gget MCP Server

General search for any biological terms using gene symbols, names, or synonyms. This is a general search that looks broadly across gene names and descriptions. For specific gene symbol searches, use search_genes_simple instead. Args: search_terms: Search terms, names, or synonyms (e.g., 'cancer' or ['apoptosis', 'death']) species: Target species (e.g., 'homo_sapiens', 'mus_musculus') Returns: SearchResult: DataFrame with search results containing Ensembl IDs and descriptions Example: Input: search_terms='apoptosis', species='homo_sapiens' Output: DataFrame with genes related to apoptosis Note: Searches broadly in "gene name" and "description" sections of Ensembl database. Results are limited to prevent overwhelming LLM context.

Search for specific genes using gene symbols with enhanced search strategy. 🚀 **BATCH PROCESSING SUPPORTED**: This function can process multiple genes in a single call! Use this tool FIRST when you have gene names/symbols and need to find their Ensembl IDs. Returns Ensembl IDs which are required for get_gene_info and get_sequences tools. IMPORTANT: Due to limitations in Ensembl search, short gene names often fail to find results. For best results, provide descriptive terms along with gene symbols: RECOMMENDED FORMAT: "GENE_SYMBOL descriptive_terms" Examples: - Instead of: "APP" - Use: "APP amyloid precursor" or "APP amyloid beta precursor protein" - Instead of: ["BACE1", "MAPT"] - Use: ["BACE1 beta secretase", "MAPT microtubule tau"] This function uses AND search for multi-word terms and OR search for single words. Args: search_terms: SINGLE gene symbol OR LIST of gene symbols with descriptive terms Single: 'APP amyloid precursor' Batch: ['BACE1 beta secretase', 'MAPT tau', 'APOE apolipoprotein'] species: Target species (e.g., 'homo_sapiens', 'mus_musculus') id_type: "gene" (default) or "transcript" - whether to return genes or transcripts Returns: SearchResult: DataFrame with gene search results containing Ensembl IDs and descriptions Results from ALL search terms are combined in a single response Example (SINGLE GENE): Input: search_terms='APP amyloid precursor', species='homo_sapiens' Output: DataFrame with APP gene and related genes Example (BATCH PROCESSING, limit number of queries to 3-5 to avoid timeouts): Input: search_terms=['APOE apolipoprotein', 'APP amyloid', 'PSEN1 presenilin'], species='homo_sapiens' Output: DataFrame with ALL three genes and their Ensembl IDs in one response Downstream tools that need the Ensembl IDs from this search: - get_gene_info: Get detailed gene information - get_sequences: Get DNA/protein sequences Note: For general biological term searches without gene focus, use search_simple.

Get detailed gene and transcript metadata using Ensembl IDs. PREREQUISITE: Use search_genes first to get Ensembl IDs from gene names/symbols. Args: ensembl_ids: One or more Ensembl gene IDs (e.g., 'ENSG00000141510' or ['ENSG00000141510']) Also supports WormBase and FlyBase IDs Returns: Dict[str, Any]: DataFrame with gene information containing metadata from multiple databases Example workflow: 1. search_genes('TP53', 'homo_sapiens') → get Ensembl ID 'ENSG00000141510' 2. get_gene_info('ENSG00000141510') Example output: DataFrame with columns like 'ensembl_id', 'symbol', 'biotype', 'chromosome', 'start', 'end', plus NCBI, UniProt, and optionally PDB information

Fetch sequences and save to local file in stdio mode. PREREQUISITE: Use search_genes first to get Ensembl IDs from gene names/symbols. Args: ensembl_ids: One or more Ensembl gene IDs (e.g., 'ENSG00000141510' or ['ENSG00000141510']) translate: If True, returns amino acid sequences; if False, returns nucleotide sequences output_path: ABSOLUTE path to output file (e.g., '/home/user/sequences.fasta'). AVOID relative paths as they cause file location issues. Auto-generated if not provided. format: Output format (currently supports 'fasta') Returns: LocalFileResult: Contains ABSOLUTE path, format, and success information instead of sequence data

Fetch FTPs for reference genomes and annotations by species from Ensembl. Args: species: Species in format "genus_species" (e.g., "homo_sapiens"). Shortcuts supported: "human", "mouse", "human_grch37" which: Which results to return. Options: 'gtf', 'cdna', 'dna', 'cds', 'cdrna', 'pep', 'all' Returns: Union[Dict[str, Any], List[str]]: Dictionary with URLs, versions, and metadata Example: Input: species="homo_sapiens", which="gtf" Output: Dictionary containing GTF URLs with Ensembl version and release info