Annotating a Research Paper

Instructions and Handbook

Fall 2019

Dr. Melissa McCartney

mmccartn@fiu.edu

Table of Contents:

For INSTRUCTORS:

1. General outline of the annotation project:

For STUDENTS:

1. What are annotated papers?

2. Annotated papers: homework assignment and pre-course survey

3. What is your role as an annotator?

4. Annotator training guide

5. Our favorite annotated papers to use as examples

6. Timeline and Rubric for your annotation project

7. Using Xodo to annotate your paper

General outline of the annotation project:

1. Picking papers:

a. Instructor selection

2. Enter paper title and student names to the google doc: https://docs.google.com/spreadsheets/d/1he0Wx_CH469QTtPBHEem4ntwKQjRH3_SG43xQkCYhw8/edit?usp=sharing

3. Once the papers have been selected, we will post them online and send a link.

a. Students will use Xodo to annotate: https://www.xodo.com/

b. Students will use their student number as their Xodo log-in

c. Papers will be housed on SitCLAB and linked to the main SitC website

4. Students complete homework assignment and pre-course assessments

a. Homework is working with an annotated paper so they understand the premise

5. Course assessments:

a. self efficacy in PSL

b. interest and performance for PSL

c. project ownership

d. group work scale

e. science identity

f. sense of belonging to the biology department

6. Students begin to annotate: see schedule and rubric here

7. Students draft podcast script: see podcast requirements here:

8. Research team edits first draft of script and annotations

9. Students make any necessary revisions

10. Students record the podcast

11. Students complete post-course assessment

What are annotated papers?

All of our annotated papers can be found on our website: http://www.scienceintheclassroom.org/

Science in the Classroom (SitC) is a collection of freely available annotated research papers.

SitC aims to help educators, undergraduates, and advanced high school students understand the research contained in scientific primary literature by using annotations and providing accompanying teaching materials.

Annotations include vocabulary, methods, descriptions of prior research, and explanations of major conclusions.

Take a tour of the SitC website: https://www.youtube.com/watch?v=xgPyxhFpviM#action=share

Annotated papers homework assignment and pre-course survey

Before you annotate a paper yourself, we want you to read an annotated paper to become familiar with the concept.

As a homework assignment, we ask you to read the following paper:

http://www.scienceintheclassroom.org/research-papers/caffeine-jolt-gives-bees-buzz-remember

Please explore this paper using the Learning Lens to get a feel how annotations work.

When you are finished, please complete the pre-course assessment provided by your Instructor on Canvas.

What is your role as an annotator?

Annotators help us deconstruct research papers for use with first year undergraduates. The papers you develop through this project will be available for use in future biology classrooms.

As annotators, you will:

· Write annotations for a research paper

· Build your communication skills as you translate complicated science for a more general audience

· Share your new knowledge of this paper as a podcast for other scientists to listen to

· Create an educational resource to be used in future introductory courses at FIU

Annotator training guide

Here, you will find details on how to write a good annotation for each required category.

Annotations

a. Hypothesis: HIGHLIGHT IN RED

· What is the main research question(s) in the paper?

· What problem is the research trying to solve?

b. Glossary terms: HIGHLIGHT IN YELLOW

· Simple and short (approximately 3 sentences)

· Don’t use the word that you’re defining in the definition

· Define acronyms

c. Real world connections: HIGHLIGHT IN BLUE

· How does this research impact daily life?

· How will this research change the world?

· How will this research affect your life?

Figures (four figures or tables total should be annotated): HIGHLIGHT IN GREEN

· Avoid jargon (student readers have likely never worked in a lab)

· Nothing is too basic

· Use this space to expand on the figures by asking questions, explaining materials/methods, embedding videos, and introducing activities

· We recommend using resources from:

· http://www.jove.com/

· https://www.hhmi.org/biointeractive

· https://www.ibiology.org/

· https://www.loc.gov/

· External links are encouraged, but avoid personal blogs, wikipedia, and content behind a paywall

Example of Figure content (feel free to draw on the figure directly with Xodo tools!):

· Graphing techniques

· Photos/videos of methods, technologies, equipment, and instruments

· Descriptions of analysis tools (statistical tests or software packages)

· If applicable, a discussion of the ethics of data collection, presentation, and analysis

Our favorite annotated paper to use as an example

https://www.xodo.com/app/#/collab/ed218441-d27d-4c6e-894d-38d6fce967d8

(give the software a few minutes to load).

Timeline and Rubric for your annotation project

Week

Dates

Annotation assignments

Points

1

8/26-8/30

Annotated paper reading assignment and homework (pre-survey)

2

9/2-9/6

Select groups and papers

Familiarize yourself with Xodo

Read your selected research paper

3

9/9-9/13

Find the hypothesis of the paper and annotate as a group

4

9/16 – 9/20

Each group member finds 8 vocabulary terms to annotate (24 vocab words total)

5

9/23 – 9/27

Each group member finds at least one real world connection to annotate (at least 4 total)

6

9/30 – 10/4

Each group member annotates one figure or table

7

10/7 – 10/11

Review your annotations

8

10/14 – 10/18

Submit the annotated paper for review

9

10/21 – 10/25

Review by research team

10

10/28–11/1

Review by research team

11

11/4 –11/8

Review by research team

12

11/11–11/15

Make any edits to annotated papers

13

11/18– 11/22

Make any edits to annotated papers

14

11/25-11/29

Make any edits to annotated papers

Using Xodo to annotate your paper

Xodo is a free website/app that allows you to annotate PDFs in real time with other collaborators: https://www.xodo.com/

Before you can begin annotating you must create a free Xodo account.

It is mandatory that you use your PANTHER ID as your Xodo user name so we are able to give you credit for the annotations you write.

Under “Account Settings” make sure you enter your PANTHER ID as your display name.

IF YOU USE YOUR REAL NAME IT WILL SHOW UP ON ALL ANNOTATED PAPERS THAT WE WILL USE IN THE FUTURE. STAY ANONYMOUS, USE YOUR PANTHER ID!!!!!

Step 1: When you have Xodo open, on the upper right hand side your display name should be there. 

Step 2: When clicked on, a scroll down menu will appear. 

Step 3: Click on settings and a box will appear. 

Step 4: Change where it says "display name" to your PANTHER ID. 

Step 5: Then click save changes and DO NOT leave the page until a blue box appears that says "Information Updated". This little blue box only appears for a second. 

The paper you will be annotating will be posted at: https://sitclab.org/

To annotate using Xodo:

A. highlight the text you want to annotate with your cursor

B. a tool box will pop up, click the highlight tool (second from left)

C. a tool bar will/should appear, click style (middle icon)

· try to zoom in on the article if you are having issues

D. select your color correlating to the annotation content

E. click on the highlighted text and to the left an annotation box will appear

F. click the three dots and choose “edit”

G. Delete ALL the text in your annotation box

H. insert your annotation

I. Remember to click ‘Save’

INCLUDE ‘How to do’ VIDEO

Hypothesis: HIGHLIGHT IN RED

Glossary terms: HIGHLIGHT IN YELLOW

Real world connections: HIGHLIGHT IN BLUE

Figures: HIGHLIGHT IN GREEN

A and B

C and D

E

· Once the page is full of annotations it can get a bit difficult to identify which annotation belongs to a specific highlight.

· You can always click on the annotation and it will show you the corresponding highlight or vice versa. It can also get a bit frustrating if you’re trying to read the article. You can always hide all the annotations by clicking hide on the right-hand side above the annotations.

· You cannot delete any annotations other that your own but you can leave comments on other’s annotations. To delete, click your annotation or highlight and click delete.

· To comment on someone else’s annotation, click on it and on the right a textbox should appear. Type your feedback and push enter.

· On the left side of the page there is a box with the different pages in the article for a quick overview. Pages with annotations or figures are easily spotted through this feature. Above it, there is a toolbar. The magnifying glass is a search bar great for finding certain phrases in the text. The one with many heads will show you everyone who is collaborating on this document and who is currently online with you. There is a chat window if you would like to share ideas or receive input or feedback.

· Feel free to explore Xodo! There are many other features available.