@wentorai/research-plugins 1.0.0 → 1.2.0

package/skills/literature/metadata/doi-content-negotiation/SKILL.md

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+---
+name: doi-content-negotiation
+description: "Retrieve structured metadata from any DOI via HTTP content negotiation"
+metadata:
+  openclaw:
+    emoji: "🔗"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["DOI", "content negotiation", "metadata retrieval", "BibTeX", "citation metadata", "linked data"]
+    source: "https://citation.crosscite.org/"
+---
+
+# DOI Content Negotiation
+
+## Overview
+
+Any DOI can return structured metadata in multiple formats through HTTP content negotiation — simply set the `Accept` header when requesting `https://doi.org/{doi}`. This is the most universal way to get citation metadata, BibTeX entries, JSON-LD, and RDF from any publisher without needing a specific API. Works for all 300M+ registered DOIs. Free, no authentication.
+
+## Usage
+
+### Basic Content Negotiation
+
+```bash
+# Get JSON citation metadata (Citeproc JSON)
+curl -LH "Accept: application/vnd.citationstyles.csl+json" \
+  "https://doi.org/10.1038/nature14539"
+
+# Get BibTeX
+curl -LH "Accept: application/x-bibtex" \
+  "https://doi.org/10.1038/nature14539"
+
+# Get RIS format
+curl -LH "Accept: application/x-research-info-systems" \
+  "https://doi.org/10.1038/nature14539"
+
+# Get formatted citation (APA style)
+curl -LH "Accept: text/x-bibliography; style=apa" \
+  "https://doi.org/10.1038/nature14539"
+
+# Get formatted citation (Chicago style)
+curl -LH "Accept: text/x-bibliography; style=chicago-author-date" \
+  "https://doi.org/10.1038/nature14539"
+```
+
+### Available Formats
+
+| Accept Header | Format | Use Case |
+|--------------|--------|----------|
+| `application/vnd.citationstyles.csl+json` | Citeproc JSON | Programmatic metadata |
+| `application/x-bibtex` | BibTeX | LaTeX bibliography |
+| `application/x-research-info-systems` | RIS | Reference managers |
+| `text/x-bibliography; style=apa` | Formatted text | Direct citation |
+| `application/rdf+xml` | RDF/XML | Linked data |
+| `text/turtle` | Turtle RDF | Linked data |
+| `application/vnd.schemaorg.ld+json` | Schema.org JSON-LD | Web metadata |
+| `application/json` | DataCite JSON | DataCite DOIs |
+| `application/vnd.crossref.unixref+xml` | Crossref XML | Full Crossref metadata |
+
+### Citation Styles
+
+Over 9,000 CSL styles available:
+
+```bash
+# APA 7th edition
+style=apa
+
+# Chicago Manual of Style (author-date)
+style=chicago-author-date
+
+# IEEE
+style=ieee
+
+# MLA
+style=modern-language-association
+
+# Harvard
+style=harvard-cite-them-right
+
+# Vancouver (medical)
+style=vancouver
+
+# Nature
+style=nature
+```
+
+## Citeproc JSON Response
+
+```json
+{
+  "DOI": "10.1038/nature14539",
+  "type": "article-journal",
+  "title": "Deep learning",
+  "author": [
+    {"given": "Yann", "family": "LeCun"},
+    {"given": "Yoshua", "family": "Bengio"},
+    {"given": "Geoffrey", "family": "Hinton"}
+  ],
+  "container-title": "Nature",
+  "volume": "521",
+  "issue": "7553",
+  "page": "436-444",
+  "issued": {"date-parts": [[2015, 5, 28]]},
+  "publisher": "Springer Science and Business Media LLC",
+  "ISSN": ["0028-0836", "1476-4687"],
+  "URL": "http://dx.doi.org/10.1038/nature14539",
+  "abstract": "Deep learning allows computational models..."
+}
+```
+
+## Python Usage
+
+```python
+import requests
+
+
+def get_metadata(doi: str) -> dict:
+    """Get structured metadata for a DOI."""
+    resp = requests.get(
+        f"https://doi.org/{doi}",
+        headers={"Accept": "application/vnd.citationstyles.csl+json"},
+        allow_redirects=True,
+    )
+    resp.raise_for_status()
+    return resp.json()
+
+
+def get_bibtex(doi: str) -> str:
+    """Get BibTeX entry for a DOI."""
+    resp = requests.get(
+        f"https://doi.org/{doi}",
+        headers={"Accept": "application/x-bibtex"},
+        allow_redirects=True,
+    )
+    resp.raise_for_status()
+    return resp.text
+
+
+def get_formatted_citation(doi: str,
+                            style: str = "apa") -> str:
+    """Get a formatted citation string."""
+    resp = requests.get(
+        f"https://doi.org/{doi}",
+        headers={
+            "Accept": f"text/x-bibliography; style={style}",
+        },
+        allow_redirects=True,
+    )
+    resp.raise_for_status()
+    return resp.text.strip()
+
+
+def batch_bibtex(dois: list) -> str:
+    """Generate BibTeX file for multiple DOIs."""
+    entries = []
+    for doi in dois:
+        try:
+            bib = get_bibtex(doi)
+            entries.append(bib)
+        except requests.HTTPError:
+            entries.append(f"% Failed to resolve: {doi}")
+    return "\n\n".join(entries)
+
+
+# Example: get metadata
+meta = get_metadata("10.1038/nature14539")
+authors = ", ".join(
+    f"{a['given']} {a['family']}" for a in meta.get("author", [])
+)
+print(f"{meta['title']}")
+print(f"  Authors: {authors}")
+print(f"  {meta.get('container-title')} ({meta.get('volume')})")
+
+# Example: get BibTeX
+bibtex = get_bibtex("10.1038/nature14539")
+print(f"\nBibTeX:\n{bibtex}")
+
+# Example: formatted APA citation
+apa = get_formatted_citation("10.1038/nature14539", "apa")
+print(f"\nAPA: {apa}")
+
+# Example: batch export
+bibliography = batch_bibtex([
+    "10.1038/nature14539",
+    "10.5555/3295222.3295349",
+])
+with open("references.bib", "w") as f:
+    f.write(bibliography)
+```
+
+## Use Cases
+
+1. **Bibliography generation**: Export BibTeX/RIS for any DOI list
+2. **Citation formatting**: Generate properly formatted citations
+3. **Metadata extraction**: Get structured metadata for data pipelines
+4. **Linked data**: Retrieve RDF for knowledge graph construction
+5. **Verification**: Confirm publication details from authoritative source
+
+## References
+
+- [DOI Content Negotiation](https://citation.crosscite.org/docs.html)
+- [Crossref Content Negotiation](https://www.crossref.org/documentation/retrieve-metadata/content-negotiation/)
+- [CSL Style Repository](https://github.com/citation-style-language/styles)

package/skills/literature/metadata/orkg-api/SKILL.md

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+---
+name: orkg-api
+description: "Query the Open Research Knowledge Graph for structured research data"
+metadata:
+  openclaw:
+    emoji: "🕸️"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["knowledge graph", "research data", "structured research", "ORKG", "research contributions", "scholarly graph"]
+    source: "https://orkg.org/"
+---
+
+# Open Research Knowledge Graph (ORKG) API
+
+## Overview
+
+The Open Research Knowledge Graph (ORKG) transforms unstructured scholarly articles into structured, machine-readable research contributions. Unlike traditional databases that store metadata (title, authors, DOI), ORKG captures the semantic content — research problems, methods, results, and their relationships. The REST API enables querying, creating, and comparing research contributions programmatically. Free, no authentication required for read operations.
+
+## API Endpoints
+
+### Base URL
+
+```
+https://orkg.org/api/
+```
+
+### Search Papers
+
+```bash
+# Search papers in ORKG
+curl "https://orkg.org/api/papers?q=climate+change+adaptation&size=20"
+
+# Get paper details by ID
+curl "https://orkg.org/api/papers/R12345"
+```
+
+### Search Resources
+
+```bash
+# Search any resource (papers, predicates, comparisons)
+curl "https://orkg.org/api/resources?q=machine+learning&size=20"
+
+# Filter by class
+curl "https://orkg.org/api/resources?q=BERT&exact=false&classes=Paper"
+```
+
+### Comparisons
+
+ORKG's unique feature — structured side-by-side comparison of papers:
+
+```bash
+# List comparisons
+curl "https://orkg.org/api/comparisons?size=10"
+
+# Get a specific comparison
+curl "https://orkg.org/api/comparisons/R54321"
+
+# Search comparisons
+curl "https://orkg.org/api/comparisons?q=sentiment+analysis"
+```
+
+### Research Contributions
+
+```bash
+# Get contributions of a paper
+curl "https://orkg.org/api/papers/R12345/contributions"
+
+# A contribution describes what a paper contributes:
+# - Research problem addressed
+# - Method used
+# - Results achieved
+# - Materials/datasets used
+```
+
+## Python Usage
+
+```python
+import requests
+
+BASE_URL = "https://orkg.org/api"
+
+def search_orkg_papers(query: str, size: int = 20) -> list:
+    """Search papers in the Open Research Knowledge Graph."""
+    resp = requests.get(f"{BASE_URL}/papers", params={"q": query, "size": size})
+    resp.raise_for_status()
+    data = resp.json()
+
+    papers = []
+    for item in data.get("content", []):
+        papers.append({
+            "id": item.get("id"),
+            "title": item.get("title"),
+            "created": item.get("created_at"),
+            "contributions": item.get("contributions", [])
+        })
+    return papers
+
+def get_paper_contributions(paper_id: str) -> dict:
+    """Get structured research contributions for a paper."""
+    resp = requests.get(f"{BASE_URL}/papers/{paper_id}/contributions")
+    resp.raise_for_status()
+    return resp.json()
+
+def search_comparisons(topic: str) -> list:
+    """Find structured paper comparisons on a topic."""
+    resp = requests.get(f"{BASE_URL}/comparisons", params={"q": topic, "size": 10})
+    resp.raise_for_status()
+    return resp.json().get("content", [])
+
+# Example usage
+papers = search_orkg_papers("transfer learning NLP")
+for p in papers:
+    print(f"[{p['id']}] {p['title']}")
+
+comparisons = search_comparisons("named entity recognition")
+for c in comparisons:
+    print(f"Comparison: {c.get('title')} ({len(c.get('contributions', []))} papers)")
+```
+
+## Key Concepts
+
+| Concept | Description | Example |
+|---------|-------------|---------|
+| **Paper** | A scholarly article with metadata | "Attention Is All You Need" |
+| **Contribution** | What a paper contributes to knowledge | "Proposes self-attention mechanism" |
+| **Research Problem** | The problem a contribution addresses | "Machine translation quality" |
+| **Predicate** | A relationship type | "has_method", "has_result", "uses_dataset" |
+| **Comparison** | Side-by-side structured comparison | "Transformer variants comparison" |
+| **Resource** | Any entity in the knowledge graph | A method, dataset, metric, or concept |
+
+## ORKG vs Traditional Databases
+
+| Feature | Traditional (S2, Crossref) | ORKG |
+|---------|---------------------------|------|
+| Content | Metadata (title, DOI, citations) | Semantic content (methods, results) |
+| Structure | Flat records | Knowledge graph with relationships |
+| Comparison | Manual (read each paper) | Automated structured comparisons |
+| Machine-readable | Bibliographic metadata only | Research contributions structured |
+| Coverage | Broad (200M+ papers) | Deep but narrower (~50K papers) |
+
+## Use Cases
+
+1. **Literature surveys**: Find existing comparisons to quickly understand a field
+2. **Method selection**: Compare methods across papers on structured criteria
+3. **Gap analysis**: Identify research problems without solutions
+4. **Reproducibility**: Access structured descriptions of experimental setups
+
+## References
+
+- [ORKG Website](https://orkg.org/)
+- [ORKG API Documentation](https://orkg.org/api/)
+- [ORKG Help Center](https://orkg.org/help-center)
+- Jaradeh, M.Y., et al. (2019). "Open Research Knowledge Graph: Next Generation Infrastructure for Semantic Scholarly Knowledge." *K-CAP 2019*.

package/skills/literature/metadata/plumx-metrics-api/SKILL.md

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+---
+name: plumx-metrics-api
+description: "Track research impact beyond citations via PlumX altmetrics API"
+metadata:
+  openclaw:
+    emoji: "📊"
+    category: "literature"
+    subcategory: "metadata"
+    keywords: ["PlumX", "altmetrics", "research impact", "social media metrics", "usage statistics", "scholarly metrics"]
+    source: "https://plumanalytics.com/"
+---
+
+# PlumX Metrics API
+
+## Overview
+
+PlumX (by Elsevier/Plum Analytics) tracks 5 categories of research impact metrics beyond traditional citations: Usage, Captures, Mentions, Social Media, and Citations. It covers 130M+ research artifacts including articles, datasets, presentations, and videos. Available via Elsevier's API infrastructure. Requires an Elsevier API key.
+
+## Metric Categories
+
+| Category | What it measures | Examples |
+|----------|-----------------|---------|
+| **Usage** | Reading/viewing | Abstract views, PDF downloads, HTML views |
+| **Captures** | Saving for later | Mendeley readers, CiteULike bookmarks |
+| **Mentions** | Commentary | Blog posts, news articles, Wikipedia refs |
+| **Social Media** | Sharing/discussion | Tweets, Facebook shares, Reddit posts |
+| **Citations** | Formal references | Scopus, CrossRef, PubMed citations |
+
+## API Endpoints
+
+### Base URL
+
+```
+https://api.elsevier.com/analytics/plumx/
+```
+
+### Get Metrics by DOI
+
+```bash
+curl -H "X-ELS-APIKey: $ELSEVIER_API_KEY" \
+  "https://api.elsevier.com/analytics/plumx/doi/10.1038/nature14539"
+```
+
+### Get Metrics by Other IDs
+
+```bash
+# By PubMed ID
+curl -H "X-ELS-APIKey: $ELSEVIER_API_KEY" \
+  "https://api.elsevier.com/analytics/plumx/pmid/25428114"
+
+# By ISBN
+curl -H "X-ELS-APIKey: $ELSEVIER_API_KEY" \
+  "https://api.elsevier.com/analytics/plumx/isbn/9780262035613"
+
+# By Scopus ID
+curl -H "X-ELS-APIKey: $ELSEVIER_API_KEY" \
+  "https://api.elsevier.com/analytics/plumx/scopusId/84920765826"
+```
+
+## Response Structure
+
+```json
+{
+  "count_categories": [
+    {
+      "name": "capture",
+      "total": 15432,
+      "count_types": [
+        {"name": "READER_COUNT", "total": 15432, "sources": [
+          {"name": "Mendeley", "total": 15432}
+        ]}
+      ]
+    },
+    {
+      "name": "socialMedia",
+      "total": 3250,
+      "count_types": [
+        {"name": "TWEET_COUNT", "total": 2800},
+        {"name": "FACEBOOK_COUNT", "total": 450}
+      ]
+    },
+    {
+      "name": "citation",
+      "total": 2100,
+      "count_types": [
+        {"name": "Scopus", "total": 1800},
+        {"name": "CrossRef", "total": 2100}
+      ]
+    },
+    {
+      "name": "usage",
+      "total": 45000,
+      "count_types": [
+        {"name": "ABSTRACT_VIEWS", "total": 30000},
+        {"name": "LINK_OUTS", "total": 15000}
+      ]
+    },
+    {
+      "name": "mention",
+      "total": 85,
+      "count_types": [
+        {"name": "NEWS_COUNT", "total": 45},
+        {"name": "BLOG_COUNT", "total": 25},
+        {"name": "WIKIPEDIA_COUNT", "total": 15}
+      ]
+    }
+  ]
+}
+```
+
+## Python Usage
+
+```python
+import os
+import requests
+
+API_KEY = os.environ["ELSEVIER_API_KEY"]
+BASE_URL = "https://api.elsevier.com/analytics/plumx"
+HEADERS = {"X-ELS-APIKey": API_KEY, "Accept": "application/json"}
+
+
+def get_plumx_metrics(doi: str) -> dict:
+    """Get PlumX metrics for a paper by DOI."""
+    resp = requests.get(
+        f"{BASE_URL}/doi/{doi}",
+        headers=HEADERS,
+    )
+    resp.raise_for_status()
+    data = resp.json()
+
+    metrics = {}
+    for cat in data.get("count_categories", []):
+        category_name = cat["name"]
+        metrics[category_name] = {
+            "total": cat["total"],
+            "breakdown": {},
+        }
+        for ct in cat.get("count_types", []):
+            metrics[category_name]["breakdown"][ct["name"]] = ct["total"]
+    return metrics
+
+
+def compare_impact(dois: list) -> list:
+    """Compare PlumX metrics across multiple papers."""
+    results = []
+    for doi in dois:
+        metrics = get_plumx_metrics(doi)
+        results.append({
+            "doi": doi,
+            "citations": metrics.get("citation", {}).get("total", 0),
+            "captures": metrics.get("capture", {}).get("total", 0),
+            "social": metrics.get("socialMedia", {}).get("total", 0),
+            "usage": metrics.get("usage", {}).get("total", 0),
+            "mentions": metrics.get("mention", {}).get("total", 0),
+        })
+    return results
+
+
+# Example: analyze a paper's multi-dimensional impact
+metrics = get_plumx_metrics("10.1038/nature14539")
+for category, data in metrics.items():
+    print(f"\n{category.upper()} (total: {data['total']})")
+    for metric_type, count in data["breakdown"].items():
+        print(f"  {metric_type}: {count}")
+
+# Example: compare two papers
+# comparison = compare_impact([
+#     "10.1038/nature14539",
+#     "10.1126/science.aax2342",
+# ])
+```
+
+## PlumX vs Other Altmetric Services
+
+| Feature | PlumX | Altmetric.com | Crossref Event Data |
+|---------|-------|---------------|---------------------|
+| Metric categories | 5 comprehensive | Attention Score | Events only |
+| Coverage | 130M+ artifacts | 30M+ outputs | DOI-based |
+| Social media | Twitter, Facebook, Reddit | Twitter, Reddit, News | Twitter, Reddit, Wikipedia |
+| Usage data | Yes (views, downloads) | No | No |
+| Capture data | Yes (Mendeley readers) | Mendeley readers | No |
+| Free access | Limited | Limited widget | Full API free |
+
+## References
+
+- [PlumX Metrics](https://plumanalytics.com/learn/about-metrics/)
+- [Elsevier Developer Portal](https://dev.elsevier.com/)
+- [PlumX API Documentation](https://dev.elsevier.com/documentation/PlumXMetricsAPI.wadl)