Medical-research-skills semantic-scholar-database

Source: https://github.com/aipoch/medical-research-skills

When to Use

• You need to find relevant papers by keyword, title, or known identifiers (e.g., Semantic Scholar Paper ID).
• You want to fetch detailed metadata for a paper (abstract, venue, year, fields of study, etc.).
• You need author-centric information such as an author profile and their publications.
• You want to explore a citation network by traversing references or citations for a given paper.
• You are building a literature review workflow that requires programmatic access to scholarly graph data.

Key Features

• Paper search via the Semantic Scholar Graph API.
• Paper details retrieval (e.g., abstract, venue, citations-related fields depending on requested fields).
• Author details retrieval (author profile and associated papers depending on requested fields).
• Citation graph traversal:
  • Fetch papers that cite a target paper (

    citations

    )
  • Fetch papers referenced by a target paper (

    references

    )
• Optional API key support for higher rate limits via environment variable.

Dependencies

• Python

  >=3.9

• requests >=2.25.0

Example Usage

import os
from scripts.client import (
    search_papers,
    get_paper_details,
    get_author_details,
    get_citations,
)

# Optional: set for higher rate limits
# os.environ["S2_API_KEY"] = "YOUR_API_KEY"

def main():
    # 1) Search papers
    results = search_papers(query="Attention Is All You Need", limit=5)
    print("Search results (top 5):")
    for i, p in enumerate(results, 1):
        # The exact keys depend on the fields requested by the client implementation.
        print(f"{i}. {p.get('title')} ({p.get('year')}) - paperId={p.get('paperId')}")

    # 2) Get paper details
    paper_id = "649def34f8be52c8b66281af98ae884c09aef38b"
    paper = get_paper_details(paper_id=paper_id)
    print("\nPaper details:")
    print("Title:", paper.get("title"))
    print("Venue:", paper.get("venue"))
    print("Year:", paper.get("year"))
    print("Abstract:", (paper.get("abstract") or "")[:300], "...")

    # 3) Get author details
    author_id = "1741101"
    author = get_author_details(author_id=author_id)
    print("\nAuthor details:")
    print("Name:", author.get("name"))
    print("AuthorId:", author.get("authorId"))

    # 4) Traverse citations / references
    citing = get_citations(paper_id=paper_id, method="citations")
    refs = get_citations(paper_id=paper_id, method="references")
    print("\nCitation traversal:")
    print("Citations count:", len(citing) if isinstance(citing, list) else "N/A")
    print("References count:", len(refs) if isinstance(refs, list) else "N/A")

if __name__ == "__main__":
    main()

Implementation Details

• API Endpoint: The skill communicates with the Semantic Scholar Graph API:
  • Base URL:

    https://api.semanticscholar.org/graph/v1/

• HTTP Client: Uses

  requests

  to perform REST calls.
• Authentication / Rate Limits:
  • If

    S2_API_KEY

    is set in the environment, requests should include it (typically via an

    x-api-key

    header) to obtain higher rate limits.
  • Without an API key, the API may enforce stricter rate limiting.
• Core Operations (as implemented in

  scripts/client.py

  ):

  • search_papers(query, limit=...)

    : queries the search endpoint and returns a list of matching papers.

  • get_paper_details(paper_id)

    : fetches metadata for a specific paper ID.

  • get_author_details(author_id)

    : fetches metadata for a specific author ID.

  • get_citations(paper_id, method="citations"|"references")

    : traverses the citation graph by selecting either inbound citations or outbound references.
• Parameters:

  • limit

    : controls the maximum number of results returned by search.

  • method

    : must be either

    "citations"

    or

    "references"

    to select traversal direction.