mygene_info read
scidex.forge.mygene_info
Look up aggregated gene metadata from MyGene.info for a list of gene symbols. MyGene.info reconciles annotations from Entrez, Ensembl, UniProt, UCSC, RefSeq, GO, KEGG, WikiPathways, Reactome, ClinVar, PharmGKB, OMIM, and 20+ other sources into a single cross-database record per gene. Batch POST endpoint — free, no auth required.
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.mygene_info``.",
"properties": {
"gene_symbols": {
"description": "HGNC gene symbols to look up (e.g. ``['BRCA1', 'EGFR']``). Queried via MyGene.info batch POST endpoint. 1–50 symbols per call.",
"items": {
"type": "string"
},
"title": "Gene Symbols",
"type": "array"
},
"species": {
"default": "human",
"description": "Species filter for MyGene.info. Default 'human'. Also accepts 'mouse', 'rat', or NCBI taxonomy IDs.",
"maxLength": 64,
"title": "Species",
"type": "string"
},
"fields": {
"default": "symbol,name,taxid,ensembl.gene,uniprot.Swiss-Prot,entrezgene,go.BP,pathway.kegg,refseq.rna,genomic_pos",
"description": "Comma-separated MyGene.info fields to return. Default: 'symbol,name,taxid,ensembl.gene,uniprot.Swiss-Prot,entrezgene,go.BP,pathway.kegg,refseq.rna,genomic_pos'.",
"maxLength": 512,
"title": "Fields",
"type": "string"
},
"limit": {
"default": 10,
"description": "Maximum results per gene symbol. Default 10.",
"maximum": 1000,
"minimum": 1,
"title": "Limit",
"type": "integer"
}
},
"required": [
"gene_symbols"
],
"title": "ForgeMyGeneIn",
"type": "object"
}Output schema
{
"$defs": {
"MyGeneResult": {
"description": "One MyGene.info gene record.",
"properties": {
"query_symbol": {
"description": "The gene symbol that was queried.",
"title": "Query Symbol",
"type": "string"
},
"mygene_id": {
"default": "",
"description": "MyGene.info internal gene ID (maps to '_id').",
"title": "Mygene Id",
"type": "string"
},
"entrezgene": {
"default": "",
"description": "NCBI Entrez Gene ID.",
"title": "Entrezgene",
"type": "string"
},
"ensembl_gene_id": {
"default": "",
"description": "Ensembl stable gene ID (e.g. 'ENSG00000139618').",
"title": "Ensembl Gene Id",
"type": "string"
},
"symbol": {
"default": "",
"description": "Official gene symbol.",
"title": "Symbol",
"type": "string"
},
"name": {
"default": "",
"description": "Official gene full name.",
"title": "Name",
"type": "string"
},
"taxid": {
"default": 0,
"description": "NCBI taxonomy ID (9606 for human).",
"title": "Taxid",
"type": "integer"
},
"uniprot_swiss_prot": {
"description": "UniProt Swiss-Prot accession(s).",
"items": {
"type": "string"
},
"title": "Uniprot Swiss Prot",
"type": "array"
},
"go_bp_terms": {
"description": "GO Biological Process term names.",
"items": {
"type": "string"
},
"title": "Go Bp Terms",
"type": "array"
},
"kegg_pathway_ids": {
"description": "KEGG pathway IDs (e.g. 'hsa:05200').",
"items": {
"type": "string"
},
"title": "Kegg Pathway Ids",
"type": "array"
},
"refseq_rna": {
"description": "RefSeq RNA accession(s) (NM_/NR_).",
"items": {
"type": "string"
},
"title": "Refseq Rna",
"type": "array"
},
"genomic_pos": {
"anyOf": [
{
"additionalProperties": true,
"type": "object"
},
{
"type": "null"
}
],
"default": null,
"description": "Genomic coordinates: {chr, start, end, strand}.",
"title": "Genomic Pos"
}
},
"required": [
"query_symbol"
],
"title": "MyGeneResult",
"type": "object"
}
},
"description": "Response shape for ``scidex.forge.mygene_info``.",
"properties": {
"gene_symbols": {
"description": "The gene symbols that were queried.",
"items": {
"type": "string"
},
"title": "Gene Symbols",
"type": "array"
},
"genes": {
"description": "MyGene.info gene records, one per queried symbol.",
"items": {
"$ref": "#/$defs/MyGeneResult"
},
"title": "Genes",
"type": "array"
},
"total_found": {
"default": 0,
"description": "Number of genes with cross-ref data populated (not notfound).",
"title": "Total Found",
"type": "integer"
},
"took_ms": {
"description": "Wall-clock time for the upstream call.",
"title": "Took Ms",
"type": "integer"
}
},
"required": [
"gene_symbols",
"took_ms"
],
"title": "ForgeMyGeneOut",
"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/mygene_info' \
-H 'authorization: Bearer $SCIDEX_JWT' \
-H 'content-type: application/json' \
-d '{
"gene_symbols": []
}'Discussion
No comments yet — be the first.