Proteomicsdb Tools

Configuration File: proteomicsdb_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the proteomicsdb_tools.json configuration file.

Available Tools

ProteomicsDB_get_expression_summary (Type: ProteomicsDBTool)

Get a tissue expression summary for a protein from ProteomicsDB, showing the top tissues/cell lin…

ProteomicsDB_get_expression_summary tool specification

Tool Information:

  • Name: ProteomicsDB_get_expression_summary

  • Type: ProteomicsDBTool

  • Description: Get a tissue expression summary for a protein from ProteomicsDB, showing the top tissues/cell lines/fluids ranked by MS-based expression level. Given a UniProt accession, returns the top N biological sources where the protein is most highly expressed (by iBAQ quantification), along with total counts of tissues, cell lines, and body fluids where the protein was detected. Useful for quickly identifying which tissues/cell lines express a protein most abundantly based on mass spectrometry evidence. Complements antibody-based tissue expression from HPA.

Parameters:

  • operation (string) (required) Operation type

  • uniprot_id (string) (required) UniProt accession for the protein (e.g., ‘P04637’ for TP53, ‘P00533’ for EGFR)

  • top_n (integer) (optional) Number of top tissues to return, ranked by expression level (default: 10)

Example Usage:

query = {
    "name": "ProteomicsDB_get_expression_summary",
    "arguments": {
        "operation": "example_value",
        "uniprot_id": "example_value"
    }
}
result = tu.run(query)

ProteomicsDB_get_protein_expression (Type: ProteomicsDBTool)

Get mass spectrometry-based protein expression data across human tissues, cell lines, and body fl…

ProteomicsDB_get_protein_expression tool specification

Tool Information:

  • Name: ProteomicsDB_get_protein_expression

  • Type: ProteomicsDBTool

  • Description: Get mass spectrometry-based protein expression data across human tissues, cell lines, and body fluids from ProteomicsDB. Given a UniProt accession (e.g., P04637 for TP53), returns quantitative expression values (log10 iBAQ or TOP3) for each biological source where the protein was detected. ProteomicsDB provides MS-based proteomics data complementary to antibody-based expression in HPA and cancer proteomics in PDC. Filter by tissue category (tissue, cell line, fluid) and calculation method (iBAQ, TOP3). Expression values are log10-transformed normalized intensities. Returns tissue name, group, category, and expression statistics per source.

Parameters:

  • operation (string) (required) Operation type

  • uniprot_id (string) (required) UniProt accession for the protein (e.g., ‘P04637’ for TP53, ‘P00533’ for EGFR, ‘P01116’ for KRAS)

  • tissue_category (string) (optional) Filter by biological source category. ‘tissue’ for normal tissues, ‘cell line’ for cell lines, ‘fluid’ for body fluids, ‘all’ for everything. Default: all.

  • calculation_method (string) (optional) Protein quantification method. iBAQ (intensity-Based Absolute Quantification) or TOP3 (sum of top 3 peptide intensities). Default: iBAQ.

Example Usage:

query = {
    "name": "ProteomicsDB_get_protein_expression",
    "arguments": {
        "operation": "example_value",
        "uniprot_id": "example_value"
    }
}
result = tu.run(query)

ProteomicsDB_list_tissues (Type: ProteomicsDBTool)

List all available tissues, cell lines, and body fluids in ProteomicsDB with their BTO ontology I…

ProteomicsDB_list_tissues tool specification

Tool Information:

  • Name: ProteomicsDB_list_tissues

  • Type: ProteomicsDBTool

  • Description: List all available tissues, cell lines, and body fluids in ProteomicsDB with their BTO ontology IDs, names, categories, and anatomical groupings. Optionally filter by category (tissue, cell line, or fluid). Returns the full catalog of biological sources for which ProteomicsDB has mass spectrometry-based proteomics data, including tissue ID (BTO identifier), name, category, and anatomical group. Useful for discovering what biological sources are available before querying specific protein expression data.

Parameters:

  • operation (string) (required) Operation type

  • tissue_category (string) (optional) Filter by biological source category. Optional - omit to list all categories.

Example Usage:

query = {
    "name": "ProteomicsDB_list_tissues",
    "arguments": {
        "operation": "example_value"
    }
}
result = tu.run(query)

ProteomicsDB_search_proteins (Type: ProteomicsDBTool)

Search ProteomicsDB for proteins by gene symbol, UniProt accession, or protein name. ProteomicsDB…

ProteomicsDB_search_proteins tool specification

Tool Information:

  • Name: ProteomicsDB_search_proteins

  • Type: ProteomicsDBTool

  • Description: Search ProteomicsDB for proteins by gene symbol, UniProt accession, or protein name. ProteomicsDB contains mass spectrometry-based proteomics data for human (and other organisms) proteins. Returns matching protein entries with UniProt IDs, gene names, protein names, entry names, and molecular masses. Useful for finding the correct UniProt accession before querying expression data with ProteomicsDB_get_protein_expression. Searches across gene name, UniProt ID, and protein name fields simultaneously.

Parameters:

  • operation (string) (required) Operation type

  • query (string) (required) Search term - gene symbol (e.g., ‘KRAS’, ‘TP53’), UniProt ID (e.g., ‘P04637’), or protein name keyword (e.g., ‘kinase’, ‘GTPase KRas’)

  • organism_id (integer) (optional) NCBI taxonomy ID for organism filter. Default: 9606 (human). Other options: 10090 (mouse), 10116 (rat).

  • max_results (integer) (optional) Maximum number of results to return (default: 20, max: 100)

Example Usage:

query = {
    "name": "ProteomicsDB_search_proteins",
    "arguments": {
        "operation": "example_value",
        "query": "example_value"
    }
}
result = tu.run(query)