Digitally Enhanced Literature Search and Management

class: center, middle, inverse, title-slide

.title[
# Digitally Enhanced Literature Search and Management
]
.subtitle[
## Module 2: Digitalisation in Research
]
.author[
### Hannah Metzler CSH Vienna & Medical University of Vienna
]

---

layout: true
<div class="my-footer"><a href = "www.hannahmetzler.eu"> Hannah Metzler </a> </div>

---
# Overview

1. AI-powered & open source tools for literature search to find relevant articles

* Workflow: **Google Scholar, Zotero + ResearchRabbit**
  
  * Finding specific articles or get an overview: **Elicit**

2. Staying informed
  * Practical exercises with these tools

3. (Collaborative) Management of literature & citations: **Zotero**

???

---

# Google Scholar

.pull-left[
* Includes all content (pre-prints etc)

* Ranks articles by citation count

* Researcher profiles with all references

* Adds content immediately: good for alerts
  * Use very specific keywords or important authors
]

.pull-right[
<img src="figures/googlescholar.png" width="600" />
]
---

## If Google Scholar does not find the pdf...

* Google Scholar usually finds open access version of articles behind paywalls

* Repositories
  * Personal website

#### Other ways to access articles:

* [CORE](https://core.ac.uk) (Plugin + Website): &ensp;
<img src="figures/core.svg" width="60" />
 * Locate free versions of articles behind paywall
 
* Absolutely never use Sci-Hub!

---
name: researchrabbit

# Smart literature search: ResearchRabbit

* ["Spotify" for papers](https://researchrabbitapp.com)

* Discover papers via recommendations based on articles you chose

* Visualize paper networks: topic, citations, references

* Collaboration networks: Discover research teams & their work

* Timelines, earlier & later work

---

---

---

# Other ResearchRabbit features
.pull-left[
Personalized alerts on new content

Comments/annotations

<img src="figures/research_rabbit_alerts.png" width="250" />
<img src="figures/research_rabbit_comments.png" width="250" />
]
.pull-right[
Share collections

<img src="figures/research_rabbit_share.png" width="320" style="display: block; margin: auto;" />
]

???

# ResearchRabbit vs. scite_

* Scite: smart citations
 * evidence for claims + context
 * 7.99$/month
 * Useful for reviews/meta-analyses
 
* ResearchRabbit: smart recommendations
 * citation and author networks
 * free
 
---
name: workflow
layout: true
<div class="my-footer">
<a href = "https://twitter.com/rdpalacio/status/1601640985858957312"> Workflow: Ruben Dario on Twitter </a>
</div>

---

## Literature search workflow

* [Zotero](www.zotero.org): powerful open source literature management
  * Organizes articles into collections (per topic or project)

.right-column[.center-right[
1. Find highly cited articles with Google Scholar
2. Open on publisher website & import to Zotero collection
3. Sync the collection with ResearchRabbit
4. Explore recommendations via ResearchRabbit
5. Add papers to Zotero collection via ResearchRabbit

<img src="figures/zotero_sync_researchrabbit.png" width="750" />
]]

.left-column[
#### Workflow
<img src="figures/zotero_addtocollection_browser.png" width="200" />
]

---
layout: true
name: elicit
<div class="my-footer"><a href = "www.hannahmetzler.eu"> Hannah Metzler </a> </div>

---

# [Elicit: The AI research assistant](www.elicit.org)

<img src="figures/elicit_start.png" width="1000" />
---

# [Elicit](www.elicit.org): useful features

- Can help you find specific studies with advanced filters
  - Comparison Google Scholar: finds highly cited/central papers
  
- Summarizes abstracts (also across several papers)
.pull-left[.center-left[
- Overview of

- Interventions
  - Outcome measures
  - Sample size
  ]]
.pull-right[
- Study information

- Sample description
  - Trustworthiness
  - How is it cited?
  - Find information within paper
]

---

## Paper overview

<img src="figures/elicit_overview.png" width="1300" />
---

## Intervention, outcome measure and sample size

---

## Study information

.pull-left[
<img src="figures/elicit_studyinfo.png" width="570" />
]
.pull-right[
<img src="figures/elicit_citations_in_context.png" width="550" />
]
---

## Find information in paper

.pull-left[

Enter a question/keyword

<img src="figures/elicit_questions.png" width="570" />
]
.pull-right[

Text is highlighted in the source

<img src="figures/elicit_question_anwers.png" width="550" />
]
---

## Find specific types of papers

.pull-left[

With keywords

<img src="figures/elicit_keyword_filters.png" width="570" />
]
.pull-right[

With filters
<img src="figures/elicit_RCTFilter.png" width="450" />
]
---

## Summaries across small sets of studies

---

# Staying informed: Exercise (15 min)

* Topic 1:  [ResearchRabbit](https://researchrabbit.ai)
      * Create a collection & explore steps from [overview slide](#researchrabbit)
      * Set an alert
      
* Topic 2: [Elicit](www.elicit.org): Explore all steps from [slides](#elicit) with a question of your interest

* Topic 3: Implement the [workflow](#workflow) 
  * Find a highly cited paper on [Google Scholar](https://scholar.google.com/) or a specific paper on [Elicit](www.elicit.org)
  * Add to a Zotero collection, and sync it with [ResearchRabbit](https://researchrabbit.ai)
  * Expand your collection

* ([Twitter](www.twitter.com): Follow the most important scholars for your research topic)

---

# Break?

* Literature management with Zotero after the break

* To follow along in Zotero:

* Installed Zotero and Connector plugin for browser?
  
  * https://www.zotero.org/download/

---

# (Collaboratively) Managing literature

.pull-left[
* Mendeley, Endnote, F1000, Citavi
* [**Zotero**](https://www.zotero.org/): Open source & flexible

* **Store, organize and cite papers**
* Store PDFs in Zotero or with links to folders

* Online storage for access everywhere
]

.pull-right[
* Organize: Collections & tags

* Citing: 
  * Add-ins for Word, GoogleDocs
  * Automated bibliographies
  
* Group libraries for sharing literature

* Marking PDFs & automatic notes
]

---

---

## Zotero features on previous slide

* My Library
* Collections
 * Subcollections 
* Items (articles)
 * Snapshot of website (available offline)
 * Attached PDFs (automatic option) 
* Item features: 
 * Info
 * Item Type: article, book chapter, report, pre-print, conference paper etc
 * Notes
 * Tags
 * Related

---

## Zotero: Getting papers into your library

.pull-left[
* Via the browser extension: 
<img src="figures/zotero_add_browser.png" width="400" />
 
* Pull PDFs into Zotero
 * Automatic meta-data & renaming
]

.pull-right[
* With item identifier (ISBN, DOI): 
<img src="figures/zotero_add_doi.png" width="500" />

* Papers get added into currently active collection
]
* Most scientific databases automatically add keywords as tags

---

## Zotero: Collections & tags for organizing papers

* Collections: each item can be in several collections

.left-column[
* Tags
* Draw onto a tag to tag many items at once
 
* Colour tags
]
.right-column[.center-right[
<img src="figures/zotero_tags.png" width="800" />
 
<img src="figures/zotero_colour_tags.png" width="250" />
<img src="figures/zotero_colour_tags_papers.png" width="500" />
]]

---

# Zotero: Features of each item

* Related articles &ensp;
<img src="figures/zotero_related_entries.png" width="730" />

* Automatic summary notes with annotations from PDF &ensp; 
 * Right click on PDF: Add notes from annotations

* Press Alt to find collection of an item &ensp;
<img src="figures/zotero_findcollection.png" width="500" />

* Drag-&-drop PDF or item entry from Zotero to send/move files or reference

---

## Notes & Annotating PDFs

---

## Zotero: Syncing libarary & PFDs

.left-column[
* 300MB: free

* 2GB: 20 Euro/year

* 6GB: 60 Euro/year
]

.right-column[.center-right[
<img src="figures/zotero_syncing.png" width="450" />
]]

---

# Search and saved searches

* Quick search: 
  * speed it up by starting with " in large collections

.pull-left[
* Advanced search: 
 * can be saved
 * constantly updating collection
]
.pull-right[
<img src="figures/zotero_advanced_search_window.png" width="550" style="display: block; margin: auto 0 auto auto;" />
]
---

## Group libraries

.pull-left[
* Invite other users to group on [zotero.org](https://www.zotero.org/groups)
 * for collaborative projects 
]
.pull-right[
in Zotero:
<img src="figures/zotero_group_libraries.png" width="300" style="display: block; margin: auto auto auto 0;" />
]
* Make collections available online
 * private or public
 * read or edit access
 * for sharing literature lists/PDFs or discover sources of others
 
---

## Zotero: Citations

.pull-left[.center-left[
* Add-ins for Word, Libre Office, Google Docs are included
 * Exporting BibTex citations for Overleaf & Latex

* Automated reference lists

* Quickly switch between citation styles
]]
.pull-right[.center-right[
GoogleDoc: 
<img src="figures/zotero_googledoc.png" width="400" />
<img src="figures/zotero_reflist.png" width="600" />
<img src="figures/zotero_citation_styles.png" width="350" />
]]

---

## Zotero: Citation tips

.pull-left[.center-left[
* Suppress authors, add text before after citation in brackets

* Word/Libre Office quicker than Google Docs 
 * Switching is difficult

* Set language to English when choosing citation style

* In Bibliography: check item type in Zotero if formatting not correct (article, book, etc)
]]
.pull-right[.center-right[
<img src="figures/zotero_suppress_prefix.png" width="500" />
]]

???

## Combine Zotero & Scite

* [Zotero plug-in](https://scite.ai/blog/introducing-the-scite-plug-in-for-zotero-61189d66120c): extra columns for citations of articles in your library
  * Right click to view Scite report

---

## Zotero: More resources

* [Documentation](https://www.zotero.org/support/start)

* [Quick start guide](https://www.zotero.org/support/quick_start_guide)

* [12 must know Zotero tips and techniques](
http://ideophone.org/12-zotero-tips-and-techniques)

* [Numerous other Add-ons](https://www.zotero.org/support/plugins)

---

## Zotero exercises for day 2

.pull-left[
* Add a paper to a collection: 
  * via plugin on publisher website
  * by pulling in a PDF
  * via DOI
  
* Add keywords in "Tags"
* Create a color tag "to read" in red

* Link it to a second related article

* Make & save an advanced search
]

.pull-right[
* Open a PDF within Zotero, mark important sentences/keywords
  * Add note from annotations
* In a Google or Word doc
  * Add a few citations, with/wo author
  * Create a reference list
  
* For [Obsidian](https://obsidian.md/) users: check out step 10-15 in this [tutorial](https://twitter.com/rdpalacio/status/1601641098535129088)
  
]