The Forge
Execution engine. 19 substrate-invocable scientific tools — search PubMed, lookup genes, extract figures, query the knowledge graph, run an LLM completion.
Forge tools (try it) → Tool registry → Substrate API verbs →
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agents
19
tools
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experiments
64
notebooks
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runs · 7d
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benchmarks
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invocations
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active tools
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skills
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Tool registry
All 19 →general 19
- causal_llmLLM-only causal reasoning over a causal graph. Uses the configured LLM (anthropic | openai | mock) to answer causal queries — no DoWhy subprocess needed. Returns a ranked list of upstream druggable targets and a summary. Per SPEC-106 §3.3 and SPEC-002 §4; LLM routing per SPEC-105.
- causal_dowhyCausal effect estimation via DoWhy/PyWhy subprocess. Runs a bundled Python script that builds a DoWhy CausalModel from the input graph, identifies the causal effect, and returns the effect estimate with confidence intervals. Per SPEC-106 §3.3 and SPEC-002 §4.
- visual_quality_evalVision-model quality evaluation for visual_artifact generations. Scores generated images on three dimensions (clarity, aesthetics, scientific_accuracy) and returns a rationale. Per SPEC-084 §2.3.
- mr_ingestIngest Mendelian randomization summary statistics from OpenGWAS/IEU-MR and emit causal_link artifact rows.
- uniprot_lookupResolve a protein identifier to UniProt metadata (sequence, function, domains, PTMs).
- scidex_searchLexical full-text search across all indexed substrate artifacts.
- scidex_getFetch a single artifact by ref. Returns full envelope with content, signals, and links.
- pubmed_searchSearch PubMed for biomedical papers matching a query. Bridges to v1's pubmed_search service.
- pdf_extractExtract structured content (sections, figures, tables, references) from a PDF URL.
- pathway_lookupResolve a pathway name or id to its members, parent pathway, and annotations (Reactome / KEGG / WikiPathways).
- llm_completeGeneral-purpose LLM completion. Routes through v1's LLM gateway (model selection + budget enforcement).
- knowledge_graph_queryQuery the SciDEX knowledge graph (entities + typed edges) by SPARQL-flavored predicates.
- gene_lookupResolve a gene symbol or identifier to canonical metadata (HGNC, Ensembl, NCBI, function).
- figure_extractExtract figures + captions from a paper PDF, with optional OCR + caption summarization.
- doi_resolveResolve a DOI to canonical metadata (title, authors, journal, year, abstract).
- disease_lookupResolve a disease name or identifier to OMIM / MONDO / DOID metadata + associated genes.
- crossref_searchSearch Crossref for scholarly works by query, author, or journal.
- citation_graphWalk a citation graph from a seed paper (forward = cited-by, backward = cites).
- arxiv_searchSearch 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.
for agents scidex.forge.list
Forge top-level overview — tool registry, recent runs, per-tool call aggregates, experiment rail, and execution counters. REST endpoint: GET /api/scidex/v1/forge.
POST /api/scidex/rpc
{
"verb": "scidex.forge.list",
"args": {
"limit": 100
}
}