@wentorai/research-plugins 1.0.0 → 1.2.0

package/skills/tools/document/zotero-style-guide/SKILL.md

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+---
+name: zotero-style-guide
+description: "Feature-rich Zotero plugin for UI customization and styling"
+metadata:
+  openclaw:
+    emoji: "🎨"
+    category: "tools"
+    subcategory: "document"
+    keywords: ["Zotero", "styling", "UI customization", "reading progress", "tags", "columns"]
+    source: "https://github.com/MuiseDestiny/zotero-style"
+---
+
+# Zotero Style Guide
+
+## Overview
+
+Zotero Style is one of the most popular Zotero plugins, adding extensive UI customization capabilities — custom columns (IF, citation count, reading progress), color-coded tags, visual indicators, and workflow enhancements. It transforms Zotero's default interface into a more informative and visually organized research library. Essential for researchers managing large paper collections.
+
+## Installation
+
+```bash
+# Download latest .xpi from GitHub releases
+# In Zotero: Tools → Add-ons → Install Add-on From File
+
+# Or install via Zotero Plugin Market
+# 1. Install zotero-addons plugin first
+# 2. Search "Zotero Style" in the marketplace
+```
+
+## Custom Columns
+
+### Impact Factor Column
+
+```json
+// Preferences → Zotero Style → Columns
+{
+  "columns": [
+    {
+      "name": "IF",
+      "field": "extra",
+      "regex": "IF:\\s*([\\d.]+)",
+      "width": 60,
+      "sortable": true
+    }
+  ]
+}
+```
+
+### Citation Count Column
+
+```json
+{
+  "columns": [
+    {
+      "name": "Citations",
+      "field": "extra",
+      "regex": "Citations:\\s*(\\d+)",
+      "width": 70,
+      "sortable": true,
+      "format": "number"
+    }
+  ]
+}
+```
+
+### Reading Progress Column
+
+```json
+{
+  "columns": [
+    {
+      "name": "Progress",
+      "type": "progress",
+      "width": 100,
+      "display": "bar",
+      "colors": {
+        "0-25": "#EF4444",
+        "25-75": "#F59E0B",
+        "75-100": "#10B981"
+      }
+    }
+  ]
+}
+```
+
+## Tag Styling
+
+```json
+// Color-coded tags for visual organization
+{
+  "tagStyles": {
+    "#important": {
+      "color": "#EF4444",
+      "emoji": "🔴",
+      "position": "left"
+    },
+    "#to-read": {
+      "color": "#3B82F6",
+      "emoji": "📖",
+      "position": "left"
+    },
+    "#methodology": {
+      "color": "#8B5CF6",
+      "position": "left"
+    },
+    "#dataset": {
+      "color": "#10B981",
+      "position": "left"
+    }
+  }
+}
+```
+
+## Item Indicators
+
+```json
+// Visual indicators in item list
+{
+  "indicators": {
+    "hasAnnotations": {
+      "icon": "📝",
+      "tooltip": "Has annotations"
+    },
+    "hasNotes": {
+      "icon": "🗒️",
+      "tooltip": "Has notes"
+    },
+    "isRetracted": {
+      "icon": "⚠️",
+      "color": "#EF4444",
+      "tooltip": "Retracted paper"
+    }
+  }
+}
+```
+
+## Workflow Integration
+
+```javascript
+// Zotero Style works with other plugins
+
+// With zotero-actions-tags: auto-tag on read
+// With zotero-better-bibtex: show citekey column
+// With zotero-pdf-translate: translation indicators
+// With zoplicate: duplicate detection badges
+
+// Custom column from Better BibTeX citekey
+{
+  "columns": [{
+    "name": "CiteKey",
+    "field": "citationKey",
+    "width": 120,
+    "plugin": "better-bibtex"
+  }]
+}
+```
+
+## Layout Customization
+
+```json
+{
+  "layout": {
+    "itemPane": {
+      "sections": ["info", "tags", "notes", "related"],
+      "defaultTab": "info"
+    },
+    "columns": {
+      "defaultVisible": [
+        "title", "creator", "year", "IF",
+        "Citations", "Progress", "tags"
+      ],
+      "defaultSort": {
+        "field": "year",
+        "direction": "desc"
+      }
+    },
+    "density": "compact"
+  }
+}
+```
+
+## Recommended Setup for Researchers
+
+```markdown
+### Suggested Columns
+1. Title (auto)
+2. Creator/Authors (auto)
+3. Year (auto)
+4. Publication
+5. IF (from Extra field)
+6. Citations (from Extra field)
+7. Reading Progress (bar)
+8. Tags (color-coded)
+9. CiteKey (if using BibTeX)
+
+### Suggested Tags
+- 🔴 #critical — Must-read papers
+- 🟡 #review — Review/survey papers
+- 🔵 #methodology — Methods papers
+- 🟢 #dataset — Dataset papers
+- 🟣 #baseline — Baseline/comparison
+- ⬜ #to-read — Reading queue
+```
+
+## Use Cases
+
+1. **Library organization**: Visual columns for quick paper assessment
+2. **Reading tracking**: Progress bars for paper reading status
+3. **Impact assessment**: IF and citation count at a glance
+4. **Visual tagging**: Color-coded categorization system
+5. **Custom workflows**: Plugin integration for automated organization
+
+## References
+
+- [Zotero Style GitHub](https://github.com/MuiseDestiny/zotero-style)
+- [Zotero Plugin Development](https://www.zotero.org/support/dev/client_coding/plugin_development)
+- [Zotero Styles Gallery](https://www.zotero.org/styles)

package/skills/tools/knowledge-graph/citation-network-builder/SKILL.md

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+---
+name: citation-network-builder
+description: "Build and analyze citation networks from academic reference data"
+metadata:
+  openclaw:
+    emoji: "spider_web"
+    category: "tools"
+    subcategory: "knowledge-graph"
+    keywords: ["citation network", "bibliometrics", "graph analysis", "co-citation", "bibliographic coupling", "network visualization"]
+    source: "wentor-research-plugins"
+---
+
+# Citation Network Builder
+
+A skill for constructing, analyzing, and visualizing citation networks from academic reference data. Covers data collection from bibliographic databases, network construction using direct citation, co-citation, and bibliographic coupling methods, community detection for identifying research clusters, and practical visualization with tools like Gephi, VOSviewer, and Python NetworkX.
+
+## Data Collection and Preparation
+
+### Source Databases
+
+Citation network analysis requires structured bibliographic data with reference lists. The choice of database determines coverage and available metadata.
+
+```
+Database Comparison for Citation Analysis:
+
+Web of Science (Clarivate):
+  - Format: ISI/WoS plain text, BibTeX, CSV
+  - Coverage: ~21,000 journals, back to 1900
+  - Strengths: Cited reference data is most complete
+  - Limits: 1,000 records per export, subscription required
+  - Best for: High-quality citation network analysis
+
+Scopus (Elsevier):
+  - Format: CSV, BibTeX, RIS
+  - Coverage: ~27,000 journals, back to 1970s for most
+  - Strengths: Broader coverage than WoS, author IDs
+  - Limits: 2,000 records per export, subscription required
+  - Best for: Broader disciplinary coverage
+
+OpenAlex (free):
+  - Format: JSON via REST API
+  - Coverage: ~250M works, all disciplines
+  - Strengths: Free, open, comprehensive, API access
+  - Limits: Reference linking less complete than WoS
+  - Best for: Large-scale analysis, reproducible research
+
+Semantic Scholar (free):
+  - Format: JSON via REST API
+  - Coverage: ~200M papers, strong in CS/Biomed
+  - Strengths: Free, citation context, citation intents
+  - Limits: Weaker coverage in humanities and social sciences
+  - Best for: CS/AI-focused networks, citation intent analysis
+```
+
+### Data Cleaning for Network Construction
+
+```python
+import pandas as pd
+
+def clean_bibliographic_data(records):
+    """
+    Clean and deduplicate bibliographic records for network construction.
+
+    Steps:
+    1. Standardize DOIs (lowercase, strip prefixes)
+    2. Deduplicate by DOI, then by title similarity
+    3. Parse reference lists into structured format
+    4. Filter records missing key fields
+    """
+    # Standardize DOIs
+    records["doi"] = (
+        records["doi"]
+        .str.lower()
+        .str.replace("https://doi.org/", "", regex=False)
+        .str.replace("http://dx.doi.org/", "", regex=False)
+        .str.strip()
+    )
+
+    # Remove duplicates by DOI
+    records = records.drop_duplicates(subset="doi", keep="first")
+
+    # Filter records without references (cannot build citation links)
+    records = records[records["references"].notna()]
+    records = records[records["references"].str.len() > 0]
+
+    return records
+```
+
+## Network Construction Methods
+
+### Direct Citation Network
+
+The simplest approach: paper A cites paper B creates a directed edge from A to B.
+
+```python
+import networkx as nx
+
+def build_direct_citation_network(records):
+    """
+    Build a directed citation network.
+    Nodes = papers, Edges = citation relationships.
+
+    Args:
+        records: DataFrame with 'doi' and 'references' columns
+                 where 'references' is a list of cited DOIs
+    Returns:
+        NetworkX DiGraph
+    """
+    G = nx.DiGraph()
+
+    for _, row in records.iterrows():
+        citing_doi = row["doi"]
+        G.add_node(citing_doi, title=row.get("title", ""),
+                   year=row.get("year", None))
+
+        for ref_doi in row["references"]:
+            G.add_edge(citing_doi, ref_doi)
+
+    return G
+```
+
+### Co-Citation Network
+
+Two papers are co-cited when a third paper cites both. Co-citation strength is the number of papers that cite both. This method identifies intellectual relationships between cited works.
+
+```python
+from itertools import combinations
+from collections import Counter
+
+def build_cocitation_network(records, min_cocitations=2):
+    """
+    Build an undirected co-citation network.
+    Nodes = cited papers, Edges = co-citation frequency.
+    """
+    pair_counts = Counter()
+
+    for _, row in records.iterrows():
+        refs = sorted(set(row["references"]))
+        for a, b in combinations(refs, 2):
+            pair_counts[(a, b)] += 1
+
+    G = nx.Graph()
+    for (a, b), count in pair_counts.items():
+        if count >= min_cocitations:
+            G.add_edge(a, b, weight=count)
+
+    return G
+```
+
+### Bibliographic Coupling Network
+
+Two papers are bibliographically coupled when they share one or more references. This method groups papers with similar theoretical or methodological foundations.
+
+```python
+def build_bibliographic_coupling_network(records, min_shared=3):
+    """
+    Build an undirected bibliographic coupling network.
+    Nodes = citing papers, Edges = number of shared references.
+    """
+    ref_sets = {}
+    for _, row in records.iterrows():
+        ref_sets[row["doi"]] = set(row["references"])
+
+    G = nx.Graph()
+    dois = list(ref_sets.keys())
+    for i in range(len(dois)):
+        for j in range(i + 1, len(dois)):
+            shared = len(ref_sets[dois[i]] & ref_sets[dois[j]])
+            if shared >= min_shared:
+                G.add_edge(dois[i], dois[j], weight=shared)
+
+    return G
+```
+
+## Network Analysis
+
+### Key Metrics
+
+```
+Node-level metrics:
+  - In-degree (direct citation): number of times a paper is cited
+    -> identifies influential papers
+  - Betweenness centrality: how often a node lies on shortest paths
+    -> identifies bridging papers connecting subfields
+  - PageRank: iterative importance score based on who cites the paper
+    -> identifies papers cited by other influential papers
+
+Network-level metrics:
+  - Density: proportion of possible edges that exist
+  - Clustering coefficient: tendency of nodes to form triangles
+  - Average path length: mean shortest path between node pairs
+  - Number of connected components: isolated clusters
+```
+
+### Community Detection
+
+Community detection algorithms identify clusters of densely connected papers, corresponding to research subfields or intellectual traditions.
+
+```python
+import community as community_louvain
+
+def detect_communities(G):
+    """
+    Detect communities using the Louvain algorithm.
+    Returns a dictionary mapping node -> community_id.
+    """
+    partition = community_louvain.best_partition(G, weight="weight")
+
+    # Summarize communities
+    communities = {}
+    for node, comm_id in partition.items():
+        communities.setdefault(comm_id, []).append(node)
+
+    for comm_id, members in sorted(communities.items()):
+        print(f"Community {comm_id}: {len(members)} papers")
+
+    return partition
+```
+
+## Visualization
+
+### Tool Recommendations
+
+```
+Gephi (desktop application):
+  - Best for: Interactive exploration of medium networks (1k-50k nodes)
+  - Layout algorithms: ForceAtlas2, Fruchterman-Reingold
+  - Export: SVG, PDF, PNG
+  - Workflow: Import GEXF/GraphML -> layout -> partition by community
+              -> adjust sizes by centrality -> export
+
+VOSviewer (desktop application):
+  - Best for: Bibliometric networks specifically
+  - Direct import from WoS/Scopus export files
+  - Built-in clustering and overlay visualizations
+  - Limitation: less customizable than Gephi
+
+Python (matplotlib, pyvis):
+  - Best for: Reproducible, scriptable visualizations
+  - Use pyvis for interactive HTML network graphs
+  - Use matplotlib for static publication-quality figures
+```
+
+Citation network analysis provides a quantitative lens on the structure of scientific knowledge, revealing invisible colleges, emerging research fronts, and foundational works that shape entire disciplines.