@wentorai/research-plugins 1.0.0 → 1.2.0

package/skills/literature/fulltext/zotero-scihub-guide/SKILL.md

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+---
+name: zotero-scihub-guide
+description: "Zotero plugin for automatic PDF retrieval from Sci-Hub"
+metadata:
+  openclaw:
+    emoji: "🔓"
+    category: "literature"
+    subcategory: "fulltext"
+    keywords: ["Zotero", "Sci-Hub", "PDF download", "open access", "full text", "paper retrieval"]
+    source: "https://github.com/ethanwillis/zotero-scihub"
+---
+
+# Zotero Sci-Hub Guide
+
+## Overview
+
+Zotero Sci-Hub is a Zotero plugin that automatically fetches PDFs from Sci-Hub when papers cannot be found through standard open-access channels. It integrates seamlessly into Zotero's existing PDF retrieval workflow — when Zotero's built-in retriever fails, the plugin automatically attempts Sci-Hub as a fallback. Useful for researchers at institutions with limited journal subscriptions.
+
+## Installation
+
+```bash
+# Download the .xpi file from GitHub releases
+# In Zotero 7: Tools → Add-ons → Install Add-on From File
+
+# Manual installation
+# 1. Go to https://github.com/ethanwillis/zotero-scihub/releases
+# 2. Download zotero-scihub-*.xpi
+# 3. In Zotero: Tools → Add-ons → gear icon → Install from file
+```
+
+## Configuration
+
+```
+# In Zotero: Edit → Preferences → Zotero Sci-Hub
+
+# Settings:
+# 1. Sci-Hub URL: Set current working mirror
+#    - The plugin ships with default URLs
+#    - Update if mirrors change
+
+# 2. Automatic mode:
+#    - ON: Try Sci-Hub automatically after Zotero fails
+#    - OFF: Only fetch via right-click menu
+
+# 3. DOI sources: Where to look for DOIs
+#    - Item DOI field
+#    - Item URL field
+#    - Item Extra field
+```
+
+## Usage Workflow
+
+```markdown
+### Automatic PDF Retrieval
+1. Add item to Zotero (via browser connector, DOI, or manual)
+2. Zotero tries built-in PDF retrieval (Open Access, institutional)
+3. If no PDF found → plugin automatically queries Sci-Hub
+4. PDF attached to Zotero item
+
+### Manual Retrieval
+1. Right-click item(s) in Zotero
+2. Select "Fetch PDF from Sci-Hub"
+3. Works for single items or batch selection
+
+### Bulk Retrieval
+1. Select multiple items (Ctrl+A for all)
+2. Right-click → "Fetch PDF from Sci-Hub"
+3. Plugin processes items sequentially with rate limiting
+```
+
+## Integration with Other Plugins
+
+```markdown
+### Recommended Plugin Stack
+1. **Zotero Connector** — Browser extension for importing items
+2. **Zotero Sci-Hub** — PDF fallback retrieval
+3. **ZotFile/ZotMoov** — Organize downloaded PDFs
+4. **Zotero Better BibTeX** — Citation key management
+5. **Zotero PDF Translate** — Translate retrieved papers
+
+### Workflow
+Import item → Auto-fetch PDF → Organize files → Read & annotate
+```
+
+## Troubleshooting
+
+```markdown
+### Common Issues
+
+**PDF not found:**
+- Check if DOI is present in item metadata
+- Try updating the Sci-Hub mirror URL
+- Some very recent papers may not be available yet
+
+**Connection errors:**
+- Current mirror may be down; try alternate URL
+- Check network/proxy settings
+- Some institutions block Sci-Hub domains
+
+**Duplicate PDFs:**
+- Disable automatic mode if using other PDF fetchers
+- Check Zotero's duplicate detection settings
+```
+
+## Programmatic Alternative
+
+```python
+# For building custom PDF retrieval pipelines
+import requests
+
+def fetch_paper_by_doi(doi, output_path):
+    """Attempt to fetch paper PDF via DOI resolution."""
+    # Try Unpaywall first (legal open access)
+    unpaywall_url = (
+        f"https://api.unpaywall.org/v2/{doi}"
+        f"?email=your@email.com"
+    )
+    resp = requests.get(unpaywall_url)
+    if resp.ok:
+        data = resp.json()
+        if data.get("is_oa") and data.get("best_oa_location"):
+            pdf_url = data["best_oa_location"].get("url_for_pdf")
+            if pdf_url:
+                pdf = requests.get(pdf_url)
+                with open(output_path, "wb") as f:
+                    f.write(pdf.content)
+                return True
+
+    # Try CORE API
+    core_url = f"https://api.core.ac.uk/v3/search/works?q=doi:{doi}"
+    resp = requests.get(core_url)
+    if resp.ok:
+        results = resp.json().get("results", [])
+        if results and results[0].get("downloadUrl"):
+            pdf = requests.get(results[0]["downloadUrl"])
+            with open(output_path, "wb") as f:
+                f.write(pdf.content)
+            return True
+
+    return False
+```
+
+## Legal Considerations
+
+```markdown
+### Open Access Alternatives
+Before using Sci-Hub, check these legal sources:
+1. **Unpaywall** — Browser extension for legal OA versions
+2. **CORE** — Aggregator of OA research papers
+3. **PubMed Central** — Free biomedical literature archive
+4. **arXiv/bioRxiv** — Preprint servers
+5. **Author websites** — Many post preprints freely
+6. **Interlibrary Loan** — Request through your library
+7. **Email the author** — Most researchers share on request
+```
+
+## Use Cases
+
+1. **PDF retrieval**: Automatic paper downloading for Zotero
+2. **Literature collection**: Build reading libraries efficiently
+3. **Systematic reviews**: Bulk-fetch papers for review pipelines
+4. **Research onboarding**: Quickly gather papers for new topics
+
+## References
+
+- [Zotero Sci-Hub GitHub](https://github.com/ethanwillis/zotero-scihub)
+- [Unpaywall](https://unpaywall.org/) — Legal OA alternative
+- [CORE](https://core.ac.uk/) — OA aggregator

package/skills/literature/metadata/academic-paper-summarizer/SKILL.md

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+---
+name: academic-paper-summarizer
+description: "Summarize academic papers with structured extraction of key elements"
+metadata:
+  openclaw:
+    emoji: "📋"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["paper summary", "structured extraction", "abstract", "key findings", "research synthesis", "literature review"]
+    source: "https://github.com/lifan0127/ai-research-assistant"
+---
+
+# Academic Paper Summarizer
+
+## Overview
+
+Academic papers are dense, technical documents that require significant time to read and understand fully. The Academic Paper Summarizer skill provides a systematic framework for extracting the essential elements from research papers into structured, reusable summaries.
+
+This skill is designed for researchers who need to rapidly process large volumes of literature—whether during a systematic review, when onboarding into a new field, or when preparing a literature review section for their own manuscripts. Rather than producing generic summaries, it enforces a structured template that captures the components most relevant to downstream academic work: research questions, methodology, key findings, limitations, and contributions to the field.
+
+The skill works with any academic paper format (PDF, HTML, plain text) and can be adapted across disciplines from biomedical sciences to social sciences, engineering, and humanities. It emphasizes fidelity to the original text while organizing information into a consistent schema that facilitates comparison across papers.
+
+## Structured Extraction Framework
+
+The core of this skill is a multi-section extraction template. When summarizing a paper, populate each of the following fields:
+
+**Bibliographic Metadata:**
+- Title, authors, journal/conference, year, DOI
+- Paper type (empirical, review, theoretical, methodological, case study)
+
+**Research Context:**
+- What gap in the literature does this paper address?
+- What is the stated research question or hypothesis?
+- How does the paper position itself relative to prior work?
+
+**Methodology Summary:**
+- Study design (experimental, observational, computational, qualitative, mixed)
+- Data sources, sample size, and key variables
+- Analytical methods and tools used
+- Any novel methodological contributions
+
+**Key Findings:**
+- Primary results stated in 3-5 bullet points
+- Statistical significance or effect sizes where reported
+- Figures and tables worth revisiting (note figure/table numbers)
+
+**Critical Assessment:**
+- Strengths of the study design and execution
+- Limitations acknowledged by authors and any additional limitations you identify
+- Potential biases or confounding factors
+- Generalizability of findings
+
+**Relevance and Connections:**
+- How does this paper connect to your current research?
+- Which references cited in this paper should you follow up on?
+- Does this paper support, contradict, or extend existing findings in your collection?
+
+## Batch Processing Workflow
+
+When processing multiple papers (e.g., during a literature review), follow this workflow for efficiency:
+
+1. **Triage pass**: Read title, abstract, and conclusions of each paper. Assign a relevance score (1-5) and decide whether to perform full extraction.
+2. **Full extraction**: For papers scoring 3+, apply the complete structured extraction template above.
+3. **Cross-paper synthesis**: After extracting 5-10 papers on a related subtopic, create a synthesis note that identifies common findings, methodological trends, and open questions.
+4. **Gap identification**: Compare your extraction set against your research questions to identify what evidence is still missing.
+
+**Example extraction prompt:**
+
+```
+Read this paper and extract the following in structured format:
+1. Bibliographic info (title, authors, year, journal, DOI)
+2. Research question / hypothesis
+3. Methodology (design, data, sample, analysis)
+4. Key findings (3-5 bullets with effect sizes)
+5. Limitations and biases
+6. Relevance to [your topic]
+7. Key references to follow up
+```
+
+## Tips for High-Quality Summaries
+
+- **Preserve author voice for claims**: When summarizing findings, note whether the authors use hedging language ("suggests", "may indicate") versus strong claims ("demonstrates", "proves"). This matters for synthesis.
+- **Note negative results**: Papers often bury non-significant findings. Explicitly extract these, as they are crucial for meta-analyses and for avoiding publication bias in your review.
+- **Tag with your own keywords**: Beyond the authors' keywords, add your own tags that connect the paper to your research framework. This makes retrieval easier later.
+- **Record page numbers**: When noting key findings or quotes, record the page number so you can return to the source quickly.
+- **Update summaries**: If you re-read a paper later with new context, update the summary rather than creating a duplicate.
+
+## Output Formats
+
+Summaries can be exported in several formats depending on your workflow:
+
+- **Markdown**: For integration with note-taking tools (Obsidian, Notion, Logseq)
+- **BibTeX annotation**: Append the summary as an `annote` field in your BibTeX entry
+- **CSV row**: For spreadsheet-based literature tracking with one row per paper
+- **JSON**: For programmatic processing or import into reference managers
+
+## References
+
+- Keshav, S. (2007). "How to Read a Paper." ACM SIGCOMM Computer Communication Review.
+- Pautasso, M. (2013). "Ten Simple Rules for Writing a Literature Review." PLOS Computational Biology.
+- AI Research Assistant: https://github.com/lifan0127/ai-research-assistant

package/skills/literature/metadata/bibliometrix-guide/SKILL.md

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+---
+name: bibliometrix-guide
+description: "Perform science mapping and bibliometric analysis with R bibliometrix"
+metadata:
+  openclaw:
+    emoji: "📉"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["bibliometrix", "bibliometrics", "science mapping", "R", "citation analysis", "research trends"]
+    source: "https://github.com/massimoaria/bibliometrix"
+---
+
+# Bibliometrix Guide
+
+## Overview
+
+Bibliometrix is an R package for comprehensive science mapping and bibliometric analysis. It imports data from Scopus, Web of Science, PubMed, and other databases, then performs co-citation analysis, keyword co-occurrence mapping, collaboration networks, thematic evolution tracking, and more. Includes Biblioshiny — a Shiny-based web interface for no-code analysis.
+
+## Installation
+
+```r
+install.packages("bibliometrix")
+
+# Or development version
+devtools::install_github("massimoaria/bibliometrix")
+```
+
+## Quick Start
+
+### Import Data
+
+```r
+library(bibliometrix)
+
+# From Scopus CSV export
+M <- convert2df("scopus_export.csv", dbsource = "scopus", format = "csv")
+
+# From Web of Science
+M <- convert2df("wos_export.txt", dbsource = "wos", format = "plaintext")
+
+# From PubMed
+M <- convert2df("pubmed_export.txt", dbsource = "pubmed", format = "pubmed")
+
+# From multiple files
+file_list <- c("data1.csv", "data2.csv")
+M <- convert2df(file_list, dbsource = "scopus", format = "csv")
+```
+
+### Descriptive Analysis
+
+```r
+# Basic bibliometric summary
+results <- biblioAnalysis(M)
+summary(results, k = 10)  # Top 10 in each category
+
+# Key metrics produced:
+# - Publication trends over time
+# - Most productive authors
+# - Most cited papers
+# - Top journals/sources
+# - Country/affiliation rankings
+# - Keyword frequency
+```
+
+### Citation Analysis
+
+```r
+# Most cited documents
+CR <- citations(M, field = "article", sep = ";")
+head(CR$Cited, 20)
+
+# Most cited first authors
+CR_auth <- citations(M, field = "author", sep = ";")
+
+# Local citations (within the dataset)
+LC <- localCitations(M)
+head(LC$Papers, 10)
+```
+
+### Network Analysis
+
+```r
+# Co-citation network
+NetMatrix <- biblioNetwork(M, analysis = "co-citation",
+                           network = "references", sep = ";")
+net <- networkPlot(NetMatrix, n = 30, type = "fruchterman",
+                   Title = "Co-citation Network")
+
+# Author collaboration network
+NetMatrix <- biblioNetwork(M, analysis = "collaboration",
+                           network = "authors", sep = ";")
+net <- networkPlot(NetMatrix, n = 50, type = "kamada",
+                   Title = "Collaboration Network")
+
+# Keyword co-occurrence
+NetMatrix <- biblioNetwork(M, analysis = "co-occurrences",
+                           network = "keywords", sep = ";")
+net <- networkPlot(NetMatrix, n = 40, type = "fruchterman",
+                   Title = "Keyword Co-occurrence")
+```
+
+### Thematic Analysis
+
+```r
+# Thematic map (strategic diagram)
+Map <- thematicMap(M, field = "DE", n = 250, minfreq = 5)
+plot(Map$map)
+
+# Quadrants:
+# Motor themes (high centrality, high density)
+# Basic themes (high centrality, low density)
+# Niche themes (low centrality, high density)
+# Emerging/declining themes (low centrality, low density)
+
+# Thematic evolution over time periods
+nexus <- thematicEvolution(M,
+    field = "DE",
+    years = c(2015, 2019, 2023),
+    n = 100, minFreq = 3)
+plotThematicEvolution(nexus$Nodes, nexus$Edges)
+```
+
+### Biblioshiny (Web Interface)
+
+```r
+# Launch interactive web dashboard
+biblioshiny()
+
+# Opens browser with GUI for:
+# - Data import from multiple sources
+# - Descriptive analysis
+# - Network visualization
+# - Thematic mapping
+# - All plots exportable
+```
+
+## Supported Data Sources
+
+| Source | Format | Import function |
+|--------|--------|----------------|
+| Scopus | CSV/BibTeX | `convert2df(..., dbsource="scopus")` |
+| Web of Science | Plain text/BibTeX | `convert2df(..., dbsource="wos")` |
+| PubMed | PubMed format | `convert2df(..., dbsource="pubmed")` |
+| Dimensions | CSV | `convert2df(..., dbsource="dimensions")` |
+| Cochrane | Plain text | `convert2df(..., dbsource="cochrane")` |
+| OpenAlex | JSON | Via API integration |
+
+## Key Analysis Types
+
+| Analysis | Function | Output |
+|----------|----------|--------|
+| Descriptive | `biblioAnalysis()` | Summary statistics |
+| Co-citation | `biblioNetwork(analysis="co-citation")` | Citation clusters |
+| Collaboration | `biblioNetwork(analysis="collaboration")` | Author networks |
+| Co-occurrence | `biblioNetwork(analysis="co-occurrences")` | Keyword maps |
+| Thematic map | `thematicMap()` | Strategic quadrant diagram |
+| Trend analysis | `fieldByYear()` | Topic evolution |
+| Country collab | `metaTagExtraction() + biblioNetwork()` | Geo collaboration |
+
+## References
+
+- [Bibliometrix](https://www.bibliometrix.org/)
+- [Bibliometrix GitHub](https://github.com/massimoaria/bibliometrix)
+- Aria, M. & Cuccurullo, C. (2017). "bibliometrix: An R-tool for comprehensive science mapping analysis." *Journal of Informetrics* 11(4): 959-975.

package/skills/literature/metadata/crossref-event-data-api/SKILL.md

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+---
+name: crossref-event-data-api
+description: "Track scholarly mentions across the web via Crossref Event Data"
+metadata:
+  openclaw:
+    emoji: "📡"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["Crossref", "event data", "altmetrics", "social media mentions", "scholarly impact", "web mentions"]
+    source: "https://www.eventdata.crossref.org/"
+---
+
+# Crossref Event Data API
+
+## Overview
+
+Crossref Event Data tracks where scholarly publications are discussed, shared, and referenced across the open web — Wikipedia citations, Twitter/X mentions, Reddit posts, blog references, policy document citations, and more. Unlike traditional citation counts, Event Data captures real-time online attention to research. Free, no authentication required.
+
+## API Endpoints
+
+### Base URL
+
+```
+https://api.eventdata.crossref.org/v1
+```
+
+### Query Events
+
+```bash
+# Get events for a specific DOI
+curl "https://api.eventdata.crossref.org/v1/events?obj-id=10.1038/nature14539&rows=20"
+
+# Filter by source
+curl "https://api.eventdata.crossref.org/v1/events?\
+obj-id=10.1038/nature14539&source=wikipedia"
+
+# Filter by date range
+curl "https://api.eventdata.crossref.org/v1/events?\
+from-occurred-date=2024-01-01&until-occurred-date=2024-12-31&source=twitter&rows=100"
+
+# Get events about a DOI prefix (publisher level)
+curl "https://api.eventdata.crossref.org/v1/events?obj-id.prefix=10.1371&rows=50"
+
+# Events from a specific source
+curl "https://api.eventdata.crossref.org/v1/events?source=reddit&rows=50"
+```
+
+### Event Sources
+
+| Source | Description | What it tracks |
+|--------|-------------|---------------|
+| `wikipedia` | Wikipedia article references | DOIs cited in Wikipedia |
+| `twitter` | Twitter/X posts | Tweets linking to DOIs |
+| `reddit` | Reddit posts/comments | Reddit links to papers |
+| `hypothesis` | Hypothesis annotations | Web annotations on papers |
+| `newsfeed` | News articles | Media coverage of research |
+| `stackexchange` | Stack Exchange Q&A | Technical discussions |
+| `web` | General web pages | Blog posts, reports |
+| `wordpressdotcom` | WordPress blogs | Blog references |
+| `datacite` | DataCite DOIs | Dataset-paper linkages |
+| `crossref` | Crossref metadata | Reference list updates |
+
+### Query Parameters
+
+| Parameter | Description | Example |
+|-----------|-------------|---------|
+| `obj-id` | DOI of the paper | `obj-id=10.1038/nature14539` |
+| `obj-id.prefix` | DOI prefix (publisher) | `obj-id.prefix=10.1371` |
+| `source` | Event source | `source=wikipedia` |
+| `from-occurred-date` | Events from date | `2024-01-01` |
+| `until-occurred-date` | Events until date | `2024-12-31` |
+| `rows` | Results per page (max 10000) | `rows=100` |
+| `cursor` | Pagination cursor | Returned in response |
+
+## Response Structure
+
+```json
+{
+  "status": "ok",
+  "message-type": "event-list",
+  "message": {
+    "total-results": 245,
+    "events": [
+      {
+        "obj_id": "https://doi.org/10.1038/nature14539",
+        "source_id": "wikipedia",
+        "subj_id": "https://en.wikipedia.org/wiki/Deep_learning",
+        "relation_type_id": "references",
+        "occurred_at": "2024-03-15T10:30:00Z",
+        "subj": {
+          "title": "Deep learning - Wikipedia",
+          "url": "https://en.wikipedia.org/wiki/Deep_learning"
+        }
+      }
+    ],
+    "next-cursor": "abc123..."
+  }
+}
+```
+
+## Python Usage
+
+```python
+import requests
+from collections import Counter
+
+BASE_URL = "https://api.eventdata.crossref.org/v1"
+
+
+def get_events(doi: str, source: str = None,
+               rows: int = 100) -> list:
+    """Get Event Data events for a DOI."""
+    params = {"obj-id": doi, "rows": rows}
+    if source:
+        params["source"] = source
+
+    resp = requests.get(f"{BASE_URL}/events", params=params)
+    resp.raise_for_status()
+    data = resp.json()
+
+    events = []
+    for ev in data.get("message", {}).get("events", []):
+        events.append({
+            "source": ev.get("source_id"),
+            "subject_url": ev.get("subj_id"),
+            "subject_title": ev.get("subj", {}).get("title", ""),
+            "relation": ev.get("relation_type_id"),
+            "date": ev.get("occurred_at", "")[:10],
+        })
+    return events
+
+
+def get_attention_summary(doi: str) -> dict:
+    """Summarize online attention for a paper."""
+    events = get_events(doi, rows=10000)
+    source_counts = Counter(e["source"] for e in events)
+    return {
+        "total_events": len(events),
+        "by_source": dict(source_counts),
+        "first_event": min((e["date"] for e in events), default=None),
+        "latest_event": max((e["date"] for e in events), default=None),
+    }
+
+
+def find_wikipedia_citations(doi: str) -> list:
+    """Find Wikipedia articles that cite a paper."""
+    events = get_events(doi, source="wikipedia")
+    return [
+        {"wikipedia_page": e["subject_title"],
+         "url": e["subject_url"],
+         "date": e["date"]}
+        for e in events
+        if e["relation"] == "references"
+    ]
+
+
+# Example: analyze online attention for a paper
+doi = "10.1038/nature14539"
+summary = get_attention_summary(doi)
+print(f"Total events: {summary['total_events']}")
+for source, count in sorted(summary["by_source"].items(),
+                             key=lambda x: -x[1]):
+    print(f"  {source}: {count}")
+
+# Example: find Wikipedia coverage
+wiki_refs = find_wikipedia_citations(doi)
+for ref in wiki_refs:
+    print(f"Cited in: {ref['wikipedia_page']} ({ref['date']})")
+```
+
+## Use Cases
+
+1. **Altmetrics research**: Measure non-traditional scholarly impact
+2. **Public engagement**: Track how research reaches public audiences
+3. **Policy monitoring**: Discover when research informs policy documents
+4. **Social media analytics**: Track paper sharing on Twitter, Reddit
+5. **Wikipedia coverage**: Find which papers are cited in encyclopedias
+
+## References
+
+- [Crossref Event Data](https://www.eventdata.crossref.org/)
+- [Event Data API Guide](https://www.eventdata.crossref.org/guide/)
+- [Event Data User Guide](https://www.crossref.org/services/event-data/)