search

Execute a literature search across Scopus, PubMed, and OpenAlex databases

vibe-science:search

Execute a literature search across databases.

When to Use

  • During /vibe-science:loop discovery phase
  • Ad-hoc searches outside the main loop
  • Exploring a tangent or serendipity lead

Usage

/vibe-science:search [query]                    # Search all databases
/vibe-science:search --scopus [query]           # Scopus only
/vibe-science:search --pubmed [query]           # PubMed only
/vibe-science:search --openalex [query]         # OpenAlex only
/vibe-science:search --author [name]            # Author search
/vibe-science:search --citations [DOI]          # Papers citing this DOI

Database Priority

  1. Scopus - Most comprehensive, has citation data
  2. PubMed - Best for biomedical, free API
  3. OpenAlex - Open data, good for connections

Search Syntax

Scopus

# Basic
TITLE-ABS-KEY(term1 AND term2)

# Phrase
TITLE-ABS-KEY("exact phrase")

# Field-specific
TITLE("in title only") AND ABS("in abstract")

# Author
AU-ID(12345678)
AUTHLAST(Smith) AND AUTHFIRST(J)

# Date range
PUBYEAR > 2020
PUBYEAR = 2023

# Document type
DOCTYPE(ar)  # articles
DOCTYPE(re)  # reviews

# Combining
TITLE-ABS-KEY("optimal transport") AND TITLE-ABS-KEY("data integration") AND PUBYEAR > 2020

# Sort (via API parameter)
&sort=citedby-count   # Most cited
&sort=pubyear         # Most recent

PubMed

# Basic
term1 AND term2

# Phrase
"exact phrase"

# Field-specific
term[Title]
term[Abstract]
term[MeSH Terms]

# Author
Smith J[Author]

# Date range
2020:2024[Publication Date]

# Article type
Review[Publication Type]

# Combining
"optimal transport"[Title] AND "data integration"[Title/Abstract] AND 2020:2024[pdat]

OpenAlex

# Search works
https://api.openalex.org/works?search=term1 term2

# Filter
?filter=publication_year:2020-2024
?filter=cited_by_count:>100
?filter=author.id:A123456

# Combining
?search=optimal transport data integration&filter=publication_year:>2020

# Sorting
&sort=cited_by_count:desc
&sort=publication_date:desc

Process

Step 1: Parse Query

Input: /vibe-science:search optimal transport data integration

Parsed:
- Terms: ["optimal transport", "data integration"]
- Databases: all
- Filters: none
- Sort: relevance

Step 2: Execute Searches

Run searches across all selected databases.

Step 3: Deduplicate and Merge

Combine results, remove duplicates, categorize.

Step 4: Identify Gaps

Gap analysis:
- "optimal transport" + "data integration": 57 papers
- "unbalanced optimal transport" + "data integration": 0 papers  ← POTENTIAL GAP
- "optimal transport" + "cross-domain transfer": 3 papers ← SPARSE AREA

Step 5: Log Results

Log to queries.log and PROGRESS.md.

Step 6: Output Summary

Report total results, key findings, identified gaps, recommended deep-dives.

Anti-Hallucination

For every search result:

  • Store DOI/PMID
  • Verify DOI resolves before citing
  • Never fabricate paper titles or authors
  • Mark confidence based on source verification