tomesphere
Server Details
Search 8.5M scientific papers with LLM TLDRs, citations, linked entities, figures, and full text.
- Status
- Healthy
- Uptime
- 100.0% over the last 24 hours
- OAuth
- Works in Glama
- Last Tested
- Transport
- Streamable HTTP · MCP 2025-03-26
- URL
- ChatGPT
- –
- Claude
- –
TDQS
Scored across 9 tools
Each tool targets a distinct resource: citations vs references cleanly split citing vs cited papers, get_paper/get_full_text/get_figures/get_entities each retrieve a different aspect of a paper, and search_papers vs similar_papers are clearly different retrieval modes. No two tools appear interchangeable.
The majority follow a consistent 'get_' + noun pattern (get_paper, get_full_text, get_entities, get_figures, get_structure), with search_papers and similar_papers as verb/adjective+noun. However, 'citations' and 'references' are bare nouns, deviating slightly from the pattern, so naming is mostly but not fully uniform.
Nine tools form a well-scoped set for a scholarly-paper server, covering discovery (search, similar), retrieval (paper, full text, figures), graph relations (references, citations), and extra metadata (entities, structures). Each tool serves a clear purpose with no redundancy.
The core workflows for finding, fetching, and exploring papers are well covered: search, metadata, full text, figures, references, citations, and entities. Minor gaps exist such as no direct author/profile lookup or batch retrieval, and some deep API-specific features are absent, but these do not block common tasks.
Available Tools
9 toolscitationsARead-onlyInspect
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.
| Name | Required | Description | Default |
|---|---|---|---|
| k | No | Max citing papers (default 25, max 100). | |
| id | Yes | arXiv ID or OpenAlex Work ID. |
get_entitiesARead-onlyInspect
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.
| Name | Required | Description | Default |
|---|---|---|---|
| id | Yes | arXiv ID, PMC ID, or 10.1101/… DOI. |
get_figuresARead-onlyInspect
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.
| Name | Required | Description | Default |
|---|---|---|---|
| id | Yes | arXiv ID, PMC ID, or 10.1101/… DOI. |
get_full_textARead-onlyInspect
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/…).
| Name | Required | Description | Default |
|---|---|---|---|
| id | Yes | arXiv ID, PMC ID, or 10.1101/… DOI. |
get_paperARead-onlyInspect
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.
| Name | Required | Description | Default |
|---|---|---|---|
| id | Yes | arXiv ID like '2401.12345' or OpenAlex Work ID like 'W4390723197'. |
get_structureARead-onlyInspect
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.
| Name | Required | Description | Default |
|---|---|---|---|
| name | Yes | Gene/protein symbol (TP53, CD44) or UniProt accession (P04637). |
referencesARead-onlyInspect
Get the papers that this paper cites (its bibliography). Use when the user asks 'what does X cite' or 'show me the references'.
| Name | Required | Description | Default |
|---|---|---|---|
| k | No | Max references (default 25, max 100). | |
| id | Yes | arXiv ID or OpenAlex Work ID. |
search_papersARead-onlyInspect
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'.
| Name | Required | Description | Default |
|---|---|---|---|
| k | No | Number of results (default 10, max 25). | |
| query | Yes | Natural-language search query. E.g. 'transformer attention efficiency', 'graph neural networks for molecular property prediction'. | |
| year_max | No | Latest publication year. | |
| year_min | No | Earliest publication year, e.g. 2024. |
similar_papersARead-onlyInspect
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'.
| Name | Required | Description | Default |
|---|---|---|---|
| k | No | Number of neighbors (default 10, max 25). | |
| id | Yes | arXiv ID or OpenAlex Work ID. |
Tool Schema Changelog
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
9 tool updates
- First observed
citations - First observed
get_entities - First observed
get_figures - First observed
get_full_text - First observed
get_paper - First observed
get_structure - First observed
references - First observed
search_papers - First observed
similar_papers
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