Digitally Enhanced Literature Search and Management

class: center, middle, inverse, title-slide

.title[
# Digitally Enhanced <br> Literature Search and Management
]
.author[
### Hannah Metzler <br><br> Complexity Science Hub & Meduni Vienna
]
.date[
### www.hannahmetzler.eu
]

---

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# Overview

1. AI-powered & open source tools for finding papers

* Paper recommendations & networks: [**ResearchRabbit**](https://researchrabbit.ai)

* Finding specific articles or get an overview: [**Elicit**](www.elicit.com)

* Exercise with ResearchRabbit or Elicit

3. (Collaborative) Management of literature & citations: [**Zotero**](www.zotero.org)

* (Exercise)

---
name: researchrabbit

# [Smart literature search: ResearchRabbit](https://researchrabbitapp.com)

* ["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

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background-image: url(figures/research_rabbit.svg)
background-size: contain
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background-image: url(figures/research_rabbit_authors.png)
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## 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="250" />
]
    
---
layout: true
name: elicit

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

* Get an overview of many studies quickly

* Useful for reviews, meta-analyses

* Recently became subscription based (10$/month) :( but has free trial credits

---

.pull-left[
## Study features
<img src="figures/elicit/study_features.png" width="250" />
<img src="figures/elicit/study_features2.png" width="210" />
<img src="figures/elicit/study_features3.png" width="190" style="display: block; margin: auto;" />

]
.pull-right[
## Filters
<img src="figures/elicit/filters.png" width="230" />
]
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background-image: url(figures/elicit/paper_overview1.png)
background-size: contain
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background-image: url(figures/elicit/paper_overview2.png)
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background-image: url(figures/elicit/custom_columns_and_link_to_text.png)
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## Custom columns and link to paper quotes
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##  Exercise: Using AI-enhanced search tools (15 min)

.pull-left[
### [ResearchRabbit](https://researchrabbit.ai)
* Create a collection 
* Add 1-5 papers (DOI/Title, ResearchRabbit's keyword search)
* Add a suggested paper to the collection
* Switch from Network to Timeline
* Display an author network
* Set an alert
* Add a comment to a paper
]

.pull-right[ 
### [Elicit](www.elicit.com)
  * Choose a research question
  * Delete an irrelevant paper
  * Select relevant study features
  * Select a filter (or use a keyword)
  * Add a custom-made column
  * Find the part of the paper describing the feature
]

---

# Managing literature - Zotero

* Store, organize and cite papers

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

* Open source & flexible

.pull-left[
* Store PDFs in Zotero or with in folders (linked files)
* Online storage for access everywhere
* Organize: Collections & tags
]
.pull-right[
* Automatic citations & bibliographies
* Group libraries for sharing literature
* Marking PDFs & automatic notes
]

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background-image: url(figures/zotero_overview.svg)
background-size: contain
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## Getting papers into (and out of) your library

.pull-left[
* Via the browser extension:  
<img src="figures/zotero_add_browser.png" width="300" />
<br><br>
* Pull PDFs into Zotero
  * Automatic meta-data & renaming
]

.pull-right[
* With item identifier (ISBN, DOI): 
<img src="figures/zotero_add_doi.png" width="400" />

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

* Move/send: Drag-&-drop PDFs to email/folder (or item entry to email/text file)

---

## Organizing with collections & tags

* Collections: each item can be in several collections
* Press Alt to find collection of item &ensp;
<img src="figures/zotero_findcollection.png" width="450" />

<img src="figures/zotero_tags.svg" width="850" />
&ensp;
<img src="figures/zotero_assign_colour_tag.svg" width="180" />
* Assign colour tags & keyboard shortcut (keys 1-9): right click
* Multiple items at once: Draw them onto tag (bottom left)
* Searching papers: combine tag search+selection with keyword search
---

## Notes & Annotating PDFs

* Automatic summary notes: Right click on PDF
<img src="figures/zotero_annotations_rightclick.png" width="180" />

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<div class = "my-footer"><span>
<a href="https://www.zotero.org/support/sync#alternative_syncing_solutions">Zotero syncing solutions</a>
</span></div>

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## Group libraries for collaborations

* Invite other users to group on [zotero.org](https://www.zotero.org/groups)
* In Zotero

<img src="figures/zotero_group_libraries.png" width="200" />
* Make collections available online

* private or public
  * read or edit access
  * for sharing literature lists/PDFs or discover sources of others
  
---

## Syncing library data & files

.pull-left[
* Library data for free
* Files (PDFs etc) are stored locally
* New PC: copy Zotero folder <br><br>
* Online storage on Zotero servers: 
<img src="figures/zotero_storage_plans.png" width="250" />
* Zotfile Add-on: Link to files in cloud (Dropbox, Google Drive...)
]

.pull-right[.center-right[
<img src="figures/zotero_syncing.png" width="350" />
<br<br>
<img src="figures/zotfile_pref.png" width="260" /><img src="figures/zotfile_linked_folder.png" width="260" />
]]

???
## 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;" />
]
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## Citations

.pull-left[.center-left[
* Add-ins for Word, Libre Office, Google Docs are included
<img src="figures/zotero_googledoc.png" width="350" />
<img src="figures/zotero_suppress_prefix.png" width="210" />

* Overleaf/Latex: Export BibTex citations (automate with Better BibTex Add-on)
]]
.pull-right[.center-right[
Automated bibliography: 
<img src="figures/zotero_reflist.png" width="600" />
<img src="figures/zotero_citation_styles.png" width="300" style="display: block; margin: auto;" />

Quickly switch between citation styles
]]

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## 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)

---
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# Optional exercises

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## Zotero exercises (15 min)

.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

* Select multiple tags

* Link item to a related article
]

.pull-right[
* Open a PDF within Zotero, mark important sentences/keywords, then add extract notes 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)
]

---
name: workflow
layout: true
<div class="my-footer"><span>
<a href = "https://twitter.com/rdpalacio/status/1601640985858957312"> Workflow: Ruben Dario on Twitter </a>
</span></div>

---

## Exercise: Literature search workflow (15 min)

.right-column[.center-right[
1. Find highly cited articles with Google Scholar (or specific articles with [Elicit](www.elicit.com))
2. Open on publisher website & import to [Zotero](www.zotero.org) collection
3. Sync the collection with [ResearchRabbit](www.researchrabbit.ai)
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" />
]

???
30 min total for the presentation (without exercises)
11 min for ResearchRabbit & Elicit
19 for Zotero