Forge Tools tair_plant

tair_plant read

scidex.forge.tair_plant

Query TAIR (The Arabidopsis Information Resource) for Arabidopsis thaliana gene annotation, GO terms, mutant allele phenotypes, and human orthologs. Accepts a gene symbol (e.g. 'FT', 'LEAFY', 'AP1') or AGI locus ID (e.g. 'AT1G65480', 'AT5G61850'). Returns the AGI locus ID, full gene name, gene type (e.g. protein-coding), chromosome, functional description, GO term annotations (go_id, go_term, go_aspect, evidence_code), phenotype records from mutant alleles (allele, phenotype, pubmed_id), and human ortholog gene symbols. If the gene is not found, not_found=True is returned — not an exception. TAIR is the authoritative reference for Arabidopsis thaliana (35K+ genes, 800K+ phenotype annotations). Fills the plant model organism gap in the SciDEX forge layer. API: api.arabidopsis.org — public REST API, no authentication required.

HTTP: POST /api/scidex/forge/tair_plant

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.tair_plant``.",
  "properties": {
    "gene": {
      "description": "Arabidopsis gene symbol (e.g. 'FT', 'LEAFY', 'AP1') or AGI locus ID (e.g. 'AT1G65480', 'AT5G61850'). Gene symbols are resolved via the TAIR gene symbol search; AGI locus IDs are queried directly.",
      "title": "Gene",
      "type": "string"
    },
    "include_phenotypes": {
      "default": true,
      "description": "If True (default), include mutant allele phenotype records. Set False to reduce response size when phenotype data is not needed.",
      "title": "Include Phenotypes",
      "type": "boolean"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeTairIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "TairGOTerm": {
      "description": "One Gene Ontology term annotation from TAIR.",
      "properties": {
        "go_id": {
          "description": "GO term ID (e.g. 'GO:0009910').",
          "title": "Go Id",
          "type": "string"
        },
        "go_term": {
          "description": "GO term name (e.g. 'negative regulation of flowering').",
          "title": "Go Term",
          "type": "string"
        },
        "go_aspect": {
          "description": "GO aspect: 'F' (molecular function), 'P' (biological process), 'C' (cellular component).",
          "title": "Go Aspect",
          "type": "string"
        },
        "evidence_code": {
          "description": "Evidence code (e.g. 'IMP', 'IDA', 'IEA').",
          "title": "Evidence Code",
          "type": "string"
        }
      },
      "required": [
        "go_id",
        "go_term",
        "go_aspect",
        "evidence_code"
      ],
      "title": "TairGOTerm",
      "type": "object"
    },
    "TairPhenotype": {
      "description": "One phenotype record from a TAIR mutant allele.",
      "properties": {
        "allele": {
          "description": "Allele name (e.g. 'ft-1', 'ft-10').",
          "title": "Allele",
          "type": "string"
        },
        "phenotype": {
          "description": "Phenotype description (e.g. 'late flowering under long days').",
          "title": "Phenotype",
          "type": "string"
        },
        "pubmed_id": {
          "anyOf": [
            {
              "type": "string"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "PubMed ID of the supporting publication, if available.",
          "title": "Pubmed Id"
        }
      },
      "required": [
        "allele",
        "phenotype"
      ],
      "title": "TairPhenotype",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.tair_plant``.",
  "properties": {
    "gene": {
      "description": "Input gene symbol or AGI locus ID as provided.",
      "title": "Gene",
      "type": "string"
    },
    "locus_id": {
      "default": "",
      "description": "AGI locus ID (e.g. 'AT1G65480'). Empty string if not found.",
      "title": "Locus Id",
      "type": "string"
    },
    "full_name": {
      "default": "",
      "description": "Full gene name (e.g. 'FLOWERING LOCUS T').",
      "title": "Full Name",
      "type": "string"
    },
    "gene_type": {
      "default": "",
      "description": "Gene type (e.g. 'protein-coding', 'lncRNA', 'pseudogene').",
      "title": "Gene Type",
      "type": "string"
    },
    "chromosome": {
      "default": "",
      "description": "Chromosome (e.g. '1', '3', 'M' for mitochondrial, 'C' for chloroplast).",
      "title": "Chromosome",
      "type": "string"
    },
    "description": {
      "default": "",
      "description": "Gene function description from TAIR.",
      "title": "Description",
      "type": "string"
    },
    "go_terms": {
      "description": "GO term annotations from TAIR (molecular function, biological process, cellular component).",
      "items": {
        "$ref": "#/$defs/TairGOTerm"
      },
      "title": "Go Terms",
      "type": "array"
    },
    "phenotypes": {
      "description": "Mutant allele phenotype records from TAIR.",
      "items": {
        "$ref": "#/$defs/TairPhenotype"
      },
      "title": "Phenotypes",
      "type": "array"
    },
    "orthologs_human": {
      "description": "Human ortholog gene symbols (e.g. ['SOX15'] for LEAFY).",
      "items": {
        "type": "string"
      },
      "title": "Orthologs Human",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True if the gene or locus ID was not found in TAIR.",
      "title": "Not Found",
      "type": "boolean"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for all upstream API calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgeTairOut",
  "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/tair_plant' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

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