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 pairwise orthologs between two whole genomes in OMA. Unlike OMA_get_orthologs, this endp…

OMA_get_genome_pair_orthologs tool specification

Tool Information:

  • Name: OMA_get_genome_pair_orthologs

  • Type: OMATool

  • Description: Retrieve pairwise orthologs between two whole genomes in OMA. Unlike OMA_get_orthologs, this endpoint has real server-side page/per_page pagination. Metadata preserves the official x-total-count and reports has_more and next_page, making the complete proteome-vs-proteome set reachable.

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) Ortholog pairs per official server page (default 20, verified through 10000). Invalid values return an error rather than being silently clamped.

  • page ([‘integer’, ‘null’]) (optional) One-based official result page (default 1). Continue with metadata.next_page while has_more is true.

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 and page through all member proteins. OMA Groups contain sets of strict 1:1…

OMA_get_group tool specification

Tool Information:

  • Name: OMA_get_group

  • Type: OMATool

  • Description: Get OMA Group details and page through all 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. Reports the true member total, returned count, and next offset so large strict-ortholog groups do not silently stop at 30 members. Group numbers are not stable/predictable identifiers to memorize – resolve the current group ID for a protein of interest via OMA_get_protein’s ‘oma_group’ field first. Verified example: group 1458663 returns the p53 OMA Group, description ‘Cellular tumor antigen p53’, fingerprint ‘ACCQRNQ’.

Parameters:

  • group_id (string) (required) OMA Group number (numeric ID). Verified example: ‘1458663’ (p53 group). Use OMA_get_protein to find the current group ID for a specific protein rather than assuming a remembered ID still maps to the same group.

  • limit (integer) (optional) Maximum group members to return.

  • offset (integer) (optional) Zero-based offset into all OMA group members.

Example Usage:

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

OMA_get_hog (Type: OMATool)#

Get complete Hierarchical Orthologous Group (HOG) information from OMA. Returns all child HOGs an…

OMA_get_hog tool specification

Tool Information:

  • Name: OMA_get_hog

  • Type: OMATool

  • Description: Get complete Hierarchical Orthologous Group (HOG) information from OMA. Returns all child HOGs and all alternative taxonomic levels, including every child’s complete alternative-level list, with explicit counts at each layer; evolutionary branches are not silently capped.

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. The upstream protein-ortholog endpoint returns its complete filtered list and ignores per_page/page, so ToolUniverse applies local per_page/offset pagination. The response reports ‘count’ (orthologs in this response) alongside ‘total_count’ (all orthologs OMA holds for the protein); these differ whenever ‘per_page’ is smaller than the full set, which is usual – P04637 has 157. When they differ ‘truncated’ is true and ‘truncation_note’ says how to widen the request; continue with metadata.next_offset while has_more is true. Treat ‘count’ as a page size and never as the number of species with an ortholog.

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, maximum 1000). OMA does not paginate this endpoint – it returns the complete ortholog set in one response – so this limit is applied by ToolUniverse after fetching; use ‘offset’ for later slices.

  • offset (integer) (optional) Zero-based offset into the complete filtered ortholog list. Continue with metadata.next_offset while has_more is true.

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 and page through OMA cross-reference matches for a gene symbol, UniProt entry name, or ot…

OMA_resolve_xref tool specification

Tool Information:

  • Name: OMA_resolve_xref

  • Type: OMATool

  • Description: Resolve and page through OMA cross-reference matches for a gene symbol, UniProt entry name, or other identifier. Returns the true match total, returned count, and next offset so broad identifiers such as BRCA2 do not silently stop at 100; feed returned OMA IDs into protein/ortholog/HOG tools.

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 cross-reference matches to return (default 25, max 1000).

  • offset (integer) (optional) Zero-based offset into all OMA cross-reference matches.

Example Usage:

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