Proteins Api Tools

Configuration File: proteins_api_tools.json Tool Type: Local Tools Count: 10

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

Available Tools

proteins_api_get_comments (Type: ProteinsAPIRESTTool)

Get functional annotations and comments for a protein from the Proteins API. Supports batch opera…

proteins_api_get_comments tool specification

Tool Information:

  • Name: proteins_api_get_comments

  • Type: ProteinsAPIRESTTool

  • Description: Get functional annotations and comments for a protein from the Proteins API. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. This includes curated comments on function, subcellular location, disease involvement, and other annotations. Note: This tool extracts comments from the main protein endpoint (the separate comments endpoint is not available). Returns all functional annotation comments.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_get_epitopes (Type: ProteinsAPIRESTTool)

Get epitope sequences for a protein. Returns B-cell and T-cell epitope information with antigenic…

proteins_api_get_epitopes tool specification

Tool Information:

  • Name: proteins_api_get_epitopes

  • Type: ProteinsAPIRESTTool

  • Description: Get epitope sequences for a protein. Returns B-cell and T-cell epitope information with antigenicity predictions. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. Note: This tool extracts epitope-related data from the main protein endpoint (the separate epitopes endpoint is not available). Returns immunology comments and epitope features if present.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_get_features (Type: ProteinsAPIRESTTool)

Get detailed sequence features for a protein, including domains, regions, motifs, modified residu…

proteins_api_get_features tool specification

Tool Information:

  • Name: proteins_api_get_features

  • Type: ProteinsAPIRESTTool

  • Description: Get detailed sequence features for a protein, including domains, regions, motifs, modified residues, and other annotated features. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. Note: This tool extracts features from the main protein endpoint (the separate features endpoint is not available). Returns all sequence feature annotations for the protein.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_get_genome_mappings (Type: ProteinsAPIRESTTool)

Get reference genome mappings for a protein using the Proteins API. Supports batch operations: pa…

proteins_api_get_genome_mappings tool specification

Tool Information:

  • Name: proteins_api_get_genome_mappings

  • Type: ProteinsAPIRESTTool

  • Description: Get reference genome mappings for a protein using the Proteins API. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. This extracts genome-related cross-references (Ensembl, RefSeq, EMBL, GenBank) from the main protein endpoint, which may contain genomic location information. Note: The separate genome endpoint is not available, so this tool extracts genome-related cross-references from the main protein data. Use UniProt or EBI Search (domain=’uniprot’) to find accessions such as ‘P05067’ or ‘P04637’.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_get_protein (Type: ProteinsAPIRESTTool)

Get comprehensive protein information from Proteins API by UniProt accession. Returns protein ann…

proteins_api_get_protein tool specification

Tool Information:

  • Name: proteins_api_get_protein

  • Type: ProteinsAPIRESTTool

  • Description: Get comprehensive protein information from Proteins API by UniProt accession. Returns protein annotations, sequences, features, and cross-references. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_get_proteomics (Type: ProteinsAPIRESTTool)

Get proteomics data for a protein including mass spectrometry evidence, PTM sites, and expression…

proteins_api_get_proteomics tool specification

Tool Information:

  • Name: proteins_api_get_proteomics

  • Type: ProteinsAPIRESTTool

  • Description: Get proteomics data for a protein including mass spectrometry evidence, PTM sites, and expression data. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. Note: This tool extracts proteomics-related data from the main protein endpoint (the separate proteomics endpoint is not available). Returns PTM comments, modified residues, and related features.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_get_publications (Type: ProteinsAPIRESTTool)

Get publications associated with a protein from the Proteins API. Supports batch operations: pass…

proteins_api_get_publications tool specification

Tool Information:

  • Name: proteins_api_get_publications

  • Type: ProteinsAPIRESTTool

  • Description: Get publications associated with a protein from the Proteins API. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. Returns literature references linked to the UniProt accession, including PubMed IDs and citation details. Note: This tool extracts publications from the main protein endpoint (the separate publications endpoint is not available). Returns all publication references.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_get_variants (Type: ProteinsAPIRESTTool)

Get variation data for a protein including disease-associated variants, natural variants, and pop…

proteins_api_get_variants tool specification

Tool Information:

  • Name: proteins_api_get_variants

  • Type: ProteinsAPIRESTTool

  • Description: Get variation data for a protein including disease-associated variants, natural variants, and population data. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. Returns variant information with positions, amino acid changes, disease associations, and evidence. Note: Not all proteins have annotated variants.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • size (integer) (optional) Maximum number of variants to return per protein (default: 100)

  • offset (integer) (optional) Offset for pagination (default: 0)

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_get_xrefs (Type: ProteinsAPIRESTTool)

Get cross-references for a protein from the Proteins API, including links to other databases (Ens…

proteins_api_get_xrefs tool specification

Tool Information:

  • Name: proteins_api_get_xrefs

  • Type: ProteinsAPIRESTTool

  • Description: Get cross-references for a protein from the Proteins API, including links to other databases (Ensembl, PDB, Reactome, EMBL, RefSeq, etc.). Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. Note: This tool extracts cross-references from the main protein endpoint (the separate xrefs endpoint is not available). Returns database cross-reference records.

Parameters:

  • accession ([‘string’, ‘array’]) (required) UniProt protein accession(s). Can be a single accession (e.g., ‘P05067’), comma-separated string (e.g., ‘P05067,P04637’), or list (e.g., [‘P05067’, ‘P04637’]). Use UniProt search or ebi_search_domain with domain=’uniprot’ to find valid accessions.

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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

proteins_api_search (Type: ProteinsAPIRESTTool)

Search proteins in Proteins API by gene name, protein name, or accession. The search intelligentl…

proteins_api_search tool specification

Tool Information:

  • Name: proteins_api_search

  • Type: ProteinsAPIRESTTool

  • Description: Search proteins in Proteins API by gene name, protein name, or accession. The search intelligently maps your query: gene names (e.g., ‘BRCA1’) search by gene parameter, accessions (e.g., ‘P05067’) search by accession parameter, and longer queries (e.g., ‘insulin’) search by protein parameter. Returns list of matching proteins with full annotations. For broader search capabilities, consider using ebi_search_domain with domain=’uniprot’.

Parameters:

  • query (string) (required) Search query. Can be: gene name (e.g., ‘BRCA1’, ‘TP53’), protein name (e.g., ‘insulin’, ‘hemoglobin’), or UniProt accession (e.g., ‘P05067’). The tool automatically determines the appropriate search parameter.

  • size (integer) (optional) Maximum number of results to return (default: 25, max: 100)

  • offset (integer) (optional) Offset for pagination (default: 0)

  • format (string) (optional) Response format. JSON is recommended for most use cases.

Example Usage:

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