Zfin Tools

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

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

Available Tools

ZFIN_get_allele (Type: AllianceGenomeTool)

Get detailed information about a specific zebrafish allele from ZFIN via the Alliance of Genome R…

ZFIN_get_allele tool specification

Tool Information:

  • Name: ZFIN_get_allele

  • Type: AllianceGenomeTool

  • Description: Get detailed information about a specific zebrafish allele from ZFIN via the Alliance of Genome Resources. Returns allele symbol, associated gene, alteration type, species, and synonyms. Useful for looking up specific zebrafish mutant lines. Example: ‘ZFIN:ZDB-ALT-210706-1’ returns the szu2 allele of pax2a with its deletion variant details.

Parameters:

  • allele_id (string) (required) ZFIN allele ID with ‘ZFIN:’ prefix. Examples: ‘ZFIN:ZDB-ALT-210706-1’ (szu2 allele of pax2a), ‘ZFIN:ZDB-ALT-980203-1590’ (tm243a allele of pax2a).

Example Usage:

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

ZFIN_get_gene (Type: AllianceGenomeTool)

Get detailed Danio rerio (zebrafish) gene information from ZFIN via the Alliance of Genome Resour…

ZFIN_get_gene tool specification

Tool Information:

  • Name: ZFIN_get_gene

  • Type: AllianceGenomeTool

  • Description: Get detailed Danio rerio (zebrafish) gene information from ZFIN via the Alliance of Genome Resources. Returns gene symbol, name, synopsis, genomic location, synonyms, and cross-references. ZFIN is the primary database for zebrafish genetics. Example: ‘ZFIN:ZDB-GENE-990415-8’ returns pax2a (paired box 2a) with its role in nervous system development.

Parameters:

  • gene_id (string) (required) ZFIN gene ID with ‘ZFIN:’ prefix. Examples: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a), ‘ZFIN:ZDB-GENE-980526-166’ (shha/sonic hedgehog a), ‘ZFIN:ZDB-GENE-990415-72’ (tp53/tumor protein p53), ‘ZFIN:ZDB-GENE-030131-7740’ (bmp4/bone morphogenetic protein 4).

Example Usage:

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

ZFIN_get_gene_alleles (Type: AllianceGenomeTool)

Get alleles and variants for a zebrafish gene from ZFIN via the Alliance of Genome Resources. Ret…

ZFIN_get_gene_alleles tool specification

Tool Information:

  • Name: ZFIN_get_gene_alleles

  • Type: AllianceGenomeTool

  • Description: Get alleles and variants for a zebrafish gene from ZFIN via the Alliance of Genome Resources. Returns mutant alleles with variant types (deletion, insertion, point mutation), molecular consequences, and phenotype/disease associations. Zebrafish genetics benefits from large-scale mutagenesis screens producing thousands of alleles. Example: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a) returns alleles like szu2 (deletion) with start_lost consequence.

Parameters:

  • gene_id (string) (required) ZFIN gene ID with ‘ZFIN:’ prefix. Examples: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a), ‘ZFIN:ZDB-GENE-990415-72’ (tp53), ‘ZFIN:ZDB-GENE-980526-166’ (shha).

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

ZFIN_get_gene_expression (Type: AllianceGenomeTool)

Get expression summary for a zebrafish gene from the Alliance of Genome Resources. Returns a ribb…

ZFIN_get_gene_expression tool specification

Tool Information:

  • Name: ZFIN_get_gene_expression

  • Type: AllianceGenomeTool

  • Description: Get expression summary for a zebrafish gene from the Alliance of Genome Resources. Returns a ribbon summary of expression across anatomical systems (nervous system, renal system, sensory system, etc.) with annotation counts. Zebrafish is a premier model for studying vertebrate development and expression. Example: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a) shows 1092 annotations including nervous system (216), renal system (60), sensory system (25).

Parameters:

  • gene_id (string) (required) ZFIN gene ID with ‘ZFIN:’ prefix. Examples: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a), ‘ZFIN:ZDB-GENE-980526-166’ (shha), ‘ZFIN:ZDB-GENE-990415-72’ (tp53).

Example Usage:

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

ZFIN_get_gene_orthologs (Type: AllianceGenomeTool)

Get orthologs of a zebrafish gene across other species from the Alliance of Genome Resources. Ret…

ZFIN_get_gene_orthologs tool specification

Tool Information:

  • Name: ZFIN_get_gene_orthologs

  • Type: AllianceGenomeTool

  • Description: Get orthologs of a zebrafish gene across other species from the Alliance of Genome Resources. Returns orthologous genes in human, mouse, fly, worm, yeast, and other model organisms. Essential for translating zebrafish findings to human gene function. Zebrafish share approximately 70% of genes with humans. Example: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a) returns human PAX2 as ortholog.

Parameters:

  • gene_id (string) (required) ZFIN gene ID with ‘ZFIN:’ prefix. Examples: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a), ‘ZFIN:ZDB-GENE-990415-72’ (tp53), ‘ZFIN:ZDB-GENE-980526-166’ (shha).

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

ZFIN_get_gene_phenotypes (Type: AllianceGenomeTool)

Get phenotype annotations for a zebrafish gene from ZFIN via the Alliance of Genome Resources. Re…

ZFIN_get_gene_phenotypes tool specification

Tool Information:

  • Name: ZFIN_get_gene_phenotypes

  • Type: AllianceGenomeTool

  • Description: Get phenotype annotations for a zebrafish gene from ZFIN via the Alliance of Genome Resources. Returns phenotypes observed when the gene is mutated or knocked out in zebrafish, including affected anatomical structures and phenotype statements. Zebrafish is widely used for forward genetic screens and disease modeling. Example: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a) returns phenotypes related to eye, kidney, and nervous system development.

Parameters:

  • gene_id (string) (required) ZFIN gene ID with ‘ZFIN:’ prefix. Examples: ‘ZFIN:ZDB-GENE-990415-8’ (pax2a), ‘ZFIN:ZDB-GENE-990415-72’ (tp53), ‘ZFIN:ZDB-GENE-980526-166’ (shha).

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

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

Example Usage:

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