@wentorai/research-plugins 1.0.0

package/skills/writing/citation/citation-style-guide/SKILL.md

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+---
+name: citation-style-guide
+description: "APA, MLA, Chicago citation format guide with CSL configuration"
+metadata:
+  openclaw:
+    emoji: "book"
+    category: "writing"
+    subcategory: "citation"
+    keywords: ["citation formatting", "CSL", "citation style", "reference management"]
+    source: "wentor-research-plugins"
+---
+
+# Citation Style Guide
+
+Master the major citation styles (APA, MLA, Chicago, IEEE, Vancouver) with examples, reference manager configuration, and CSL customization.
+
+## Citation Style Overview
+
+| Style | Primary Discipline | In-Text Format | Reference List Name |
+|-------|-------------------|----------------|-------------------|
+| APA 7th | Psychology, social sciences, education | (Author, Year) | References |
+| MLA 9th | Humanities, literature, languages | (Author Page) | Works Cited |
+| Chicago (Author-Date) | Social sciences, natural sciences | (Author Year) | References |
+| Chicago (Notes-Bib) | History, arts, humanities | Footnotes/endnotes | Bibliography |
+| IEEE | Engineering, computer science | [1] numbered | References |
+| Vancouver | Medicine, biomedical sciences | (1) numbered | References |
+| Harvard | General, UK/Australia universities | (Author Year) | Reference List |
+| Nature | Multidisciplinary sciences | Superscript numbered | References |
+
+## APA 7th Edition
+
+### In-Text Citations
+
+```
+One author:     (Smith, 2023)     or   Smith (2023) found that...
+Two authors:    (Smith & Jones, 2023)
+3+ authors:     (Smith et al., 2023)
+Direct quote:   (Smith, 2023, p. 45)
+Multiple works: (Jones, 2021; Smith, 2023)
+Same author, same year: (Smith, 2023a, 2023b)
+Organization:   (World Health Organization [WHO], 2023)
+                then subsequent: (WHO, 2023)
+```
+
+### Reference List Examples
+
+```
+# Journal article
+Smith, J. A., & Jones, B. C. (2023). Title of the article in sentence
+    case. Journal Name in Title Case, 45(2), 123-145.
+    https://doi.org/10.1234/example
+
+# Book
+Williams, R. T. (2022). Title of the book in sentence case (3rd ed.).
+    Publisher Name. https://doi.org/10.1234/example
+
+# Chapter in edited book
+Chen, L. (2023). Chapter title. In A. Editor & B. Editor (Eds.),
+    Book title (pp. 50-75). Publisher. https://doi.org/10.1234/example
+
+# Conference paper
+Lee, S., & Park, J. (2023). Paper title. In Proceedings of the 2023
+    Conference Name (pp. 100-110). Publisher.
+    https://doi.org/10.1234/example
+
+# Webpage
+National Institutes of Health. (2023, March 15). Page title.
+    https://www.nih.gov/example
+
+# Preprint
+Garcia, M. (2023). Title of preprint. arXiv.
+    https://doi.org/10.48550/arXiv.2301.12345
+
+# Dataset
+Johnson, K. (2023). Dataset title (Version 2.0) [Data set]. Repository.
+    https://doi.org/10.1234/example
+```
+
+## MLA 9th Edition
+
+### In-Text Citations
+
+```
+One author:     (Smith 45)         or   Smith argues that "..." (45).
+Two authors:    (Smith and Jones 45)
+3+ authors:     (Smith et al. 45)
+No page number: (Smith)
+Multiple works: (Smith 45; Jones 67)
+```
+
+### Works Cited Examples
+
+```
+# Journal article
+Smith, John A., and Beth C. Jones. "Article Title in Title Case."
+    Journal Name, vol. 45, no. 2, 2023, pp. 123-45.
+    https://doi.org/10.1234/example.
+
+# Book
+Williams, Rose T. Title of Book in Italics. 3rd ed., Publisher, 2022.
+
+# Chapter in edited book
+Chen, Li. "Chapter Title." Book Title, edited by Amy Editor and
+    Bob Editor, Publisher, 2023, pp. 50-75.
+
+# Website
+"Page Title." Site Name, Organization, 15 Mar. 2023,
+    www.example.com/page.
+```
+
+## IEEE Style
+
+### In-Text Citations
+
+IEEE uses numbered references in square brackets, in order of first appearance:
+
+```
+As shown in [1], deep learning has achieved...
+Several studies [2]-[5] have demonstrated...
+Smith et al. [6] proposed...
+```
+
+### Reference List Examples
+
+```
+# Journal article
+[1] J. A. Smith and B. C. Jones, "Article title in sentence case,"
+    J. Name Abbreviated, vol. 45, no. 2, pp. 123-145, Feb. 2023,
+    doi: 10.1234/example.
+
+# Conference paper
+[2] S. Lee and J. Park, "Paper title," in Proc. Conf. Name,
+    City, Country, 2023, pp. 100-110.
+
+# Book
+[3] R. T. Williams, Book Title in Italics, 3rd ed. City, Country:
+    Publisher, 2022.
+
+# Online source
+[4] Author, "Page title," Website, date. [Online]. Available:
+    https://www.example.com
+```
+
+## Using CSL (Citation Style Language)
+
+CSL is the standard format used by Zotero, Mendeley, and other reference managers to define citation styles. Over 10,000 CSL styles are available at github.com/citation-style-language/styles.
+
+### Installing a CSL Style in Zotero
+
+1. Visit the Zotero Style Repository: zotero.org/styles
+2. Search for your target journal or style (e.g., "Nature", "APA 7th")
+3. Click to install directly into Zotero
+4. In Zotero, go to Settings > Cite > Styles to manage installed styles
+
+### CSL Style Structure
+
+```xml
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0">
+  <info>
+    <title>Custom Style</title>
+    <id>http://www.example.com/custom-style</id>
+  </info>
+
+  <!-- How in-text citations appear -->
+  <citation>
+    <sort>
+      <key variable="author"/>
+      <key variable="issued"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter="; ">
+      <group delimiter=", ">
+        <names variable="author">
+          <name form="short" and="symbol"/>
+        </names>
+        <date variable="issued" form="text" date-parts="year"/>
+      </group>
+    </layout>
+  </citation>
+
+  <!-- How the bibliography/reference list appears -->
+  <bibliography>
+    <sort>
+      <key variable="author"/>
+      <key variable="issued"/>
+    </sort>
+    <layout>
+      <!-- Define reference formatting here -->
+    </layout>
+  </bibliography>
+</style>
+```
+
+## BibTeX Entry Types
+
+For LaTeX users, correct entry types ensure proper formatting:
+
+```bibtex
+@article{smith2023,
+  author  = {Smith, John A. and Jones, Beth C.},
+  title   = {Article Title},
+  journal = {Journal Name},
+  year    = {2023},
+  volume  = {45},
+  number  = {2},
+  pages   = {123--145},
+  doi     = {10.1234/example}
+}
+
+@inproceedings{lee2023,
+  author    = {Lee, Sam and Park, Jin},
+  title     = {Paper Title},
+  booktitle = {Proceedings of the 2023 Conference},
+  year      = {2023},
+  pages     = {100--110},
+  doi       = {10.1234/example}
+}
+
+@book{williams2022,
+  author    = {Williams, Rose T.},
+  title     = {Book Title},
+  edition   = {3rd},
+  publisher = {Publisher Name},
+  year      = {2022}
+}
+
+@misc{garcia2023preprint,
+  author = {Garcia, Maria},
+  title  = {Title of Preprint},
+  year   = {2023},
+  eprint = {2301.12345},
+  archiveprefix = {arXiv},
+  primaryclass  = {cs.CL}
+}
+```
+
+## Quick Decision Guide
+
+| If your field is... | Use this style | LaTeX bibliography style |
+|--------------------|---------------|------------------------|
+| Psychology, education | APA 7th | `apacite` or `biblatex-apa` |
+| Literature, languages | MLA 9th | `biblatex-mla` |
+| History, arts | Chicago Notes | `chicago-authordate` |
+| Engineering, CS (IEEE venues) | IEEE | `IEEEtran` |
+| Medicine, clinical | Vancouver | `vancouver` |
+| Natural sciences (Nature group) | Nature | `naturemag` |
+| Economics | Chicago Author-Date | `chicago-authordate` |
+| Check specific journal | Journal's author guidelines | See journal website |

package/skills/writing/citation/reference-manager-comparison/SKILL.md

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+---
+name: reference-manager-comparison
+description: "Compare Zotero, Mendeley, EndNote, and Paperpile for research use"
+metadata:
+  openclaw:
+    emoji: "card_index_dividers"
+    category: "writing"
+    subcategory: "citation"
+    keywords: ["reference manager", "Zotero", "Mendeley", "EndNote", "Paperpile", "citation management"]
+    source: "wentor-research-plugins"
+---
+
+# Reference Manager Comparison
+
+A skill for selecting and configuring the right reference management tool for your research workflow. Provides an in-depth comparison of Zotero, Mendeley, EndNote, and Paperpile across features, pricing, integration, collaboration, and discipline-specific needs.
+
+## Feature Comparison
+
+### Overview Matrix
+
+| Feature | Zotero | Mendeley | EndNote | Paperpile |
+|---------|--------|----------|---------|-----------|
+| Cost | Free (300MB cloud) | Free (2GB cloud) | ~$275 or institutional | $36/year (academic) |
+| Platform | Win/Mac/Linux | Win/Mac/Linux | Win/Mac | Web + Chrome |
+| Word plugin | Yes | Yes | Yes | Yes (Google Docs too) |
+| LaTeX export | BibTeX, BibLaTeX | BibTeX | BibTeX | BibTeX |
+| PDF annotation | Basic (built-in reader) | Yes | Yes | Yes |
+| Group libraries | Yes (unlimited, 300MB free) | Yes (limited free) | Via EndNote Online | Yes |
+| Browser extension | Excellent (Zotero Connector) | Web Importer | Capture (limited) | Excellent |
+| Open source | Yes (GPLv3) | No | No | No |
+| Offline access | Full | Full | Full | Limited |
+| Storage upgrade | $20/year (2GB) | $55/year (5GB) | Unlimited (desktop) | Unlimited |
+
+## Zotero
+
+### Strengths
+
+```
+- Free and open source with strong community
+- Best browser extension for capturing metadata
+- Excellent plugin ecosystem:
+  * Better BibTeX (superior LaTeX integration)
+  * ZotFile (PDF management and renaming)
+  * Zotero OCR (extract text from scanned PDFs)
+  * Scite (citation context analysis)
+- Works on all platforms including Linux
+- Syncs across devices; self-hosting is possible
+- Transparent data format (SQLite, exportable)
+```
+
+### Zotero Setup for Researchers
+
+```python
+def recommended_zotero_plugins() -> list[dict]:
+    """
+    Essential Zotero plugins for academic researchers.
+    """
+    return [
+        {
+            "name": "Better BibTeX",
+            "purpose": "Automatic .bib file export, stable citation keys",
+            "install": "github.com/retorquere/zotero-better-bibtex",
+            "priority": "Essential for LaTeX users"
+        },
+        {
+            "name": "ZotFile",
+            "purpose": "Rename and organize attached PDFs",
+            "install": "zotfile.com",
+            "priority": "Highly recommended"
+        },
+        {
+            "name": "Zotero Storage Scanner",
+            "purpose": "Find broken attachments and duplicates",
+            "install": "Available via Zotero plugin manager",
+            "priority": "Useful for library maintenance"
+        },
+        {
+            "name": "DOI Manager",
+            "purpose": "Fetch missing DOIs for your references",
+            "install": "Available via Zotero plugin manager",
+            "priority": "Recommended for bibliography accuracy"
+        }
+    ]
+```
+
+## Mendeley
+
+### Strengths
+
+```
+- Free with generous 2GB cloud storage
+- Built-in PDF reader with annotation tools
+- Mendeley Suggest recommends related papers
+- Strong institutional adoption
+- Social features (researcher profiles, groups)
+```
+
+### Limitations
+
+```
+- Owned by Elsevier (data privacy concerns for some users)
+- Desktop app development has slowed (focus shifted to web)
+- Limited plugin ecosystem compared to Zotero
+- BibTeX export can have formatting inconsistencies
+- Group library size limitations on free tier
+```
+
+## EndNote
+
+### Strengths
+
+```
+- Deep integration with Web of Science
+- Mature product with decades of development
+- Excellent Word plugin (Cite While You Write)
+- Strong institutional support and training resources
+- Handles very large libraries (10,000+ references) well
+```
+
+### Limitations
+
+```
+- Expensive for individual purchase
+- No Linux support
+- Closed format (vendor lock-in risk)
+- Steeper learning curve
+- Limited free collaboration features
+```
+
+## Paperpile
+
+### Strengths
+
+```
+- Excellent Google Docs and Google Scholar integration
+- Clean, modern interface
+- Very fast browser-based workflow
+- Built-in PDF viewer with annotation
+- Automatic metadata extraction from PDFs
+```
+
+### Limitations
+
+```
+- No desktop app (requires internet for full functionality)
+- Chrome-only browser extension
+- No Linux-native app (web-based works on all platforms)
+- Smaller user community than Zotero or Mendeley
+```
+
+## Decision Guide
+
+### Choosing by Use Case
+
+```
+If you use LaTeX primarily:
+  -> Zotero + Better BibTeX (best .bib integration)
+
+If you use Google Docs primarily:
+  -> Paperpile (native Docs integration)
+
+If your institution provides it:
+  -> EndNote (maximize institutional support)
+
+If you want free + open source:
+  -> Zotero (no contest)
+
+If you need built-in recommendations:
+  -> Mendeley or Paperpile (suggest related papers)
+
+If you collaborate heavily:
+  -> Zotero groups or Paperpile shared folders
+
+If you have a very large library (50,000+ items):
+  -> EndNote or Zotero (both handle large libraries well)
+```
+
+## Migration Between Tools
+
+### Exporting and Importing
+
+All major reference managers support BibTeX and RIS export formats, making migration possible:
+
+```
+Export from source tool:
+  - Zotero: File > Export Library > BibTeX/RIS
+  - Mendeley: Tools > Export (BibTeX)
+  - EndNote: File > Export > RIS/BibTeX
+  - Paperpile: Settings > Export > BibTeX
+
+Import to target tool:
+  - Drag and drop the exported file into the new tool
+  - Review imported entries for metadata accuracy
+  - Re-attach PDFs if they did not transfer automatically
+```
+
+### What Transfers and What Does Not
+
+| Data | Transfers? | Notes |
+|------|-----------|-------|
+| Metadata (title, author, year) | Yes | Via BibTeX/RIS |
+| PDFs | Sometimes | Depends on export settings |
+| Annotations/highlights | Rarely | Usually tool-specific format |
+| Folder/collection structure | Sometimes | Zotero RDF preserves collections |
+| Tags | Usually | Via RIS or Zotero RDF |
+| Notes | Sometimes | Check export format |
+
+Choose your reference manager early in your research career and invest time in organizing your library -- the cost of switching grows with library size.

package/skills/writing/citation/zotero-api/SKILL.md

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+---
+name: zotero-api
+description: "Reference management library and collections API"
+metadata:
+  openclaw:
+    emoji: "🔍"
+    category: "writing"
+    subcategory: "citation"
+    keywords: ["reference management", "citation management", "bibliography organization", "literature import"]
+    source: "https://www.zotero.org/support/dev/web_api/v3/basics"
+---
+
+# Zotero API Guide
+
+## Overview
+
+Zotero is a free, open-source reference management software designed to help researchers collect, organize, cite, and share bibliographic references. The Zotero Web API provides programmatic access to user and group libraries stored on Zotero servers, enabling integration with research workflows, automated bibliography management, and custom tool development.
+
+The API supports reading and writing items (books, journal articles, conference papers, web pages, and dozens of other item types), organizing items into collections, managing tags, retrieving attachment metadata, and accessing shared group libraries. It follows RESTful conventions and supports JSON and Atom response formats, making it straightforward to integrate with existing research infrastructure.
+
+Researchers, librarians, research software developers, and digital humanities scholars use the Zotero API to build literature review tools, automate citation workflows, synchronize reference libraries across platforms, generate bibliographies programmatically, and create custom research management dashboards. The API is particularly popular in digital humanities projects where large bibliographic datasets need programmatic manipulation.
+
+## Authentication
+
+Authentication is optional for reading public libraries but required for accessing private libraries and all write operations. Zotero uses API keys for authentication.
+
+1. Log in to your Zotero account at https://www.zotero.org/
+2. Navigate to https://www.zotero.org/settings/keys
+3. Create a new API key with appropriate permissions (read/write access to personal or group libraries)
+4. Include the key in the `Zotero-API-Key` header
+
+```bash
+# Authenticated request
+curl -H "Zotero-API-Key: YOUR_API_KEY" "https://api.zotero.org/users/USER_ID/items"
+
+# Public group library (no auth needed)
+curl "https://api.zotero.org/groups/GROUP_ID/items"
+```
+
+Your user ID can be found at https://www.zotero.org/settings/keys alongside your API key settings.
+
+## Core Endpoints
+
+### users/{id}/items: User Library Items
+
+Retrieve, search, and manage items in a user's personal Zotero library.
+
+- **URL**: `GET https://api.zotero.org/users/{userID}/items`
+- **Parameters**:
+
+| Parameter  | Type   | Required | Description                                              |
+|------------|--------|----------|----------------------------------------------------------|
+| userID     | int    | Yes      | Zotero user ID (in URL path)                             |
+| q          | string | No       | Quick search query (searches title, creator, year)       |
+| qmode      | string | No       | Search mode: `titleCreatorYear` or `everything`          |
+| itemType   | string | No       | Filter by type: `journalArticle`, `book`, `conferencePaper`, etc. |
+| tag        | string | No       | Filter by tag (can be repeated for multiple tags)        |
+| sort       | string | No       | Sort field: `dateAdded`, `dateModified`, `title`, `creator` |
+| direction  | string | No       | Sort direction: `asc` or `desc`                          |
+| limit      | int    | No       | Results per request (default 25, max 100)                |
+| start      | int    | No       | Pagination offset                                        |
+| format     | string | No       | Response format: `json` (default), `atom`, `bib`, `keys` |
+
+- **Example**:
+
+```bash
+# Get all journal articles tagged "machine learning"
+curl -H "Zotero-API-Key: YOUR_KEY" \
+  "https://api.zotero.org/users/12345/items?itemType=journalArticle&tag=machine+learning&format=json"
+
+# Search for items by keyword
+curl -H "Zotero-API-Key: YOUR_KEY" \
+  "https://api.zotero.org/users/12345/items?q=neural+networks&format=json"
+```
+
+- **Response**: Returns array of item objects, each containing `key`, `version`, `data` (with `itemType`, `title`, `creators`, `abstractNote`, `date`, `DOI`, `url`, `tags`, `collections`, `relations`), and `links`.
+
+### groups/{id}/items: Group Library Items
+
+Access items in shared group libraries, which are commonly used for collaborative research projects and reading groups.
+
+- **URL**: `GET https://api.zotero.org/groups/{groupID}/items`
+- **Parameters**:
+
+| Parameter | Type   | Required | Description                                         |
+|-----------|--------|----------|-----------------------------------------------------|
+| groupID   | int    | Yes      | Zotero group ID (in URL path)                       |
+| q         | string | No       | Quick search query                                  |
+| itemType  | string | No       | Filter by item type                                 |
+| tag       | string | No       | Filter by tag                                       |
+| sort      | string | No       | Sort field                                          |
+| limit     | int    | No       | Results per request (max 100)                       |
+| start     | int    | No       | Pagination offset                                   |
+| format    | string | No       | Response format: `json`, `atom`, `bib`, `keys`      |
+
+- **Example**:
+
+```bash
+# List items in a public group library
+curl "https://api.zotero.org/groups/67890/items?format=json&limit=50"
+
+# Get formatted bibliography from a group
+curl "https://api.zotero.org/groups/67890/items?format=bib&style=apa"
+```
+
+- **Response**: Same structure as user library items. Group items may include additional access control metadata depending on the group's privacy settings.
+
+## Rate Limits
+
+No strict rate limits are enforced, but Zotero asks users to limit requests to a reasonable rate. The API uses conditional requests via `If-Modified-Since-Version` headers for efficient synchronization. Responses include a `Last-Modified-Version` header that should be stored and used in subsequent requests to only retrieve changed items. Batch operations are supported for creating/updating multiple items in a single request (up to 50 items per write request).
+
+## Common Patterns
+
+### Export a Bibliography in a Specific Citation Style
+
+Generate a formatted bibliography from a Zotero collection:
+
+```python
+import requests
+
+headers = {"Zotero-API-Key": "YOUR_KEY"}
+
+# Get items formatted as APA bibliography
+resp = requests.get(
+    "https://api.zotero.org/users/12345/collections/ABCDEF/items",
+    headers=headers,
+    params={"format": "bib", "style": "apa", "limit": 100}
+)
+print(resp.text)
+```
+
+### Sync Library Items to a Custom Database
+
+Efficiently synchronize Zotero items using version tracking:
+
+```python
+import requests
+
+headers = {"Zotero-API-Key": "YOUR_KEY"}
+last_version = 0  # Store this between syncs
+
+resp = requests.get(
+    "https://api.zotero.org/users/12345/items",
+    headers={**headers, "If-Modified-Since-Version": str(last_version)},
+    params={"format": "json", "limit": 100}
+)
+
+if resp.status_code == 200:
+    items = resp.json()
+    last_version = resp.headers["Last-Modified-Version"]
+    for item in items:
+        print(f"Updated: {item['data'].get('title', 'No title')} (v{item['version']})")
+elif resp.status_code == 304:
+    print("No changes since last sync")
+```
+
+### Analyze Research Library by Tag Distribution
+
+Explore the thematic distribution of a research library:
+
+```python
+import requests
+from collections import Counter
+
+headers = {"Zotero-API-Key": "YOUR_KEY"}
+
+resp = requests.get(
+    "https://api.zotero.org/users/12345/items",
+    headers=headers,
+    params={"format": "json", "limit": 100, "itemType": "journalArticle"}
+)
+
+tag_counts = Counter()
+for item in resp.json():
+    for tag in item["data"].get("tags", []):
+        tag_counts[tag["tag"]] += 1
+
+for tag, count in tag_counts.most_common(20):
+    print(f"  {tag}: {count}")
+```
+
+## References
+
+- Official Web API documentation: https://www.zotero.org/support/dev/web_api/v3/basics
+- API key management: https://www.zotero.org/settings/keys
+- Item types and fields: https://api.zotero.org/itemTypes
+- Zotero homepage: https://www.zotero.org/
+- Citation styles: https://www.zotero.org/styles