Uniprot Tools

Configuration File: uniprot_tools.json Tool Type: Local Tools Count: 12

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

Available Tools

UniProt_get_alternative_names_by_accession (Type: UniProtRESTTool)

Extract all alternative names (alternativeNames) from UniProtKB entry.

UniProt_get_alternative_names_by_accession tool specification

Tool Information:

• Name: UniProt_get_alternative_names_by_accession

• Type: UniProtRESTTool

• Description: Extract all alternative names (alternativeNames) from UniProtKB entry.

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_get_disease_variants_by_accession (Type: UniProtRESTTool)

Extract all variants (feature type = VARIANT) and their related annotations from UniProtKB entry.

UniProt_get_disease_variants_by_accession tool specification

Tool Information:

• Name: UniProt_get_disease_variants_by_accession

• Type: UniProtRESTTool

• Description: Extract all variants (feature type = VARIANT) and their related annotations from UniProtKB entry.

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_get_entry_by_accession (Type: UniProtRESTTool)

Get the complete JSON entry for a specified UniProtKB accession.

UniProt_get_entry_by_accession tool specification

Tool Information:

• Name: UniProt_get_entry_by_accession

• Type: UniProtRESTTool

• Description: Get the complete JSON entry for a specified UniProtKB accession.

Parameters:

• accession (string) (required) UniProtKB entry accession, e.g., P05067.

Example Usage:

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

UniProt_get_function_by_accession (Type: UniProtRESTTool)

Extract functional annotations from UniProtKB entry (Comment type = FUNCTION).

UniProt_get_function_by_accession tool specification

Tool Information:

• Name: UniProt_get_function_by_accession

• Type: UniProtRESTTool

• Description: Extract functional annotations from UniProtKB entry (Comment type = FUNCTION).

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_get_isoform_ids_by_accession (Type: UniProtRESTTool)

Extract all splice isoform IDs from UniProtKB entry (isoformNames).

UniProt_get_isoform_ids_by_accession tool specification

Tool Information:

• Name: UniProt_get_isoform_ids_by_accession

• Type: UniProtRESTTool

• Description: Extract all splice isoform IDs from UniProtKB entry (isoformNames).

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_get_organism_by_accession (Type: UniProtRESTTool)

Extract the organism scientific name from UniProtKB entry.

UniProt_get_organism_by_accession tool specification

Tool Information:

• Name: UniProt_get_organism_by_accession

• Type: UniProtRESTTool

• Description: Extract the organism scientific name from UniProtKB entry.

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_get_ptm_processing_by_accession (Type: UniProtRESTTool)

Extract all PTM and processing sites from UniProtKB entry (feature type = MODIFIED RESIDUE or SIG…

UniProt_get_ptm_processing_by_accession tool specification

Tool Information:

• Name: UniProt_get_ptm_processing_by_accession

• Type: UniProtRESTTool

• Description: Extract all PTM and processing sites from UniProtKB entry (feature type = MODIFIED RESIDUE or SIGNAL, etc.).

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_get_recommended_name_by_accession (Type: UniProtRESTTool)

Extract the recommended protein name (recommendedName) from UniProtKB entry.

UniProt_get_recommended_name_by_accession tool specification

Tool Information:

• Name: UniProt_get_recommended_name_by_accession

• Type: UniProtRESTTool

• Description: Extract the recommended protein name (recommendedName) from UniProtKB entry.

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_get_sequence_by_accession (Type: UniProtRESTTool)

Extract the canonical sequence from UniProtKB entry.

UniProt_get_sequence_by_accession tool specification

Tool Information:

• Name: UniProt_get_sequence_by_accession

• Type: UniProtRESTTool

• Description: Extract the canonical sequence from UniProtKB entry.

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_get_subcellular_location_by_accession (Type: UniProtRESTTool)

Extract subcellular localization annotations from UniProtKB entry (Comment type = SUBCELLULAR LOC…

UniProt_get_subcellular_location_by_accession tool specification

Tool Information:

• Name: UniProt_get_subcellular_location_by_accession

• Type: UniProtRESTTool

• Description: Extract subcellular localization annotations from UniProtKB entry (Comment type = SUBCELLULAR LOCATION).

Parameters:

• accession (string) (required) UniProtKB accession, e.g., P05067.

Example Usage:

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

UniProt_id_mapping (Type: UniProtRESTTool)

Map IDs between different databases (e.g., Ensembl to UniProt, Gene Name to UniProt). Supports ba…

UniProt_id_mapping tool specification

Tool Information:

• Name: UniProt_id_mapping

• Type: UniProtRESTTool

• Description: Map IDs between different databases (e.g., Ensembl to UniProt, Gene Name to UniProt). Supports batch mapping and async task processing. Use this to convert between different database identifiers.

Parameters:

• ids (unknown) (required) ID(s) to map. Can be single string or array of strings, e.g., ‘ENSG00000141510’ or [‘MEIOB’, ‘TP53’]

• from_db (string) (required) Source database. Examples: ‘Ensembl’, ‘Gene_Name’, ‘RefSeq_Protein’, ‘PDB’, ‘EMBL’

• to_db (string) (optional) Target database (default: ‘UniProtKB’)

• max_wait_time (integer) (optional) Maximum time to wait for async task completion in seconds (default: 30)

Example Usage:

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

UniProt_search (Type: UniProtRESTTool)

Search UniProtKB database with flexible query syntax. Returns protein entries with accession numb…

UniProt_search tool specification

Tool Information:

• Name: UniProt_search

• Type: UniProtRESTTool

• Description: Search UniProtKB database with flexible query syntax. Returns protein entries with accession numbers and metadata. Query syntax supports: field searches (gene:TP53, organism_id:9606, reviewed:true), ranges (length:[100 TO 500], mass:[20000 TO 50000]), wildcards (gene:MEIOB*), boolean operators (AND/OR/NOT), and parentheses for grouping. Examples: ‘gene:TP53 AND organism_id:9606’, ‘length:[400 TO 500] AND reviewed:true’, ‘tissue:brain NOT organism_id:10090’.

Parameters:

• query (string) (required) Search query using UniProt syntax. Simple: ‘MEIOB’, ‘insulin’. Field searches: ‘gene:TP53’, ‘protein_name:insulin’, ‘organism_id:9606’, ‘reviewed:true’. Ranges: ‘length:[100 TO 500]’, ‘mass:[20000 TO 50000]’. Wildcards: ‘gene:MEIOB*’. Boolean: ‘gene:TP53 AND organism_id:9606’, ‘tissue:brain OR tissue:liver’, ‘reviewed:true NOT fragment:true’. Use parentheses for grouping: ‘(organism_id:9606 OR organism_id:10090) AND gene:TP53’. Note: ‘organism:’ auto-converts to ‘organism_id:’.

• organism (string) (optional) Optional organism filter. Use common names (‘human’, ‘mouse’, ‘rat’, ‘yeast’) or taxonomy ID (‘9606’). Automatically combined with query using AND. Will not duplicate if organism is already in query.

• limit (integer) (optional) Maximum number of results to return (default: 25, max: 500). Accepts string or integer.

• min_length (integer) (optional) Minimum sequence length. Auto-converts to ‘length:[min TO *]’ range query.

• max_length (integer) (optional) Maximum sequence length. Auto-converts to ‘length:[* TO max]’ range query.

• fields (array) (optional) List of field names to return (e.g., [‘accession’,’gene_primary’,’length’,’organism_name’]). When specified, returns raw API response with requested fields. Common fields: accession, id, gene_names, gene_primary, protein_name, organism_name, organism_id, length, mass, sequence, reviewed, cc_function. See UniProt API docs for full list. Default (no fields): returns formatted response with accession, id, protein_name, gene_names, organism, length.

Example Usage:

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

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