Flybase Tools

Configuration File: flybase_tools.json Tool Type: Local Tools Count: 6

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

Available Tools

FlyBase_get_gene (Type: AllianceGenomeTool)

Get detailed Drosophila melanogaster (fruit fly) gene information from FlyBase via the Alliance o…

FlyBase_get_gene tool specification

Tool Information:

  • Name: FlyBase_get_gene

  • Type: AllianceGenomeTool

  • Description: Get detailed Drosophila melanogaster (fruit fly) gene information from FlyBase via the Alliance of Genome Resources. Returns gene symbol, name, synopsis, genomic location, synonyms, and cross-references. FlyBase is the primary database for Drosophila genetics. Example: ‘FB:FBgn0003996’ returns the white (w) gene with its function as an ABCG2-class transporter.

Parameters:

  • gene_id (string) (required) FlyBase gene ID with ‘FB:’ prefix. Examples: ‘FB:FBgn0003996’ (white/w), ‘FB:FBgn0000490’ (decapentaplegic/dpp), ‘FB:FBgn0004647’ (Notch/N), ‘FB:FBgn0000546’ (eyeless/ey), ‘FB:FBgn0003731’ (hedgehog/hh).

Example Usage:

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

FlyBase_get_gene_alleles (Type: AllianceGenomeTool)

Get alleles and variants for a Drosophila gene from FlyBase via the Alliance of Genome Resources….

FlyBase_get_gene_alleles tool specification

Tool Information:

  • Name: FlyBase_get_gene_alleles

  • Type: AllianceGenomeTool

  • Description: Get alleles and variants for a Drosophila gene from FlyBase via the Alliance of Genome Resources. Returns allele symbols, categories (insertion, point mutation, etc.), associated phenotypes, disease annotations, and variant details including genomic coordinates. Example: ‘FB:FBgn0000490’ (dpp) returns alleles like dpp[MI03752] with variant location and molecular consequence.

Parameters:

  • gene_id (string) (required) FlyBase gene ID with ‘FB:’ prefix. Examples: ‘FB:FBgn0003996’ (white/w), ‘FB:FBgn0000490’ (dpp), ‘FB:FBgn0004647’ (Notch/N).

  • limit (integer) (optional) Maximum number of alleles to return (1-100). Default: 20.

  • page (integer) (optional) Page number for pagination. Default: 1.

Example Usage:

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

FlyBase_get_gene_disease_models (Type: AllianceGenomeTool)

Get disease models involving a Drosophila gene from the Alliance of Genome Resources. Drosophila …

FlyBase_get_gene_disease_models tool specification

Tool Information:

  • Name: FlyBase_get_gene_disease_models

  • Type: AllianceGenomeTool

  • Description: Get disease models involving a Drosophila gene from the Alliance of Genome Resources. Drosophila is a powerful model organism for human disease research. Returns genotype-based disease models with associated human disease names and Disease Ontology IDs. Example: ‘FB:FBgn0000490’ (dpp) has 946 disease model entries including models for ALS, Parkinson’s disease, and other neurodegenerative conditions.

Parameters:

  • gene_id (string) (required) FlyBase gene ID with ‘FB:’ prefix. Examples: ‘FB:FBgn0000490’ (dpp), ‘FB:FBgn0004647’ (Notch/N), ‘FB:FBgn0003996’ (white/w).

  • limit (integer) (optional) Maximum number of disease models to return (1-100). Default: 20.

  • page (integer) (optional) Page number for pagination. Default: 1.

Example Usage:

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

FlyBase_get_gene_expression (Type: AllianceGenomeTool)

Get expression summary for a Drosophila gene from the Alliance of Genome Resources. Returns a rib…

FlyBase_get_gene_expression tool specification

Tool Information:

  • Name: FlyBase_get_gene_expression

  • Type: AllianceGenomeTool

  • Description: Get expression summary for a Drosophila gene from the Alliance of Genome Resources. Returns a ribbon summary of expression across anatomical systems (nervous system, integumental system, reproductive system, etc.) with annotation counts. Useful for understanding where a fly gene is expressed. Example: ‘FB:FBgn0000490’ (dpp) shows expression in alimentary system (43 annotations), integumental system (56), respiratory system (32).

Parameters:

  • gene_id (string) (required) FlyBase gene ID with ‘FB:’ prefix. Examples: ‘FB:FBgn0000490’ (dpp), ‘FB:FBgn0003996’ (white/w), ‘FB:FBgn0004647’ (Notch/N).

Example Usage:

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

FlyBase_get_gene_interactions (Type: AllianceGenomeTool)

Get molecular or genetic interactions for a Drosophila gene from the Alliance of Genome Resources…

FlyBase_get_gene_interactions tool specification

Tool Information:

  • Name: FlyBase_get_gene_interactions

  • Type: AllianceGenomeTool

  • Description: Get molecular or genetic interactions for a Drosophila gene from the Alliance of Genome Resources. Molecular interactions are physical protein-protein interactions. Genetic interactions are phenotype-based (suppression, enhancement, etc.). Returns interacting gene pairs with species and interaction type. Example: ‘FB:FBgn0000490’ (dpp) has 169 genetic interactions including genetic suppression with anchor.

Parameters:

  • gene_id (string) (required) FlyBase gene ID with ‘FB:’ prefix. Examples: ‘FB:FBgn0003996’ (white/w), ‘FB:FBgn0000490’ (dpp), ‘FB:FBgn0004647’ (Notch/N).

  • interaction_type (string) (optional) Type of interaction: ‘molecular’ (physical PPI) or ‘genetic’ (phenotype-based). Default: ‘molecular’.

  • limit (integer) (optional) Maximum number of interactions to return (1-100). Default: 20.

  • page (integer) (optional) Page number for pagination. Default: 1.

Example Usage:

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

FlyBase_get_gene_orthologs (Type: AllianceGenomeTool)

Get orthologs of a Drosophila gene across other species from the Alliance of Genome Resources. Re…

FlyBase_get_gene_orthologs tool specification

Tool Information:

  • Name: FlyBase_get_gene_orthologs

  • Type: AllianceGenomeTool

  • Description: Get orthologs of a Drosophila gene across other species from the Alliance of Genome Resources. Returns orthologous genes in human, mouse, zebrafish, worm, yeast, and other model organisms with prediction method details and best-score indicators. Essential for translational research from fly models to human disease genes. Example: ‘FB:FBgn0004647’ (Notch) returns orthologs including human NOTCH1-4.

Parameters:

  • gene_id (string) (required) FlyBase gene ID with ‘FB:’ prefix. Examples: ‘FB:FBgn0004647’ (Notch/N), ‘FB:FBgn0003996’ (white/w), ‘FB:FBgn0000546’ (eyeless/ey).

  • limit (integer) (optional) Maximum number of orthologs to return (1-100). Default: 20.

  • page (integer) (optional) Page number for pagination. Default: 1.

  • stringency (string) (optional) Stringency filter for orthology calls: ‘stringent’ (high confidence) or ‘moderate’. Default: ‘stringent’.

Example Usage:

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