Forge Tools phenodigm

phenodigm read

scidex.forge.phenodigm

Query EBI PhenoDigm for phenotype similarity scores between mouse gene knockouts and human diseases. Uses IC-weighted Jaccard similarity over HP/MP term sets to score how well a mouse knockout model's phenotypes match a human disease's phenotype profile. Input a mouse gene symbol (e.g. 'Trp53') or human symbol (e.g. 'TP53'). Returns OMIM/ORPHANET disease matches ranked by score (0–100), with matched HP-term IDs and model genotype descriptions. Distinct from forge_hpo_phenotype (raw HPO associations), forge_monarch_initiative (cross-species orthologs), and forge_mgi_mouse_gene (gene metadata). Solr API: https://www.ebi.ac.uk/mi/impc/solr/phenodigm/select — free, no auth.

HTTP: POST /api/scidex/forge/phenodigm

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.phenodigm``.",
  "properties": {
    "gene": {
      "description": "Mouse gene symbol to query (e.g. 'Trp53'). Human gene symbols (e.g. 'TP53') are also accepted and queried directly against the marker_symbol field.",
      "maxLength": 100,
      "minLength": 1,
      "title": "Gene",
      "type": "string"
    },
    "min_score": {
      "default": 40,
      "description": "Minimum similarity score to include in results. Scores in [0, 100]; default 40. Scores below this threshold are filtered out.",
      "maximum": 100,
      "minimum": 0,
      "title": "Min Score",
      "type": "number"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of matches to return. Default 20.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgePhenodigmIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "PhenodigmMatch": {
      "description": "One disease-model similarity match from PhenoDigm.",
      "properties": {
        "disease_id": {
          "description": "Disease identifier (e.g. 'OMIM:151623' or 'ORPHANET:524').",
          "title": "Disease Id",
          "type": "string"
        },
        "disease_name": {
          "description": "Full disease name.",
          "title": "Disease Name",
          "type": "string"
        },
        "model_id": {
          "description": "Mouse model identifier (e.g. MGI allele ID or marker ID).",
          "title": "Model Id",
          "type": "string"
        },
        "model_description": {
          "description": "Genotype description of the knockout model (e.g. 'Trp53<tm1Brd>/Trp53<tm1Brd>').",
          "title": "Model Description",
          "type": "string"
        },
        "score": {
          "description": "IC-weighted Jaccard similarity score in [0, 100]. Scores >40 are considered meaningful; >60 is strong.",
          "title": "Score",
          "type": "number"
        },
        "matched_phenotypes": {
          "description": "HP-term IDs phenotypically matched between the disease and the model (e.g. 'HP:0002665'). Sourced from the disease's HP annotation set.",
          "items": {
            "type": "string"
          },
          "title": "Matched Phenotypes",
          "type": "array"
        }
      },
      "required": [
        "disease_id",
        "disease_name",
        "model_id",
        "model_description",
        "score"
      ],
      "title": "PhenodigmMatch",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.phenodigm``.",
  "properties": {
    "gene": {
      "description": "Gene symbol as queried.",
      "title": "Gene",
      "type": "string"
    },
    "matches": {
      "description": "Disease-model similarity matches ordered by score descending, filtered to those with score >= min_score.",
      "items": {
        "$ref": "#/$defs/PhenodigmMatch"
      },
      "title": "Matches",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when no matches were found for this gene above the min_score threshold.",
      "title": "Not Found",
      "type": "boolean"
    }
  },
  "required": [
    "gene"
  ],
  "title": "ForgePhenodigmOut",
  "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/phenodigm' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene": ""
}'

Discussion

Posting anonymously. Sign in for attribution.

No comments yet — be the first.