API

OrganoidBench API

Read-only registry data and structured submission endpoints.

Overview

Public pages read from the same D1-backed registry data exposed here.

Unknown or unmeasured fields return null.

Current methodology: 1.0.0 (released 2026-04-20).

Endpoints

Method	Path	Description
GET	/api/v1/health	Registry counts and current methodology version.
GET	/api/v1/leaderboard	Flattened leaderboard rows. Query: track, organization, status, runStatus, limit.
GET	/api/v1/leaderboard/facets	Facet values for filters (tracks, tasks, orgs, modalities, access, review statuses).
GET	/api/v1/leaderboard/export.csv	Same rows as /leaderboard, returned as CSV.
GET	/api/v1/systems	All registered systems.
GET	/api/v1/systems/{id_or_slug}	One system with source, dataset, setup, and runs.
GET	/api/v1/systems/{id}/runs	Benchmark runs for a system.
GET	/api/v1/systems/{id}/metrics	Per-run metric values, derivations, and citations.
GET	/api/v1/systems/{id}/provenance	Provenance event log for a system.
GET	/api/v1/datasets	All ingested datasets.
GET	/api/v1/datasets/{id_or_slug}	One dataset with files, license, and source.
GET	/api/v1/datasets/{id}/files	File listing for a dataset.
GET	/api/v1/datasets/{id}/linked-systems	Systems that reference this dataset.
GET	/api/v1/sources	All ingested sources (papers, preprints, data records).
GET	/api/v1/sources/{id_or_doi}	One source with linked datasets and systems.
GET	/api/v1/organizations	Labs and consortia with artifact counts.
GET	/api/v1/organizations/{id}	One organization with full artifact list.
GET	/api/v1/tracks	Benchmark tracks with metric definitions.
GET	/api/v1/tracks/{slug}	One track with metrics, tasks, and scoring formula.
GET	/api/v1/tracks/{slug}/leaderboard	Leaderboard filtered to one track.
GET	/api/v1/tasks	All tasks across all tracks.
GET	/api/v1/tasks/{slug}	One task with its registered systems and runs.
GET	/api/v1/methodology/current	Current scoring methodology version.
GET	/api/v1/methodology/{version}	A specific methodology version.
POST	/api/v1/submissions	Submit a system, dataset, or result for review.
POST	/api/v1/corrections	File a correction or dispute against an existing record.

Submission

Public submissions use GitHub Issues. The API endpoint is for structured intake.

Submission bodyPOST /api/v1/submissions

{
  "submitterEmail": "researcher@example.org",
  "submitterName": "Researcher Name",
  "affiliation": "Example Lab",
  "submissionType": "system",
  "title": "Source-backed organoid recording system",
  "proposedSystemName": "Source-backed organoid recording system",
  "proposedTrackSlug": "signal-quality",
  "proposedTaskSlug": "baseline-recording",
  "benchmarkTrack": "signal-quality",
  "task": "baseline-recording",
  "organizationName": "Example Lab",
  "sourceUrl": "https://doi.org/10.0000/example",
  "paperUrl": "https://doi.org/10.0000/example",
  "datasetUrl": "https://zenodo.org/records/0000000",
  "codeUrl": "https://github.com/example/repo",
  "organoidType": "not reported",
  "recordingPlatform": "not reported",
  "notes": "Brief context for curator review.",
  "limitations": "Known limitations or not reported."
}

Status vocabulary

Verification status (systems, datasets)

draftCreated, nothing reviewed.
source_verifiedSource URL resolves, DOI recorded.
data_ingestedData files enumerated.
unscoredReviewed, but no run has a published composite.
provisionalScored once, awaiting independent replication.
scoredComposite published under current methodology.
curator_reviewedReviewed manually after ingestion.
publishedPassed full review and is cited in the leaderboard.
disputedFlagged by a correction.
deprecatedSuperseded or retracted.

Derivation method (metric values)

computedComputed from source-backed data or code.
extracted_from_paperReported in a source paper.
submittedSubmitter provided the value.
curator_estimatedCurator estimate from source-backed evidence.