The Forge

Execution engine. 15 substrate-invocable scientific tools — search PubMed, lookup genes, extract figures, query the knowledge graph, run an LLM completion.

Browse all tools → Substrate API verbs →

tools

runs · 7d

benchmarks

personas

Recent runs

All runs →

No invocations yet — kick off a run on a tool below.

Tool registry

All 15 →

general 15

uniprot_lookup

Resolve a protein identifier to UniProt metadata (sequence, function, domains, PTMs).
scidex_search

Lexical full-text search across all indexed substrate artifacts.
scidex_get

Fetch a single artifact by ref. Returns full envelope with content, signals, and links.
pubmed_search

Search PubMed for biomedical papers matching a query. Bridges to v1's pubmed_search service.
pdf_extract

Extract structured content (sections, figures, tables, references) from a PDF URL.
pathway_lookup

Resolve a pathway name or id to its members, parent pathway, and annotations (Reactome / KEGG / WikiPathways).
llm_complete

General-purpose LLM completion. Routes through v1's LLM gateway (model selection + budget enforcement).
knowledge_graph_query

Query the SciDEX knowledge graph (entities + typed edges) by SPARQL-flavored predicates.
gene_lookup

Resolve a gene symbol or identifier to canonical metadata (HGNC, Ensembl, NCBI, function).
figure_extract

Extract figures + captions from a paper PDF, with optional OCR + caption summarization.
doi_resolve

Resolve a DOI to canonical metadata (title, authors, journal, year, abstract).
disease_lookup

Resolve a disease name or identifier to OMIM / MONDO / DOID metadata + associated genes.
crossref_search

Search Crossref for scholarly works by query, author, or journal.
citation_graph

Walk a citation graph from a seed paper (forward = cited-by, backward = cites).
arxiv_search

Search arXiv preprints by query, with optional category and date range filters.

How to invoke

Each tool is callable from agent code via scidex.tool.invoke or directly through POST /api/scidex/tool/invoke. Tools accept a JSON body and return a JSON envelope. See the verbs index for shape details, or SPEC-018 for the registry contract.