Oma Tools

Configuration File: oma_tools.json Tool Type: Local Tools Count: 4

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

Available Tools

OMA_get_group (Type: OMATool)

Get OMA Group details including member proteins. OMA Groups contain sets of strict 1:1 orthologs …

OMA_get_group tool specification

Tool Information:

  • Name: OMA_get_group

  • Type: OMATool

  • Description: Get OMA Group details including member proteins. OMA Groups contain sets of strict 1:1 orthologs across all genomes, ensuring each species contributes at most one gene. This is the most stringent orthology definition in OMA. Example: group 1388790 returns the p53 OMA Group with fingerprint ‘HKKGEPC’, description ‘cellular tumor antigen p53’, and members from fish, mammals, and other vertebrates.

Parameters:

  • group_id (string) (required) OMA Group number (numeric ID). Examples: ‘1388790’ (p53 group), ‘839588’ (EGFR group). Use OMA_get_protein to find the group ID for a specific protein.

Example Usage:

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

OMA_get_hog (Type: OMATool)

Get Hierarchical Orthologous Group (HOG) information from OMA. HOGs represent groups of genes tha…

OMA_get_hog tool specification

Tool Information:

  • Name: OMA_get_hog

  • Type: OMATool

  • Description: Get Hierarchical Orthologous Group (HOG) information from OMA. HOGs represent groups of genes that descended from a single ancestral gene within a given taxonomic range. HOGs capture the full evolutionary history of gene families including gene duplications. Example: HOG:E0739094 returns the p53 HOG at the Euteleostomi level with description ‘cellular tumor antigen p53’, completeness score 0.65, and child HOGs for fish, mammals, etc.

Parameters:

  • hog_id (string) (required) Hierarchical Orthologous Group ID. Examples: ‘HOG:E0739094’ (p53 family), ‘HOG:E0817124’ (insulin family). Use OMA_get_protein to find the HOG ID for a specific protein.

Example Usage:

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

OMA_get_orthologs (Type: OMATool)

Get pairwise orthologs for a protein from the OMA (Orthologous MAtrix) Browser. Returns orthologo…

OMA_get_orthologs tool specification

Tool Information:

  • Name: OMA_get_orthologs

  • Type: OMATool

  • Description: Get pairwise orthologs for a protein from the OMA (Orthologous MAtrix) Browser. Returns orthologous proteins across species with relationship type (1:1, 1:many, many:1, many:many), evolutionary distance, and alignment score. OMA orthologs are inferred using a rigorous algorithm that provides high-confidence predictions. Example: P04637 (human p53) returns orthologs in 200+ species including Mus musculus, Danio rerio, and Drosophila melanogaster.

Parameters:

  • protein_id (string) (required) UniProt accession (e.g., ‘P04637’ for human p53) or OMA ID.

  • rel_type ([‘string’, ‘null’]) (optional) Filter by orthology relationship type. Options: ‘1:1’ (one-to-one), ‘1:n’ (one-to-many), ‘n:1’ (many-to-one), ‘n:m’ (many-to-many). Leave empty for all types.

  • per_page ([‘integer’, ‘null’]) (optional) Number of orthologs to return (default: 20, max: 100).

Example Usage:

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

OMA_get_protein (Type: OMATool)

Get protein information from the OMA (Orthologous MAtrix) Browser by UniProt accession or OMA ID….

OMA_get_protein tool specification

Tool Information:

  • Name: OMA_get_protein

  • Type: OMATool

  • Description: Get protein information from the OMA (Orthologous MAtrix) Browser by UniProt accession or OMA ID. OMA is a comprehensive orthology database covering 2,600+ complete genomes. Returns protein details including species, genomic location, OMA group membership, and Hierarchical Orthologous Group (HOG) assignment. Example: P04637 returns human TP53 with OMA ID HUMAN31534, HOG:E0739094.3a.3b.3b, and genomic locus on chromosome 17.

Parameters:

  • protein_id (string) (required) UniProt accession (e.g., ‘P04637’ for human p53) or OMA ID (e.g., ‘HUMAN31534’). UniProt accessions are recommended for cross-database compatibility.

Example Usage:

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