MCP Radar
MCP Server

tomesphere

com.tomesphere/tomesphere
Science & Engineering Search & Research Public & reachable MCP 2026-07-28

What this MCP does

Searches and retrieves scientific papers, full text, citations, figures, linked biomedical entities, related papers, and protein structure references.

Capabilities

Tools

9 tools
citations
Get papers that cite the given paper (who refers to this work). Use when the user asks 'who cites X', 'what's the impact', or wants follow-up work. Note: 2024+ citation coverage is sparse; indexing in progress.
Read only Open world
Input schema 
{'type': 'object', 'required': ['id'], 'properties': {'k': {'type': 'integer', 'default': 25, 'description': 'Max citing papers (default 25, max 100).'}, 'id': {'type': 'string', 'description': 'arXiv ID or OpenAlex Work ID.'}}}
get_entities
Get the biomedical entities linked to a paper: genes, proteins, chemicals, diseases, species, mutations, cell lines, and clinical-trial (NCT) IDs. Accepts an arXiv ID, PMC ID, or bioRxiv/medRxiv DOI.
Read only Open world
Input schema 
{'type': 'object', 'required': ['id'], 'properties': {'id': {'type': 'string', 'description': 'arXiv ID, PMC ID, or 10.1101/… DOI.'}}}
get_figures
Get a paper's real figure images — URLs, labels, and captions. Most biomedical papers have figures; arXiv papers often don't. Accepts an arXiv ID, PMC ID, or bioRxiv/medRxiv DOI.
Read only Open world
Input schema 
{'type': 'object', 'required': ['id'], 'properties': {'id': {'type': 'string', 'description': 'arXiv ID, PMC ID, or 10.1101/… DOI.'}}}
get_full_text
Fetch a paper's full body text as Markdown (methods, results, protocols, inline tables) — use for deep questions the abstract can't answer. Accepts an arXiv ID (2401.12345), a PMC ID (PMC5339222), or a bioRxiv/medRxiv DOI (10.1101/…).
Read only Open world
Input schema 
{'type': 'object', 'required': ['id'], 'properties': {'id': {'type': 'string', 'description': 'arXiv ID, PMC ID, or 10.1101/… DOI.'}}}
get_paper
Fetch a paper's full metadata: title, authors, year, abstract, TLDR (LLM-generated), key findings, citation count, GitHub repos, HuggingFace models/datasets, videos, peer reviews, and links. Accepts an arXiv ID (e.g. '2401.12345' or '1706.03762v5') or an OpenAlex Work ID (e.g. 'W4390723197'). Use when the user names a specific paper or pastes an arXiv link.
Read only Open world
Input schema 
{'type': 'object', 'required': ['id'], 'properties': {'id': {'type': 'string', 'description': "arXiv ID like '2401.12345' or OpenAlex Work ID like 'W4390723197'."}}}
get_structure
Resolve a gene/protein name (e.g. 'TP53', 'CD44') or UniProt accession to its 3D structure — returns the UniProt accession + AlphaFold model URL (and PDB when available). Great for a gene named in a paper's entities.
Read only Open world
Input schema 
{'type': 'object', 'required': ['name'], 'properties': {'name': {'type': 'string', 'description': 'Gene/protein symbol (TP53, CD44) or UniProt accession (P04637).'}}}
references
Get the papers that this paper cites (its bibliography). Use when the user asks 'what does X cite' or 'show me the references'.
Read only Open world
Input schema 
{'type': 'object', 'required': ['id'], 'properties': {'k': {'type': 'integer', 'default': 25, 'description': 'Max references (default 25, max 100).'}, 'id': {'type': 'string', 'description': 'arXiv ID or OpenAlex Work ID.'}}}
search_papers
Search 8.5 million academic papers (arXiv + biomedical: PMC / bioRxiv / medRxiv, all disciplines) by topic, keyword, author, or linked entity (gene / protein / disease). Each hit returns id, title, TLDR, type, and links. Use to find papers about a topic, e.g. 'transformer efficiency' or 'CRISPR base editing'.
Read only Open world
Input schema 
{'type': 'object', 'required': ['query'], 'properties': {'k': {'type': 'integer', 'default': 10, 'description': 'Number of results (default 10, max 25).'}, 'query': {'type': 'string', 'description': "Natural-language search query. E.g. 'transformer attention efficiency', 'graph neural networks for molecular property prediction'."}, 'year_max': {'type': 'integer', 'description': 'Latest publication year.'}, 'year_min': {'type': 'integer', 'description': 'Earliest publication year, e.g. 2024.'}}}
similar_papers
Find papers semantically similar to a given paper using SPECTER2 embeddings (trained on scientific-citation triplets). Returns nearest neighbors with TLDR. Use when the user wants 'papers like X' or 'what's adjacent to this work'.
Read only Open world
Input schema 
{'type': 'object', 'required': ['id'], 'properties': {'k': {'type': 'integer', 'default': 10, 'description': 'Number of neighbors (default 10, max 25).'}, 'id': {'type': 'string', 'description': 'arXiv ID or OpenAlex Work ID.'}}}
History

Recent tool changes

Added
get_structure
Sept. 17, 2026, 12:38 p.m.
Added
get_entities
Sept. 17, 2026, 12:38 p.m.
Added
get_figures
Sept. 17, 2026, 12:38 p.m.
Added
get_full_text
Sept. 17, 2026, 12:38 p.m.
Added
references
Sept. 17, 2026, 12:38 p.m.
Added
citations
Sept. 17, 2026, 12:38 p.m.
Added
similar_papers
Sept. 17, 2026, 12:38 p.m.
Added
get_paper
Sept. 17, 2026, 12:38 p.m.
Added
search_papers
Sept. 17, 2026, 12:38 p.m.
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