Pombase Tools

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

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

Available Tools

PomBase_get_gene (Type: PomBaseTool)

Get detailed gene information from PomBase for fission yeast (S. pombe) by systematic ID. Returns…

PomBase_get_gene tool specification

Tool Information:

  • Name: PomBase_get_gene

  • Type: PomBaseTool

  • Description: Get detailed gene information from PomBase for fission yeast (S. pombe) by systematic ID. Returns gene name, protein product, InterPro domain annotations, deletion viability, UniProt cross-reference, and transmembrane domain coordinates. S. pombe is a key model organism for cell cycle, chromosome biology, and RNA processing research. Example: SPBC11B10.09 returns cdc2 (cyclin-dependent kinase), essential for cell division.

Parameters:

  • gene_id (string) (required) PomBase systematic gene identifier. Examples: ‘SPBC11B10.09’ (cdc2), ‘SPAC2F7.03c’ (pom1), ‘SPAC1002.17c’ (ase1).

Example Usage:

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

PomBase_get_gene_phenotypes (Type: PomBaseTool)

Get phenotype annotations for a fission yeast (S. pombe) gene from PomBase. Returns deletion viab…

PomBase_get_gene_phenotypes tool specification

Tool Information:

  • Name: PomBase_get_gene_phenotypes

  • Type: PomBaseTool

  • Description: Get phenotype annotations for a fission yeast (S. pombe) gene from PomBase. Returns deletion viability, FYPO (Fission Yeast Phenotype Ontology) term annotations with evidence codes. S. pombe phenotypes are a key resource for understanding gene function in cell biology. Example: SPBC11B10.09 (cdc2) is inviable when deleted, reflecting its essential role in cell division.

Parameters:

  • gene_id (string) (required) PomBase systematic gene identifier. Examples: ‘SPBC11B10.09’ (cdc2), ‘SPAC2F7.03c’ (pom1).

Example Usage:

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

PomBase_get_go_annotations (Type: PomBaseTool)

Get Gene Ontology annotations (biological_process / molecular_function / cellular_component) for …

PomBase_get_go_annotations tool specification

Tool Information:

  • Name: PomBase_get_go_annotations

  • Type: PomBaseTool

  • Description: Get Gene Ontology annotations (biological_process / molecular_function / cellular_component) for a fission-yeast (S. pombe) gene from PomBase, with per-aspect counts and resolved term names. Example: SPBC11B10.09 (cdc2) returns BP terms like GO:0000082 ‘G1/S transition of mitotic cell cycle’, plus MF and CC terms.

Parameters:

  • gene_id (string) (required) PomBase systematic ID. Examples: ‘SPBC11B10.09’ (cdc2).

Example Usage:

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

PomBase_get_interactions (Type: PomBaseTool)

Get physical and genetic interactions for a fission-yeast (S. pombe) gene from PomBase, each with…

PomBase_get_interactions tool specification

Tool Information:

  • Name: PomBase_get_interactions

  • Type: PomBaseTool

  • Description: Get physical and genetic interactions for a fission-yeast (S. pombe) gene from PomBase, each with evidence method, reference (PMID), throughput, and source database. Example: SPBC11B10.09 (cdc2) has ~100 physical interactions (e.g. SPAC1006.03c/red1 via Affinity Capture-MS, PMID:24713849, BIOGRID) and ~118 genetic interactions.

Parameters:

  • gene_id (string) (required) PomBase systematic ID. Examples: ‘SPBC11B10.09’ (cdc2).

Example Usage:

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

PomBase_get_orthologs (Type: PomBaseTool)

Get human and S. cerevisiae orthologs of a fission-yeast (S. pombe) gene from PomBase. Returns or…

PomBase_get_orthologs tool specification

Tool Information:

  • Name: PomBase_get_orthologs

  • Type: PomBaseTool

  • Description: Get human and S. cerevisiae orthologs of a fission-yeast (S. pombe) gene from PomBase. Returns ortholog IDs with taxon (9606=human via HGNC, 4932=budding yeast via systematic name). Example: SPBC11B10.09 (cdc2) returns human CDKs HGNC:1722/1771/1772 (taxon 9606) and S. cerevisiae CDC28 / YBR160W (taxon 4932).

Parameters:

  • gene_id (string) (required) PomBase systematic ID. Examples: ‘SPBC11B10.09’ (cdc2), ‘SPAC1006.03c’ (red1).

Example Usage:

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

PomBase_search_genes (Type: PomBaseTool)

Search PomBase for fission yeast (S. pombe) genes by name, systematic ID, or protein product keyw…

PomBase_search_genes tool specification

Tool Information:

  • Name: PomBase_search_genes

  • Type: PomBaseTool

  • Description: Search PomBase for fission yeast (S. pombe) genes by name, systematic ID, or protein product keyword. Searches across 12,600+ gene entries. Returns matching genes with systematic IDs, gene names, and protein products. Example: searching ‘kinase’ returns CDK and other kinase genes; searching ‘cdc’ returns cell division cycle genes.

Parameters:

  • query (string) (required) Search query - gene name, systematic ID prefix, or product keyword. Examples: ‘cdc2’, ‘kinase’, ‘SPAC’, ‘pom1’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum results to return (1-50, default 10).

Example Usage:

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