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 ClinVar, COSMIC, and other variant annotations. Suppor…

proteins_api_get_variants tool specification

Tool Information:

  • Name: proteins_api_get_variants

  • Type: ProteinsAPIRESTTool

  • Description: Get variation data for a protein including ClinVar, COSMIC, and other variant annotations. Supports batch operations: pass a list of accessions or comma-separated string to retrieve multiple proteins in parallel. Note: Variations endpoint may not be available for all proteins. If this returns 404, use proteins_api_get_protein instead which includes variant information. Returns variant information with clinical significance and population frequencies.

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_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. Returns search results matching the query. Note: The Proteins AP…

proteins_api_search tool specification

Tool Information:

  • Name: proteins_api_search

  • Type: ProteinsAPIRESTTool

  • Description: Search proteins in Proteins API. Returns search results matching the query. Note: The Proteins API search endpoint may have limitations. For reliable protein search, consider using ebi_search_domain with domain=’uniprot’ instead. This tool attempts to search by name or accession, but may not work for all query types.

Parameters:

  • query (string) (required) Search query (e.g., protein name, gene name, organism). Internally converted to ‘q’ parameter for Proteins API.

  • size (integer) (optional) Number of results to return (default: 25)

  • 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)