API contract version: 1.0

Documentation generated: 2026-10-02T15:55:34Z

Overview

The MorPhiC Integrated Read API exposes read-optimised views over submitted study metadata, GeneDB reference data, and analysis rollups. It is designed for portal features, reporting tables, gene search, and submissions-side target gene validation.

The API is backed by materialised MongoDB collections built offline by the integrated data builder. The public endpoints are read-only.

Service URLs

Production (stable public service):

https://integrated-read-api.archive.morphic.bio

Development (testing and unreleased data):

https://integrated-read-api.dev.archive.morphic.bio

All endpoint paths in this document are relative to one of these base URLs. Public applications and reproducible analyses should use production.

For example:

export MORPHIC_API_BASE_URL=https://integrated-read-api.archive.morphic.bio
curl "$MORPHIC_API_BASE_URL/api/read/summary"

The HTTP transcripts below are generated from executable API tests against the production base URL. For local development only, replace the base URL with http://localhost:8080.

Stability and backward compatibility

The current endpoints constitute the MorPhiC Integrated Read API v1 contract. Additive endpoints and response fields may be introduced within v1. Existing documented fields and endpoints will not be removed or renamed within v1.

Any future backward-incompatible change will use a new major API version. The previous version will remain available during a documented migration period, and deprecations will be announced in the API documentation and changelog.

The API contract version is independent of the MorPhiC data release. Responses may expose newer catalogue records as data releases are published without changing the API contract version.

Pagination

Paged endpoints accept page and size. The first page is page=0. Paged read endpoints cap size at 500. Gene reference search caps size at 100.

Summary

Returns high-level counts for the materialised read collections. The repositoryBrokering object groups dataset counts by GEO/ENA accession coverage.

Request

GET /api/read/summary HTTP/1.1
Host: integrated-read-api.archive.morphic.bio

Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 325

{
  "assayCount" : 2,
  "collectionCount" : 3,
  "referenceGeneCount" : 19260,
  "geneCount" : 105,
  "repositoryBrokering" : {
    "geoOnly" : 3,
    "enaOnly" : 4,
    "geoAndEna" : 12,
    "other" : 0,
    "none" : 1
  },
  "cellLineCount" : 3,
  "contextCount" : 123,
  "datasetCount" : 20,
  "analysisResultCount" : 42
}

Response fields

Path Type Description

geneCount

Number

Number of MorPhiC gene rollup records.

referenceGeneCount

Number

Number of HGNC reference gene records.

datasetCount

Number

Number of study/dataset rollup records.

collectionCount

Number

Number of related-study collection records.

contextCount

Number

Number of gene x dataset context records.

assayCount

Number

Number of distinct assay values.

cellLineCount

Number

Number of distinct cell line values.

analysisResultCount

Number

Total analysis result count across gene rollups.

repositoryBrokering

Object

Dataset counts grouped by public repository accession coverage.

repositoryBrokering.geoOnly

Number

Datasets with GEO accessions but no ENA accessions.

repositoryBrokering.enaOnly

Number

Datasets with ENA accessions but no GEO accessions.

repositoryBrokering.geoAndEna

Number

Datasets with both GEO and ENA accessions.

repositoryBrokering.other

Number

Datasets with accessions that are not classified as GEO or ENA.

repositoryBrokering.none

Number

Datasets without any accession-derived repository classification.

Genes

Lists MorPhiC genes that appear in the integrated study/dataset read model. Use this endpoint for the Data Catalog gene view.

Gene path identifiers accept either the stable HGNC ID or a resolvable display symbol. Prefer HGNC IDs for programmatic clients and MCP tools; use symbols for human-facing navigation.

Endpoints

GET /api/read/genes
GET /api/read/genes/{hgncIdOrSymbol}
GET /api/read/genes/{hgncIdOrSymbol}/datasets

Request

GET /api/read/genes?q=PAX&assay=RNA-seq&modelSystem=Primitive+syncytium&cellLine=KOLF2.2J&status=analysed&page=0&size=10 HTTP/1.1
Host: integrated-read-api.archive.morphic.bio

Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 746

{
  "items" : [ {
    "symbol" : "PAX6",
    "hgnc_id" : "HGNC:8620",
    "full_name" : "paired box 6",
    "protein_class" : "homeodomain transcription factor (PC00119)",
    "synonyms" : [ "D11S812E", "AN", "WAGR" ],
    "previous_symbols" : [ "AN1", "AN2" ],
    "resolvable_symbols" : [ "PAX6", "D11S812E", "AN", "WAGR", "AN1", "AN2" ],
    "dataset_count" : 5,
    "assay_count" : 1,
    "assays" : [ "RNA-seq" ],
    "model_systems" : [ "Cortical brain organoid", "Primitive syncytium" ],
    "cell_lines" : [ "KOLF2.2J" ],
    "analysis_result_count" : 8,
    "statuses" : [ "analysed", "dynamic_ready", "precomputed", "submitted" ]
  } ],
  "page" : {
    "number" : 0,
    "size" : 10,
    "totalElements" : 1,
    "totalPages" : 1
  }
}

Query parameters

Parameter Description

q

Optional text search over gene symbol, HGNC ID, full name, synonyms, and previous symbols.

assay

Filter by assay present in the gene rollup.

modelSystem

Filter by model system present in the gene rollup.

cellLine

Filter by cell line present in the gene rollup.

status

Filter by status flag, for example analysed or dynamic_ready.

page

Zero-based page number.

size

Page size. Capped at 500.

Response fields

Path Type Description

items

Array

Gene rollup records.

items[].symbol

String

Approved/display gene symbol.

items[].hgnc_id

String

Stable HGNC identifier.

items[].full_name

String

Approved HGNC gene name.

items[].dataset_count

Number

Number of datasets associated with the gene.

items[].analysis_result_count

Number

Number of analysis results associated with the gene.

items[].statuses

Array

Integrated status flags available for this gene.

page

Object

Pagination metadata.

Each gene includes a datasets array. Each entry represents one exact gene/dataset context and contains study_id, study_label, model_system, cell_line, assay, perturbation_type, and center. Clients can use these scalar values to build valid filter combinations without creating cross-product combinations from dataset-level arrays.

Datasets

Lists study/dataset rollups. Use this endpoint for the Data Catalog dataset view. Public studies are included even when they do not yet have target genes or linked analysis results. Dataset rows include raw accessions plus derived repositories, repository_accessions, and repository_brokering fields. These fields let the portal display whether a dataset has GEO accessions, ENA accessions, both, another repository, or no public repository accession yet. Dataset rows also include analysis_centers when linked GeneDB analysis results identify the analysis provider.

Dataset path identifiers accept either the SubmissionsDB study ID or the study/dataset label. Prefer study_id for programmatic clients; use labels for human-facing navigation.

Endpoints

GET /api/read/datasets
GET /api/read/datasets/{datasetIdOrLabel}
GET /api/read/datasets/{datasetIdOrLabel}/genes

Request

GET /api/read/datasets?q=JAX&dpc=JAX&assay=RNA-seq&modelSystem=Primitive+syncytium&cellLine=KOLF2.2J&analysisCenter=Fred-Hutch&page=0&size=10 HTTP/1.1
Host: integrated-read-api.archive.morphic.bio

Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1234

{
  "items" : [ {
    "study_id" : "675416f3e0e750692acd5eb1",
    "study_label" : "JAX_RNAseq7_Reversion",
    "study_title" : "Study 7- RNA-seq of male KOLF2.2J hiPSC-derived differentiated cells",
    "study_description" : "RNA-seq study of reverted null alleles in KOLF2.2J differentiated cells.",
    "dpc" : "JAX",
    "release_status" : null,
    "submission_date" : "2024-12-07T09:35:47.104+00:00",
    "public_release_date" : null,
    "accessions" : [ "ERP166966", "GSE288287" ],
    "repositories" : [ "ENA", "GEO" ],
    "repository_accessions" : {
      "ena" : [ "ERP166966" ],
      "geo" : [ "GSE288287" ],
      "other" : [ ]
    },
    "repository_brokering" : {
      "ena" : true,
      "geo" : true,
      "both" : true,
      "other" : false,
      "none" : false
    },
    "assays" : [ "RNA-seq" ],
    "model_systems" : [ "Primitive syncytium" ],
    "cell_lines" : [ "KOLF2.2J" ],
    "analysis_centers" : [ "Fred-Hutch" ],
    "perturbation_types" : [ "CRISPR-Cas9 KO" ],
    "target_gene_count" : 5,
    "target_genes" : [ "EPAS1", "GCM1", "GRHL1", "PAX6", "PPARG" ],
    "analysis_result_count" : 7
  } ],
  "page" : {
    "number" : 0,
    "size" : 10,
    "totalElements" : 1,
    "totalPages" : 1
  }
}

Query parameters

Parameter Description

q

Optional text search over study label, title, description, target genes, and accessions.

dpc

Filter by data production centre.

assay

Filter by assay.

modelSystem

Filter by model system.

cellLine

Filter by cell line.

analysisCenter

Filter by analysis centre/provider.

page

Zero-based page number.

size

Page size. Capped at 500.

Response fields

Path Type Description

items

Array

Study/dataset rollup records.

items[].study_id

String

Stable SubmissionsDB study identifier.

items[].study_label

String

Human-readable study/dataset label.

items[].dpc

String

Data production centre.

items[].assays

Array

Assays represented in the dataset.

items[].perturbation_types

Array

Perturbation types represented in the dataset.

items[].repositories

Array

Public repositories represented by the dataset accessions, for example ENA and GEO.

items[].repository_accessions

Object

Accessions grouped by repository.

items[].repository_brokering

Object

Boolean repository coverage flags derived from accessions.

items[].analysis_centers

Array

Analysis centres represented by linked analysis results.

items[].target_genes

Array

Target genes listed for the dataset.

page

Object

Pagination metadata.

Collections

Lists automatically derived related-study collections. Collections group public datasets that share the same data production centre, model system, and perturbation strategy. They are intended for the Data Catalog collection view and for navigation from a collection to its member datasets.

Collection path identifiers use the stable deterministic collection_id generated by the read-model builder.

Endpoints

GET /api/read/collections
GET /api/read/collections/{collectionId}
GET /api/read/collections/{collectionId}/datasets

Request

GET /api/read/collections?q=Cortical&dpc=JAX&modelSystem=Cortical+brain+organoid&perturbationType=CRISPR-Cas9+KO&page=0&size=10 HTTP/1.1
Host: integrated-read-api.archive.morphic.bio

Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 617

{
  "items" : [ {
    "collection_id" : "collection-1",
    "title" : "JAX: Cortical brain organoid - CRISPR-Cas9 KO",
    "description" : "Related JAX studies.",
    "dpc" : "JAX",
    "model_system" : "Cortical brain organoid",
    "perturbation_type" : "CRISPR-Cas9 KO",
    "assays" : [ "RNA-seq" ],
    "cell_lines" : [ "KOLF2.2J" ],
    "study_ids" : [ "study-1", "study-2" ],
    "study_labels" : [ "JAX_RNAseq4_ExEm_brain", "JAX_RNAseq5_ExE_CBO" ],
    "dataset_count" : 2,
    "target_gene_count" : 12
  } ],
  "page" : {
    "number" : 0,
    "size" : 10,
    "totalElements" : 1,
    "totalPages" : 1
  }
}

Query parameters

Parameter Description

q

Optional text search over collection title, description, member study labels, and target genes.

dpc

Filter by data production centre.

modelSystem

Filter by model system.

perturbationType

Filter by perturbation strategy/type.

page

Zero-based page number.

size

Page size. Capped at 500.

Response fields

Path Type Description

items

Array

Related-study collection rollup records.

items[].collection_id

String

Stable deterministic collection identifier.

items[].title

String

Human-readable collection title.

items[].description

String

Short collection description, when available.

items[].dpc

String

Data production centre shared by collection members.

items[].model_system

String

Model system shared by collection members.

items[].perturbation_type

String

Perturbation strategy/type shared by collection members.

items[].assays

Array

Assays represented across member datasets.

items[].cell_lines

Array

Cell lines represented across member datasets.

items[].study_ids

Array

Stable study IDs for member datasets.

items[].study_labels

Array

Labels for member datasets.

items[].dataset_count

Number

Number of member datasets/studies.

items[].target_gene_count

Number

Number of unique target genes across member datasets.

page

Object

Pagination metadata.

Get one collection

GET /api/read/collections/collection-1 HTTP/1.1
Host: integrated-read-api.archive.morphic.bio
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 122

{
  "collection_id" : "collection-1",
  "title" : "JAX: Cortical brain organoid - CRISPR-Cas9 KO",
  "dataset_count" : 2
}

Path parameters

Table 1. /api/read/collections/{collectionId}
Parameter Description

collectionId

Stable deterministic collection identifier.

Get collection member datasets

GET /api/read/collections/collection-1/datasets?page=0&size=10 HTTP/1.1
Host: integrated-read-api.archive.morphic.bio
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 240

{
  "items" : [ {
    "study_id" : "study-1",
    "study_label" : "JAX_RNAseq4_ExEm_brain",
    "collection_ids" : [ "collection-1" ]
  } ],
  "page" : {
    "number" : 0,
    "size" : 10,
    "totalElements" : 1,
    "totalPages" : 1
  }
}

Path parameters

Table 2. /api/read/collections/{collectionId}/datasets
Parameter Description

collectionId

Stable deterministic collection identifier.

Query parameters

Parameter Description

page

Zero-based page number.

size

Page size. Capped at 500.

Response fields

Path Type Description

items

Array

Dataset rollups that belong to the collection.

items[].study_id

String

Stable SubmissionsDB study identifier.

items[].study_label

String

Human-readable study/dataset label.

items[].collection_ids

Array

Collection IDs assigned to this dataset.

page

Object

Pagination metadata.

Gene Dataset Contexts

Returns the combined gene x dataset context records. This is the most detailed read model and includes gene metadata, study metadata, experiment fields, analysis availability, and provenance.

Common filters include:

Parameter Description

gene

Gene symbol, synonym, or previous symbol.

hgncId

HGNC identifier, for example HGNC:3374.

studyId

Study identifier from the submissions system.

datasetLabel

Study or dataset label.

dpc

Data production centre, for example JAX.

assay

Assay type, for example RNA-seq.

modelSystem

Model system.

cellLine

Cell line.

analysisCenter

Analysis centre/provider, for example Fred-Hutch.

hasAnalysisResults

Whether the context has analysis results.

status

Status flag such as submitted, analysed, precomputed, or dynamic_ready.

Request

GET /api/read/gene-dataset-contexts?hgncId=HGNC%3A3374&studyId=675416f3e0e750692acd5eb1&dpc=JAX&assay=RNA-seq&modelSystem=Primitive+syncytium&cellLine=KOLF2.2J&analysisCenter=Fred-Hutch&hasAnalysisResults=true&status=analysed&page=0&size=25 HTTP/1.1
Host: integrated-read-api.archive.morphic.bio

Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 2166

{
  "items" : [ {
    "context_id" : "81daddfadc916df179e355632eb5706484f8d628d6d8374c4d89bab6c23ede19",
    "gene" : {
      "symbol" : "EPAS1",
      "hgnc_id" : "HGNC:3374",
      "full_name" : "endothelial PAS domain protein 1",
      "protein_class" : "basic helix-loop-helix transcription factor (PC00055)",
      "synonyms" : [ "MOP2", "PASD2", "HIF2A", "HLF", "BHLHE73" ],
      "previous_symbols" : [ ],
      "resolvable_symbols" : [ "EPAS1", "MOP2", "PASD2", "HIF2A", "HLF", "BHLHE73" ]
    },
    "study" : {
      "study_id" : "675416f3e0e750692acd5eb1",
      "study_label" : "JAX_RNAseq7_Reversion",
      "study_title" : "Study 7- RNA-seq of male KOLF2.2J hiPSC-derived differentiated cells",
      "dpc" : "JAX",
      "release_status" : null,
      "submission_date" : "2024-12-07T09:35:47.104+00:00",
      "public_release_date" : null,
      "accessions" : [ "ERP166966", "GSE288287" ],
      "repositories" : [ "ENA", "GEO" ],
      "repository_accessions" : {
        "ena" : [ "ERP166966" ],
        "geo" : [ "GSE288287" ],
        "other" : [ ]
      },
      "repository_brokering" : {
        "ena" : true,
        "geo" : true,
        "both" : true,
        "other" : false,
        "none" : false
      }
    },
    "experiment" : {
      "assay" : "RNA-seq",
      "model_system" : "Primitive syncytium",
      "cell_line" : "KOLF2.2J",
      "sample_type" : "cell line",
      "perturbation_type" : "CRISPR-Cas9 KO"
    },
    "analysis" : {
      "has_analysis_results" : true,
      "result_types" : [ "DE" ],
      "analysis_count" : 2,
      "analysis_centers" : [ "Fred-Hutch" ],
      "dataset_id" : "16c89c9de3728f35dadc1c164309c16557f72db2",
      "default_condition_id" : "EPAS1_reverted",
      "de_summary" : {
        "n_total" : 20041,
        "n_significant" : 30,
        "n_up" : 5,
        "n_down" : 25,
        "median_abs_log2fc" : 0.541
      }
    },
    "status" : {
      "submitted" : true,
      "public" : false,
      "analysed" : true,
      "precomputed" : true,
      "dynamic_ready" : true
    }
  } ],
  "page" : {
    "number" : 0,
    "size" : 25,
    "totalElements" : 1,
    "totalPages" : 1
  }
}

Query parameters

Parameter Description

hgncId

Stable HGNC identifier.

studyId

Stable SubmissionsDB study identifier.

dpc

Filter by data production centre.

assay

Filter by assay.

modelSystem

Filter by model system.

cellLine

Filter by cell line.

analysisCenter

Filter by analysis centre/provider.

hasAnalysisResults

Filter by analysis availability.

status

Filter by status flag, for example analysed.

page

Zero-based page number.

size

Page size. Capped at 500.

Response fields

Path Type Description

items

Array

Gene x dataset context records.

items[].context_id

String

Stable derived identifier for this gene x dataset context.

items[].gene

Object

Resolved gene metadata.

items[].study

Object

Study/dataset metadata.

items[].experiment

Object

Experiment metadata, including assay and perturbation type.

items[].analysis

Object

Analysis availability and summary metadata.

items[].status

Object

Integrated status flags.

page

Object

Pagination metadata.

Gene Dataset Summary Report

Returns a flattened reporting view suitable for consortium tables and exports.

Use this endpoint when a client needs one row per gene/dataset context for reporting, export, or downstream tabular analysis.

Request

GET /api/read/reports/gene-dataset-summary?gene=EPAS1&dpc=JAX&assay=RNA-seq&modelSystem=Primitive+syncytium&analysisCenter=Fred-Hutch&hasAnalysisResults=true&page=0&size=100 HTTP/1.1
Host: integrated-read-api.archive.morphic.bio

Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 786

{
  "items" : [ {
    "gene" : "EPAS1",
    "hgnc_id" : "HGNC:3374",
    "dataset" : "JAX_RNAseq7_Reversion",
    "study_id" : "675416f3e0e750692acd5eb1",
    "analysis_dataset_id" : "16c89c9de3728f35dadc1c164309c16557f72db2",
    "analysis_center" : "Fred-Hutch",
    "dpc" : "JAX",
    "assay" : "RNA-seq",
    "submission_date" : "2024-12-07T09:35:47.104+00:00",
    "public_release_date" : null,
    "model_system" : "Primitive syncytium",
    "cell_line" : "KOLF2.2J",
    "has_analysis_results" : true,
    "analysis_count" : 2,
    "clonal_cell_lines_per_gene" : null,
    "dracc_processed_v1_internal_release" : null,
    "dracc_processed_latest_internal_release" : null
  } ],
  "page" : {
    "number" : 0,
    "size" : 100,
    "totalElements" : 1,
    "totalPages" : 1
  }
}

Query parameters

Parameter Description

gene

Filter by gene symbol or resolvable alias.

dpc

Filter by data production centre.

assay

Filter by assay.

modelSystem

Filter by model system.

analysisCenter

Filter by analysis centre/provider.

hasAnalysisResults

Filter by analysis availability.

page

Zero-based page number.

size

Page size. Capped at 500.

Response fields

Path Type Description

items

Array

Flattened reporting rows.

items[].gene

String

Gene symbol.

items[].hgnc_id

String

Stable HGNC identifier.

items[].dataset

String

Study/dataset label.

items[].study_id

String

Stable SubmissionsDB study identifier.

items[].analysis_dataset_id

String

GeneDB analysis dataset identifier, where available.

items[].analysis_center

String

Analysis centre/provider for linked analysis results, where available.

items[].has_analysis_results

Boolean

Whether analysis results are available for this row.

page

Object

Pagination metadata.

Additional example

GET /api/read/reports/gene-dataset-summary?dpc=JAX&assay=RNA-seq&hasAnalysisResults=true&size=100

HGNC Reference Search

Searches the HGNC-backed reference gene collection. This endpoint supports autocomplete and can optionally limit results to genes present in MorPhiC data or genes on the provisional MorPhiC programme gene list. Each result distinguishes genes represented in submitted/ingested MorPhiC contexts (studied_in_morphic) from genes with at least one linked GeneDB analysis result (analysed_in_morphic).

Request

GET /api/read/gene-reference/search?q=PAX&morphicOnly=true&programmeOnly=true&size=5 HTTP/1.1
Host: integrated-read-api.archive.morphic.bio

Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 321

[ {
  "symbol" : "PAX6",
  "hgnc_id" : "HGNC:8620",
  "full_name" : "paired box 6",
  "morphic" : true,
  "studied_in_morphic" : true,
  "analysed_in_morphic" : true,
  "morphic_provisional" : true,
  "morphic_programme_gene" : true,
  "provisional_centres" : [ "JAX", "MSK" ],
  "ensembl_gene_id" : "ENSG00000007372"
} ]

Query parameters

Parameter Description

q

Search text. Matches HGNC ID, approved symbol, synonyms, previous symbols, and search prefixes.

morphicOnly

When true, returns only genes present in MorPhiC integrated data.

programmeOnly

When true, returns genes present in MorPhiC integrated data or the provisional MorPhiC programme gene list.

size

Maximum number of results to return. Capped at 100.

Response fields

Path Type Description

[].hgnc_id

String

HGNC identifier.

[].symbol

String

Approved HGNC gene symbol.

[].full_name

String

Approved HGNC gene name.

[].morphic

Boolean

Backward-compatible flag for whether this gene is present in MorPhiC integrated data.

[].studied_in_morphic

Boolean

Whether this gene is present in MorPhiC integrated data.

[].analysed_in_morphic

Boolean

Whether this gene has at least one linked GeneDB analysis result.

[].morphic_provisional

Boolean

Whether this gene appears in the provisional MorPhiC programme gene list.

[].morphic_programme_gene

Boolean

Whether this gene is either studied in MorPhiC data or listed as a provisional MorPhiC programme gene.

[].provisional_centres

Array

DPC flags from the provisional MorPhiC programme gene list.

[].ensembl_gene_id

String

Ensembl gene identifier from the provisional MorPhiC programme gene list, where available.

JASPAR Matrix Profiles

Returns one versioned JASPAR 2020 CORE vertebrate position frequency matrix by matrix ID. The API serves the packaged non-redundant set by default; deployments can select the redundant set with JASPAR_PROFILE_SET=redundant.

GET /api/read/jaspar/matrix/MA0069.1

Malformed IDs return 400; well-formed IDs absent from the configured profile set return 404.

Bulk Gene Validation

Validates user-provided target gene values against the HGNC-backed reference collection. Inputs may be HGNC IDs, approved symbols, synonyms, or previous symbols.

The response groups inputs into:

Group Meaning

valid

A single HGNC record matched the input.

invalid

No HGNC record matched the input.

ambiguous

More than one HGNC record matched the input and a curator/user decision is needed.

Request

POST /api/read/gene-reference/validate HTTP/1.1
Content-Type: application/json
Content-Length: 53
Host: integrated-read-api.archive.morphic.bio

{
  "genes" : [ "PAX6", "HGNC:3374", "not-a-gene" ]
}

Response

HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 1198

{
  "invalid" : [ {
    "reason" : "No matching HGNC gene found",
    "input" : "not-a-gene"
  } ],
  "valid" : [ {
    "input" : "PAX6",
    "matched_by" : "symbol",
    "hgnc_id" : "HGNC:8620",
    "symbol" : "PAX6",
    "full_name" : "paired box 6",
    "synonyms" : [ "D11S812E", "AN", "WAGR" ],
    "previous_symbols" : [ "AN1", "AN2" ],
    "morphic" : true,
    "studied_in_morphic" : true,
    "analysed_in_morphic" : true,
    "morphic_provisional" : true,
    "morphic_programme_gene" : true,
    "provisional_centres" : [ "JAX" ],
    "ensembl_gene_id" : "ENSG00000007372",
    "study_count" : 5,
    "dataset_count" : 5
  }, {
    "input" : "HGNC:3374",
    "matched_by" : "hgnc_id",
    "hgnc_id" : "HGNC:3374",
    "symbol" : "EPAS1",
    "full_name" : "endothelial PAS domain protein 1",
    "synonyms" : [ "MOP2", "PASD2", "HIF2A", "HLF", "BHLHE73" ],
    "previous_symbols" : [ ],
    "morphic" : true,
    "studied_in_morphic" : true,
    "analysed_in_morphic" : false,
    "morphic_provisional" : false,
    "morphic_programme_gene" : true,
    "provisional_centres" : [ ],
    "ensembl_gene_id" : null,
    "study_count" : 3,
    "dataset_count" : 3
  } ],
  "ambiguous" : [ ]
}

Request fields

Path Type Description

genes

Array

Gene inputs to validate. Values may be HGNC IDs, approved symbols, synonyms, or previous symbols.

Response fields

Path Type Description

valid

Array

Inputs that matched exactly one HGNC reference gene.

valid[].input

String

Original input value.

valid[].hgnc_id

String

Matched HGNC identifier.

valid[].symbol

String

Matched approved HGNC symbol.

invalid

Array

Inputs that did not match any HGNC reference gene.

invalid[].input

String

Original invalid input value.

invalid[].reason

String

Reason the input was not accepted.

ambiguous

Array

Inputs that matched more than one HGNC reference gene.

Swagger / OpenAPI

Swagger remains available as an endpoint-level reference and live testing surface:

https://integrated-read-api.archive.morphic.bio/swagger-ui/index.html

The machine-readable OpenAPI description is available at:

https://integrated-read-api.archive.morphic.bio/v3/api-docs

Use these generated docs for curated examples, response explanations, and stable documentation snippets.