Oma Tools

Configuration File: oma_tools.json Tool Type: Local Tools Count: 7

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

Available Tools

OMA_get_genome_pair_orthologs (Type: OMATool)

Retrieve the complete set of pairwise orthologs between TWO whole genomes (proteome-vs-proteome) …

OMA_get_genome_pair_orthologs tool specification

Tool Information:

• Name: OMA_get_genome_pair_orthologs

• Type: OMATool

• Description: Retrieve the complete set of pairwise orthologs between TWO whole genomes (proteome-vs-proteome) in OMA. Unlike OMA_get_orthologs (which returns orthologs of a single query protein), this returns every orthologous protein PAIR between two species genomes – the data used to build species-pair ortholog tables, dN/dS panels, and comparative-genomics / synteny analyses. Each pair reports entry_1 and entry_2 (omaid, canonical_id, species, HOG/group), the relationship type (1:1, 1:n, n:1, n:m), evolutionary distance, and alignment score. Provide species codes (e.g. genome1=’HUMAN’, genome2=’MOUSE’) or NCBI taxon IDs. Results are paginated; use per_page and page. Example: genome1=’HUMAN’, genome2=’MOUSE’ returns pairs such as HUMAN01436 (NK2R_HUMAN) <-> MOUSE00001 (NK2R_MOUSE), rel_type 1:1.

Parameters:

• genome1 (string) (required) First genome: UniProt species code (e.g. ‘HUMAN’, ‘PANTR’) or NCBI taxon ID (e.g. ‘9606’).

• genome2 (string) (required) Second genome: UniProt species code (e.g. ‘MOUSE’, ‘PANTR’) or NCBI taxon ID (e.g. ‘10090’).

• per_page ([‘integer’, ‘null’]) (optional) Number of ortholog pairs to return per page (default: 20, max: 100). The full proteome-vs-proteome set is large; paginate with ‘page’.

• page ([‘integer’, ‘null’]) (optional) Page number for paginated results (default: 1).

Example Usage:

query = {
    "name": "OMA_get_genome_pair_orthologs",
    "arguments": {
        "genome1": "example_value",
        "genome2": "example_value"
    }
}
result = tu.run(query)

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:F0782425 returns the p53 HOG at the Euteleostomi level with description ‘cellular tumor antigen p53’, completeness score 0.61, and child HOGs for fish, mammals, etc.

Parameters:

• hog_id (string) (required) Hierarchical Orthologous Group ID. Examples: ‘HOG:F0782425’ (p53 family), ‘HOG:F0798498’ (insulin family). Use OMA_get_protein to find the current HOG ID for a specific protein (the ‘oma_hog_id’ field). Note: OMA reassigns HOG IDs between releases, so IDs from older releases may return ‘no longer valid’.

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:F0782425.2c.7a, 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)

OMA_get_protein_go (Type: OMATool)

Get Gene Ontology (GO) functional annotations for a specific OMA protein. OMA attaches per-entry …

OMA_get_protein_go tool specification

Tool Information:

• Name: OMA_get_protein_go

• Type: OMATool

• Description: Get Gene Ontology (GO) functional annotations for a specific OMA protein. OMA attaches per-entry GO annotations with the aspect (biological_process / molecular_function / cellular_component), information content (ic), evidence code (e.g. IDA, NAS, IEA), and a literature reference (PMID). Other OMA tools return orthology / HOG / group membership but not these functional annotations. Accepts an OMA ID (e.g. ‘HUMAN17018’) or UniProt accession (e.g. ‘P04637’); use OMA_resolve_xref or OMA_get_protein first if you only have a gene symbol. Example: protein_id=’HUMAN17018’ returns GO:0060261 ‘positive regulation of transcription initiation by RNA polymerase II’, aspect biological_process, ic 8.27, evidence IDA, reference PMID:12218053.

Parameters:

• protein_id (string) (required) OMA ID (e.g. ‘HUMAN17018’) or UniProt accession (e.g. ‘P04637’).

• aspect ([‘string’, ‘null’]) (optional) Optional GO aspect filter: ‘biological_process’, ‘molecular_function’, or ‘cellular_component’. Leave empty for all aspects.

Example Usage:

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

OMA_resolve_xref (Type: OMATool)

Resolve a gene name, gene symbol, UniProt entry name, or any cross-reference identifier to OMA pr…

OMA_resolve_xref tool specification

Tool Information:

• Name: OMA_resolve_xref

• Type: OMATool

• Description: Resolve a gene name, gene symbol, UniProt entry name, or any cross-reference identifier to OMA protein entries. This is the entry point into the OMA toolchain when you only have a common identifier (e.g. ‘BRCA2’ or ‘MED4_HUMAN’) rather than a UniProt accession or OMA ID. OMA_get_protein only accepts a UniProt accession (P04637) or OMA ID (HUMAN31534); use this tool first to obtain the entry_nr / oma_id / genome for the gene of interest, then feed the oma_id into OMA_get_protein, OMA_get_orthologs, OMA_get_protein_go, etc. Example: search=’MED4_HUMAN’ returns entry_nr 24423700, oma_id HUMAN17018, species Homo sapiens (taxon 9606); search=’BRCA2’ returns matching OMA entries across species.

Parameters:

• search (string) (required) Gene symbol (e.g. ‘BRCA2’), UniProt entry name (e.g. ‘MED4_HUMAN’), or any cross-reference identifier to resolve to OMA entries.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of cross-reference matches to return (default: 25, max: 100).

Example Usage:

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

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