tomesphere

Tools

Token cost is the o200k count of the tools list JSON, including schemas, before any tool is called.

• 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, TL

• 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 a

• 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 '

• 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

• references

  Get the papers that this paper cites (its bibliography). Use when the user asks 'what does X cite' or 'show me the references'.

• 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

• 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.

• 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.

• 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 p