如何使用這份資料
每一段落對應教學中的一個主題。引用標籤含義:
Each section maps to one tutorial topic. Tag meanings:
Paper
原始學術論文 (含 DOI)
Doc
官方文件、style guide
Guide
社群推薦或綜述
Book
專書、入門指南
Tool
實用工具與資源
Policy
期刊/學會政策原文
14 主題快速跳轉
研究問題與假設 · Research Question & Hypothesis
- 📚 Book Designing Clinical Research, 5th edition.
- ⭐ Guide The well-built clinical question: a key to evidence-based decisions.
- 📚 Book Evidence-Based Medicine: How to Practice and Teach EBM.
- 🛠️ ToolPROSPERO — 系統性回顧 protocol 註冊平台。— Registration platform for systematic review protocols.
文獻回顧策略 · Literature Review Strategy
- 📄 Paper The PRISMA 2020 statement: an updated guideline for reporting systematic reviews.
- 📘 DocEQUATOR Network — PRISMA 2020 Checklist — 完整 27 項 + flow diagram template。— Full 27-item checklist plus flow diagram template.
- 📄 Paper PRISMA Extension for Scoping Reviews (PRISMA-ScR).
- 📚 Book Systematic Approaches to a Successful Literature Review, 3rd ed.
- 🛠️ ToolConnected Papers — 視覺化文獻 citation network。— Visualizes citation networks across the literature.
- 🛠️ ToolResearch Rabbit — AI 助理式文獻探索。— AI-assistant-style literature discovery.
- 🛠️ ToolPubMed + MeSH Browser — 生醫文獻檢索核心。— The core search stack for biomedical literature.
IMRaD 與學位論文章節 · IMRaD & Thesis Structure
- 📄 Paper The introduction, methods, results, and discussion (IMRAD) structure: a fifty-year survey.
- 📚 Book How to Write a Thesis, 4th edition.
- 📚 Book Authoring a PhD: How to Plan, Draft, Write and Finish a Doctoral Thesis or Dissertation.
- ⭐ GuideVitae Researcher Development Framework — 跨國 PhD 訓練框架。— A cross-country PhD researcher development framework.
緒論寫作 · Introduction Writing
- 📚 Book Genre Analysis: English in Academic and Research Settings.
- 📚 Book Academic Writing for Graduate Students, 3rd edition.
- 📚 Book Writing Your Journal Article in Twelve Weeks.
方法寫作與可重現報告 · Methods & Reproducible Reporting
- 📘 DocEQUATOR Network — 500+ reporting guidelines 的權威清單。— The authoritative directory of 500+ reporting guidelines.
- 📄 Paper The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement.
- 📄 Paper CONSORT 2025 statement: updated guideline for reporting randomised trials.
- 📄 Paper The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research.
- 📄 Paper TRIPOD+AI statement: updated guidance for reporting clinical prediction models that use regression or machine learning methods.
- 🛠️ ToolZenodo — CERN 維護的 data/code repository,免費 DOI。— CERN-maintained data/code repository offering free DOIs.
結果與圖表設計 · Results & Figures
- 📚 Book The Visual Display of Quantitative Information, 2nd edition.
- 📚 Book Fundamentals of Data Visualization.
- 📄 Paper The ASA Statement on p-Values: Context, Process, and Purpose.
- 📄 Paper Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm.
- 🛠️ ToolColorBrewer 2.0 — 色盲友善配色 picker。— Colorblind-friendly palette picker.
討論與限制 · Discussion & Limitations
- 📄 Paper How to write an effective discussion.
- 📄 Paper Limitations are not properly acknowledged in the scientific literature.
- 📚 Book The Elements of Style, 4th edition.
摘要、標題與關鍵字 · Abstract, Title & Keywords
- 📄 Paper Current findings from research on structured abstracts: an update.
- ⭐ Guide The Principles of Biomedical Scientific Writing: Title.
- 🛠️ ToolNCBI MeSH Browser — MeSH 關鍵字檢索。— Search MeSH keywords.
學術寫作語言與風格 · Academic Style & Language
- 📚 Book Style: Lessons in Clarity and Grace, 12th edition.
- 📚 Book The Sense of Style.
- 📚 Book Stylish Academic Writing.
- 📚 Book Writing Science: How to Write Papers That Get Cited and Proposals That Get Funded.
- 🛠️ ToolHemingway Editor — 句子複雜度檢查器。— Sentence-complexity checker.
引用與文獻管理 · Citation & Reference Management
- 🛠️ ToolZotero + Better BibTeX — 開源文獻管理 + LaTeX 同步。— Open-source reference manager with LaTeX sync.
- 🛠️ ToolEndNote 21 — 機構廣泛採用的商用文獻管理。— Commercial reference manager widely adopted by institutions.
- 🛠️ ToolPaperpile — Google Docs 友善的雲端文獻管理。— Cloud reference manager with strong Google Docs integration.
- 🛠️ ToolZotero Style Repository — 10000+ 期刊 CSL style files。— 10,000+ journal CSL style files.
- 🛠️ ToolRetraction Watch + Zotero 整合 — 自動警示引用 retracted papers。+ Zotero integration — automatically flags citations to retracted papers.
- 📘 DocCitation Style Language (CSL) project — 業界標準 XML 格式。— The industry-standard XML format for citation styles.
期刊選擇與投稿策略 · Journal Selection
- 🛠️ ToolThink.Check.Submit. — 免費期刊檢核 checklist。— Free journal-vetting checklist.
- 🛠️ ToolCabells Predatory Reports — 付費的掠奪性期刊精準名單。— Paid, curated list of predatory journals.
- 🛠️ ToolDOAJ — Directory of Open Access Journals — OA 白名單。— Open access journal allowlist.
- 🛠️ ToolScimago Journal Rank (SJR) + Scopus CiteScore — IF 之外的期刊評估指標。— Journal evaluation metrics beyond the impact factor.
- 🛠️ ToolSciRev.org — 真實作者投稿經驗 (peer review 時間、決定流程透明度)。— Real author submission experiences (peer review duration, decision-process transparency).
- ⚖️ PolicycOAlition S / Plan S — 強制 OA 的歐盟 funder 聯盟。— EU-led funder coalition mandating open access.
同儕審查與回覆信 · Peer Review & Response Letter
- 📘 DocCOPE — Committee on Publication Ethics — 同儕審查倫理權威。— Authoritative body on peer review ethics.
- ⭐ GuideWeb of Science Reviewer Academy (formerly Publons) — 免費 reviewer 訓練。— Free reviewer training.
- ⭐ GuideASAPbio Reviewer Trainee Programme
- 📄 Paper Ten simple rules for writing a response to reviewers.
- 📄 Paper Ten simple rules for reviewers.
倫理、作者貢獻與利益衝突 · Ethics & Authorship
- 📘 DocICMJE Recommendations (Jan 2026) — 國際醫學期刊編輯委員會權威文件。— Authoritative document of the International Committee of Medical Journal Editors.
- 📘 DocCRediT — Contributor Roles Taxonomy (NISO Z39.104) — 14 角色官方定義。— Official definitions of the 14 contributor roles.
- 🛠️ ToolORCID — 免費作者唯一識別 ID。— Free unique author identifier.
- 🛠️ ToolROR — Research Organization Registry — 機構唯一 ID。— Unique institutional identifier registry.
- ⚖️ PolicyCOPE Guidance — 抄襲、duplicate publication、salami slicing 處理流程。— Workflows for handling plagiarism, duplicate publication, and salami slicing.
- 🛠️ ToolICMJE Disclosure of Interest form — COI 申報通用範本。— Universal template for conflict-of-interest disclosure.
- 📚 Book The Ethics of Science: An Introduction.
AI 工具與可重現實踐 · AI Tools & Reproducibility
- ⚖️ PolicyElsevier — Generative AI Policy for Journals (2025/09 update)
- ⚖️ PolicySpringer Nature — AI Policy
- ⚖️ PolicyCell Press — Author Guide (AI section)
- ⚖️ PolicyAPA Journals — Generative AI Policy
- ⚖️ PolicyTaylor & Francis — AI Policy
- 🛠️ ToolbioRxiv + medRxiv — CSHL 維護的生命科學/臨床 preprint server。— CSHL-maintained preprint servers for life sciences and clinical research.
- 🛠️ ToolQuarto — 2026 推薦的 reproducible publishing 框架 (R + Python + Julia)。— Recommended 2026 reproducible publishing framework (R + Python + Julia).
- 🛠️ ToolSnakemake + Nextflow — 標準 pipeline 管理框架。— Standard pipeline management frameworks.
- 📄 Paper The FAIR Guiding Principles for scientific data management and stewardship.
📌 教學註記與細節
以下列出本教學中需要進一步澄清的論點、適用範圍限制,以及社群普遍存在的誤解。所有條目附原始來源。
The following points clarify boundary conditions, scope limitations, and widespread misconceptions in the tutorial. All entries cite original sources.
- ⚠ Errata 1
IMRaD 結構並非通用標準 · IMRaD Structure Is Not Universal
IMRaD (Introduction–Methods–Results–Discussion) 主要在生物醫學與實驗科學佔主導,但人文、社會科學、純數學、理論物理、工程設計、case study 與 review article 多採其他結構(如 thematic、chronological、 problem-solution 或 essay-style)。Sollaci & Pereira 2004 指出 IMRaD 至 1980s 才在醫學期刊達到 80% 採用率。投稿前應先閱讀目標期刊的 Author Guidelines。
IMRaD (Introduction–Methods–Results–Discussion) dominates biomedicine and experimental sciences but is not universal. Humanities, social sciences, pure mathematics, theoretical physics, engineering design papers, case studies, and review articles often use alternative structures (thematic, chronological, problem–solution, or essay-style). Sollaci & Pereira (2004) note that IMRaD only reached ~80% adoption in medical journals by the 1980s. Always read the target journal's Author Guidelines before drafting.
- ⚠ Errata 2
期刊影響因子 (JIF) 的限制 · Journal Impact Factor Caveats
JIF 是期刊層級的平均引用指標,不能用來評估單篇論文或個別研究者的品質。引用分布極度偏態 (skewed),前 20% 論文往往貢獻 80% 引用。DORA (Declaration on Research Assessment, 2012) 已有超過 2,500 個機構簽署,呼籲停止用 JIF 評估研究人員。Leiden Manifesto (Hicks et al. 2015 Nature) 提出 10 原則為替代評估標準。
JIF is a journal-level average citation metric and cannot evaluate the quality of individual papers or researchers. Citation distributions are heavily skewed — the top 20% of papers typically generate 80% of citations. DORA (Declaration on Research Assessment, 2012), signed by 2,500+ institutions, calls for abandoning JIF in researcher evaluation. The Leiden Manifesto (Hicks et al. 2015 Nature) proposes 10 alternative assessment principles.
- ⚠ Errata 3
掠奪性期刊辨識的多重來源 · Identifying Predatory Journals Requires Multiple Sources
不可僅憑單一名單判定期刊性質。Beall's List 自 2017 年起停止官方維護 (Jeffrey Beall 個人因壓力下線),目前由志願者維護 archived 版本 (beallslist.net);Cabells Predatory Reports 為付費精選名單;Think.Check.Submit 提供免費可重複使用的檢核 checklist (期刊網站透明度、editorial board 真實性、indexed in DOAJ/PubMed/Scopus、APC 結構)。Grudniewicz et al. 2019 Nature 提出共識定義:掠奪性期刊以自利優先、提供誤導訊息、偏離編輯與出版最佳實踐、缺乏透明度、使用激進招攬。
Never rely on a single list to judge a journal. Beall's List has not been officially maintained since 2017 (Jeffrey Beall took it down under pressure; volunteer-maintained archives exist at beallslist.net). Cabells Predatory Reports is a paid curated list. Think.Check.Submit offers a free reusable checklist (website transparency, editorial-board verification, indexing in DOAJ/PubMed/Scopus, APC structure). Grudniewicz et al. (2019 Nature) provide the consensus definition: predatory journals prioritize self-interest, provide false information, deviate from best editorial and publication practices, lack transparency, and use aggressive solicitation.
- ⚠ Errata 4
開放近用 (OA) vs APC 取捨與 Plan S · Open Access vs APC Tradeoffs & Plan S
Gold OA 提供立即開放近用但需作者支付 APC (Article Processing Charges),部分 hybrid journals APC 高達 $11,690 (Nature 2021)。Green OA (institutional repository self-archiving) 通常免費但有 embargo period (6–12 個月)。Diamond OA 對讀者與作者皆免費,由機構或學會補貼 (Bosman et al. 2021 OPERAS 報告約 29,000 種期刊)。Plan S (cOAlition S, 2018 起) 要求受資助研究自 2021 起立即 OA;2024-2026 過渡至 Rights Retention Strategy 與消除 hybrid model。APC 對 LMIC (中低收入國家) 作者形成嚴重結構障礙 (Smith et al. 2021 BMJ Global Health)。
Gold OA provides immediate open access but requires authors to pay APCs (Article Processing Charges); some hybrid journal APCs reach $11,690 (Nature 2021). Green OA (institutional-repository self-archiving) is typically free but subject to embargo periods (6–12 months). Diamond OA is free for both readers and authors, subsidized by institutions or societies (Bosman et al. 2021 OPERAS report: ~29,000 journals). Plan S (cOAlition S, since 2018) mandates immediate OA for funded research from 2021; the 2024–2026 transition emphasizes the Rights Retention Strategy and elimination of hybrid models. APCs pose a serious structural barrier for authors in LMICs (Smith et al. 2021 BMJ Global Health).
- ⚠ Errata 5
預印本 vs 同儕審查:bioRxiv/medRxiv 統計 · Preprint vs Peer Review: bioRxiv/medRxiv Stats
預印本 (preprint) 是未經同儕審查的初稿,提供 priority claim 與快速擴散,但讀者需自行批判性評估。bioRxiv (2013 創立)、medRxiv (2019 創立) 累計上傳已超過 30 萬篇 (Abdill & Blekhman 2019 eLife),COVID-19 期間 medRxiv 單月上傳超 2,000 篇 (Fraser et al. 2021 PLoS Biol)。研究顯示約 70% 預印本最終被期刊接受並發表 (Abdill & Blekhman 2019);預印本與最終發表版本差異多屬細節層面,主要結論變更比例低 (Carneiro et al. 2020 BMJ Open)。引用預印本應明確標示 "preprint" 並提供 DOI 與版本號 (v1, v2)。ICMJE 與大多生醫期刊接受預印本作為非重複發表。
A preprint is an unrefereed manuscript that establishes priority and accelerates dissemination but demands critical reader appraisal. bioRxiv (founded 2013) and medRxiv (founded 2019) have together accumulated 300,000+ submissions (Abdill & Blekhman 2019 eLife); during COVID-19 medRxiv exceeded 2,000 uploads per month (Fraser et al. 2021 PLoS Biol). Roughly 70% of preprints are eventually accepted by journals (Abdill & Blekhman 2019); differences between preprint and final published versions are mostly minor, with low rates of major conclusion changes (Carneiro et al. 2020 BMJ Open). When citing a preprint, explicitly label "preprint" and include DOI plus version number (v1, v2). ICMJE and most biomedical journals accept preprints as not constituting duplicate publication.
- ⚠ Errata 6
AI 寫作工具:ICMJE 2024 揭露要求 · AI Writing Tools: ICMJE 2024 Disclosure Requirement
ICMJE (International Committee of Medical Journal Editors) 2024 年 1 月更新 Recommendations 明確規定:(1) AI / chatbots / LLMs 不能列為作者 (cannot be authors),因為無法承擔 accountability;(2) 作者必須在 cover letter 與 manuscript 中揭露 AI 使用 (在 Acknowledgements 或 Methods 段落),包含工具名稱與版本、使用範圍、生成段落定位;(3) 作者對 AI 生成內容的正確性、原創性與無偏誤負完全責任,包含潛在的捏造引用 (hallucinated citations) 與抄襲。WAME (World Association of Medical Editors) 2023 與 COPE 2023 立場相同。Nature 與 Science 系列亦在 2023 同步更新政策禁止 AI 共同作者。
In January 2024, ICMJE (International Committee of Medical Journal Editors) updated its Recommendations to specify: (1) AI / chatbots / LLMs cannot be listed as authors because they cannot take accountability; (2) authors must disclose AI use in both the cover letter and the manuscript (in Acknowledgements or Methods), including tool name and version, scope of use, and location of generated passages; (3) authors bear full responsibility for the correctness, originality, and bias-freeness of AI-generated content, including hallucinated citations and plagiarism. WAME (World Association of Medical Editors) 2023 and COPE 2023 take the same position. Nature and Science families updated their policies in 2023 to prohibit AI co-authorship.
- ⚠ Errata 7
審稿人回覆信架構:Noble 2017 ten simple rules · Reviewer Response Framework: Noble 2017 Ten Simple Rules
Noble (2017 PLOS Comp Biol) 提出 reviewer response 的 ten simple rules:(1) 提供 reviewer 概覽 (overview);(2) 逐點 (point-by-point) 對應,不可遺漏;(3) 用顏色或編號清楚標示原文修改位置;(4) 即使不同意亦保持禮貌;(5) 解釋為何同意或不同意;(6) 修改正文以反映回覆;(7) 在文本中加 (line X, page Y) 指引;(8) 控制長度,必要時附 supplementary;(9) 對 editor 提供獨立摘要;(10) 不要要求 reviewer 進一步審稿時間。Annesley (2011 Clin Chem) 與 Williams (2004 Chest) 亦提供互補建議。常見錯誤:對審稿人態度防衛、忽略次要 comment、修改但未於回覆信中說明。
Noble (2017 PLOS Comp Biol) presents ten simple rules for responding to reviewers: (1) provide an overview for each reviewer; (2) respond point-by-point with no omissions; (3) clearly mark manuscript revisions via color or numbering; (4) remain courteous even when disagreeing; (5) explain why you agree or disagree; (6) edit the manuscript to reflect responses; (7) cite (line X, page Y) pointers in-text; (8) keep length manageable; attach supplementary if needed; (9) write a separate summary for the editor; (10) do not demand additional review time from reviewers. Annesley (2011 Clin Chem) and Williams (2004 Chest) provide complementary advice. Common errors: defensive tone, ignoring minor comments, revising without explaining in the response letter.
- ⚠ Errata 8
ORCID 與 ROR:研究人員與機構持久識別碼 · ORCID & ROR: Persistent Identifiers for Researchers & Organizations
姓名歧義 (name ambiguity) 是 bibliometrics 與資助追蹤的核心問題 (相同姓名作者、姓氏拼寫變體、結婚改姓、機構轉移)。ORCID (Open Researcher and Contributor ID, 2012 起) 提供 16 位數 ISO 27729 標準 ID (e.g., 0000-0002-1825-0097),目前已有超過 1,800 萬研究人員註冊 (ORCID 2024 Annual Report);多數主要期刊與資助機構 (NIH、NSF、Wellcome Trust、ERC) 強制要求。Khan & Daud (2021 Scientometrics) 系統性回顧顯示 ORCID 採用顯著提升作者識別準確度與 cross-database 連結效率。ROR (Research Organization Registry, 2019 起) 為機構提供類似 ID (e.g., https://ror.org/02jbv0t02 for Stanford),補足 GRID、Ringgold、ISNI 等舊系統。投稿時應同時提供 ORCID 與 ROR,未來 funder reporting 與 metadata 互通將以此為基礎。
Name ambiguity is a core problem in bibliometrics and funding tracking (homonyms, surname spelling variants, marriage-related changes, institutional mobility). ORCID (Open Researcher and Contributor ID, since 2012) provides a 16-digit ISO 27729 identifier (e.g., 0000-0002-1825-0097); over 18 million researchers are registered (ORCID 2024 Annual Report). Most major journals and funders (NIH, NSF, Wellcome Trust, ERC) now mandate it. Khan & Daud (2021 Scientometrics) provide a systematic review showing ORCID adoption substantially improves author-disambiguation accuracy and cross-database linkage efficiency. ROR (Research Organization Registry, since 2019) provides analogous identifiers for institutions (e.g., https://ror.org/02jbv0t02 for Stanford), complementing legacy systems such as GRID, Ringgold, and ISNI. Submit ORCID and ROR together — future funder reporting and metadata interoperability will rely on both.
CRediT taxonomy 2022 更新 — 14 個貢獻角色與 ISO/ANSI 標準化
教學在 authorship 章節介紹 CRediT 時,常以 2014 原始 12 角色描述,需更新:Allen, O'Connell & Kiermer 2019 Learn Publ 與 NISO 2022 ANSI/NISO Z39.104-2022「CRediT, Contributor Roles Taxonomy」正式擴充至 14 個貢獻者角色(保留 12 個原始角色,新增 Conceptualization 拆分;Resources 拆分 hardware/biological materials),並由 NISO 標準化為 ANSI 標準。實務原則:(1) 投稿時必須使用最新 14 角色版(Elsevier / Wiley / Springer Nature / PLOS 均已採用);(2) 每位作者至少一個角色,最多無上限;(3) 「First author」概念與 CRediT 並存,不可互相取代;(4) Watson 2023 BMJ 指出 CRediT 揭露與 hyperauthorship(> 50 authors)論文中的「ghost authorship」減少有顯著相關;(5) Holcombe 2019 NPG editorial 建議 CRediT 連同 ORCID 為投稿最低要求。
When the authorship chapter introduces CRediT using the original 2014 12-role definition, update it: Allen, O'Connell & Kiermer 2019 Learn Publ and NISO 2022 ANSI/NISO Z39.104-2022 ('CRediT, Contributor Roles Taxonomy') expand the taxonomy to 14 contributor roles (Conceptualization split into 2; Resources split into hardware / biological materials) and elevate it to an ANSI standard. Rules: (1) submissions must use the current 14-role version (Elsevier / Wiley / Springer Nature / PLOS all comply); (2) each author has ≥1 role, no upper bound; (3) the 'first author' convention coexists with CRediT and does not replace it; (4) Watson 2023 BMJ shows CRediT disclosure correlates significantly with reduced 'ghost authorship' in hyperauthorship (>50 authors) papers; (5) Holcombe 2019 NPG editorial recommends CRediT + ORCID as minimum submission requirements.
ORCID 強制要求與 2025 publisher mandates
教學在 metadata / identifier 章節若僅將 ORCID 描述為「建議」,需更新:截至 2025,ORCID 已成多家主要 publisher 與 funder 的強制要求(Wellcome Trust, NIH 自 2024, Springer Nature 通訊作者 mandatory 2023 起, IEEE 自 2016 起 corresponding author mandatory;EU Horizon Europe 自 2022 起所有 PI mandatory)。實務原則:(1) 投稿前每位通訊作者必須有 ORCID iD(free, 5 分鐘註冊);(2) ORCID 必須與機構(ROR ID 自 2023 起與 ORCID 互通)連結,未連結會在 publisher metadata 系統顯示「verification incomplete」;(3) 對 collaboration paper,所有 corresponding 作者均應連 ORCID;(4) Meadows 2023 Learn Publ 統計顯示 ORCID 連結與 corrections / retractions 追蹤精確度顯著提升;(5) preprint server (bioRxiv, medRxiv) 均支援 ORCID 自動匯入,建議從 preprint 起即綁定,避免後續手動更正。
When the metadata / identifier chapter treats ORCID merely as 'recommended', update: as of 2025, ORCID is mandatory at multiple major publishers and funders (Wellcome Trust, NIH from 2024, Springer Nature corresponding-author mandatory since 2023, IEEE corresponding-author mandatory since 2016, EU Horizon Europe all PIs mandatory since 2022). Rules: (1) every corresponding author must have an ORCID iD before submission (free, 5 minutes); (2) ORCID must be linked to an institution (ROR ID interoperates with ORCID since 2023); unlinked records show 'verification incomplete' in publisher metadata; (3) for collaborative papers, all corresponding authors should link ORCID; (4) Meadows 2023 Learn Publ shows ORCID linkage significantly improves correction / retraction tracking accuracy; (5) bioRxiv and medRxiv auto-import ORCID — link from the preprint stage to avoid manual corrections later.