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PDF下載連結

我發現youtube 影片會不見，詳見Youtube播放清單

提問可以加入Apen Academy，或直接在這裡提問，可以直接在文字上加註

How I Streamline Literature Review with AI tools

林協霆


和信治癌中心醫院腫瘤內科部

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Introduction


Note

Goal of this lecuture: Provide a variety of methods for everyone to evaluate their own needs and configure and build their own workflow.

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Mindsets: KISS

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The Great Note-Taking Odyssey. This meme ruined my life and sent me on… | by David Molina Cavazos | May, 2024 | Medium

Personal Experience

Inclusion Criteria

  • Free and open-source software (FOSS)
  • 100% Your Data, ❤️ markdown
  • Vivid Plugin Ecosystem
  • Customization
  • Scalability
  • Community support

Obsidian, Loqseq, Zotero

Exclusion Criteria

  • 🤑 Paid
  • Unique Note Filetype

Notion, Heptabase, Endnote, Mendeley

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Zettelkasten Method

  • The building blocks of a Zettelkasten are the inbox, the note archive, and the reference manager.
  • Don’t use categories. Use tags instead
  • Set links between notes.

:::free

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  • The server hosting the image is unavailable
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:::split

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:::

  1. Getting Started • Zettelkasten Method
  2. (19) X 上的 Eugene Yan：「Regular note-taking didn't work for me. Notes stay separate—connections are not made. I fixed this by building a Zettelkasten using @RoamResearch. (Zettelkasten originates from highly prolific sociologist Niklas Luhmann. He wrote 70 books & 500 scholarly articles.) Thread 👇 https://t.co/exVfl5EYXT」 / X
  3. The Zettelkasten Method Lacks a Spaced Repetition Scheduler and Here's One Easy Fix - Master How To Learn

Building A Digital Second Brain

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Forte T. Building a Second Brain: A Proven Method to Organise Your Digital Life and Unlock Your Creative Potential. Paperback edition. Profile Books; 2023.

Recommend Workflow







G



A_O

Pubmed

Google

Perplexity

SciSpace

RSS readers

ResearchRabbit



B_O

Zotero

Raindrop



A_O->B_O





C_O

Zotero

Obsidian

ChatGPT

Sider

ChatBox



B_O->C_O





D_O

GoogleDoc

Zettlr

Marp

Quarto



C_O->D_O





Note_Taking
Distill



Express
Express



Note_Taking->Express





Capture
Capture



Organize
Organize



Capture->Organize





Organize->Note_Taking





C
C



O
O




D
D




E
E

Image Not Showing Possible Reasons
  • The image file may be corrupted
  • The server hosting the image is unavailable
  • The image path is incorrect
  • The image format is not supported
Learn More →

Capture

Workflow







G



A

Pubmed

Google

Perplexity

SciSpace

RSS readers

ResearchRabbit



B

Zotero

Raindrop



A->B





C

Zotero

Obsidian

ChatGPT

Sider

ChatBox



B->C





D

GoogleDoc

Zettlr

Marp

Quarto



C->D





Note_Taking
Distill



Express
Express



Note_Taking->Express





Capture
Capture



Organize
Organize



Capture->Organize





Organize->Note_Taking

Google Capture Operators

Pubmed Advanced Capture

  • 進入到Advanced Capture Results - PubMed
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  • 試一下
    • ("clinical trial"[Publication Type])
    • ("2023/01/01"[Date - Publication] : "3000"[Date - Publication])
    • ("keywords your want to search"[Title/Abstract])

RSS 訂閱

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  • The server hosting the image is unavailable
  • The image path is incorrect
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Image Not Showing Possible Reasons
  • The image file may be corrupted
  • The server hosting the image is unavailable
  • The image path is incorrect
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Create RSS Feeds in PubMed. NLM Technical Bulletin. 2020 Jul–Aug

Plugin

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AI tools

GPTs

自行試用

Perplexity

:::half

Perplexity

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:::split

FYI

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:::

AI Chat for scientific PDFs | SciSpace

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Open AI API

h:350 按 create new secret key

Warning

Keep Your API keys Safe !

取個名字後建立

Important

目前 API key 的計價方法是要先加值後才能用，建議存個 20 美金就很夠用了，也可以設定自動加值

Sider

安裝 Chrome 外掛：Sider，最好的 ChatGPT 瀏覽器擴展，在所有網站的側邊欄中提供人工智慧助手。

:::half

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:::split

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:::

Immersive Translate

Immersive Translate - Bilingual Webpage Translation Extension_PDF Document Translation Tool


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Chatbox

w:1000px

AnythingLLM

Tavily AI

Elevate your AI's capabilities with a search engine built specifically for AI agents (LLMs), delivering real-time, accurate, and factual results at speed.

需要輸入你的 OpenAI API w:850px

GPT researcher

Organize

Workflow







G



A

Pubmed

Google

Perplexity

SciSpace

RSS readers

ResearchRabbit



B

Zotero

Raindrop



A->B





C

Zotero

Obsidian

ChatGPT

Sider

ChatBox



B->C





D

GoogleDoc

Zettlr

Marp

Quarto



C->D





Organize
Organize



Distill
Distill



Organize->Distill





Capture
Capture



Capture->Organize





Express
Express



Distill->Express

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Organize Citation, the simple method

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Bibliography Filetypes

RIS CSV JSON BibTeX Txt

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Tip

Try: BibTeX converters and generators - BibTeX.com

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BibTeX.com

Zotero

:::free

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:::split

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:::

Quick Start Add Item Organizeion Chrome Extension PDF Reader

不要勾選檔案同步

快速複製，項目格式選擇 AMA

引用的文件編輯器，視需求安裝 Microsoft Word

來源目錄，選擇一個雲端可以同步的空間

ResearchRabbit

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Citationchaser

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Zotero Plugins

插件安裝方法

  • 前往對應的插件網址，確認是否為 Zotero 7 的版本。
  • 下載對應的安裝文件（xpi 檔案）。
  • 在 Zotero 中，選擇「工具」>「附加元件」>「從檔案安裝附加元件」，選擇下載的檔案進行安裝

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Where can I find plugins

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外掛安裝必要的就好，裝太多會速度變慢，經驗談。

Better BibTex for Zotero

必裝，Make Zotero useful for us LaTex holdouts.

重要設定：citation key: auth.lower + "_" + veryshorttitle(1).lower + "_" + year

輸入畫面

下載連結

What is Bibtex

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BibTeX format explained [with examples] - BibTeX.com. Paperpile. Accessed May 26, 2024. https://www.bibtex.com/g/bibtex-format/

Attanger

Attachment Manager for Zotero

Subfolder 選擇 collection，會按照目前的 collection 的資料夾層級整理 pdf

PDF-Translate

Translate PDF, EPub, webpage, metadata, annotations, notes to the target language. Support 20+ translate services.

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:::half

ZotLit

ZotLit is a third-party project that aims to facilitate the integration between Obsidian.md and Zotero, by providing a set of community plugins for both Obsidian and Zotero.

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:::split

Other Methods

:::

Distill

Workflow







G



A

Pubmed

Google

Perplexity

SciSpace

RSS readers

ResearchRabbit



B

Zotero

Raindrop



A->B





C

Zotero

Obsidian

ChatGPT

Sider

ChatBox



B->C





D

GoogleDoc

Zettlr

Marp

Quarto



C->D





Capture
Capture



Organize
Organize



Capture->Organize





Distill
Distill



Organize->Distill





Express
Express



Distill->Express

Obsidian

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see groepl/Obsidian-Zettelkasten-Starter-Kit: A Starter Kit for Obsidian with all essential elements to build up your own Zettelkasten system.

Install Obsidian Plugins

偏好設定 → 第三方外掛程式 → 關閉「受限模式」 → 社群外掛程式 → 瀏覽

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:::split

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:::

Zotlit

How does it work?







G



Zotero


Zotero



SqliteDatabase


~/Zotero/
zotero.sqlite



Zotero->SqliteDatabase





data

🔑@CitationKey

Metadata:
Author, Title, Years, DOI...

Notes



SqliteDatabase->Zotero





Obsidian


Obsidian



SqliteDatabase->Obsidian





Obsidian->SqliteDatabase





LiteratureNote



📔Literature
Note
CitationKey.md



Obsidian->LiteratureNote


Templates



Link



🔗Link
[@CitationKey]



Obsidian->Link


Templates

Zotlit: Create Lit Note from Zotero

選擇條目 → 右鍵 → Obsidian Action → Create Literature Notes(s) → Open Link

:::half

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:::split

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:::

ZotLit: Add Citation in Obsidian

輸入[@ → 自動跳出條目選單

:::half

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:::split

  • [@ will output as [@citationKey]
  • [@/
  • If there's a lit note already created, such as citationKey.md, will output as [[citationKey|(Author, 2022)]]
  • and will be previewed as (Author, 2022)

:::

Create Zotlit Template

偏好設定 → Zotlit → Template → 點→📂

Tip

Create zt-****.eta.md files in ZtTemplates folder

組態範本 – ZotLit

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zt-note

zt-annot.eta

zt-annots.eta

zt-cite2.eta

@youtube

Other plugins that may help

  • Zotero Integration
  • Reference Map
  • Copilot
  • Excalidraw
  • Imgur
  • Slurp

Notero = Notion + Zotero

@youtube

:::half

Prompts

Sider ChatGPT ChatBox Gemini …

General Use

Q: {第一行，針對輸入內容所提出的具體問題，問題描述要包含所提供的內容} 🙋

## {第二行，以有力的 20 個字的標題把讀者注意力抓過來}

**{有力的開場/導言：直接、簡短、犀利的一句話}**

## 重點整理：📍

{條列式重點，儘可能詳細說明，Nested Lists}

## 重要名詞解釋及中英對照：🔠

{條列式中英對照}

:::split

Q: 新冠疫苗接種後出現罕見症狀 VITT 與由抗 PF4 抗體引起的血小板減少症是什麼？🙋

疫苗誘發的罕見血栓症：🩺

疫苗接種後出現抗 PF4 抗體引起的罕見症狀

重點整理：📍

  • 新冠疫苗接種後可能引起罕見症狀 VITT
    • 由抗 PF4 抗體導致的血小板活化
    • 在兩種腺病毒載體疫苗(Oxford–AstraZeneca 和 Johnson & Johnson–Janssen)後出現
  • 患者通常有多處或不尋常的血栓，如腦靜脈窦和腹部靜脈
  • 血中 d-二聚體水平升高

重要名詞解釋及中英對照：🔠

:::

For Trials

In markdown bullet points:

1. Design: Trial phase, II, III, or an meta-analysis, single center or multi-center, randomized or not, or open-label or blind, etc.
2. number of patients, and patients characteristics
3. agent: medication use in this trial, both intervention and control, with dose
4. Treatment line
5. Trial Acronym (if provided)
6. compare efficacy in one markdown table
7. compare toxicity in another markdown table (if provided)
8. one line summarize

:::half

  • Design: Phase 3, multinational, open-label, randomized trial
  • Number of patients: 608 patients
  • Patients characteristics: Previously untreated unresectable or metastatic urothelial carcinoma
  • Trial Acronym: CheckMate 901, ClinicalTrials.gov number NCT03036098

:::split

Outcome Nivolumab Combination Gemcitabine-Cisplatin Alone
Overall Survival 21.7 months 18.9 months
Progression-Free Survival 7.9 months 7.6 months
Objective Response 57.6% (complete response 21.7%) 43.1% (complete response 11.8%)

:::

Express

Workflow







G



A

Pubmed

Google

Perplexity

SciSpace

RSS readers

ResearchRabbit



B

Zotero

Raindrop



A->B





C

Zotero

Obsidian

ChatGPT

Sider

ChatBox



B->C





D

GoogleDoc

Zettlr

Marp

Quarto



C->D





Capture
Capture



Organize
Organize



Capture->Organize





Distill
Distill



Organize->Distill





Express
Express



Distill->Express

Google Doc

趕時間的人用這個最簡單

AI Writing assistance

Figure: width:550px
Figure: width:550px

Warning

網頁版 App 重啟後會遺失資料

Obsidian Text Generator

安裝外掛

Figure: width:1150px

Talers

  • Figure: width:1150px

Tip

See here for more writing-assistants

Word and LibreOffice

在 zotero 的設定裡會引導你安裝

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:::half

Zettlr

Zotero → Collection → 右鍵 → Export Collection

Figure: height:250px

:::split

Note

Choose a CSL files

Figure: height:250px

---
title: "My document"
bibliography: ./assets/references.bib
---

:::

Marp

Figure: height:550px

Quarto

Figure: height:450px

@youtube

Take Home Messages







G



A

Pubmed

Google

Perplexity

SciSpace

RSS readers

ResearchRabbit



B

Zotero

Raindrop



A->B





C

Zotero

Obsidian

ChatGPT

Sider

ChatBox



B->C





D

GoogleDoc

Zettlr

Marp

Quarto



C->D





Note_Taking
Distill



Express
Express



Note_Taking->Express





Capture
Capture



Organize
Organize



Capture->Organize





Organize->Note_Taking

Important

Keep It Simple, Stupid

Thank you for your time and attention

Have a nice day

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Last changed by 
 
Hsieh-Ting Lin
林協霆醫師，內科醫師，現任職於和信治癌中心醫院腫瘤內科部 🩸🦀🦎
1
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1150

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