Appris Tools

Configuration File: appris_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

APPRIS_get_functional_annotations (Type: APPRISTool)

Get detailed functional annotations for gene isoforms from APPRIS, including structural domains (…

APPRIS_get_functional_annotations tool specification

Tool Information:

  • Name: APPRIS_get_functional_annotations

  • Type: APPRISTool

  • Description: Get detailed functional annotations for gene isoforms from APPRIS, including structural domains (spade), functional residues (firestar), 3D structure coverage (matador3d), cross-species conservation (corsair), transmembrane helices (thump), signal peptides (crash), and proteomics evidence (proteo).

Annotations are grouped by type. Optionally filter by transcript_id to focus on a specific isoform.

Available methods: appris, firestar, matador3d, spade, corsair, thump, crash, proteo, tsl

Parameters:

  • gene_id (string) (required) Ensembl gene ID (e.g., ENSG00000141510 for TP53).

  • species (string) (optional) Species name (e.g., homo_sapiens).

  • methods (string) (optional) Comma-separated analysis methods to retrieve (e.g., ‘firestar,spade,corsair’). Leave empty for all.

  • transcript_id (string) (optional) Optional Ensembl transcript ID to filter results for a specific isoform (e.g., ENST00000269305).

Example Usage:

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

APPRIS_get_isoforms (Type: APPRISTool)

Get all transcript isoforms and their APPRIS annotations for a gene. APPRIS classifies isoforms a…

APPRIS_get_isoforms tool specification

Tool Information:

  • Name: APPRIS_get_isoforms

  • Type: APPRISTool

  • Description: Get all transcript isoforms and their APPRIS annotations for a gene. APPRIS classifies isoforms as PRINCIPAL (most functionally important) or ALTERNATIVE based on structural, functional, and evolutionary evidence.

Requires an Ensembl gene ID (ENSG…). Use HGNC_fetch_gene_by_symbol or Ensembl tools to convert gene symbols to Ensembl IDs first.

Reliability levels: PRINCIPAL:1 (highest) through PRINCIPAL:5, MINOR (alternative), or ‘No Principal Isoform’.

Parameters:

  • gene_id (string) (required) Ensembl gene ID (e.g., ENSG00000141510 for TP53, ENSG00000012048 for BRCA1).

  • species (string) (optional) Species name in lowercase with underscore (e.g., homo_sapiens, mus_musculus, danio_rerio).

Example Usage:

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

APPRIS_get_principal_isoform (Type: APPRISTool)

Get the principal (most functionally important) transcript isoform for a gene as determined by th…

APPRIS_get_principal_isoform tool specification

Tool Information:

  • Name: APPRIS_get_principal_isoform

  • Type: APPRISTool

  • Description: Get the principal (most functionally important) transcript isoform for a gene as determined by the APPRIS database.

APPRIS selects the principal isoform based on protein structure (matador3d, spade), functional residues (firestar), cross-species conservation (corsair), transmembrane topology (thump, crash), and proteomics evidence (proteo).

Requires an Ensembl gene ID (ENSG…). Use HGNC_fetch_gene_by_symbol to convert gene symbols first.

Parameters:

  • gene_id (string) (required) Ensembl gene ID (e.g., ENSG00000141510 for TP53).

  • species (string) (optional) Species name (e.g., homo_sapiens, mus_musculus).

Example Usage:

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