by jotting down a simpler explanation of a concept in the margins. That's annotation—helping to make the text more accessible and understandable for you.

Abstract: On the other hand, an abstract is a short summary of a document's main points. Think of it as a mini version of the text. If you've ever written a research paper, you've probably had to include an abstract at the beginning. It gives readers a snapshot of what the document covers so they can decide if they want to read the whole thing.

So, in a nutshell, an annotation is more about adding value to the text, while an abstract is about summarizing it. Both have their places and can be super helpful when dealing with complex or lengthy texts. Understanding the difference between the two is another step in mastering the art of reading and writing effectively.

Now, let's shift gears and explore how annotation plays a role in the digital learning space. With the advent of technology, education isn't limited to chalkboards and textbooks anymore. We've moved onto laptops, tablets, and even mobile phones. So, where does the definition of annotation fit in this digital world?

In digital learning, annotation takes on a slightly different form. Instead of scribbling in the margins of a book, you're adding notes to a PDF, highlighting text in an eBook, or leaving comments on a shared document.

Let's say you're studying for a history exam with a friend, and you're both using the same digital textbook. You come across a paragraph that you think is particularly important, so you highlight it and leave a note saying, "Must remember for the exam!" When your friend opens the book on their device, they can see your annotation and benefit from it. This is the power of annotation in digital learning—it promotes collaboration and makes studying a more interactive experience.

And it's not just for students, either. Teachers can use digital annotation to provide feedback on assignments, clarify points in a lecture, or share additional resources. In a world where online learning is becoming the norm, understanding and using digital annotation is a skill worth mastering.

Having explored the definition of annotation in various contexts, it's exciting to imagine where it might head in the future. As we continue to integrate technology into our lives, the role and methods of annotation are likely to evolve with it.

Imagine a world where every bit of text you interact with—be it a digital book, an online article, or even a social media post—can be annotated with your thoughts, questions, or insights. And not just that, imagine those annotations being instantly shareable with anyone around the globe. We're already seeing glimpses of this in digital learning platforms, as we previously discussed.

Moreover, the rise of artificial intelligence might add another layer to annotation. Imagine AI systems that can automatically highlight important parts of a text, suggest resources for further reading, or even generate annotations based on your personal learning style. Now that's a future worth looking forward to!

While we are not there yet, the journey towards that future is already underway. And as we make strides in this direction, the definition of annotation will continue to expand and adapt. It's a fascinating field that underscores the importance of understanding, interpreting, and communicating information in our increasingly interconnected world.

If you're looking to improve your annotation skills and learn more about organizing your creative projects, check out Ansh Mehra's workshop, ' Documentation for Creative People on Notion .' This workshop will provide you with practical tips and techniques for effective annotation, as well as help you develop a comprehensive documentation system for your creative work.

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How to Annotate an Article

Last Updated: September 26, 2023 Fact Checked

This article was co-authored by Emily Listmann, MA . Emily Listmann is a private tutor in San Carlos, California. She has worked as a Social Studies Teacher, Curriculum Coordinator, and an SAT Prep Teacher. She received her MA in Education from the Stanford Graduate School of Education in 2014. There are 9 references cited in this article, which can be found at the bottom of the page. This article has been fact-checked, ensuring the accuracy of any cited facts and confirming the authority of its sources. This article has been viewed 399,853 times.

Annotating a text means that you take notes in the margins and make other markings for reading comprehension. Many people use annotation as part of academic research or to further their understanding of a certain work. To annotate an article, you'll need to ask questions as you go through the text, focus on themes, circle terms you don't understand, and write your opinions on the text's claims. You can annotate an article by hand or with an online note-taking program.

Following General Annotation Procedures

• Background on the author
• Themes throughout the text
• The author’s purpose for writing the text
• The author’s thesis
• Points of confusion
• How the text compares to other texts you are analyzing on the same topic
• Questions to ask your teacher or questions to bring up in class discussions

• Later on, you can gather all of these citations together to form a bibliography or works cited page, if required.
• If you are working with a source that frequently changes, such as a newspaper or website, make sure to mark down the accession date or number (the year the piece was acquired and/or where it came from).

• If you were given an assignment sheet with listed objectives, you might look over your completed annotation and check off each objective when finished. This will ensure that you’ve met all of the requirements.

• You can also write down questions that you plan to bring up during a class discussion. For example, you might write, “What does everyone think about this sentence?” Or, if your reading connects to a future writing assignment, you can ask questions that connect to that work.

• You could write, “Connects to the theme of hope and redemption discussed in class.”

• Use whatever symbol marking system works for you. Just make sure that you are consistent in your use of certain symbols.
• As you review your notes, you can create a list of all of the particular words that are circled. This may make it easier to look them up.
• For example, if the tone of the work changes mid-paragraph, you might write a question mark next to that section.

• To increase your reading comprehension even more, you might want to write down the thesis statement in the margins in your own words.
• The thesis sentence might start with a statement, such as, “I argue…”

• For example, reading online reviews can help you to determine whether or not the work is controversial or has been received without much fanfare.
• If there are multiple authors for the work, start by researching the first name listed.

• You might write, “This may contradict any earlier section.” Or, “I don’t agree with this.”

Annotating an Article by Hand

• You can also file away this paper copy for future reference as you continue your research.

• If you are visual learner, you might consider developing a notation system involving various colors of highlighters and flags.

• Depending on how you’ve taken your notes, you could also remove these Post-its to create an outline prior to writing.

• This rough annotation can then be used to create a larger annotated bibliography. This will help you to see any gaps in your research as well. [11] X Research source

Annotating an Article on a Webpage

• You could also use a program, such as Evernote, MarkUp.io, Bounce, Shared Copy, WebKlipper, or Springnote. Be aware that some of these programs may require a payment for access.

• Depending on your program, you may be able to respond to other people’s comments. You can also designate your notes as private or public.

Community Q&A

• Annotating takes extra time, so make sure to set aside enough time for you to complete your work. [15] X Research source Thanks Helpful 0 Not Helpful 0
• If traditional annotation doesn’t appeal to you, then create a dialectical journal where you write down any quotes that speak to you. Thanks Helpful 0 Not Helpful 0

• If you end up integrating your notes into a written project, make sure to keep your citation information connected. Otherwise, you run the risk of committing plagiarism. Thanks Helpful 0 Not Helpful 0

You Might Also Like

• ↑ https://research.ewu.edu/writers_c_read_study_strategies
• ↑ http://penandthepad.com/annotate-newspaper-article-7730073.html
• ↑ https://www.hunter.cuny.edu/rwc/handouts/the-writing-process-1/invention/Annotating-a-Text/
• ↑ https://learningcenter.unc.edu/tips-and-tools/annotating-texts/
• ↑ https://www.biologycorner.com/worksheets/annotate.html
• ↑ https://owl.purdue.edu/owl/general_writing/common_writing_assignments/annotated_bibliographies/annotated_bibliography_samples.html
• ↑ https://elearningindustry.com/the-5-best-free-annotation-tools-for-teachers
• ↑ http://www.macworld.com/article/1162946/software-productivity/how-to-annotate-pdfs.html
• ↑ http://www.une.edu/sites/default/files/Reading-and-Annotating.pdf

About This Article

To annotate an article, start by underlining the thesis, or the main argument that the author is making. Next, underline the topic sentences for each paragraph to help you focus on the themes throughout the text. Then, in the margins, write down any questions that you have or those that you’d like your teacher to help you answer. Additionally, jot down your opinions, such as “I don’t agree with this section” to create personal connections to your reading and make it easier to remember the information. For more advice from our Education reviewer, including how to annotate an article on a web page, keep reading. Did this summary help you? Yes No

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Annotating Texts

What is annotation.

Annotation can be:

• A systematic summary of the text that you create within the document
• A key tool for close reading that helps you uncover patterns, notice important words, and identify main points
• An active learning strategy that improves comprehension and retention of information

Why annotate?

• Isolate and organize important material
• Identify key concepts
• Monitor your learning as you read
• Make exam prep effective and streamlined
• Can be more efficient than creating a separate set of reading notes

How do you annotate?

Summarize key points in your own words .

• Use headers and words in bold to guide you
• Look for main ideas, arguments, and points of evidence
• Notice how the text organizes itself. Chronological order? Idea trees? Etc.

Circle key concepts and phrases

• What words would it be helpful to look-up at the end?
• What terms show up in lecture? When are different words used for similar concepts? Why?

Write brief comments and questions in the margins

• Be as specific or broad as you would like—use these questions to activate your thinking about the content
• See our handout on reading comprehension tips for some examples

Use abbreviations and symbols

• Try ? when you have a question or something you need to explore further
• Try ! When something is interesting, a connection, or otherwise worthy of note
• Try * For anything that you might use as an example or evidence when you use this information.
• Ask yourself what other system of symbols would make sense to you.

Highlight/underline

• Highlight or underline, but mindfully. Check out our resource on strategic highlighting for tips on when and how to highlight.

Use comment and highlight features built into pdfs, online/digital textbooks, or other apps and browser add-ons

• Are you using a pdf? Explore its highlight, edit, and comment functions to support your annotations
• Some browsers have add-ons or extensions that allow you to annotate web pages or web-based documents
• Does your digital or online textbook come with an annotation feature?
• Can your digital text be imported into a note-taking tool like OneNote, EverNote, or Google Keep? If so, you might be able to annotate texts in those apps

What are the most important takeaways?

• Annotation is about increasing your engagement with a text
• Increased engagement, where you think about and process the material then expand on your learning, is how you achieve mastery in a subject
• As you annotate a text, ask yourself: how would I explain this to a friend?
• Put things in your own words and draw connections to what you know and wonder

The table below demonstrates this process using a geography textbook excerpt (Press 2004):

A common concern about annotating texts: It takes time!

Yes, it can, but that time isn’t lost—it’s invested.

Spending the time to annotate on the front end does two important things:

• It saves you time later when you’re studying. Your annotated notes will help speed up exam prep, because you can review critical concepts quickly and efficiently.
• It increases the likelihood that you will retain the information after the course is completed. This is especially important when you are supplying the building blocks of your mind and future career.

One last tip: Try separating the reading and annotating processes! Quickly read through a section of the text first, then go back and annotate.

Works consulted:

Nist, S., & Holschuh, J. (2000). Active learning: strategies for college success. Boston: Allyn and Bacon. 202-218.

Simpson, M., & Nist, S. (1990). Textbook annotation: An effective and efficient study strategy for college students. Journal of Reading, 34: 122-129.

Press, F. (2004). Understanding earth (4th ed). New York: W.H. Freeman. 208-210.

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How to Annotate Texts

Use the links below to jump directly to any section of this guide:

Annotation Fundamentals

How to start annotating , how to annotate digital texts, how to annotate a textbook, how to annotate a scholarly article or book, how to annotate literature, how to annotate images, videos, and performances, additional resources for teachers.

Writing in your books can make you smarter. Or, at least (according to education experts), annotation–an umbrella term for underlining, highlighting, circling, and, most importantly, leaving comments in the margins–helps students to remember and comprehend what they read. Annotation is like a conversation between reader and text. Proper annotation allows students to record their own opinions and reactions, which can serve as the inspiration for research questions and theses. So, whether you're reading a novel, poem, news article, or science textbook, taking notes along the way can give you an advantage in preparing for tests or writing essays. This guide contains resources that explain the benefits of annotating texts, provide annotation tools, and suggest approaches for diverse kinds of texts; the last section includes lesson plans and exercises for teachers.

Why annotate? As the resources below explain, annotation allows students to emphasize connections to material covered elsewhere in the text (or in other texts), material covered previously in the course, or material covered in lectures and discussion. In other words, proper annotation is an organizing tool and a time saver. The links in this section will introduce you to the theory, practice, and purpose of annotation. 

How to Mark a Book, by Mortimer Adler

This famous, charming essay lays out the case for marking up books, and provides practical suggestions at the end including underlining, highlighting, circling key words, using vertical lines to mark shifts in tone/subject, numbering points in an argument, and keeping track of questions that occur to you as you read. 

How Annotation Reshapes Student Thinking (TeacherHUB)

In this article, a high school teacher discusses the importance of annotation and how annotation encourages more effective critical thinking.

The Future of Annotation (Journal of Business and Technical Communication)

This scholarly article summarizes research on the benefits of annotation in the classroom and in business. It also discusses how technology and digital texts might affect the future of annotation. 

Annotating to Deepen Understanding (Texas Education Agency)

This website provides another introduction to annotation (designed for 11th graders). It includes a helpful section that teaches students how to annotate reading comprehension passages on tests.

Once you understand what annotation is, you're ready to begin. But what tools do you need? How do you prepare? The resources linked in this section list strategies and techniques you can use to start annotating. 

What is Annotating? (Charleston County School District)

This resource gives an overview of annotation styles, including useful shorthands and symbols. This is a good place for a student who has never annotated before to begin.

How to Annotate Text While Reading (YouTube)

This video tutorial (appropriate for grades 6–10) explains the basic ins and outs of annotation and gives examples of the type of information students should be looking for.

Annotation Practices: Reading a Play-text vs. Watching Film (U Calgary)

This blog post, written by a student, talks about how the goals and approaches of annotation might change depending on the type of text or performance being observed. 

Annotating Texts with Sticky Notes (Lyndhurst Schools)

Sometimes students are asked to annotate books they don't own or can't write in for other reasons. This resource provides some strategies for using sticky notes instead.

Teaching Students to Close Read...When You Can't Mark the Text (Performing in Education)

Here, a sixth grade teacher demonstrates the strategies she uses for getting her students to annotate with sticky notes. This resource includes a link to the teacher's free Annotation Bookmark (via Teachers Pay Teachers).

Digital texts can present a special challenge when it comes to annotation; emerging research suggests that many students struggle to critically read and retain information from digital texts. However, proper annotation can solve the problem. This section contains links to the most highly-utilized platforms for electronic annotation.

Evernote is one of the two big players in the "digital annotation apps" game. In addition to allowing users to annotate digital documents, the service (for a fee) allows users to group multiple formats (PDF, webpages, scanned hand-written notes) into separate notebooks, create voice recordings, and sync across all sorts of devices. 

OneNote is Evernote's main competitor. Reviews suggest that OneNote allows for more freedom for digital note-taking than Evernote, but that it is slightly more awkward to import and annotate a PDF, especially on certain platforms. However, OneNote's free version is slightly more feature-filled, and OneNote allows you to link your notes to time stamps on an audio recording.

Diigo is a basic browser extension that allows a user to annotate webpages. Diigo also offers a Screenshot app that allows for direct saving to Google Drive.

While the creators of Hypothesis like to focus on their app's social dimension, students are more likely to be interested in the private highlighting and annotating functions of this program.

Foxit PDF Reader

Foxit is one of the leading PDF readers. Though the full suite must be purchased, Foxit offers a number of annotation and highlighting tools for free.

Nitro PDF Reader

This is another well-reviewed, free PDF reader that includes annotation and highlighting. Annotation, text editing, and other tools are included in the free version.

Goodreader is a very popular Mac-only app that includes annotation and editing tools for PDFs, Word documents, Powerpoint, and other formats.

Although textbooks have vocabulary lists, summaries, and other features to emphasize important material, annotation can allow students to process information and discover their own connections. This section links to guides and video tutorials that introduce you to textbook annotation. 

Annotating Textbooks (Niagara University)

This PDF provides a basic introduction as well as strategies including focusing on main ideas, working by section or chapter, annotating in your own words, and turning section headings into questions.

A Simple Guide to Text Annotation (Catawba College)

The simple, practical strategies laid out in this step-by-step guide will help students learn how to break down chapters in their textbooks using main ideas, definitions, lists, summaries, and potential test questions.

Annotating (Mercer Community College)

This packet, an excerpt from a literature textbook, provides a short exercise and some examples of how to do textbook annotation, including using shorthand and symbols.

Reading Your Healthcare Textbook: Annotation (Saddleback College)

This powerpoint contains a number of helpful suggestions, especially for students who are new to annotation. It emphasizes limited highlighting, lots of student writing, and using key words to find the most important information in a textbook. Despite the title, it is useful to a student in any discipline.

Annotating a Textbook (Excelsior College OWL)

This video (with included transcript) discusses how to use textbook features like boxes and sidebars to help guide annotation. It's an extremely helpful, detailed discussion of how textbooks are organized.

Because scholarly articles and books have complex arguments and often depend on technical vocabulary, they present particular challenges for an annotating student. The resources in this section help students get to the heart of scholarly texts in order to annotate and, by extension, understand the reading.

Annotating a Text (Hunter College)

This resource is designed for college students and shows how to annotate a scholarly article using highlighting, paraphrase, a descriptive outline, and a two-margin approach. It ends with a sample passage marked up using the strategies provided. 

Guide to Annotating the Scholarly Article (ReadWriteThink.org)

This is an effective introduction to annotating scholarly articles across all disciplines. This resource encourages students to break down how the article uses primary and secondary sources and to annotate the types of arguments and persuasive strategies (synthesis, analysis, compare/contrast).

How to Highlight and Annotate Your Research Articles (CHHS Media Center)

This video, developed by a high school media specialist, provides an effective beginner-level introduction to annotating research articles. 

How to Read a Scholarly Book (AndrewJacobs.org)

In this essay, a college professor lets readers in on the secrets of scholarly monographs. Though he does not discuss annotation, he explains how to find a scholarly book's thesis, methodology, and often even a brief literature review in the introduction. This is a key place for students to focus when creating annotations. 

A 5-step Approach to Reading Scholarly Literature and Taking Notes (Heather Young Leslie)

This resource, written by a professor of anthropology, is an even more comprehensive and detailed guide to reading scholarly literature. Combining the annotation techniques above with the reading strategy here allows students to process scholarly book efficiently. 

Annotation is also an important part of close reading works of literature. Annotating helps students recognize symbolism, double meanings, and other literary devices. These resources provide additional guidelines on annotating literature.

AP English Language Annotation Guide (YouTube)

In this ~10 minute video, an AP Language teacher provides tips and suggestions for using annotations to point out rhetorical strategies and other important information.

Annotating Text Lesson (YouTube)

In this video tutorial, an English teacher shows how she uses the white board to guide students through annotation and close reading. This resource uses an in-depth example to model annotation step-by-step.

Close Reading a Text and Avoiding Pitfalls (Purdue OWL)

This resources demonstrates how annotation is a central part of a solid close reading strategy; it also lists common mistakes to avoid in the annotation process.

AP Literature Assignment: Annotating Literature (Mount Notre Dame H.S.)

This brief assignment sheet contains suggestions for what to annotate in a novel, including building connections between parts of the book, among multiple books you are reading/have read, and between the book and your own experience. It also includes samples of quality annotations.

AP Handout: Annotation Guide (Covington Catholic H.S.)

This annotation guide shows how to keep track of symbolism, figurative language, and other devices in a novel using a highlighter, a pencil, and every part of a book (including the front and back covers).

In addition to written resources, it's possible to annotate visual "texts" like theatrical performances, movies, sculptures, and paintings. Taking notes on visual texts allows students to recall details after viewing a resource which, unlike a book, can't be re-read or re-visited ( for example, a play that has finished its run, or an art exhibition that is far away). These resources draw attention to the special questions and techniques that students should use when dealing with visual texts.

How to Take Notes on Videos (U of Southern California)

This resource is a good place to start for a student who has never had to take notes on film before. It briefly outlines three general approaches to note-taking on a film. 

How to Analyze a Movie, Step-by-Step (San Diego Film Festival)

This detailed guide provides lots of tips for film criticism and analysis. It contains a list of specific questions to ask with respect to plot, character development, direction, musical score, cinematography, special effects, and more. 

How to "Read" a Film (UPenn)

This resource provides an academic perspective on the art of annotating and analyzing a film. Like other resources, it provides students a checklist of things to watch out for as they watch the film.

Art Annotation Guide (Gosford Hill School)

This resource focuses on how to annotate a piece of art with respect to its formal elements like line, tone, mood, and composition. It contains a number of helpful questions and relevant examples. 

Photography Annotation (Arts at Trinity)

This resource is designed specifically for photography students. Like some of the other resources on this list, it primarily focuses on formal elements, but also shows students how to integrate the specific technical vocabulary of modern photography. This resource also contains a number of helpful sample annotations.

How to Review a Play (U of Wisconsin)

This resource from the University of Wisconsin Writing Center is designed to help students write a review of a play. It contains suggested questions for students to keep in mind as they watch a given production. This resource helps students think about staging, props, script alterations, and many other key elements of a performance.

This section contains links to lessons plans and exercises suitable for high school and college instructors.

Beyond the Yellow Highlighter: Teaching Annotation Skills to Improve Reading Comprehension (English Journal)

In this journal article, a high school teacher talks about her approach to teaching annotation. This article makes a clear distinction between annotation and mere highlighting.

Lesson Plan for Teaching Annotation, Grades 9–12 (readwritethink.org)

This lesson plan, published by the National Council of Teachers of English, contains four complete lessons that help introduce high school students to annotation.

Teaching Theme Using Close Reading (Performing in Education)

This lesson plan was developed by a middle school teacher, and is aligned to Common Core. The teacher presents her strategies and resources in comprehensive fashion.

Analyzing a Speech Using Annotation (UNC-TV/PBS Learning Media)

This complete lesson plan, which includes a guide for the teacher and relevant handouts for students, will prepare students to analyze both the written and presentation components of a speech. This lesson plan is best for students in 6th–10th grade.

Writing to Learn History: Annotation and Mini-Writes (teachinghistory.org)

This teaching guide, developed for high school History classes, provides handouts and suggested exercises that can help students become more comfortable with annotating historical sources.

Writing About Art (The College Board)

This Prezi presentation is useful to any teacher introducing students to the basics of annotating art. The presentation covers annotating for both formal elements and historical/cultural significance.

Film Study Worksheets (TeachWithMovies.org)

This resource contains links to a general film study worksheet, as well as specific worksheets for novel adaptations, historical films, documentaries, and more. These resources are appropriate for advanced middle school students and some high school students. 

Annotation Practice Worksheet (La Guardia Community College)

This worksheet has a sample text and instructions for students to annotate it. It is a useful resource for teachers who want to give their students a chance to practice, but don't have the time to select an appropriate piece of text. 

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Information Literacy Research Skill Building: What is an Annotation?

• Basic Timeline for Information
• Research Process Podcast
• Library Lingo
• Popular vs Scholarly Sources
• Primary vs Secondary Sources
• Advanced Database Searching
• Advanced Searching Techniques
• Choosing Search Terms video
• Database Evaluation
• Dissertations and Theses
• Identifying Main Concepts
• Citations to Articles
• Journal Title Abbreviations – Finding the Real Title
• Evaluating Sources: The CRAAP Test
• Peer Reviewed Journals, Refereed, and Juried Journals
• Popular vs Scholarly Information
• Article Evaluation Flow Chart

What is an Annotation?

• Most of us are probably more familiar with seeing or writing “summaries” or “abstracts” of articles or information we find. Summaries or abstracts basically rehash the content of the material. Writing annotations, however, require a different approach. Annotations, on the other hand, look at the material a little more objectively. When writing an annotation, you should consider who wrote it and why. Consult the Elements of an Annotation below for more detail.

Elements of an Annotation

• Identification and qualifications of the author: Did a journalist, scientist, politician, professor, or a lay person write the material? What do you know about the person?
• Major thesis, theories and ideas: What is the basic idea the author is trying to convey? What is the message?
• Audience and level of reading difficulty: For whom is the article written? Does the author use simple language? Scientific language? A particular jargon or specialized terms?
• Bias or standpoint of the author in relation to his theme: Does the author have a particular axe to grind, point to make, or something to sell (even if it is an idea)? What does the author have to gain or lose?
• Relationship of the work to other works in the field: Compared to other things you have read about the topic, what does this particular source add to your knowledge? Why is it worthy of inclusion into your project? What purpose does it serve? (This means you have to have already read a number of other materials on the topic before you can accurately annotate something.)
• Conclusions, findings, results : What is your basic assessment of the article based on everything else you know?
• Special features. If the work is long enough (a book or extensive article) you may want to briefly explain how it is organized. If there are indexes, statistical tables, pictures, or a bibliography, your reader will want to know.
• Annotations are short - not over 150 words. Because annotations are usually just a paragraph long, they need to be very succinct and to the point. You shouldn’t feel like you need to add “filler” information, especially if you cover all the annotation elements listed above. Annotations are also written in 3rd person.

Article Annotation Activity

• After you read the annotation, see if you can identify which annotation elements correspond with the bold text you see in the text of the annotation.
• Remember, there is no one correct to annotate an article, as long as most of the seven elements outlined above are addressed. When you evaluate an information source, pick out and make judgments about what you think is important based on how the item relates to your research.

Article Annotation

• Annotation of “Tells of Vaccine to Stop Influenza.” New York Times. October 2, 1918. ProQuest Historical News York Times (1851-2003). Pg. 10: This primary source article was written at the time of the 1918 flu outbreak by a New York Times journalist. It is a basic, unbiased report of information the author received from the U.S. Army. As a NYT’s article, it was written for the public at a basic reading level , and accounts for the development of immunization against the Spanish Flu . This would have been spectacular news at this point in time. The article, it turns out, was not accurate , as no immunization against the flu was ever found. In the second paragraph, there is evidence that Army doctors reporting this information have an interest in consoling the American public from “undue alarm.” This comment by Dr. Copeland, Health Commissioner of New York City, supports the idea that there was great concern in keeping the public confident that the matter was under control – even when the worst of the pandemic was hitting America. ACTIVITY: Look at the text in bold in the annotation above. Try to match each phrase in bold font with one of the seven annotation elements listed on the front of this handout. There may be more than one answer for each phrase you see in bold.

Original Article

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• Last Updated: May 19, 2022 1:56 PM
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Writers' Center

Eastern Washington University

Reading and Study Strategies

What is annotating and why do it, annotation explained, steps to annotating a source, annotating strategies.

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What is Annotating?

Annotating is any action that deliberately interacts with a text to enhance the reader's understanding of, recall of, and reaction to the text. Sometimes called "close reading," annotating usually involves highlighting or underlining key pieces of text and making notes in the margins of the text. This page will introduce you to several effective strategies for annotating a text that will help you get the most out of your reading.

Why Annotate?

By annotating a text, you will ensure that you understand what is happening in a text after you've read it. As you annotate, you should note the author's main points, shifts in the message or perspective of the text, key areas of focus, and your own thoughts as you read. However, annotating isn't just for people who feel challenged when reading academic texts. Even if you regularly understand and remember what you read, annotating will help you summarize a text, highlight important pieces of information, and ultimately prepare yourself for discussion and writing prompts that your instructor may give you. Annotating means you are doing the hard work while you read, allowing you to reference your previous work and have a clear jumping-off point for future work.

1. Survey : This is your first time through the reading

You can annotate by hand or by using document software. You can also annotate on post-its if you have a text you do not want to mark up. As you annotate, use these strategies to make the most of your efforts:

• Include a key or legend on your paper that indicates what each marking is for, and use a different marking for each type of information. Example: Underline for key points, highlight for vocabulary, and circle for transition points.
• If you use highlighters, consider using different colors for different types of reactions to the text. Example: Yellow for definitions, orange for questions, and blue for disagreement/confusion.
• Dedicate different tasks to each margin: Use one margin to make an outline of the text (thesis statement, description, definition #1, counter argument, etc.) and summarize main ideas, and use the other margin to note your thoughts, questions, and reactions to the text.

Lastly, as you annotate, make sure you are including descriptions of the text as well as your own reactions to the text. This will allow you to skim your notations at a later date to locate key information and quotations, and to recall your thought processes more easily and quickly.

• Next: Using a Dictionary >>
• Last Updated: Apr 25, 2024 2:50 PM
• URL: https://research.ewu.edu/writers_c_read_study_strategies

• How to Annotate

Where to Make Notes

First, determine how you will annotate the text you are about to read. 

If it is a printed article, you may be able to just write in the margins. A colored pen might make it easier to see than black or even blue. 

If it is an article posted on the web, you could also you Diigo , which is a highlighting and annotating tool that you can use on the website and even share your notes with your instructor. Other note-taking plug-ins for web browsers might serve a similar function. 

If it is a textbook that you do not own (or wish to sell back), use post it notes to annotate in the margins.

You can also use a notebook to keep written commentary as you read in any platform, digital or print. If you do this, be sure to leave enough information about the specific text you’re responding to that you can find it later if you need to. (Make notes about page number, which paragraph it is, or even short quotes to help you locate the passage again.)

What Notes to Make

Now you will annotate the document by adding your own words, phrases, and summaries to the written text. For the following examples, the article “ Guinea Worm Facts ” was used.

• Scan the document you are annotating. Some obvious clues will be apparent before you read it, such as titles or headers for sections. Read the first paragraph. Somewhere in the first (or possibly the second) paragraph should be a BIG IDEA about what the article is going to be about. In the margins, near the top, write down the big idea of the article in your own words. This shouldn’t be more than a phrase or a sentence. This big idea is likely the article’s thesis.
• Underline topic sentences or phrases that express the main idea for that paragraph or section. You should never underline more than 5 words, though for large paragraphs or blocks of text, you can use brackets. (Underlining long stretches gets messy, and makes it hard to review the text later.) Write in the margin next to what you’ve underlined a summary of the paragraph or the idea being expressed.

• “Depending on the outcome of the assessment, the commission recommends to WHO which formerly endemic countries should be declared free of transmission, i.e., certified as free of the disease.” –> ?? What does this mean? Who is WHO?
• “Guinea worm disease incapacitates victims for extended periods of time making them unable to work or grow enough food to feed their families or attend school.” –> My dad was sick for a while and couldn’t work. This was hard on our family.
• “Guinea worm disease is set to become the second human disease in history, after smallpox, to be eradicated.” –> Eradicated = to put an end to, destroy

To summarize how you will annotate text:

1. Identify the BIG IDEA 2. Underline topic sentences or main ideas 3. Connect ideas with arrows 4. Ask questions 5. Add personal notes 6. Define technical words

Like many skills, annotating takes practice. Remember that the main goal for doing this is to give you a strategy for reading text that may be more complicated and technical than what you are used to.

• Revision and Adaptation. Provided by : Lumen Learning. License : CC BY-NC: Attribution-NonCommercial
• How to Annotate Text. Provided by : Biology Corner. Located at : https://biologycorner.com/worksheets/annotate.html . License : CC BY-NC: Attribution-NonCommercial
• Image of taking notes. Authored by : Security & Defence Agenda. Located at : https://flic.kr/p/8NunXe . License : CC BY: Attribution
• Table of Contents

Instructor Resources (available upon sign-in)

• Overview of Instructor Resources
• Quiz Survey

Reading: Types of Reading Material

• Introduction to Reading
• Outcome: Types of Reading Material
• Characteristics of Texts, Part 1
• Characteristics of Texts, Part 2
• Characteristics of Texts, Part 3
• Characteristics of Texts, Conclusion
• Self Check: Types of Writing

Reading: Reading Strategies

• Outcome: Reading Strategies
• The Rhetorical Situation
• Academic Reading Strategies
• Self Check: Reading Strategies

Reading: Specialized Reading Strategies

• Outcome: Specialized Reading Strategies
• Online Reading Comprehension
• How to Read Effectively in Math
• How to Read Effectively in the Social Sciences
• How to Read Effectively in the Sciences
• 5 Step Approach for Reading Charts and Graphs
• Self Check: Specialized Reading Strategies

Reading: Vocabulary

• Outcome: Vocabulary
• Strategies to Improve Your Vocabulary
• Using Context Clues
• The Relationship Between Reading and Vocabulary
• Self Check: Vocabulary

Reading: Thesis

• Outcome: Thesis
• Locating and Evaluating Thesis Statements
• The Organizational Statement
• Self Check: Thesis

Reading: Supporting Claims

• Outcome: Supporting Claims
• Types of Support
• Supporting Claims
• Self Check: Supporting Claims

Reading: Logic and Structure

• Outcome: Logic and Structure
• Rhetorical Modes
• Inductive and Deductive Reasoning
• Diagramming and Evaluating Arguments
• Logical Fallacies
• Evaluating Appeals to Ethos, Logos, and Pathos
• Self Check: Logic and Structure

Reading: Summary Skills

• Outcome: Summary Skills
• Paraphrasing
• Quote Bombs
• Summary Writing
• Self Check: Summary Skills
• Conclusion to Reading

Writing Process: Topic Selection

• Introduction to Writing Process
• Outcome: Topic Selection
• Starting a Paper
• Choosing and Developing Topics
• Back to the Future of Topics
• Developing Your Topic
• Self Check: Topic Selection

Writing Process: Prewriting

• Outcome: Prewriting
• Prewriting Strategies for Diverse Learners
• Rhetorical Context
• Working Thesis Statements
• Self Check: Prewriting

Writing Process: Finding Evidence

• Outcome: Finding Evidence
• Using Personal Examples
• Performing Background Research
• Listening to Sources, Talking to Sources
• Self Check: Finding Evidence

Writing Process: Organizing

• Outcome: Organizing
• Moving Beyond the Five-Paragraph Theme
• Introduction to Argument
• The Three-Story Thesis
• Organically Structured Arguments
• Logic and Structure
• The Perfect Paragraph
• Introductions and Conclusions
• Self Check: Organizing

Writing Process: Drafting

• Outcome: Drafting
• From Outlining to Drafting
• Flash Drafts
• Self Check: Drafting

Writing Process: Revising

• Outcome: Revising
• Seeking Input from Others
• Responding to Input from Others
• The Art of Re-Seeing
• Higher Order Concerns
• Self Check: Revising

Writing Process: Proofreading

• Outcome: Proofreading
• Lower Order Concerns
• Proofreading Advice
• "Correctness" in Writing
• The Importance of Spelling
• Punctuation Concerns
• Self Check: Proofreading
• Conclusion to Writing Process

Research Process: Finding Sources

• Introduction to Research Process
• Outcome: Finding Sources
• The Research Process
• Finding Sources
• What are Scholarly Articles?
• Finding Scholarly Articles and Using Databases
• Database Searching
• Advanced Search Strategies
• Preliminary Research Strategies
• Reading and Using Scholarly Sources
• Self Check: Finding Sources

Research Process: Source Analysis

• Outcome: Source Analysis
• Evaluating Sources
• CRAAP Analysis
• Evaluating Websites
• Synthesizing Sources
• Self Check: Source Analysis

Research Process: Writing Ethically

• Outcome: Writing Ethically
• Academic Integrity
• Defining Plagiarism
• Avoiding Plagiarism
• Using Sources in Your Writing
• Self Check: Writing Ethically

Research Process: MLA Documentation

• Introduction to MLA Documentation
• Outcome: MLA Documentation
• MLA Document Formatting
• MLA Works Cited
• Creating MLA Citations
• MLA In-Text Citations
• Self Check: MLA Documentation
• Conclusion to Research Process

Grammar: Nouns and Pronouns

• Introduction to Grammar
• Outcome: Nouns and Pronouns
• Pronoun Cases and Types
• Pronoun Antecedents
• Try It: Nouns and Pronouns
• Self Check: Nouns and Pronouns

Grammar: Verbs

• Outcome: Verbs
• Verb Tenses and Agreement
• Non-Finite Verbs
• Complex Verb Tenses
• Try It: Verbs
• Self Check: Verbs

Grammar: Other Parts of Speech

• Outcome: Other Parts of Speech
• Comparing Adjectives and Adverbs
• Adjectives and Adverbs
• Conjunctions
• Prepositions
• Try It: Other Parts of Speech
• Self Check: Other Parts of Speech

Grammar: Punctuation

• Outcome: Punctuation
• End Punctuation
• Hyphens and Dashes
• Apostrophes and Quotation Marks
• Brackets, Parentheses, and Ellipses
• Semicolons and Colons
• Try It: Punctuation
• Self Check: Punctuation

Grammar: Sentence Structure

• Outcome: Sentence Structure
• Parts of a Sentence
• Common Sentence Structures
• Run-on Sentences
• Sentence Fragments
• Parallel Structure
• Try It: Sentence Structure
• Self Check: Sentence Structure

Grammar: Voice

• Outcome: Voice
• Active and Passive Voice
• Using the Passive Voice
• Conclusion to Grammar
• Try It: Voice
• Self Check: Voice

Success Skills

• Introduction to Success Skills
• Habits for Success
• Critical Thinking
• Time Management
• Writing in College
• Computer-Based Writing
• Conclusion to Success Skills

Understanding & Interacting with a Text

Annotations, definition and purpose.

Annotating literally means taking notes within the text as you read.  As you annotate, you may combine a number of reading strategies—predicting, questioning, dealing with patterns and main ideas, analyzing information—as you physically respond to a text by recording your thoughts.  Annotating may occur on a first or second reading of the text, depending on the text’s difficulty or length. You may annotate in different formats, either in the margins of the text or in a separate notepad or document. The main thing to remember is that annotation is at the core of active reading. By reading carefully and pausing to reflect upon, mark up, and add notes to a text as you read, you can greatly improve your understanding of that text.

Think of annotating a text in terms of having a conversation with the author in real time. You wouldn’t sit passively while the author talked at you. You wouldn’t be able to get clarification or ask questions.  Your thought processes would probably close down and you would not engage in thinking about larger meanings related to the topic. Conversation works best when people are active participants. Annotation is a form of active involvement with a text.

Reasons to Annotate

There are a number of reasons to annotate a text:

• Annotation ultimately saves reading time. While it may take more time up front as you read, annotating while you read can help you avoid having to re-read passages in order to get the meaning. That’s because…
• Annotation improves understanding. By pausing to reflect as you read, annotating a text helps you figure out if you’re understanding what you’re reading. If not, you can immediately re-read or seek additional information to improve your understanding. This is called “monitoring comprehension.”
• Annotation increases your odds of remembering what you’ve read, because you write those annotations in your own words, making the information your own. You also leave behind a set of notes that can help you find key information the next time you need to refer to that text.
• Annotation provides a record of your deeper questions and thoughts as you read, insights related to analyzing, interpreting, and going beyond the text into related issues.  Annotations such as these will be useful when you’re asked to respond to a text through reacting, applying, analyzing, and synthesizing, since these types of annotations record your own thoughts.  Much academic work in college is intended to get you to offer your own, informed thoughts (as opposed to simple recall and regurgitation of information); annotating a text helps you capture key personal, analytical insights as you read.

The following video offers a brief, clear example of annotating a text.

What to Annotate

You’ll find that you’re annotating differently in different texts, depending on your background knowledge of the topic, your own ease with reading the text, and the type of text, among other variables.  There’s no single formula for annotating a text.  Instead, there are different types of annotations that you may make, depending on the particular text.

• Mark the thesis or main idea sentence, if there is one in the text.  Or note the implied main idea.  In either case, phrase that main idea in your own words.
• Mark places that seem important, interesting, and/or confusing.
• Note your agreement or disagreement with an idea in the text.
• Link a concept in the text to your own experience.
• Write a reminder to look up something – an unknown word, a difficult concept, or a related idea that occurred to you.
• Record questions you have about what you are reading. These questions generally fall into two different categories, to clarify meaning and to evaluate what you’ve read.
• Note any biases unstated assumptions (your own included).
• Paraphrase a difficult passage by putting it into your own words.
• Summarize a lengthy section of a text to extract the main ideas–again in your own words.
• Note important transition words that show a shift in thought; transitions show how the author is linking ideas.  This is especially important if you’re reading and annotating a text intended to persuade the reader to a particular point of view, as it allows you to clarify and evaluate the author’s line of reasoning.
• Note repeated words or phrases; it’s likely that such emphasis relates to a key concept or main idea.
• Note the writer’s tone—straightforward, sarcastic, sincere, witty—and how it influences the ideas presented.
• Note idea linkages between this text and another text.
• Note idea linkages between this text and key concepts or theories of a discipline. For example, does the author offer examples relating to theories of motivation that you’re studying in a psychology class?
• And more…again, annotations vary according to the text and your background in the text’s topic.

View the following video, which reviews reading strategies for approximately the first three minutes and then moves into a comprehensive discussion of the types of things to annotate in non-fiction texts.

How to Annotate

Make sure to annotate through writing.  Do not – do not –  simply highlight or underline existing words in the text.  While your annotations may start with a few underlined words or sentences, you should always complete your thoughts through a written annotation that identifies why you underlined those words (e.g., key ideas, your own reaction to something, etc.). The pitfall of highlighting is that readers tend to do it too much, and then have to go back to the original text and re-read most of it.  By writing annotations in your own words, you’ve already moved to a higher level in your conversation with the text.

If you don’t want to write in a margin of a book or article, use sticky notes for your annotations.  If the text is in electronic form, then the format itself may have built-in annotation tools, or write in a Word document which allows you to paste sentences and passages that you want to annotate.

You may also want to create your own system of symbols to mark certain things such as main idea (*), linkage to ideas in another text (+), confusing information that needs to be researched further (!), or similar idea (=). The symbols and marks should make sense to you, and you should apply them consistently from text to text, so that they become an easy shorthand for annotation. However, annotations should not consist of symbols only; you need to include words to remember why you marked the text in that particular place.

Above all, be selective about what to mark; if you end up annotating most of a page or even most of a paragraph, nothing will stand out, and you will have defeated the purpose of annotating.

Here’s one brief example of annotation:

Sample Annotation

What follows is a sample annotation of the first few paragraphs of an article from CNN, “One quarter of giant panda habitat lost in Sichuan quake,” July 29, 2009. Sample annotations are in color. 

“The earthquake in Sichuan, southwestern China, last May left around 69,000 people dead and 15 million people displaced. Now ecologists have assessed the earthquake’s impact on biodiversity look this word up and the habitat for some of the last existing wild giant pandas.

According to the report published in “Frontiers in Ecology and the Environment,” 23 percent of the pandas’ habitat in the study area was destroyed, and fragmentation of the remaining habitat could hinder panda reproduction. How was this data gathered? Do we know that fragmentation will hinder panda reproduction?  

The Sichuan region is designated as a global hotspot for biodiversity, according to Conservation International. Home to more than 12,000 species of plants and 1.122 species of vertebrates, the area includes more than half of the habitat for the Earth’s wild giant panda population, said study author Weihua Xu of the Chinese Academy of Sciences in Beijing.” So can we assume that having so much of the pandas/ habitat destroyed will impact other species here?

Link to two additional examples of what and how to annotate

• Invention: Annotating a Text from Hunter College, included as a link in Maricopa Community College’s Reading 100 open educational resource. There’s a very clearly-annotated sample text at the end of this handout.
• Ethnic Varieties by Walt Wolfram, included as a link in Let’s Get Writing.

Summary: Annotation = Making Connections

The video below offers a review of reading concepts in the first part, focused on the concept of reading as connecting with a text.  From approximately mid-way to the end, the video offers a good extended example and discussion of annotating a text.

Note: if you want to try annotating an article and find the one in the video difficult to read, you may want to practice on a similar article about the same topic, “ Tinker V. Des Moines Independent Community School District: Kelly Shackelford on Symbolic Speech ” on the blog of the U.S. Supreme Court.

Read the paragraphs from “ Cultural Relativism ” that deal with the sociological perspective. Annotate the paragraphs with insights, questions, and thoughts that occur to you as you read.

• Annotations, includes material adapted from Excelsior College Online Reading Lab, Let's Get Writing, UMRhetLab, Reading 100, and Basic Reading and Writing; attributions below. Authored by : Susan Oaks. License : CC BY-NC-SA: Attribution-NonCommercial-ShareAlike
• Annotating: Creating an Annotation System. Provided by : Excelsior College. Located at : https://owl.excelsior.edu/orc/what-to-do-while-reading/annotating/annotating-creating-an-annotation-system/ . Project : Excelsior College Online Reading lab. License : CC BY: Attribution
• Chapter 1 - Critical Reading. Authored by : Elizabeth Browning. Provided by : Virginia Western Community College. Located at : https://vwcceng111.pressbooks.com/chapter/chapter-1-critical-reading/#whileyouread . Project : Let's Get Writing. License : CC BY-NC-SA: Attribution-NonCommercial-ShareAlike
• Strategies for Active Reading. Authored by : Guy Krueger.. Provided by : University of Mississippi. Located at : https://courses.lumenlearning.com/olemiss-writing100/chapter/strategies-for-active-reading/ . Project : UMRhetLab. License : CC BY: Attribution
• Annotating a Text (from Hunter College). Provided by : Maricopa Community College. Located at : https://learn.maricopa.edu/courses/904536/files/32965647?module_item_id=7199522 . Project : Reading 100. License : CC BY: Attribution
• Summary Skills. Provided by : Lumen Learning. Located at : https://courses.lumenlearning.com/suny-basicreadingwriting/chapter/outcome-summary-skills/ . Project : Basic Reading and Writing. License : CC BY: Attribution
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Introduction to Research: Annotating Articles

• Search Tips
• Using the Library Search
• Google Scholar Library Links
• Using Academic Search Premier
• Using Ebook Central
• Using JSTOR
• Google Search Strategies
• Evaluating Sources

Annotating Articles

• Searching for Images
• Meet with a Librarian
• Chicago Style

For this course, you must annotate an article about an issue facing college students. Below is a guide on how to effectively annotate an article. The previous page in this module went over APA citation style, which is required for the annotation for your assignment!

• Download a printer friendly version

Creating an Annotation

An annotation is a brief descriptive and evaluative paragraph that goes beyond a mere summary of a source. The annotation identifies the accuracy, relevancy, and quality of a source, often as it pertains to your research topic or assignment. This worksheet will help you in building a source annotation.

The Citation

Always start your annotation with the full citation of the source. Consult your APA Citation Guide for help on building your citation.

The Annotation

Answering the following questions will help you to write an annotation for any given source. 

Now that you’ve answered the questions above, piece together your answers into a coherent and well-formed paragraph. Congratulations! You have just created an annotation!

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• Next: Searching for Images >>
• Last Updated: May 10, 2024 4:16 PM
• URL: https://nsc.libguides.com/research

What Is an Annotation in Reading, Research, and Linguistics?

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• An Introduction to Punctuation
• Ph.D., Rhetoric and English, University of Georgia
• M.A., Modern English and American Literature, University of Leicester
• B.A., English, State University of New York

An annotation is a note, comment, or  concise statement of the key ideas in a text or a portion of a text and is commonly used in reading instruction and in research . In corpus linguistics , an annotation is a coded note or comment that identifies specific linguistic features of a word or sentence.

One of the most common uses of annotations is in essay composition, wherein a student might annotate a larger work he or she is referencing, pulling and compiling a list of quotes to form an argument. Long-form essays and term papers, as a result, often come with an annotated bibliography , which includes a list of references as well as brief summaries of the sources.

There are many ways to annotate a given text, identifying key components of the material by underlining, writing in the margins, listing cause-effect relationships, and noting confusing ideas with question marks beside the statement in the text.

Identifying Key Components of a Text

When conducting research, the process of annotation is almost essential to retaining the knowledge necessary to understand a text's key points and features and can be achieved through a number of means.

Jodi Patrick Holschuh and Lori Price Aultman describe a student's goal for annotating text in "Comprehension Development," wherein the students "are responsible for pulling out not only the main points of the text but also the other key information (e.g., examples and details) that they will need to rehearse for exams."

Holschuh and Aultman go on to describe the many ways a student may isolate key information from a given text, including writing brief summaries in the student's own words, listing out characteristics and cause-and-effect relations in the text, putting key information in graphics and charts, marking possible test questions, and underlining keywords or phrases or putting a question mark next to confusing concepts.

REAP: A Whole-Language Strategy

According to Eanet & Manzo's 1976 "Read-Encode-Annotate-Ponder" strategy for teaching students language and reading comprehension , annotation is a vital part of a students' ability to understand any given text comprehensively.

The process involves the following four steps: Read to discern the intent of the text or the writer's message; Encode the message into a form of self-expression, or write it out in student's own words; Analyze by writing this concept in a note; and Ponder or reflect on the note, either through introspection or discussing with peers.

Anthony V. Manzo and Ula Casale Manzo describe the notion in "Content Area Reading: A Heuristic Approach" as among the earliest strategies developed to stress the use of writing as a means of improving thinking and reading," wherein these annotations "serve as alternative perspectives from which to consider and evaluate information and ideas."

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• Coherence in Composition
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• Abstracting & Transcribing Genealogical Documents
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How to Write an Annotated Bibliography - APA Style (7th Edition)

What is an annotation, how is an annotation different from an abstract, what is an annotated bibliography, types of annotated bibliographies, descriptive or informative, analytical or critical, to get started.

An annotation is more than just a brief summary of an article, book, website, or other type of publication. An annotation should give enough information to make a reader decide whether to read the complete work. In other words, if the reader were exploring the same topic as you, is this material useful and if so, why?

While an abstract also summarizes an article, book, website, or other type of publication, it is purely descriptive. Although annotations can be descriptive, they also include distinctive features about an item. Annotations can be evaluative and critical as we will see when we look at the two major types of annotations.

An annotated bibliography is an organized list of sources (like a reference list). It differs from a straightforward bibliography in that each reference is followed by a paragraph length annotation, usually 100–200 words in length.

Depending on the assignment, an annotated bibliography might have different purposes:

• Provide a literature review on a particular subject
• Help to formulate a thesis on a subject
• Demonstrate the research you have performed on a particular subject
• Provide examples of major sources of information available on a topic
• Describe items that other researchers may find of interest on a topic

There are two major types of annotated bibliographies:

A descriptive or informative annotated bibliography describes or summarizes a source as does an abstract; it describes why the source is useful for researching a particular topic or question and its distinctive features. In addition, it describes the author's main arguments and conclusions without evaluating what the author says or concludes.

For example:

McKinnon, A. (2019). Lessons learned in year one of business.  Journal of Legal Nurse Consulting ,  30 (4), 26–28. This article describes some of the difficulties many nurses experience when transitioning from nursing to a legal nurse consulting business. Pointing out issues of work-life balance, as well as the differences of working for someone else versus working for yourself, the author offers their personal experience as a learning tool. The process of becoming an entrepreneur is not often discussed in relation to nursing, and rarely delves into only the first year of starting a new business. Time management, maintaining an existing job, decision-making, and knowing yourself in order to market yourself are discussed with some detail. The author goes on to describe how important both the nursing professional community will be to a new business, and the importance of mentorship as both the mentee and mentor in individual success that can be found through professional connections. The article’s focus on practical advice for nurses seeking to start their own business does not detract from the advice about universal struggles of entrepreneurship makes this an article of interest to a wide-ranging audience.

An analytical or critical annotation not only summarizes the material, it analyzes what is being said. It examines the strengths and weaknesses of what is presented as well as describing the applicability of the author's conclusions to the research being conducted.

Analytical or critical annotations will most likely be required when writing for a college-level course.

McKinnon, A. (2019). Lessons learned in year one of business.  Journal of Legal Nurse Consulting ,  30 (4), 26–28. This article describes some of the difficulty many nurses experience when transitioning from nursing to a nurse consulting business. While the article focuses on issues of work-life balance, the differences of working for someone else versus working for yourself, marketing, and other business issues the author’s offer of only their personal experience is brief with few or no alternative solutions provided. There is no mention throughout the article of making use of other research about starting a new business and being successful. While relying on the anecdotal advice for their list of issues, the author does reference other business resources such as the Small Business Administration to help with business planning and professional organizations that can help with mentorships. The article is a good resource for those wanting to start their own legal nurse consulting business, a good first advice article even. However, entrepreneurs should also use more business research studies focused on starting a new business, with strategies against known or expected pitfalls and issues new businesses face, and for help on topics the author did not touch in this abbreviated list of lessons learned.

Now you are ready to begin writing your own annotated bibliography.

• Choose your sources - Before writing your annotated bibliography, you must choose your sources. This involves doing research much like for any other project. Locate records to materials that may apply to your topic.
• Review the items - Then review the actual items and choose those that provide a wide variety of perspectives on your topic. Article abstracts are helpful in this process.
• The purpose of the work
• A summary of its content
• Information about the author(s)
• For what type of audience the work is written
• Its relevance to the topic
• Any special or unique features about the material
• Research methodology
• The strengths, weaknesses or biases in the material

Annotated bibliographies may be arranged alphabetically or chronologically, check with your instructor to see what he or she prefers.

Please see the  APA Examples page  for more information on citing in APA style.

• Last Updated: Aug 8, 2023 11:27 AM
• URL: https://libguides.umgc.edu/annotated-bibliography-apa

• Research Guides
• CECH Library

How to Write an Annotated Bibliography

Writing annotations.

• Introduction
• New RefWorks
• Formatting Citations
• Sample Annotated Bibliographies

An annotation is a brief note following each citation listed on an annotated bibliography.  The goal is to briefly summarize the source and/or explain why it is important for a topic.  They are typically a single concise paragraph, but might be longer if you are summarizing and evaluating.

Annotations can be written in a variety of different ways and it’s important to consider the style you are going to use.  Are you simply summarizing the sources, or evaluating them?  How does the source influence your understanding of the topic?  You can follow any style you want if you are writing for your own personal research process, but consult with your professor if this is an assignment for a class.

Annotation Styles

• Combined Informative/Evaluative Style - This style is recommended by the library as it combines all the styles to provide a more complete view of a source.  The annotation should explain the value of the source for the overall research topic by providing a summary combined with an analysis of the source.  

Aluedse, O. (2006). Bullying in schools: A form of child abuse in schools.  Educational Research Quarterly ,  30 (1), 37.

The author classifies bullying in schools as a “form of child abuse,” and goes well beyond the notion that schoolyard bullying is “just child’s play.” The article provides an in-depth definition of bullying, and explores the likelihood that school-aged bullies may also experience difficult lives as adults. The author discusses the modern prevalence of bullying in school systems, the effects of bullying, intervention strategies, and provides an extensive list of resources and references.

Statistics included provide an alarming realization that bullying is prevalent not only in the United States, but also worldwide. According to the author, “American schools harbor approximately 2.1 million bullies and 2.7 million victims.” The author references the National Association of School Psychologists and quotes, “Thus, one in seven children is a bully or a target of bullying.” A major point of emphasis centers around what has always been considered a “normal part of growing up” versus the levels of actual abuse reached in today’s society.

The author concludes with a section that addresses intervention strategies for school administrators, teachers, counselors, and school staff. The concept of school staff helping build students’ “social competence” is showcased as a prevalent means of preventing and reducing this growing social menace. Overall, the article is worthwhile for anyone interested in the subject matter, and provides a wealth of resources for researching this topic of growing concern.

(Renfrow & Teuton, 2008)

• Informative Style -  Similar to an abstract, this style focuses on the summarizing the source.  The annotation should identify the hypothesis, results, and conclusions presented by the source.

Plester, B., Wood, C, & Bell, V. (2008). Txt msg n school literacy: Does texting and knowledge of text abbreviations adversely affect children's literacy attainment? Literacy , 42(3), 137-144.

Reports on two studies that investigated the relationship between children's texting behavior, their knowledge of text abbreviations, and their school attainment in written language skills. In Study One, 11 to 12 year-old children reported their texting behavior and translated a standard English sentence into a text message and vice versa. In Study Two, children's performance on writing measures were examined more specifically, spelling proficiency was also assessed, and KS2 Writing scores were obtained. Positive correlations between spelling ability and performance on the translation exercise were found, and group-based comparisons based on the children's writing scores also showed that good writing attainment was associated with greater use of texting abbreviations (textisms), although the direction of this association is not clear. Overall, these findings suggest that children's knowledge of textisms is not associated with poor written language outcomes for children in this age range. 

(Beach et al., 2009)

• Evaluative Style - This style analyzes and critically evaluates the source.  The annotation should comment on the source's the strengths, weaknesses, and how it relates to the overall research topic.

Amott, T. (1993). Caught in the Crisis: Women in the U.S. Economy Today . New York: Monthly Review Press.

A very readable (140 pp) economic analysis and information book which I am currently considering as a required collateral assignment in Economics 201. Among its many strengths is a lucid connection of "The Crisis at Home" with the broader, macroeconomic crisis of the U.S. working class (which various other authors have described as the shrinking middle class or the crisis of de-industrialization).

(Papadantonakis, 1996)

• Indicative Style - This style of annotation identifies the main theme and lists the significant topics included in the source.  Usually no specific details are given beyond the topic list . 

Example: 

Gambell, T.J., & Hunter, D. M. (1999). Rethinking gender differences in literacy. Canadian Journal of Education , 24(1) 1-16.

Five explanations are offered for recently assessed gender differences in the literacy achievement of male and female students in Canada and other countries. The explanations revolve around evaluative bias, home socialization, role and societal expectations, male psychology, and equity policy.

(Kerka & Imel, 2004)

Beach, R., Bigelow, M., Dillon, D., Dockter, J., Galda, L., Helman, L., . . . Janssen, T. (2009). Annotated Bibliography of Research in the Teaching of English.  Research in the Teaching of English,   44 (2), 210-241. Retrieved from http://www.jstor.org/stable/27784357

Kerka, S., & Imel, S. (2004). Annotated bibliography: Women and literacy.  Women's Studies Quarterly,  32 (1), 258-271. Retrieved from http://search.proquest.com/docview/233645656?accountid=2909

Papadantonakis, K. (1996). Selected Annotated Bibliography for Economists and Other Social Scientists.  Women's Studies Quarterly,   24 (3/4), 233-238. Retrieved from http://www.jstor.org/stable/40004384

Renfrow, T.G., & Teuton, L.M. (2008). Schoolyard bullying: Peer victimization an annotated bibliography. Community & Junior College Libraries, 14(4), 251-­275. doi:10.1080/02763910802336407

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• Next: Sample Annotated Bibliographies >>
• Last Updated: Feb 27, 2023 10:50 AM
• URL: https://guides.libraries.uc.edu/annotated_bibliography

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How To Annotate An Article Effectively [Tips + Tools]

Annotating an article goes over and above just simply writing down notes. It is a worthwhile activity, which when done correctly can help you to actively read and understand the text you're reading.

If you wanted to read something, you used to have to go to a library or bookstore. But now you can get access to thousands of free books and articles online. And thanks to the rise of the digital era , you don’t even need to leave home anymore.

However, how often have you found yourself reading an article or blog post only to realize that you don’t remember anything from it? This is because you weren't actively taking in anything you were reading.

This can easily be rectified if you annotate an article while reading it.

In order to get the most out of reading, you should always make comments or highlight important parts of the text. This way, your brain stays active and you can easily refer back to them later.

You can annotate articles by hand on a piece of paper, however, if you want to do it online, there are plenty of tools available to help you out.

• First Of All, What Is Annotation?🤷‍♀️
• Why Should You Take The Time Out To Annotate When Reading?🧐

7 Steps For How To Annotate An Article Effectively🔥

How to optimize your annotation process🌟.

• How To Use The Various Online Annotation Tools: Markup Vs. Kami📝
• Conclusion🙌

Important disclosure: we're proud affiliates of some tools mentioned in this guide. If you click an affiliate link and subsequently make a purchase, we will earn a small commission at no additional cost to you (you pay nothing extra). For more information, read our affiliate disclosure .

First Of All, What Is Annotation? 🤷‍♀️

Annotation is simply making personal notes and adding explanations or comments on top of an image or document.

Annotating is about drawing attention to specific words, phrases, or themes in the article.

There are three main methods of annotation:

Highlighting

• Adding comments.

Each method has its advantages and disadvantages.

When highlighting, you add color to specific word s or phrases.

Advantages of highlighting text are that it's easy to do and actually doesn't require any special software.

A disadvantage of highlighting text is that it may not show up well when printed out and depending on the color used, the contrast can make it hard to read the words.

Tagging allows you to assign keywords to different sections of the text.

Advantages of tagging include easily being able to search for specific tags and locate associated text.

The disadvantages of tagging are that it requires more work than highlighting since you must first create a list of keywords before assigning each one of them to the text.

Comments are generally more personal than either of these two methods. They are usually written by the reader and reflect the readers' thoughts and feelings towards what they are reading.

The advantages of leaving your comments when annotating are article are that writing is an active learning strategy and you're more likely to remember what you've written. The disadvantages of commenting are that it takes time to write a comment.

The best way to annotate an article is by using all three methods at once.

Why Should You Take The Time Out To Annotate When Reading? 🧐

The main advantage of annotating articles is that it helps you retain information better.

It is one of the best active reading strategies.

When you annotate, you're forced to pay attention to the text and therefore you'll learn faster. It also makes you think harder so you'll understand things better. This is particularly helpful with complex reading material.

Another advantage of effective annotation is being more aware of what you're reading. You will naturally begin to notice the important points in the text or relevant pieces of information. This will help you focus on those areas.

You can even use annotations as a study tool.

If you annotate articles, digital textbooks, or academic texts, you'll find yourself referring back to it often. This is because you'll be easily reminded of the key points.

You can then go back and reread the highlighted passages without having to worry about remembering where you left off. This is particularly useful if you are a student who is studying for an exam or trying to learn a new concept.

The disadvantages of annotating are that you might feel like you're wasting time. However trust me, you aren't ! One way to eliminate this feeling is to annotate the articles you are reading online rather than print them out and annotate them by hand.

Annotating online allows you to quickly make corrections to your annotations, something that may not be so easy by hand.

Plus when annotating online you have easy access to your annotations wherever you may be. You can just save the page with your annotations and continue reading later. No need to carry around stacks of printed-out articles with you.

Oh and you're also helping to save the environment too by reducing your paper usage & printing!

That's why I say, online annotation all the way!

Alright, so you know all about what annotation is and why it is important, which is great. But how do you actually go about annotating an article?

Below are seven steps you can follow when annotating an article:

• Scan For Important Details
• Skim For More Information
• Underline Or Highlight Key Points
• Read The Entire Article Thoroughly
• Make Your Notes
• Quickly Summarize The Key Ideas
• Create An Outline

1. Scan For Important Details

The first step when annotating an article is to scan the article for details that are relevant to what you want to learn from the article.

Usually, when you are scanning you read the title of the articles, the headings, the abstract, and the conclusion of the article so you can grasp some idea of the direction of the article.

2. Skim For More Information

You then need to skim-read the article to get a general and clearer idea of what it's about.

It doesn't matter if you don't fully understand everything but you want to get a sense of the topic and its central theme . This means you are looking for keywords, key concepts, terms, phrases, abbreviations, etc.

A good tactic when skimming through an article is to read the first sentence or two of the first paragraphs.

3. Underline Or Highlight Key Points

Your next step is to then underline or highlight the most important points in the article that you have picked up on through your initial readings.

These could be the main ideas in texts, facts, statistics, quotes, examples, etc. that you found interesting and relevant.

4. Read The Entire Article Thoroughly

Once you've underlined the key points, you should read the entire article again. Slowly and carefully.

Reading the article in its entirety helps to reinforce the key points you've already identified.

In addition, it gives you a chance to look at the different parts of the article and see how they relate to each other.

It is good practice at this point to circle any unfamiliar words and to look them up. Noting down the meanings of the words both mentally and on the article itself.

5. Make Your Notes

Now that you've read the entire article, you can start making your personal notes. You can make these notes in the margin, at the end of the article, or on a new page entirely.

Write down any questions you still have about the article, any points you want to remember, or anything else you'd like to add.

Keep in mind that the notes you take don't have to be words, they can also be visuals.

6. Quickly Summarize The Key Ideas

After you've finished writing down your thoughts, you can summarize the main ideas of the article into one sentence.

For example, if you were annotating the article " Why Do We Have A Short Attention Span? ", you would write down something like:

"Short attention spans are caused by our fast-paced world."

It is important in your summary that you make connections between the key ideas in the article.

7. Create An Outline

Finally, once you've summarized the major ideas of the piece, create an outline . This will help you organize your notes as well as give you a deeper understanding of the article overall.

An outline is simply a list of the key ideas of the document. It's not meant to be exhaustive, nor does it have to include every single detail.

An outline is usually made up of three sections:

• Title - What is this document about?
• Body - What did we learn from this article?
• Conclusions - How does this article affect us today?

You are now ready to get started annotating articles. This extremely useful skill is a vital one to learn, however, you can take it a step further and optimize your annotation processes.

Some people are annotation naturals, but with others, it requires a bit more practice. Below are some tips and tricks to help you annotate articles online more efficiently and effectively:

An Annotation Tool Is Your Best Friend 💕

Use a legend 🔑, make use of your colors wisely 🎨.

• Different Margin Different Task ☝️

Note Down Descriptions & Reactions ✍️

Did someone say snapchat 👻, be critical 🧠, use abbreviations or symbols *️⃣.

Annotation tools are useful because they allow you to easily mark up text and highlight important parts of an article. They also let you take notes and record your thoughts.

There are many online annotation tools available, including Markup by Kdan Mobile, Cronycle & Kami.

Markup is an all-in-one annotation tool - meaning you can use it to personally annotate articles online and websites ( & PDFs too if you’re using the iOS app ).

The tool combines note-taking with artificial intelligence, ensuring that you are actively reading with great efficiency.

The more you use Markup, the more helpful it becomes as it remembers the types of articles you have read and the content within them, and then it suggests articles of a similar nature.

With Markup you can save all your annotations in one place, for easy access and you can quickly share them amongst your peers.

You can get started with Markup for free. However, if you are looking to upgrade your functions and features then the paid pricing plans start at $39.99 per user per month billed annually.

From the outset, Croncyle may not look like an annotation tool. It in fact advertises itself as a marketing intelligence platform.

However, it does have a very nifty annotation feature for PDFs, saved web pages, and online articles. All you have to do is save the article to one of your boards and then you can get started highlighting, adding comments, and tagging.

After you have annotated the article you can review all of the comments you made, extract highlighted text, and then share it with whoever you wish.

Unfortunately, there is no free plan for Croncyle, and their paid plans start at $49 per user per month, paid annually.

Kami may market itself as a digital classroom tool , however, it can be used by anybody, in any industry.

With Kami, you can take a PDF document, a Word document, images, and conventional articles and transform them into a beautifully annotated end result. And then you can save and share those documents as you please.

One particularly useful feature of Kami that sets itself apart from the other two tools we have mentioned is that you can annotate in written words, visuals, videos, or voice recordings.

Kami offers its’ users a completely free version , or they can upgrade to the Teacher Plan which is $99 per year. It just depends on the extent of your needs.

Using annotation tools can save you valuable time. However, there are some things to keep in mind before using them.

First, you'll need to find a tool that works with your device. Some apps work only on certain devices (iPhones, iPads), while others may require a web browser.

Second, you need to think about your annotation needs and which tool best suits those.

For example , if you're looking for a simple way to quickly note down key points, then you might choose to use a basic highlighting app. If you're looking for more advanced features such as adding images, formatting text, or recording audio clips, then you may want to consider a more complex tool.

Third, make sure you know how to use the tool properly. You should always start off by reading through the documentation first. Then, practice using the tool until you feel comfortable doing so.

Lastly, make sure the tool fits into your budget . There are free options out there, but you may want to invest in a paid option if you plan on making heavy use of it.

Always make use of a key or legend when annotating articles online. A legend is a quick reference guide that explains what each symbol means.

A legend can be used at any point during the process, whether you're writing annotations directly on the page or creating a summary.

It's very helpful to add a legend to a document because it helps other readers ( or you at a later stage ) understand what you mean. It will also help you organize your thoughts and remember what you've written.

When creating a legend, try to stick to 3-5 symbols per section.

When annotating you need to be careful of your color choices. Avoid using too many colors. Instead, pick just two or three main colors.

The reason why you need to limit yourself to these colors is that most people have limited vision. When you use too many colors, it becomes difficult for people to read what you wrote.

If you do decide to use multiple colors, make sure to use contrasting ones instead of monochromatic ones. If you don't it may be hard to distinguish one color from the next. For instance, if you use red and pink together, then you will struggle to tell where one ends and the next begins.

Avoid using bright colors like yellow or orange. These colors tend to distract from the content. Also, avoid using colors that are too dark as they will make it hard to read the text.

You should also use a different color for each type of reaction , e.g. green for questions, red for confusion, and purple for agreement.

Different Margin Different Task☝️

Try to make your annotations as logical as possible. Use one margin for tagging and another margin for making comments. Or one margin for reactions and the other for questions.

This makes it easier to follow along with the article themes.

When annotating an article it is important to note down descriptions of what is written as well as your reactions to the key concepts. Noting down reactions allows you to go back to this section and understand how it initially made you feel and your thought process at the time.

If you're not sure about something, then write it down, and question it. This will give you time to think about it before you continue.

Noting your thoughts helps you better understand the article when you review it again at a later stage.

This one is for students. Did you know you can annotate articles on Snapchat? Yes, it’s true!

All you need to do is take a screenshot of the article you want to annotate.

Then, open up the image editor and paste the article. Once you've done that, you can begin adding your own notes and reactions by tapping on the screen.

Another way to do this is to subscribe to one of the news accounts on Snapchat, open up an article of interest, screenshot it and get annotating.

You can also easily share your annotations with friends.

It is important when annotating an article to be critical of what is written. Don't just accept everything at face value.

Really think about what the article is saying and the implications of such.

Think about what you would say in response to the author's arguments. Would you agree or disagree? Why?

To make your life easier, you can always abbreviate certain words or you can use symbols to represent certain things. This is particularly useful for repeated concepts or themes as it saves you time in writing it out.

For example , instead of writing ‘theory’ all over the place, you could simply put ‘T’. Also saving you space for more elaborate descriptions. Or try using a '?' mark if something in the article requires more research on your behalf.

Just make sure you include these abbreviations and symbols in your legend so that you know exactly what they mean!

The last thing you want is to forget their meaning and have to annotate the article from scratch.

How To Use The Various Online Annotation Tools: Markup Vs. Kami 📝

Maybe using online annotation tools sounds daunting to you but we are here to show you otherwise. Using these tools couldn't be any easier.

Markup is a unique annotation tool as it allows you to highlight and annotate any article online. No need to download the article or have it on your google drive.

In fact, you don’t even have to download anything - not even the tool itself, as all you have to do, is add it as an extension to your browser.

Go to the Markup website . Click on the relevant button to take you to your Chrome or Edge extension web store.

Add the Markup extension to your browser. No account is needed! You may want to pin it to your extensions bar for easy access.

Go to the article you want to annotate. Click on the Markup extension button and a drop-down annotation menu will appear ( as seen above ).

As you can see with Markup you can highlight text, add tags, add annotations, automatically summarize the article (a very useful feature) and then share your annotations with other people.

Plus they offer you pro tips for using the tool!

Select the text you want , and as long as the ‘Text Highlighter’ toggle is set to on, a Markups button will appear next to your text.

Click this button and it will give you the option to highlight your text - in multiple different colors!

If you want to annotate your text all you need to do is select your text, click the annotation button that pops up next to your text, and type in your note. You can even change the note color.

It really is that easy.

Click ‘Annotations ’ on the side panel to view all the notes and highlighted text you’ve added.

This quickly shows you everything you deemed important in the article and allows you to easily navigate to any section.

Click ‘Share’, and then click ‘Include highlights and notes’ to share your annotated article with anyone via a link or across your Facebook, Twitter, and Weibo social networks.

Kami is an annotation tool that is aimed at the education industry. Because of this, it functions mainly to annotate articles that are either saved onto a drive or downloaded onto the computer.

Unlike with Markup, you cannot annotate straight onto an article on a website. However, it still fulfills its purpose perfectly.

Go to their website , create an account, and log in. Then open your file from Google Docs or Drive, My Computer, or OneDrive. Or create one using the various templates.

Once your article is uploaded you’ll get access to a number of annotation tools , all present in the bar on the left-hand side of your screen.

There are also a number of functional options in the top right-hand corner - open file, save, share, download, etc.

Click on the highlighter icon and highlight your text in multiple colors. You can also underline important text or strike it through if it isn’t relevant.

Click on the comments icon to add notes in multiple forms - written, audio, video, or visual. Plus you can tag your notes in different colors so you know which are related and which aren't.

You can even add text boxes, shapes, and drawings to the actual article itself.

Click on the download icon to export your document - with or without the annotations.

Which tool is best?

That depends on your needs as a person. If you have a whole lot of downloaded articles, go with Kami, but if you want to save time and annotate directly online, then Markup is the tool for you.

Or you can always explore the other annotation tools we mentioned in this article…

Conclusion 🙌

Without annotation, it becomes easy to read through an article and not remember anything afterward. This isn’t ideal - especially if you are a student.

Annotating an article online is an important skill if you want to not only read the text but actually actively take in what it is saying. Many people view annotation as tedious, however, there are a number of tools available to help you.

And using them couldn’t be any easier.

After reading this article you should have everything you need to effectively and efficiently annotate your articles. What are you waiting for?

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How to Prepare an Annotated Bibliography: The Annotated Bibliography

• The Annotated Bibliography
• Fair Use of this Guide

Explanation, Process, Directions, and Examples

What is an annotated bibliography.

An annotated bibliography is a list of citations to books, articles, and documents. Each citation is followed by a brief (usually about 150 words) descriptive and evaluative paragraph, the annotation. The purpose of the annotation is to inform the reader of the relevance, accuracy, and quality of the sources cited.

Annotations vs. Abstracts

Abstracts are the purely descriptive summaries often found at the beginning of scholarly journal articles or in periodical indexes. Annotations are descriptive and critical; they may describe the author's point of view, authority, or clarity and appropriateness of expression.

The Process

Creating an annotated bibliography calls for the application of a variety of intellectual skills: concise exposition, succinct analysis, and informed library research.

First, locate and record citations to books, periodicals, and documents that may contain useful information and ideas on your topic. Briefly examine and review the actual items. Then choose those works that provide a variety of perspectives on your topic.

Cite the book, article, or document using the appropriate style.

Write a concise annotation that summarizes the central theme and scope of the book or article. Include one or more sentences that (a) evaluate the authority or background of the author, (b) comment on the intended audience, (c) compare or contrast this work with another you have cited, or (d) explain how this work illuminates your bibliography topic.

Critically Appraising the Book, Article, or Document

For guidance in critically appraising and analyzing the sources for your bibliography, see How to Critically Analyze Information Sources . For information on the author's background and views, ask at the reference desk for help finding appropriate biographical reference materials and book review sources.

Choosing the Correct Citation Style

Check with your instructor to find out which style is preferred for your class. Online citation guides for both the Modern Language Association (MLA) and the American Psychological Association (APA) styles are linked from the Library's Citation Management page .

Sample Annotated Bibliography Entries

The following example uses APA style ( Publication Manual of the American Psychological Association , 7th edition, 2019) for the journal citation:

Waite, L., Goldschneider, F., & Witsberger, C. (1986). Nonfamily living and the erosion of traditional family orientations among young adults. American Sociological Review, 51 (4), 541-554. The authors, researchers at the Rand Corporation and Brown University, use data from the National Longitudinal Surveys of Young Women and Young Men to test their hypothesis that nonfamily living by young adults alters their attitudes, values, plans, and expectations, moving them away from their belief in traditional sex roles. They find their hypothesis strongly supported in young females, while the effects were fewer in studies of young males. Increasing the time away from parents before marrying increased individualism, self-sufficiency, and changes in attitudes about families. In contrast, an earlier study by Williams cited below shows no significant gender differences in sex role attitudes as a result of nonfamily living.

This example uses MLA style ( MLA Handbook , 9th edition, 2021) for the journal citation. For additional annotation guidance from MLA, see 5.132: Annotated Bibliographies .

Waite, Linda J., et al. "Nonfamily Living and the Erosion of Traditional Family Orientations Among Young Adults." American Sociological Review, vol. 51, no. 4, 1986, pp. 541-554. The authors, researchers at the Rand Corporation and Brown University, use data from the National Longitudinal Surveys of Young Women and Young Men to test their hypothesis that nonfamily living by young adults alters their attitudes, values, plans, and expectations, moving them away from their belief in traditional sex roles. They find their hypothesis strongly supported in young females, while the effects were fewer in studies of young males. Increasing the time away from parents before marrying increased individualism, self-sufficiency, and changes in attitudes about families. In contrast, an earlier study by Williams cited below shows no significant gender differences in sex role attitudes as a result of nonfamily living.

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Tambíen disponible en español: Cómo Preparar una Bibliografía Anotada

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Annotating a text, or marking the pages with notes, is an excellent, if not essential, way to make the most out of the reading you do for college courses. Annotations make it easy to find important information quickly when you look back and review a text. They help you familiarize yourself with both the content and organization of what you read. They provide a way to begin engaging with ideas and issues directly through comments, questions, associations, or other reactions that occur to you as you read. In all these ways, annotating a text makes the reading process an active one, not just background for writing assignments, but an integral first step in the writing process.

A well-annotated text will accomplish all of the following:

• clearly identify where in the text important ideas and information are located
• express the main ideas of a text
• trace the development of ideas/arguments throughout a text
• introduce a few of the reader’s thoughts and reactions

Ideally, you should read a text through once before making major annotations. You may just want to circle unfamiliar vocabulary or concepts. This way, you will have a clearer idea about where major ideas and important information are in the text, and your annotating will be more efficient.

A brief description and discussion of four ways of annotating a text— highlighting/underlining, paraphrase/summary of main ideas, descriptive outline, and comments/responses —and a sample annotated text follow:

HIGHLIGHTING/UNDERLINING

Highlighting or underlining key words and phrases or major ideas is the most common form of annotating texts. Many people use this method to make it easier to review material, especially for exams. Highlighting is also a good way of picking out specific language within a text that you may want to cite or quote in a piece of writing. However, over-reliance on highlighting is unwise for two reasons. First, there is a tendency to highlight more information than necessary, especially when done on a first reading. Second, highlighting is the least active form of annotating. Instead of being a way to begin thinking and interacting with ideas in texts, highlighting can become a postponement of that process.

On the other hand, highlighting is a useful way of marking parts of a text that you want to make notes about. And it’s a good idea to highlight the words or phrases of a text that are referred to by your other annotations.

PARAPHRASE/SUMMARY OF MAIN IDEAS

Going beyond locating important ideas to being able to capture their meaning through paraphrase is a way of solidifying your understanding of these ideas. It’s also excellent preparation for any writing you may have to do based on your reading. A series of brief notes in the margins beside important ideas gives you a handy summary right on the pages of the text itself, and if you can take the substance of a sentence or paragraph and condense it into a few words, you should have little trouble clearly demonstrating your understanding of the ideas in question in your own writing.

DESCRIPTIVE OUTLINE

A descriptive outline shows the organization of a piece of writing, breaking it down to show where ideas are introduced and where they are developed. A descriptive outline allows you to see not only where the main ideas are but also where the details, facts, explanations, and other kinds of support for those ideas are located.

A descriptive outline will focus on the function of individual paragraphs or sections within a text. These functions might include any of the following:

• summarizing a topic/argument/etc.
• introducing an idea
• adding explanation
• giving examples
• providing factual evidence
• expanding or limiting the idea
• considering an opposing view
• dismissing a contrary view
• creating a transition
• stating a conclusion

This list is hardly exhaustive and it’s important to recognize that several of these functions may be repeated within a text, particularly ones that contain more than one major idea.

Making a descriptive outline allows you to follow the construction of the writer’s argument and/or the process of his/her thinking. It helps identify which parts of the text work together and how they do so.

COMMENTS/RESPONSES

You can use annotation to go beyond understanding a text’s meaning and organization by noting your reactions—agreement/disagreement, questions, related personal experience, connection to ideas from other texts, class discussions, etc. This is an excellent way to begin formulating your own ideas for writing assignments based on the text or on any of the ideas it contains.

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Annotating text: The complete guide to close reading

As students, researchers, and self-learners, we understand the power of reading and taking smart notes . But what happens when we combine those together? This is where annotating text comes in.

Annotated text is a written piece that includes additional notes and commentary from the reader. These notes can be about anything from the author's style and tone to the main themes of the work. By providing context and personal reactions, annotations can turn a dry text into a lively conversation.

Creating text annotations during close readings can help you follow the author's argument or thesis and make it easier to find critical points and supporting evidence. Plus, annotating your own texts in your own words helps you to better understand and remember what you read.

This guide will take a closer look at annotating text, discuss why it's useful, and how you can apply a few helpful strategies to develop your annotating system.

What does annotating text mean?

Text annotation refers to adding notes, highlights, or comments to a text. This can be done using a physical copy in textbooks or printable texts. Or you can annotate digitally through an online document or e-reader.

Generally speaking, annotating text allows readers to interact with the content on a deeper level, engaging with the material in a way that goes beyond simply reading it. There are different levels of annotation, but all annotations should aim to do one or more of the following:

• Summarize the key points of the text
• Identify evidence or important examples
• Make connections to other texts or ideas
• Think critically about the author's argument
• Make predictions about what might happen next

When done effectively, annotation can significantly improve your understanding of a text and your ability to remember what you have read.

What are the benefits of annotation?

There are many reasons why someone might wish to annotate a document. It's commonly used as a study strategy and is often taught in English Language Arts (ELA) classes. Students are taught how to annotate texts during close readings to identify key points, evidence, and main ideas.

In addition, this reading strategy is also used by those who are researching for self-learning or professional growth. Annotating texts can help you keep track of what you’ve read and identify the parts most relevant to your needs. Even reading for pleasure can benefit from annotation, as it allows you to keep track of things you might want to remember or add to your personal knowledge management system .

Annotating has many benefits, regardless of your level of expertise. When you annotate, you're actively engaging with the text, which can help you better understand and learn new things . Additionally, annotating can save you time by allowing you to identify the most essential points of a text before starting a close reading or in-depth analysis.

There are few studies directly on annotation, but the body of research is growing. In one 2022 study, specific annotation strategies increased student comprehension , engagement, and academic achievement. Students who annotated read slower, which helped them break down texts and visualize key points. This helped students focus, think critically , and discuss complex content.

Annotation can also be helpful because it:

• Allows you to quickly refer back to important points in the text without rereading the entire thing
• Helps you to make connections between different texts and ideas
• Serves as a study aid when preparing for exams or writing essays
• Identifies gaps in your understanding so that you can go back and fill them in

The process of annotating text can make your reading experience more fruitful. Adding comments, questions, and associations directly to the text makes the reading process more active and enjoyable.

Be the first to try it out!

We're developing ABLE, a powerful tool for building your personal knowledge, capturing information from the web, conducting research, taking notes, and writing content.

How do you annotate text?

There are many different ways to annotate while reading. The traditional method of annotating uses highlighters, markers, and pens to underline, highlight, and write notes in paper books. Modern methods have now gone digital with apps and software. You can annotate on many note-taking apps, as well as online documents like Google Docs.

While there are documented benefits of handwritten notes, recent research shows that digital methods are effective as well. Among college students in an introductory college writing course, those with more highlighting on digital texts correlated with better reading comprehension than those with more highlighted sections on paper.

No matter what method you choose, the goal is always to make your reading experience more active, engaging, and productive. To do so, the process can be broken down into three simple steps:

• Do the first read-through without annotating to get a general understanding of the material.
• Reread the text and annotate key points, evidence, and main ideas.
• Review your annotations to deepen your understanding of the text.

Of course, there are different levels of annotation, and you may only need to do some of the three steps. For example, if you're reading for pleasure, you might only annotate key points and passages that strike you as interesting or important. Alternatively, if you're trying to simplify complex information in a detailed text, you might annotate more extensively.

The type of annotation you choose depends on your goals and preferences. The key is to create a plan that works for you and stick with it.

Annotation strategies to try

When annotating text, you can use a variety of strategies. The best method for you will depend on the text itself, your reason for reading, and your personal preferences. Start with one of these common strategies if you don't know where to begin.

• Questioning: As you read, note any questions that come to mind as you engage in critical thinking . These could be questions about the author's argument, the evidence they use, or the implications of their ideas.
• Summarizing: Write a brief summary of the main points after each section or chapter. This is a great way to check your understanding, help you process information , and identify essential information to reference later.
• Paraphrasing: In addition to (or instead of) summaries, try paraphrasing key points in your own words. This will help you better understand the material and make it easier to reference later.
• Connecting: Look for connections between different parts of the text or other ideas as you read. These could be things like similarities, contrasts, or implications. Make a note of these connections so that you can easily reference them later.
• Visualizing: Sometimes, it can be helpful to annotate text visually by drawing pictures or taking visual notes . This can be especially helpful when trying to make connections between different ideas.
• Responding: Another way to annotate is to jot down your thoughts and reactions as you read. This can be a great way to personally engage with the material and identify any areas you need clarification on.

Combining the three-step annotation process with one or more strategies can create a customized, powerful reading experience tailored to your specific needs.

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7 tips for effective annotations

Once you've gotten the hang of the annotating process and know which strategies you'd like to use, there are a few general tips you can follow to make the annotation process even more effective.

1. Read with a purpose. Before you start annotating, take a moment to consider what you're hoping to get out of the text. Do you want to gain a general overview? Are you looking for specific information? Once you know what you're looking for, you can tailor your annotations accordingly.

2. Be concise. When annotating text, keep it brief and focus on the most important points. Otherwise, you risk annotating too much, which can feel a bit overwhelming, like having too many tabs open . Limit yourself to just a few annotations per page until you get a feel for what works for you.

3. Use abbreviations and symbols. You can use abbreviations and symbols to save time and space when annotating digitally. If annotating on paper, you can use similar abbreviations or symbols or write in the margins. For example, you might use ampersands, plus signs, or question marks.

4. Highlight or underline key points. Use highlighting or underlining to draw attention to significant passages in the text. This can be especially helpful when reviewing a text for an exam or essay. Try using different colors for each read-through or to signify different meanings.

5. Be specific. Vague annotations aren't very helpful. Make sure your note-taking is clear and straightforward so you can easily refer to them later. This may mean including specific inferences, key points, or questions in your annotations.

6. Connect ideas. When reading, you'll likely encounter ideas that connect to things you already know. When these connections occur, make a note of them. Use symbols or even sticky notes to connect ideas across pages. Annotating this way can help you see the text in a new light and make connections that you might not have otherwise considered.

7. Write in your own words. When annotating, copying what the author says verbatim can be tempting. However, it's more helpful to write, summarize or paraphrase in your own words. This will force you to engage your information processing system and gain a deeper understanding.

These tips can help you annotate more effectively and get the most out of your reading. However, it’s important to remember that, just like self-learning , there is no one "right" way to annotate. The process is meant to enrich your reading comprehension and deepen your understanding, which is highly individual. Most importantly, your annotating system should be helpful and meaningful for you.

Engage your learning like never before by learning how to annotate text

Learning to effectively annotate text is a powerful tool that can improve your reading, self-learning , and study strategies. Using an annotating system that includes text annotations and note-taking during close reading helps you actively engage with the text, leading to a deeper understanding of the material.

Try out different annotation strategies and find what works best for you. With practice, annotating will become second nature and you'll reap all the benefits this powerful tool offers.

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Schematic representation of the peer-reviewed process of TE curation

Improvement of the transposable element libraries

To generate the TE libraries, we first ran RepeatModeler and RepeatModeler2 on H. exemplaris and R. varieornatus , respectively, and obtained 519 and 898 consensus sequences (Table  1 ). Then the course participants manually curated as many consensus sequences as possible. In about three course days plus voluntary efforts by some participants after each course, the participants were able to curate 274 consensus sequences (53%) of the H. exemplaris library and 139 consensus sequences (15%) of the R. varieornatus library (Table S1 -3). Given the lack of previously curated libraries from closely related species, most of the consensus sequences were automatically classified as “Unknown” by RepeatModeler, but the thorough process of manual curation successfully reclassified 296 unknown consensus sequences (out of a total of 413 curated sequences, 71%) into known categories of elements. After manual curation, we found that most of the two species’ libraries are comprised of DNA transposons and a minority of retrotransposons (Table  1 ). Since many consensus sequences remained uncurated and unclassified, it is possible that the relative percentages of the categories change in the future, but we expect, especially from the composition of the H. exemplaris library, to mostly find additional (non-autonomous) DNA transposons among the unclassified.

The process of manual curation improved the overall level of TE classification of the libraries but also the quality of the individual consensus sequences by correctly identifying their termini and in general by extending their sequence. Indeed, by comparing the lengths of the consensus sequences for the same element, we can notice a marked increase in length after curation (Fig.  2 ).

Comparison of the length of the consensus sequences before and after manual curation

Diversity of transposable elements

When looking at the diversity of repeats in the curated libraries (combined libraries comprising curated and uncurated consensus sequences), we identified a total of 437 Class II DNA consensus sequences belonging to the superfamilies/clades CMC, MULE, TcMar, Sola, PiggyBac, PIF-Harbinger, Zator, hAT, Maverick, P and Zisupton. Many of these elements are non-autonomous and show a remarkable diversity and complexity of internal structures (Fig.  3 ) which emphasizes the need for complete, curated consensus sequences to be able to properly classify internal repeat structures and infer their mode of accumulation in the genome. For Class I retrotransposons, we found 47 LINEs belonging to the superfamilies/clades L1, I, CR1, CRE, R2, R2-NesL, L2, RTE-X and RTE-BovB and another 40 LTRs belonging to the superfamilies/clades DIRS, Gypsy, Ngaro and Pao. The REPET library generated for R. varieornatus (Table S4 ) consists of a total of 130 consensus sequences, with the majority classified as DNA transposons (129), similar to the curated consensus generated from RepeatModeler output (Table S3 ). However, several superfamilies manually identified in the RepeatModeler library, including Zator, MULE, and P, were not detected in the REPET one. These differences may be attributed to variations in underlying software and also to differences in curation and decision-making processes.

Dotplots of six DNA transposons from the library of Hypsibius exemplaris produced with the MAFFT online server. These elements were selected by course participants for aesthetic reasons

To highlight the importance of generating and using custom repeat libraries for the organisms of interest as well as their curation, we masked the two tardigrade genomes and compared how the annotation and accumulation patterns change when using general repeat libraries (in this case the Repbase library for Arthropoda) and species-specific ones before and after curation (Fig.  4 ; Table  2 and S5). The use of the known repeats for Arthropoda available on Repbase provided a poor and insufficient annotation for both species (all the following percentages are given for H. exemplaris and then for R. varieornatus ) where only 1.95% and 0.26% of the assemblies were annotated as interspersed repeats and the accumulation patterns were characterized only by likely old insertions. Then the use of species-specific, albeit uncurated, libraries completely changed the percentage of TEs annotated (16.38% and 15.66%) and their accumulation patterns that showed many recently accumulated insertions. While the shape and percentages of the repeat landscapes did not drastically change after the manual curation of the libraries, the curated libraries clearly highlighted a large accumulation of DNA transposons in recent and ancient times alike that were either not present in the other landscapes or were hidden among the “unknown” repeats. Especially for R. varieornatus , the curation highlighted a higher accumulation of repeats in the very recent times (1–5% of divergence). This higher accumulation of DNA transposons in recent times is also in line with the finding of multiple putatively active transposable element subfamilies (Table  3 ). Finally, the use of the repeat library of one species to annotate the other species (reciprocal masking) resulted to be almost as insufficient as the use of the Repbase library for Arthropoda, stressing once again how important it is to have a capillary knowledge of the repeatome for correct biological interpretations.

Repeat landscapes of the genomes of H. exemplaris and R. varieornatus annotated with the Repbase (Arthropoda clade), uncurated and curated of both tardigrades combined libraries, and with libraries of the reciprocal species (only species-specific repeats). The divergence from consensus calculated with the Kimura 2-parameter distance model is shown on the x-axis. The percentage of genome annotated is shown on the y-axis

As a demonstrative example of the contribution of the collaborative curation process in providing novel insights into TE diversity, taxonomic distribution and biology, we decided to deeply characterize consensus sequences that we classified as Tc4. These elements have a rather limited taxonomic distribution, few references in the literature exist, and they incompletely duplicate the target site upon transposition [ 26 ] which can impose challenges for their classification. The Tc4 transposons are DDD elements firstly discovered in Caenorhabditis elegans [ 26 ] where they recognize the interrupted palindrome CTNAG as target site for insertion, and cause duplication of only the central TNA trinucleotide. Regarding their taxonomic distribution, consensus sequences for Tc4 elements are known and deposited only for nematodes and arthropods in RepeatPeps, Repbase and DFAM. Phylogenetic analyses based on DDD segments confidently placed the four tardigrade Tc4 consensus sequences identified in R. varieornatus within the Tc4 clade in a sister relationship with arthropod elements and with a branching pattern that reassembles the Panarthropoda group (tardigrades + onychophorans + arthropods) within Ecdysozoa [ 27 ] (Fig.  5 A). The DDD catalytic domain is highly conserved between different phyla (Fig.  5 B) and the target site of tardigrades mirrors what was previously observed in nematodes (i.e., C|TNA|G where “|” marks the transposase cut site; Fig.  5 C-D). We could therefore hypothesize that these elements first originated during the diversification of Ecdysozoa. However, broader comparative analyses involving more early-diverging Metazoa clades are necessary to confirm this lineage-specific origin.

Characterization and phylogenetic analyses of Tc4 elements. ( A ) Phylogenetic tree of Tc4 consensus sequences based on DDD catalytic domains identified in the R. varieornatus consensus sequences, highlighted in bold and orange, together with representative sequences extracted from the RepeatPeps library from nematodes (pink) and insects (green). All nodes received maximal support value. ( B ) Alignment of DDD catalytic domains of sequences included in phylogenetic analyses. Residues conserved in more than 80% of the sequences are colored. Arrows highlight catalytic DDD residues. Sequence logos of 5’ ( C ) and 3’ ( D ) ends of Tc4 elements used to curate the R. varieornatus consensus sequences. Black and purple arrows denote terminal inverted repeats (TIRs) and target site duplications (TSDs), respectively. The purple dotted line marks the transposase cut on the CTNAG target site

Contributions from the course participants

During both editions of the course, participants were free to explore their favorite topics within the scope of the syllabus and we share two contributions developed by the participants that can be useful for the entire community. First, an additional repeat library of 130 consensus sequences (119 of which are DNA transposons) was produced with the use of REPET for R. varieornatus (Table S4 ). Second, a guide for the classification of TEs from multisequence alignments (File S1) that can be a useful starting point for beginners and complementary to more extensive guides [ 13 , 14 ].

As shown here and in many other studies, repeat annotation is key to correctly identify and interpret patterns of genome evolution and proper annotation is based on a thorough curation of the repeat libraries [ 8 , 9 , 28 ]. However, it is hard for curation efforts to keep up with the sheer number of genome assemblies released every year as curation done by single laboratories may require months or even years for a single genome. Tools like TE-Aid [ 13 ] and EarlGrey [ 29 ] are rapidly spreading and gaining popularity to facilitate TE curation processes [ 30 , 31 , 32 , 33 ]. Despite these advancements, until fully automatized, reliable tools are developed and there are manual curation training sets for understudied taxa, we emphasize the need to implement manual curation for repeat libraries as well as to find alternative ways to deal with the curation of hundreds of new libraries. Here we presented one such alternative approach, namely a peer-reviewed course sourcing effort designed to be as reproducible and comparable as possible and where the hands-on tutorials were designed to be meaningful for the participants because they dealt with real unexplored data and directly contributed to the scientific community. The two iterations of this course sourcing effort resulted in the successful curation of hundreds of new and diverse TEs. While the repeat libraries presented here were not completely curated and classified, we would like to highlight that TE curation can be considered as a “cumulative” effort of a community. The more people learn how to curate, the more teachers are educated and the faster the process becomes. Therefore, we hope that this experience and teaching framework can be of use for the genome research community and that it can be applicable to other types of data/analyses that need manual curation (e.g., genome assemblies [ 21 , 22 ] and gene annotations).

Materials and methods

Genome assemblies.

For this study, we used the genome assemblies of the two tardigrade species: Hypsibius exemplaris  (formerly identified as Hypsibius dujardini ; GCA_002082055.1) and Ramazzottius varieornatus (GCA_001949185.1) produced by sequencing a pool of male and female individuals by Yoshida et al. [ 23 ]. The Hypsibius exemplaris genome was assembled using long PacBio and short Illumina reads whereas the Ramazzottius varieornatus genome was assembled using a combination of Sanger and Illumina reads [ 23 ].

Raw repetitive element library

To start the de novo characterization of TEs, we ran RepeatModeler on H. exemplaris and RepeatModeler2 on R. varieornatus [ 34 ] using the option -LTR_struct and obtained a library of raw consensus sequences for each of the genomes. RepeatModeler and not RepeatModeler2 was used on H. exemplaris since at the time of the first edition of the course in 2018, only RepeatModeler was available. RepeatModeler and RepeatModeler2 automatically named the consensus sequences with the prefix “rnd” that we replaced with the abbreviations of the species names: “hypDuj” for H. exemplaris and “ramVar” for R. varieornatus . Note that the abbreviation “hypDuj” was assigned prior to the scientific name change from H. dujardini to H. exemplaris . Despite this, we have chosen to retain “hypDuj” in the final repeat library for the sake of simplicity.

The two libraries were then compared to find similar sequences belonging either to the same family or subfamily by using, respectively, the 80-80-80 rule [ 35 ] and the 95-80-98 rule [ 36 ]. The rules were applied by masking the library of R. varieornatus with the library of H. exemplaris using RepeatMasker [ 37 ] and by parsing the resulting. out table with awk.

Manual curation of the consensus sequences

After the generation of the libraries of raw consensus sequences, we proceeded with the collaborative peer-reviewed manual curation step. For example in the second iteration of the course, the participants were split into ten groups and each group received about 80 consensus sequences to curate.

The curation of the raw consensus sequences followed a “Blast-Extend-Extract” process. The first step of the curation consisted in the alignment of the raw consensus sequences to the genome of origin using BLAST [ 38 ]. The best 20 BLASTN hits were selected, extended by 2 kb at both ends and aligned to their raw consensus sequence with MAFFT [ 39 ] which produced a multisequence alignment for each consensus sequence ready to be manually curated (script RMDL_curation_pipeline.pl, first published in [ 40 ]).

Each of the multisequence alignment was then inspected to: (1) find the actual boundaries of the repetitive element; (2) build a new consensus sequence with Advanced Consensus Maker ( https://hcv.lanl.gov/content/sequence/CONSENSUS/AdvConExplain.html ); (3) fix ambiguous base and gap calls in the new consensus sequence following the majority rule; (4) find sequence hallmarks to define the repetitive elements as transposable elements (e.g., target site duplication, long terminal repeats, terminal inverted repeats or other motifs). Every new consensus sequence was reported in a common Excel table (Table S1 ). To quantitatively measure the improvement of the repeat libraries after manual curation, we compared the length of consensus sequences before and after curation.

In all the figures and tables, the term “curated” indicates that the library mentioned contains manually curated consensus sequences as well as all the consensus sequences that remained uncurated. Finally, we consider each consensus sequence as a proxy for a transposable element subfamily. However, the consensus sequences were not checked for redundancy and not clustered into families and subfamilies using the 80-80-80 or 95-80-98 rules for nomenclature because the focus of the study was on classifying the consensus sequences into superfamilies and orders of transposable elements.

The code used to produce the consensus sequences and their alignments is provided as tutorial on the GitHub repository https://github.com/ValentinaPeona/TardigraTE .

Classification

The new consensus sequences were classified using sequence characteristics retrieved by the alignments (e.g., target site duplications, terminal repeats) and homology information retrieved through masking the sequences with Censor [ 41 , 42 ] following the recommendations from [ 35 ] and [ 43 ]. When the information retrieved by the alignments and Censor was not enough to provide a reliable classification of the elements, the sequences were further analyzed for the presence of informative protein domains using the Conserved Domain Database [ 44 , 45 , 46 ].

Since the course participants in general had never curated transposable element alignments before, we decided to implement a peer-review process. For the first course ( H. exemplaris ), the results of each participant were sent to another participant to check the curated alignments and independently retrieve key information for the classification. The independent sequences and classifications would be compared and fixed if necessary. In the second course ( R. varieornatus ), all sequences were inspected by the same 3 reviewers and only these applied the same process as previously described.

Comparative analysis of the repetitive content

The genome assemblies of both tardigrade species were masked with RepeatMasker 4.1.10 using four different types of TE libraries: (1) known Arthropoda consensus sequences from Repbase; (2) uncurated raw consensus sequences from the respective species; (3) curated consensus sequences together with the consensus sequences that were not curated from the respective species; (4) curated consensus sequences together with the consensus sequences that were curated from the other species. The RepeatMasker output files were then used to get the percentages of the genomes annotated as TEs and to visualize the landscapes of the accumulation of repeats.

Finally, we estimated the number of putative active transposable elements in the two genomes by filtering the RepeatMasker annotation for elements that show at least 10 copies with 0% divergence from their consensus sequences.

Characterization of Tc4 elements

During the manual curation process, participants found types of DNA transposons that are currently considered to have a rather restricted phylogenetic distribution like Tc4 elements, therefore more in-depth analyses were run on these elements. The protein domains of known Tc elements were compared to the Tc4 consensus sequences from the tardigrade species and phylogenetic relationships were established.

Protein homologies of the partially curated repeat libraries were collected using BLASTX (e-value 1e-05) [ 47 ] against a database of TE-related protein (RepeatPeps library) provided with the RepeatMasker installation. We extracted the amino acid translation of each hit on Tc4 elements based on the coordinates reported in the BLASTX output. Resulting protein sequences were aligned together with all members of the TcMar group present in RepeatPeps library using MAFFT ( L-INS-i mode) [ 48 ] and the alignment was manually inspected to identify and isolate the catalytic DDD domain. The resulting trimmed alignment was used for phylogenetic inference with IQ-TREE-2 [ 49 ], identifying the best-fit evolutionary model with ModelFinder2 and assessing nodal support with 1000 UltraFastBootstrap replicates [ 50 ]. The resulting maximum likelihood tree was mid-point rooted and the Tc4 subtree extracted for visualization purposes. The alignment with all members of the TcMar superfamily and the resulting phylogenetic tree can be found in File S2 and S3, respectively.

The DDD segments of Tc4 elements were re-aligned using T-Coffee in expresso mode [ 51 ] to produce conservation scores. A sequence logo of 5’ and 3’ boundaries of identified Tc4 elements was produced extracting all sequences used to curate the four R. varieornatus Tc4 elements and keeping the first 15 bp and 11 bp before and after the terminal inverted repeats (TIRs), respectively.

Additional transposable element library

Participants ran REPET V3.0 [ 52 ] to produce a de novo transposable element library for R. varieornatus in parallel to the one generated by RepeatModeler2. A custom TE library composed by repeats from Repbase and from H. exemplaris was used to aid REPET in the classification process. Only consensus sequences that showed two or more full-length copies in the R. varieornatus genome were retained in the new library. Furthermore, the consensus sequences were scanned for protein domains and presence of TIRs or long terminal repeats (LTRs).

Data availability

Data is provided within the manuscript or supplementary information files.

Abbreviations

Long Terminal Repeats

Transposable Element

Terminal Inverted Repeats

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Acknowledgements

Part of the analysis were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX), National Academic Infrastructure for Supercomputing in Sweden (NAISS), partially funded by the Swedish Research Council through grant agreement no. 2022-06725 and CSC-IT Finland. We thank the three anonymous reviewers and Irina Arkhipova for their useful and detailed comments on the manuscript.

declaration.

Open access funding provided by Uppsala University. This study was supported by grants from Swedish Research Council Vetenskapsrådet (2020–04436 to AS; 2022–06195 to VP), the Swedish Research Council Formas (2017 − 01597 to AS), the Canziani bequest and the ‘Ricerca Fondamentale Orientata’ (RFO) funding from the University of Bologna to JM.

Open access funding provided by Uppsala University.

Author information

Valentina Peona and Jacopo Martelossi contributed equally to this work.

Authors and Affiliations

Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, SE-752 36, Sweden

Valentina Peona, Yifan Pei & Alexander Suh

Swiss Ornithological Institute Vogelwarte, Sempach, CH-6204, Switzerland

Valentina Peona

Department of Bioinformatics and Genetics, Swedish Natural History Museum, Stockholm, Sweden

Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, Bologna, 40126, Italy

Jacopo Martelossi

New York University Abu Dhabi, Saadiyat Island, United Arab Emirates

Dareen Almojil

Skolkovo Institute of Science and Technology, Moscow, Russia

Julia Bocharkina

Natural History Museum, Oslo University, Oslo, Norway

Ioana Brännström

Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden

Anglia Ruskin University, East Rd, Cambridge, CB1 1PT, UK

University of Arizona, Tucson, AZ, USA

Evolutionary Genetics Department, Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany

Tomàs Carrasco-Valenzuela

Berlin Center for Genomics in Biodiversity Research, 14195, Berlin, Germany

Reed College, Portland, OR, United States of America

Jon DeVries

Department of Ecology and Evolution, The University of Chicago, Chicago, IL, 60637, USA

Meredith Doellman

Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA

Evolutionary Biology & Ecology, University of Freiburg, Freiburg, Germany

Daniel Elsner

Research Unit Comparative Microbiome Analysis (COMI), Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, Neuherberg, Germany

Pamela Espíndola-Hernández

Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK

Guillermo Friis Montoya

Institute of Evolution and Ecology, University of Tuebingen, Tuebingen, Germany

Bence Gaspar

Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic

Danijela Zagorski

Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland

Paweł Hałakuc

Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary

Beti Ivanovska

The Natural History Museum, Cromwell Road, London, SW6 7SJ, UK

Christopher Laumer

Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

Robert Lehmann

LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt, Germany

Ljudevit Luka Boštjančić & Maria Anna Nilsson

Department of Genetics, Environment & Evolution, Centre for Biodiversity & Environment Research, University College London, London, UK

Rahia Mashoodh

Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic

Sofia Mazzoleni

INBIOS-Conservation Genetic Lab, University of Liege, Liege, Belgium

Alice Mouton

Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany

Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland

Giacomo Potente

German Cancer Research Center, NGS Core Facility, DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany

Panagiotis Provataris

Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, Madrid, 28006, Spain

José Ramón Pardos-Blas

Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India

Ravindra Raut

Molecular Ecology Group (MEG), National Research Council of Italy – Water Research Institute (CNR-IRSA), Verbania, Italy

Tomasa Sbaffi

Eurofins Genomics Europe Pharma and Diagnostics Products & Services Sales GmbH, Ebersberg, Germany

Florian Schwarz

Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland

Jessica Stapley

Tree of Life, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK

Lewis Stevens

Department of Botany, Jagannath Univerity, Dhaka, 1100, Bangladesh

Nusrat Sultana

Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic

Radka Symonova

Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, 40014, Finland

Mohadeseh S. Tahami

Centogene GmbH, Am Strande 7, 18055, Rostock, Germany

Department of Ecology & Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America

Zell- und Molekularbiologie der Pflanzen, Technische Universität Dresden, Dresden, Germany

Abdullah Yusuf

Physalia-courses, 10249, Berlin, Germany

Carlo Pecoraro

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK

Alexander Suh

Present address: Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 160, 53113, Bonn, Germany

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AS conceived the project and VP contributed to its development. VP and JM analyzed the final data. AS, VP, JM wrote the manuscript, and all authors revised the manuscript. MST, AM, DA, JS, GP provided additional contributions to the teaching material. VP, JM, DA, JB, IB, MB, AC, TCV, JDV, MD, DE, PEH, GFM, BG, DZ, PH, BI, CL, RL, LLB, RM, SM, AM, MAN, YP, GP, PP, JRPB, RR, TS, FS, JS, LS, NS, RS, MST, AU, HY, AY, AS contributed to the curation of the repeat library. CP provided and maintained the computational infrastructure during the courses. Valentina Peona and Jacopo Martelossi contributed equally to this work. All course participants are listed in alphabetical order.

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Correspondence to Valentina Peona , Jacopo Martelossi or Alexander Suh .

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Carlo Pecoraro is founder of Physalia-courses (http://www.physalia-courses.org/) but had no role in the design of the study.

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Peona, V., Martelossi, J., Almojil, D. et al. Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective. Mobile DNA 15 , 10 (2024). https://doi.org/10.1186/s13100-024-00319-8

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Michael Cohen Was Paid to Fix Trump’s Problems. Now He’s One of Them.

Mr. Cohen once called himself Donald J. Trump’s “designated thug.” Will he help bring about the ex-president’s downfall?

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By Ben Protess ,  Jonah E. Bromwich ,  Jonathan Swan ,  Maggie Haberman and William K. Rashbaum

Donald J. Trump has always surrounded himself with lawyers — all types of lawyers. There are the television-friendly talking heads. The polished criminal practitioners. The pit-bull litigators, the corporate suits and the legal advisers with their own legal troubles.

And then there was the singular Michael D. Cohen, lawyer by trade and enforcer by nature. With the loyalty of a surrogate son, he kept Mr. Trump’s secrets and cleaned up his messes. He was the fixer.

This week, however, Mr. Cohen is poised to unfix Mr. Trump’s life. When he takes the stand as a vital witness at Mr. Trump’s criminal trial in Manhattan, Mr. Cohen will unearth some of the secrets he buried, revealing a mess that prosecutors say his former boss was desperate to hide.

The Links Between Trump and 3 Hush-Money Deals

Here’s how key figures involved in making hush-money payoffs on behalf of Donald J. Trump are connected.

It will represent a pivotal moment of the trial, and the climax of a decades-long relationship between two New York loudmouths who used each other, betrayed each other and will now face off on the biggest stage: The first criminal trial of an American president.

Interviews with 10 of Mr. Cohen’s allies and adversaries, as well as a review of court records and Mr. Cohen’s books, paint a portrait of a once-obscure operator who came to play an outsized role in American politics, a man whose relationship with the former president traced an arc from asset to threat.

From the stand, Mr. Cohen will tell of his greatest coup in Mr. Trump’s employ, the time when he paid $130,000 to suppress a porn star’s story of a sexual encounter with Mr. Trump. He did so, he will say, at his boss’s direction. And, illuminating what prosecutors say is the cover-up at the heart of the case, he is expected to offer his firsthand account of how, after the 2016 election, the new president reimbursed him for the hush money, but falsified records to disguise those payments as legal expenses.

Mr. Trump denies any role in falsifying the records, and says he never had sex with the porn star, Stormy Daniels. His lawyers dispute that any crime occurred.

Despite months of preparation, Mr. Cohen, 57, will be unpredictable on the stand, prone as he is to both tirades and charm.

Prosecutors acknowledged on Friday having little control over Mr. Cohen, who, despite their admonitions, has taunted Mr. Trump throughout the trial. In a recent TikTok video, Mr. Trump’s lawyers complained, he wore a shirt with a picture of the former president behind bars, prompting the judge to request that he keep quiet.

But prosecutors, who are offering Mr. Cohen nothing in return, have little leverage to rein him in. Unlike a traditional cooperating witness who trades testimony for leniency, he has already spent more than a year in federal prison for paying the hush money and committing other crimes.

That experience, contrasted with that of other Trump aides who avoided indictment or received pardons, has catalyzed his anger. Mr. Cohen, whose self-image remains inextricably tied to Mr. Trump, has transformed himself from lackey to antagonist, adopting a new identity, but with the same personality.

Craving public redemption, Mr. Cohen has fashioned himself as a standard-bearer of the anti-Trump resistance, seeking what he once called a “way to right some of the many wrongs I committed at his behest.” And since his prison stint, he has made money from their feud. There have been books bluntly titled “Disloyal” and “Revenge,” and a podcast called “Mea Culpa.”

Under questioning from prosecutors, his testimony could play out like a cinematic thriller, as he casts himself as a consigliere turned state’s evidence. This is the story Mr. Cohen told when he testified before Congress, where he estimated he had made 500 threats at Mr. Trump’s behest, and at a New York civil trial, where he accused the former president of fraud.

At that trial, the defense accused Mr. Cohen of perjury. Now, Mr. Trump’s team in the criminal case is expected to escalate those attacks, painting Mr. Cohen as a rogue actor whose fixes caused more problems than they solved. They have promised to seize on Mr. Cohen’s credibility and criminal record — Mr. Trump is fond of noting that he is a “convicted liar” — and portray him as a scorned underling seeking revenge against the former president.

Prosecutors from the Manhattan district attorney’s office have already anticipated those lines of attack — and leaned into them. While the prosecutors introduced witnesses to corroborate much of Mr. Cohen’s account, they have invited those same witnesses to cast him as a bully, a nervous wreck and, as one person put it, a “jerk.”

The intent is to suck the air out of the defense’s attacks and desensitize the jury to Mr. Cohen’s baggage, turning him into an object of amusement. Already, his name has drawn smiles from some of the jurors, who will now evaluate his credibility for themselves.

Who Are Key Players in the Trump Manhattan Criminal Trial?

The first criminal trial of former President Donald J. Trump is underway. Take a closer look at central figures related to the case.

“He was everything Trump wanted,” said Donny Deutsch, a television personality and advertising executive who is close with Mr. Cohen and was once friendly with Mr. Trump. “He’s aggressive, he’s tenacious, he’s a bulldozer, and so what you’re hearing in court, a lot of the perceived negatives, is what made him a positive for Trump.”

Mr. Deutsch recalled that, years ago, after he had implied on television that Mr. Trump was racist, Mr. Cohen called to complain. “Donald is really upset,” Mr. Cohen said. “Can you talk to him, tell him you don’t think he’s a racist?”

Mr. Cohen, who learned from and parroted his boss, acknowledged in his memoir that he had been Mr. Trump’s “designated thug.”

Their relationship, defined by abuse and subservience, imploded soon after the hush-money deal came to light in 2018. Mr. Trump washed his hands of Mr. Cohen, who in turn vowed to flip.

Ever since, they have waged public combat with one another. Mr. Trump sued Mr. Cohen and called him a “rat.” Mr. Cohen sued Mr. Trump and called him a “mob boss.”

But, as the trial approached, people close to him say, Mr. Cohen’s notoriety as a Trump nemesis took a personal toll that left him anguished. He privately conveyed a fear for his safety, though he ultimately concluded he had no choice but to testify.

After the trial started, Mr. Cohen pledged to “sit my ass in that witness stand,” and “just tell the truth.”

‘He said he was a lawyer.’

Mr. Cohen, the son of a Holocaust survivor, had idolized Mr. Trump since his youth on Long Island. And after buying apartments in two of Mr. Trump’s New York buildings in the early 2000s, he caught Mr. Trump’s eye during a dispute with the condo board at Trump World Tower in New York.

Mr. Trump saw his potential as an enforcer, and soon Mr. Cohen received an office on the 26th floor of Trump Tower.

But Mr. Cohen’s colleagues at the Trump family real estate business saw his job as something of a mystery. They spotted him inside Mr. Trump’s office, overheard him yelling from his own and watched him walk the hallways with a pistol strapped to his ankle.

A prosecutor last week asked a former co-worker about Mr. Cohen’s precise position at the company, the Trump Organization.

“He said he was a lawyer,” Jeffrey McConney, Mr. Trump’s former corporate controller, replied dryly, eliciting laughter from the courtroom.

Mr. Cohen was indeed a lawyer, in the sense that he had graduated from law school, worked as a personal injury lawyer and occasionally performed tasks that approximated legal work under the amorphous title of executive vice president of the Trump Organization and “special counsel” to Mr. Trump.

But more often than not, Mr. Cohen’s tasks were unrelated to the law — and sometimes, at odds with it.

There was the time, Mr. Cohen recounted in “Disloyal,” that he threatened to tank a paint company with bad publicity to get thousands of gallons of free paint for Mr. Trump’s golf resort outside Miami.

And the time Mr. Cohen hired a computer programmer to rig an online CNBC poll to ensure that Mr. Trump would rank among the most influential business people alive.

And the time he threatened to ruin the college admission prospects of a child whose family was a tenant in a Trump building, so that they would not obstruct a renovation.

Mr. Cohen never much liked the term fixer. But the role had special meaning to Mr. Trump, who was always on the lookout for someone to emulate his earliest lawyer, Roy M. Cohn, an unscrupulous defender known for scorched-earth tactics honed while working for Mafia bosses and the Communist-hunting Senator Joseph McCarthy.

Mr. Cohen updated the part for the digital era, helping Mr. Trump draft some of his nastiest social media snipes, not at political enemies, but instead at fellow celebrities such as the actress Rosie O’Donnell.

He also scouted the occasional deal, including foreign projects that never materialized, like a plan for a Trump Tower in Moscow that caught the interest of federal investigators and ultimately led to one of Mr. Cohen’s guilty pleas. (He admitted to lying to Congress about the deal out of loyalty to Mr. Trump.)

Mr. Cohen also protected the Trump family, emails and other records show. He helped Mr. Trump’s youngest son, Barron, find a private school. He helped his oldest, Donald Trump Jr., dig out of an ill-fated business venture. And, on occasion, Mr. Cohen has said, Mr. Trump put Mr. Cohen on the phone with his wife, Melania, to reassure her that he hadn’t been unfaithful.

In return, Mr. Trump subjected Mr. Cohen to ridicule. Over their decade together, Mr. Trump stiffed him on bonuses and threatened to fire him at least twice.

But Mr. Cohen kept searching for new ways to win the dollops of approbation he craved, including by nurturing his nascent political hopes.

Mr. Cohen, who indulged his own political aspirations as a failed City Council candidate, was one of the strongest believers in Mr. Trump as a possible president when he flirted with running in 2012. Mr. Cohen set up a website, ShouldTrumpRun.org, and went on a scouting trip to Iowa.

Although he had no formal role on the 2016 campaign, Mr. Cohen nonetheless raised millions of dollars, recruited Black supporters and was an enthusiastic booster of Mr. Trump on television.

But his greatest service came behind the scenes, arranging payoffs to two women who had threatened to go public with stories about having sex with a married Mr. Trump. One, Karen McDougal, struck a $150,000 deal with Mr. Trump’s allies at The National Enquirer, who bought and buried the former Playboy model’s story.

The second woman was the porn star, Ms. Daniels, who described her encounter with Mr. Trump in graphic detail on the witness stand last week. When Mr. Trump was slow to pay the $130,000 hush money, Mr. Cohen dug into his own pocket.

Mr. Trump repaid him monthly through the first year of the presidency. Mr. Cohen was no longer a Trump Organization employee, and Mr. Trump had excluded him from a job in Washington. But Mr. Cohen’s email signature now carried a loftier title: personal lawyer to the president.

When one of Mr. Trump’s friends asked Mr. Trump why he kept Mr. Cohen so close, Mr. Trump replied, “He has his purpose.”

The knock at the door

In the early morning hours of April 9, 2018, as Mr. Cohen puttered around a New York hotel room sipping coffee in a pair of Nike shorts, he heard a knock on the door.

Peering through the peephole, he saw a row of badges. It was the F.B.I.

The swarm of agents was at the hotel, where Mr. Cohen was staying while his apartment was undergoing repairs, with a warrant to seize evidence of various crimes, including that the hush money had constituted an illegal donation to Mr. Trump’s campaign. By midday, they had also searched his office, his home and his safe deposit box.

People who saw Mr. Cohen afterward described a suicidal man who paced the room, refusing to spend a single day in jail.

Mr. Trump was enraged as well. On the day of the search, he declared it “a disgraceful situation.”

Initially, Mr. Trump came to Mr. Cohen’s defense, publicly flattering Mr. Cohen as a “good man” and privately phoning him with a message: Stay strong. The support soon faded, the phone stopped ringing and the public praise dried up.

Not even a month after the raid, Mr. Trump called into one of his favorite television shows, “Fox & Friends,” and distanced himself, saying Mr. Cohen had handled just “a tiny, tiny little fraction” of his legal work. Mr. Trump added: “From what I understand, they’re looking at his businesses,” nodding to the tax and bank crimes to which Mr. Cohen would ultimately plead guilty.

By June, Mr. Trump’s company used that same logic to stop paying Mr. Cohen’s mounting legal bills. It was the final straw for Mr. Cohen, who hired Lanny J. Davis, a veteran Washington lawyer and public relations strategist with close ties to Democratic politicians. He also told friends that he was willing to cooperate with prosecutors.

When he pleaded guilty to federal charges that August, Mr. Cohen for the first time stood up in a courtroom to accuse the man he had once protected, saying he had paid the hush money “at the direction of” his former boss.

He told a judge, while being sentenced to prison, “I felt it was my duty to cover up his dirty deeds.”

In 2020, Mr. Cohen was released on furlough during the coronavirus pandemic. But the Federal Bureau of Prisons sent him back behind bars in Otisville, N.Y., after he refused to sign paperwork barring him from publishing a book during the remainder of his sentence. A judge later called his second imprisonment “retaliatory.”

His friends say he remains tortured.

“He doesn’t revel in any of this,” said Omarosa Manigault Newman, a former White House aide. “If Michael had his way, he would still be working with Trump.”

‘You’re not on your podcast.’

At first, the performance was surprisingly smooth.

Mr. Cohen took the stand at Mr. Trump’s civil fraud trial in October 2023 and did what the New York attorney general had asked: He testified that Mr. Trump had directed him years earlier to manipulate internal records to make the developer look richer than he was.

Then it was the defense’s turn.

Alina Habba, Mr. Trump’s lawyer, paced in front of the bench. She smiled as she reintroduced herself to Mr. Cohen and, minutes later, attacked him as a disgraced former lawyer and a serial liar who had perjured himself even while pleading guilty to a federal crime.

“You have lied under oath numerous times, Mr. Cohen, isn’t that correct?” Ms. Habba asked. Mr. Cohen acknowledged that it was.

He fought back, noting that when he had lied in court, he had often done so for Mr. Trump. He even lodged his own objections, citing legal precedents, though he had lost his law license after pleading guilty years earlier.

“You don’t get to object,” Ms. Habba told him, later reminding him, “You’re not on your podcast.”

Though the judge found that Mr. Cohen had been “credible,” his unpredictability on the witness stand stood as a cautionary tale for prosecutors in Mr. Trump’s criminal case.

The Donald Trump Indictment, Annotated

The indictment unveiled in April 2023 centers on a hush-money deal with a porn star, but a related document alleges a broader scheme to protect Donald J. Trump’s 2016 campaign.

Anticipating attacks on his credibility, the prosecutors have sought to corroborate his story during the first three weeks of testimony, introducing evidence in support of his assertion that Mr. Trump directed the hush-money deal.

Hope Hicks, Mr. Trump’s former spokeswoman, scoffed at the notion that Mr. Cohen would have made the $130,000 hush-money payment to Ms. Daniels out of the kindness of his heart because doing so “would be out of character for Michael,” an insulting comment that nonetheless supported Mr. Cohen’s story.

They also elicited testimony from another former Trump aide who confirmed that Mr. Cohen was scheduled to meet with Mr. Trump in the White House in early February 2017. At that meeting, Mr. Cohen has said, he and Mr. Trump confirmed their plan to falsify the records.

And prosecutors made sure to enter into evidence the voice of a man who had once found Mr. Cohen essential.

“Michael Cohen is a very talented lawyer,” Mr. Trump said, in a recording from a news conference in 2017 that was played in the courtroom. “He’s a good lawyer at my firm.”

Ben Protess is an investigative reporter at The Times, writing about public corruption. He has been covering the various criminal investigations into former President Trump and his allies. More about Ben Protess

Jonah E. Bromwich covers criminal justice in New York, with a focus on the Manhattan district attorney’s office and state criminal courts in Manhattan. More about Jonah E. Bromwich

Jonathan Swan is a political reporter covering the 2024 presidential election and Donald Trump’s campaign. More about Jonathan Swan

Maggie Haberman is a senior political correspondent reporting on the 2024 presidential campaign, down ballot races across the country and the investigations into former President Donald J. Trump. More about Maggie Haberman

William K. Rashbaum is a Times reporter covering municipal and political corruption, the courts and broader law enforcement topics in New York. More about William K. Rashbaum

Our Coverage of the Trump Hush-Money Trial

News and Analysis

Michael Cohen was paid to fix Donald Trump’s problems. Now, as he prepares to take the stand in Trump’s criminal trial, he’s one of them .

Ahead of Cohen’s testimony, Justice Juan Merchan told prosecutors to keep Cohen from speaking about the case .

Witnesses have described Trump monitoring the minutiae of his business , a portrait prosecutors are drawing to help convince the jury that he couldn’t have helped but oversee the hush-money payment.

More on Trump’s Legal Troubles

Key Inquiries: Trump faces several investigations  at both the state and the federal levels, into matters related to his business and political careers.

Case Tracker:  Keep track of the developments in the criminal cases  involving the former president.

What if Trump Is Convicted?: Could he go to prison ? And will any of the proceedings hinder Trump’s presidential campaign? Here is what we know , and what we don’t know .

Trump on Trial Newsletter: Sign up here  to get the latest news and analysis  on the cases in New York, Florida, Georgia and Washington, D.C.

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Computer Science > Machine Learning

Title: selective fine-tuning on llm-labeled data may reduce reliance on human annotation: a case study using schedule-of-event table detection.

Abstract: Large Language Models (LLMs) have demonstrated their efficacy across a broad spectrum of tasks in healthcare applications. However, often LLMs need to be fine-tuned on task-specific expert annotated data to achieve optimal performance, which can be expensive and time consuming. In this study, we fine-tune PaLM-2 with parameter efficient fine-tuning (PEFT) using noisy labels obtained from gemini-pro 1.0 for the detection of Schedule-of-Event (SoE) tables, which specify care plan in clinical trial protocols. We introduce a filtering mechanism to select high-confidence labels for this table classification task, thereby reducing the noise in the auto-generated labels. We show that fine-tuned PaLM-2 with those labels achieves performance that exceeds the gemini-pro 1.0 and other LLMs. Furthermore, its performance is close to a PaLM-2 fine-tuned on labels obtained from non-expert annotators. Our results show that leveraging LLM-generated labels through powerful models like gemini-pro can potentially serve as a viable strategy for improving LLM performance through fine-tuning in specialized tasks, particularly in domains where expert annotations are scarce, expensive, or time-consuming to obtain.

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