Sgd Protein Tools

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

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

Available Tools

SGD_get_literature (Type: SGDProteinTool)

Get categorized literature references for a budding-yeast (Saccharomyces cerevisiae) gene from th…

SGD_get_literature tool specification

Tool Information:

  • Name: SGD_get_literature

  • Type: SGDProteinTool

  • Description: Get categorized literature references for a budding-yeast (Saccharomyces cerevisiae) gene from the Saccharomyces Genome Database (SGD). Returns reference counts per curation category (primary, review, interaction, phenotype, GO, disease, PTM, regulation, additional, high-throughput) plus a capped list of the most relevant references for each category, each with citation, PubMed ID, year, and SGD reference link. Useful for surveying the curated literature behind a yeast gene’s annotations. The ‘locus’ argument accepts a standard gene name (e.g. ‘ACT1’), a systematic name (e.g. ‘YAL001C’), or an SGD ID (e.g. ‘S000001855’). No API key required.

Parameters:

  • locus (string) (required) Yeast gene identifier: standard gene name (e.g. ‘ACT1’), systematic/ORF name (e.g. ‘YAL001C’), or SGD ID (e.g. ‘S000001855’).

Example Usage:

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

SGD_get_protein_domains (Type: SGDProteinTool)

Get mapped protein domains for a budding-yeast (Saccharomyces cerevisiae) gene from the Saccharom…

SGD_get_protein_domains tool specification

Tool Information:

  • Name: SGD_get_protein_domains

  • Type: SGDProteinTool

  • Description: Get mapped protein domains for a budding-yeast (Saccharomyces cerevisiae) gene from the Saccharomyces Genome Database (SGD). Returns domain hits from Pfam, InterPro, SMART, PROSITE, CDD, Gene3D, SUPERFAMILY, PANTHER, and PRINTS, each with the domain accession, description, source database, and start/end residue coordinates on the protein. The ‘locus’ argument accepts a standard gene name (e.g. ‘ACT1’), a systematic name (e.g. ‘YFL039C’), or an SGD ID (e.g. ‘S000001855’). No API key required.

Parameters:

  • locus (string) (required) Yeast gene identifier: standard gene name (e.g. ‘ACT1’), systematic/ORF name (e.g. ‘YFL039C’), or SGD ID (e.g. ‘S000001855’).

Example Usage:

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

SGD_get_ptm_sites (Type: SGDProteinTool)

Get curated post-translational modification (PTM) sites for a budding-yeast (Saccharomyces cerevi…

SGD_get_ptm_sites tool specification

Tool Information:

  • Name: SGD_get_ptm_sites

  • Type: SGDProteinTool

  • Description: Get curated post-translational modification (PTM) sites for a budding-yeast (Saccharomyces cerevisiae) gene from the Saccharomyces Genome Database (SGD). Returns modified residues such as phosphorylation, ubiquitination, acetylation, methylation, and succinylation, each with the modification type, the residue letter, its position in the protein sequence, and the supporting reference (citation + PubMed ID). The ‘locus’ argument accepts a standard gene name (e.g. ‘ACT1’), a systematic name (e.g. ‘YAL001C’), or an SGD ID (e.g. ‘S000001855’). No API key required.

Parameters:

  • locus (string) (required) Yeast gene identifier: standard gene name (e.g. ‘ACT1’), systematic/ORF name (e.g. ‘YAL001C’), or SGD ID (e.g. ‘S000001855’).

Example Usage:

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