Resolve an ambiguous gene symbol, alias, or accession to an authoritative entity.

Args: query: Gene symbol (e.g. TP53), alias (e.g. HER2, p53), or accession. taxon_id: NCBI Taxonomy ID (default: 9606 for human). chromosome: Optional chromosome hint for disambiguation (e.g. '17' or 'chr17'). locus_type: Optional biotype hint (e.g. 'protein-coding', 'pseudogene').

Returns: JSON string containing the resolved canonical gene entity, cross-references, and match audit trail.

Fetch structured protein details from UniProt by primary accession.

Args: accession: UniProt accession ID (e.g. P04637).

Returns: JSON string containing protein name, gene, length, mass, and organism.

Resolve a list of gene identifiers/aliases in batch with concurrency control and performance metrics.

Args: queries: List of gene symbols or aliases (e.g. ["TP53", "HER2", "EGFR", "7157", "P04637"]). taxon_id: NCBI Taxonomy ID (default: 9606 for human). concurrency: Maximum concurrent requests (default: 10).

Returns: JSON string containing the batch resolution summary, success rate, and resolved entities.

Fetch transcripts, canonical isoform, and exon structures from Ensembl.

Args: query: Ensembl Gene ID (e.g. ENSG00000141510) or gene symbol (e.g. TP53). species: Species name (default: 'homo_sapiens' or 'mus_musculus').

Returns: JSON string containing gene coordinates and transcript variants with exon models.

Identify corresponding orthologous genes across species via Ensembl.

Args: query: Gene symbol (e.g. TP53) or Ensembl Gene ID (e.g. ENSG00000141510). target_species: Target species (default: 'mus_musculus', 'danio_rerio', etc.). source_species: Source species (default: 'homo_sapiens').

Returns: JSON string containing list of orthologous genes with identity and relation type.

Resolve mouse gene details and MGI identifiers (Mus musculus).

Args: query: Mouse gene symbol (e.g. 'Trp53') or MGI ID (e.g. 'MGI:98834') or Ensembl ID.

Returns: JSON string containing the resolved mouse gene entity with MGI identifier.

Fetch Gene Ontology functional annotations (MF, BP, CC) for a gene or protein.

Args: query: Gene symbol (e.g. 'TP53'), alias, or UniProt accession (e.g. 'P04637'). taxon_id: NCBI Taxonomy ID (default: 9606 for human). aspect: Optional filter: 'molecular_function', 'biological_process', or 'cellular_component'. limit: Maximum number of annotations per aspect (default: 25).

Returns: JSON string containing the functional profile structured into MF, BP, and CC with evidence codes.

Fetch metadata and functional definition for a Gene Ontology (GO) term ID.

Args: go_id: Gene Ontology identifier (e.g. 'GO:0006915').

Returns: JSON string containing term name, definition, aspect, and synonyms.

Fetch biological pathways involving a gene or protein from Reactome.

Args: query: Gene symbol (e.g. 'TP53'), alias, or UniProt accession (e.g. 'P04637'). taxon_id: NCBI Taxonomy ID (default: 9606 for human). species: Species name (default: 'Homo sapiens'). limit: Maximum number of pathways to return (default: 20).

Returns: JSON string containing the list of pathways with names, stable IDs, and Reactome links.

Fetch detailed information for a Reactome pathway by its stable identifier.

Args: st_id: Reactome pathway stable ID (e.g. 'R-HSA-5357801' for Programmed Cell Death).

Returns: JSON string containing pathway name, species, summary text, and diagram availability.

Resolve a disease name, synonym, or MONDO identifier against the MONDO Disease Ontology.

Args: query: Disease name (e.g. 'Li-Fraumeni syndrome', 'Breast cancer'), synonym, or ID ('MONDO:0018875'). limit: Maximum number of matches to return (default: 5).

Returns: JSON string containing the list of resolved disease entities with MONDO IDs, definitions, and cross-references.

Fetch evidence-backed therapeutic target-disease associations from Open Targets Platform.

Args: gene: Gene symbol (e.g. 'TP53', 'BRAF', 'EGFR') or Ensembl Gene ID ('ENSG00000141510'). limit: Maximum number of top disease associations to return (default: 10).

Returns: JSON string containing associated diseases, evidence scores (0.0-1.0), and datatype evidence breakdowns.

Fetch authoritative supporting scientific literature from Europe PMC / PubMed.

Args: query: Gene symbol (e.g. 'TP53'), disease name, or scientific query string. limit: Maximum number of peer-reviewed publications to return (default: 5).

Returns: JSON string containing publication titles, journal, year, authors, abstract, and citation counts.

Fetch detailed metadata for a specific scientific paper by PMID, PMCID, or DOI.

Args: identifier: Publication identifier (e.g. PMID '30514107', PMCID 'PMC6280721', or DOI '10.1038/s41586-018-0774-4').

Returns: JSON string containing full paper metadata, abstract, and direct web links.

Construct an ontological Knowledge Subgraph centered on a biological entity (PRD-21).

Connects the seed gene across multiple biological layers:

• Encoded proteins (UniProt)

• Transcripts (Ensembl)

• Reactome pathways

• Gene Ontology terms (processes & molecular functions)

• Disease associations with evidence scores (Open Targets)

• Key supporting peer-reviewed publications (Europe PMC)

Args: query: Gene symbol (e.g. 'TP53', 'BRCA1', 'EGFR') or alias. taxon_id: NCBI Taxonomy ID (default: 9606 for human). include_pathways: Include Reactome pathway nodes and edges (default: True). include_go: Include Gene Ontology nodes and edges (default: True). include_diseases: Include Open Targets disease association nodes and edges (default: True). include_literature: Include Europe PMC publication nodes and edges (default: True).

Returns: JSON string representing the connected subgraph nodes, edges, weights, and provenance.

Enumerate graph paths from a source gene to a target entity (PRD-22).

Paths follow edges drawn from curated databases; each hop reports its source database and score if the source provides one. Scores are products of source-provided weights, not probabilities. Literature edges are keyword hits and are only used when target_type is 'publication'.

Args: source_query: Origin gene symbol or alias (e.g. 'TP53'). target_query: Target identifier (e.g. 'MONDO:0005575', 'R-HSA-69563') or a whole-phrase name (e.g. 'colorectal cancer'). max_hops: Maximum edges to traverse, 1 to 6 (default: 3). min_score: Minimum product of source-provided scores, 0.0 to 1.0 (default: 0.0). target_type: Optional node type filter: gene, protein, transcript, pathway, disease, publication, go_term.

Returns: JSON string with paths, matched targets, and warnings. On invalid input, a JSON object with an 'error' field.