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 the complete InterPro match and transmembrane-domain lists with explicit counts, plus product, deletion viability, and cross-references. S. pombe is a key model organism for cell cycle, chromosome biology, and RNA processing research. Example: SPAC1093.06c (dhc1) returns all 29 annotated domain matches.

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

PomBase_get_gene_phenotypes tool specification

Tool Information:

  • Name: PomBase_get_gene_phenotypes

  • Type: PomBaseTool

  • Description: Get all phenotype annotations for a fission yeast (S. pombe) gene from PomBase. Returns deletion viability and the complete set of both single-locus and multi-locus FYPO (Fission Yeast Phenotype Ontology) annotations; phenotype_count is the full returned count. S. pombe phenotypes are a key resource for understanding gene function in cell biology. Example: SPBC11B10.09 (cdc2) has hundreds of phenotype annotations and is inviable when deleted.

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 the complete Gene Ontology annotation set (biological_process / molecular_function / cellular…

PomBase_get_go_annotations tool specification

Tool Information:

  • Name: PomBase_get_go_annotations

  • Type: PomBaseTool

  • Description: Get the complete Gene Ontology annotation set (biological_process / molecular_function / cellular_component) for a fission-yeast (S. pombe) gene from PomBase, with full per-aspect counts and resolved term names. No aspect is silently capped. Example: SPBC11B10.09 (cdc2) returns all BP, MF, and CC annotations.

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 gene from PomBase, each with evidence, …

PomBase_get_interactions tool specification

Tool Information:

  • Name: PomBase_get_interactions

  • Type: PomBaseTool

  • Description: Get physical and genetic interactions for a fission-yeast gene from PomBase, each with evidence, reference, throughput, and source. The two lists are independently paginated: continue with next_physical_offset and/or next_genetic_offset while the corresponding has_more field is true. Example: cdc2 has about 100 physical and 118 genetic records.

Parameters:

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

  • limit (integer) (optional) Maximum records returned from each interaction list in this page.

  • physical_offset (integer) (optional) Zero-based physical-interaction offset; continue with next_physical_offset.

  • genetic_offset (integer) (optional) Zero-based genetic-interaction offset; continue with next_genetic_offset.

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 all PomBase fission-yeast genes by name, systematic ID, or product keyword with complete l…

PomBase_search_genes tool specification

Tool Information:

  • Name: PomBase_search_genes

  • Type: PomBaseTool

  • Description: Search all PomBase fission-yeast genes by name, systematic ID, or product keyword with complete local limit/offset pagination. Metadata reports total_matches, has_more, and next_offset; continue while more matches remain.

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 in this page (1-50, default 10).

  • offset (integer) (optional) Zero-based offset in the complete filtered match list. Continue with metadata.next_offset.

Example Usage:

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