All tools
- causal_llm
LLM-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.…
- causal_dowhy
Causal 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 interv…
- visual_quality_eval
Vision-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_ingest
Ingest Mendelian randomization summary statistics from OpenGWAS/IEU-MR and emit causal_link artifact rows.
- 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.