oma_orthologs read
scidex.forge.oma_orthologs
Look up protein orthologs in the OMA Browser REST API by OMA entry ID, numeric entry number, or canonical protein identifier such as a UniProt accession. Returns OMA ortholog records with species, NCBI taxon ID, relationship type, HOG/group identifiers, locus metadata, score, and distance. Supports optional OMA rel_type filtering such as '1:1'.
Invoke
Calls scidex.tool.invoke on the substrate with
this tool name. Edit the JSON below — it must match the
input schema. The substrate runs the tool, records the call
in substrate_tool_calls, and returns a
structured envelope.
Sign in to invoke this tool. Schema and curl snippet are visible to anyone.
Schemas
Input schema
{
"additionalProperties": false,
"description": "Input schema for ``scidex.forge.oma_orthologs``.",
"properties": {
"protein_id": {
"description": "OMA protein entry identifier: OMA ID, numeric entry number, or canonical protein identifier such as a UniProt accession (for example, 'P04637').",
"maxLength": 80,
"minLength": 1,
"title": "Protein Id",
"type": "string"
},
"rel_type": {
"anyOf": [
{
"enum": [
"1:1",
"1:n",
"m:1",
"m:n"
],
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "Optional OMA relationship filter. Use '1:1' for one-to-one orthologs, or leave unset to return all ortholog relationship types.",
"title": "Rel Type"
},
"limit": {
"default": 100,
"description": "Maximum number of ortholog records to return.",
"maximum": 500,
"minimum": 1,
"title": "Limit",
"type": "integer"
}
},
"required": [
"protein_id"
],
"title": "ForgeOMAOrthologsIn",
"type": "object"
}Output schema
{
"$defs": {
"OMAOrtholog": {
"description": "One OMA ortholog record.",
"properties": {
"entry_nr": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "OMA internal numeric entry ID.",
"title": "Entry Nr"
},
"oma_id": {
"default": "",
"description": "OMA protein identifier, e.g. HUMAN07666.",
"title": "Oma Id",
"type": "string"
},
"canonical_id": {
"default": "",
"description": "Canonical protein identifier from OMA, often a UniProt or RefSeq accession.",
"title": "Canonical Id",
"type": "string"
},
"entry_url": {
"default": "",
"description": "OMA API URL for this protein entry.",
"title": "Entry Url",
"type": "string"
},
"sequence_length": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Protein sequence length.",
"title": "Sequence Length"
},
"species_code": {
"default": "",
"description": "OMA five-letter species code.",
"title": "Species Code",
"type": "string"
},
"species_name": {
"default": "",
"description": "Scientific species name.",
"title": "Species Name",
"type": "string"
},
"taxon_id": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "NCBI taxonomy ID for the species.",
"title": "Taxon Id"
},
"rel_type": {
"default": "",
"description": "OMA relationship type, e.g. '1:1' or '1:n'.",
"title": "Rel Type",
"type": "string"
},
"score": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "OMA orthology confidence score.",
"title": "Score"
},
"distance": {
"anyOf": [
{
"type": "number"
},
{
"type": "null"
}
],
"default": null,
"description": "OMA evolutionary distance value.",
"title": "Distance"
},
"oma_group": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "OMA group ID when available.",
"title": "Oma Group"
},
"oma_hog_id": {
"default": "",
"description": "Hierarchical orthologous group ID.",
"title": "Oma Hog Id",
"type": "string"
},
"chromosome": {
"default": "",
"description": "Chromosome or contig label.",
"title": "Chromosome",
"type": "string"
},
"locus_start": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Genomic locus start coordinate.",
"title": "Locus Start"
},
"locus_end": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Genomic locus end coordinate.",
"title": "Locus End"
},
"locus_strand": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"description": "Genomic strand, usually 1 or -1.",
"title": "Locus Strand"
},
"is_main_isoform": {
"anyOf": [
{
"type": "boolean"
},
{
"type": "null"
}
],
"default": null,
"description": "Whether OMA marks this protein as the main isoform.",
"title": "Is Main Isoform"
}
},
"title": "OMAOrtholog",
"type": "object"
}
},
"description": "Response shape for ``scidex.forge.oma_orthologs``.",
"properties": {
"protein_id": {
"description": "The protein identifier that was queried.",
"title": "Protein Id",
"type": "string"
},
"orthologs": {
"items": {
"$ref": "#/$defs/OMAOrtholog"
},
"title": "Orthologs",
"type": "array"
},
"total_orthologs": {
"default": 0,
"description": "Total ortholog records returned by OMA before applying ``limit``.",
"title": "Total Orthologs",
"type": "integer"
},
"returned": {
"default": 0,
"description": "Number of ortholog records returned.",
"title": "Returned",
"type": "integer"
},
"not_found": {
"default": false,
"description": "True when OMA cannot resolve the ID.",
"title": "Not Found",
"type": "boolean"
},
"detail": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"description": "OMA not-found or ambiguity detail when available.",
"title": "Detail"
},
"source": {
"default": "OMA Browser REST API (omabrowser.org)",
"description": "Data source identifier.",
"title": "Source",
"type": "string"
},
"took_ms": {
"default": 0,
"description": "Wall-clock time for the upstream call.",
"title": "Took Ms",
"type": "integer"
}
},
"required": [
"protein_id"
],
"title": "ForgeOMAOrthologsOut",
"type": "object"
}curl snippet
Replace $SCIDEX_JWT with a valid bearer token. Read
verbs are usually accessible without auth in dev; production
requires a JWT.
curl -sS -X POST '/api/scidex/forge/oma_orthologs' \
-H 'authorization: Bearer $SCIDEX_JWT' \
-H 'content-type: application/json' \
-d '{
"protein_id": ""
}'Discussion
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