Uniprot Tools

Configuration File: uniprot_tools.json Tool Type: Local Tools Count: 17

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. WARNING: This tool returns the c…

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. WARNING: This tool returns the complete UniProtKB entry, which can be extremely large (40,000+ lines for some entries) and may cause LLM context limits to be exceeded or crashes. For most use cases, consider using more specific extraction tools instead: UniProt_get_function_by_accession, UniProt_get_sequence_by_accession, UniProt_get_recommended_name_by_accession, UniProt_get_organism_by_accession, UniProt_get_subcellular_location_by_accession, UniProt_get_disease_variants_by_accession, or UniProt_get_ptm_processing_by_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_proteome (Type: UniProtRESTTool)

Get proteome information by proteome ID. Returns comprehensive proteome data including taxonomy, …

UniProt_get_proteome tool specification

Tool Information:

• Name: UniProt_get_proteome

• Type: UniProtRESTTool

• Description: Get proteome information by proteome ID. Returns comprehensive proteome data including taxonomy, components, gene/protein counts, and annotation scores. Proteome IDs are typically in format UP000005640 (human), UP000000589 (mouse), etc. Use UniProt search with proteome filters to find proteome IDs for specific organisms.

Parameters:

• proteome_id (string) (required) UniProt proteome ID (e.g., ‘UP000005640’ for human, ‘UP000000589’ for mouse). Find proteome IDs using UniProt search with proteome filters or by querying organism-specific proteomes.

Example Usage:

query = {
    "name": "UniProt_get_proteome",
    "arguments": {
        "proteome_id": "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_get_uniparc_entry (Type: UniProtRESTTool)

Get UniParc entry by UniParc ID (UPI). UniParc is a non-redundant archive of all publicly availab…

UniProt_get_uniparc_entry tool specification

Tool Information:

• Name: UniProt_get_uniparc_entry

• Type: UniProtRESTTool

• Description: Get UniParc entry by UniParc ID (UPI). UniParc is a non-redundant archive of all publicly available protein sequences. Returns sequence, cross-references, and sequence features. UniParc IDs are in format UPI000002ED67. Use UniProt_get_entry_by_accession to find the UniParc ID for a UniProt entry (in extraAttributes.uniParcId).

Parameters:

• upi (string) (required) UniParc ID (UPI) in format UPI000002ED67. Find UPI from UniProt entry (extraAttributes.uniParcId) or use UniProt_search_uniparc.

Example Usage:

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

UniProt_get_uniref_cluster (Type: UniProtRESTTool)

Get UniRef cluster information by cluster ID. UniRef clusters group proteins that share 100% (Uni…

UniProt_get_uniref_cluster tool specification

Tool Information:

• Name: UniProt_get_uniref_cluster

• Type: UniProtRESTTool

• Description: Get UniRef cluster information by cluster ID. UniRef clusters group proteins that share 100% (UniRef100), 90% (UniRef90), or 50% (UniRef50) sequence identity. Returns cluster metadata, representative member, member count, and member list. Cluster IDs are in format UniRef100_P04637, UniRef90_P04637, or UniRef50_P04637.

Parameters:

• cluster_id (string) (required) UniRef cluster ID (e.g., ‘UniRef50_P04637’, ‘UniRef90_P04637’, ‘UniRef100_P04637’). Use UniProt_get_uniref_search to find cluster IDs.

Example Usage:

query = {
    "name": "UniProt_get_uniref_cluster",
    "arguments": {
        "cluster_id": "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)

UniProt_search_uniparc (Type: UniProtRESTTool)

Search UniParc entries. Returns UniParc entries matching the query. Use this to find UniParc entr…

UniProt_search_uniparc tool specification

Tool Information:

• Name: UniProt_search_uniparc

• Type: UniProtRESTTool

• Description: Search UniParc entries. Returns UniParc entries matching the query. Use this to find UniParc entries for specific proteins or sequences. Query syntax supports protein accessions, gene names, organism filters, etc.

Parameters:

• query (string) (required) Search query. Examples: ‘P04637’ (protein accession), ‘name:TP53’, ‘organism_id:9606’ (human). Supports UniProt query syntax.

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

Example Usage:

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

UniProt_search_uniref (Type: UniProtRESTTool)

Search UniRef clusters. Returns clusters matching the query. Use this to find UniRef clusters for…

UniProt_search_uniref tool specification

Tool Information:

• Name: UniProt_search_uniref

• Type: UniProtRESTTool

• Description: Search UniRef clusters. Returns clusters matching the query. Use this to find UniRef clusters for specific proteins or organisms. Query syntax supports protein accessions, gene names, organism filters, etc.

Parameters:

• query (string) (required) Search query. Examples: ‘P04637’ (protein accession), ‘name:TP53’, ‘organism_id:9606’ (human). Supports UniProt query syntax.

• cluster_type (string) (optional) UniRef cluster type: UniRef100 (100% identity), UniRef90 (90% identity), UniRef50 (50% identity)

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

Example Usage:

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

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