generated: '2026-08-21'
method: derived
source: openapi/genialis-base-openapi.yaml
api: Genialis Expressions API
note: >-
  Derived from the 205 component schemas and the $ref / RelationshipDict links
  between them, plus the resource roots the live API index at
  https://app.genialis.com/api/ returns. Genialis publishes no object reference, so
  no id-prefix scheme could be searched; ids are plain integers (observed: data id
  1083792, collection id 3).
id_scheme:
  type: integer
  prefixed: false
  evidence: 'GET /api/data?limit=1 -> results[0].id = 1083792; GET /api/collection?limit=1 -> results[0].id = 3'
core_concept: >-
  Resolwe's model: a Collection groups Samples (entities); each Sample owns Data
  objects; each Data object is the output of a Process run; DescriptorSchema defines
  the shape of the metadata descriptors attached to Collections, Samples and Data;
  AnnotationField/AnnotationValue carry structured sample metadata; Variant /
  VariantCall / VariantAnnotation carry the genomic call layer; Prediction* carry
  model outputs.
entities:
- name: Data
  path: /api/data
  description: A single unit of data — the input to or the output of a process run.
  relationships:
  - to: Process
    type: belongs_to
    via: process
  - to: Collection
    type: belongs_to
    via: collection
  - to: Entity
    type: belongs_to
    via: entity
    note: Entity is the internal name for Sample.
  - to: DescriptorSchema
    type: belongs_to
    via: descriptor_schema
  - to: User
    type: belongs_to
    via: contributor
  - to: Data
    type: has_many
    via: /api/data/{id}/children
  - to: Data
    type: belongs_to
    via: /api/data/{id}/parents
  status_enum_schema: DataStatus
- name: Sample
  aka: Entity
  path: /api/sample
  relationships:
  - to: Collection
    type: belongs_to
    via: collection
  - to: Data
    type: has_many
    via: /api/sample/{id}/data (reverse of Data.entity)
  - to: AnnotationValue
    type: has_many
    via: /api/annotation_value?entity=
  - to: User
    type: belongs_to
    via: contributor
- name: Collection
  path: /api/collection
  relationships:
  - to: Sample
    type: has_many
    via: Entity.collection
  - to: Data
    type: has_many
    via: Data.collection
  - to: Relation
    type: has_many
    via: Relation.collection
  - to: DescriptorSchema
    type: belongs_to
    via: descriptor_schema
- name: Relation
  path: /api/relation
  description: Typed grouping of samples within a collection (series, replicate groups, comparisons).
  relationships:
  - to: Collection
    type: belongs_to
    via: collection
  - to: RelationPartition
    type: has_many
    via: partitions
- name: Process
  path: /api/process
  description: A registered analysis workflow definition with typed inputs and outputs.
  relationships:
  - to: Data
    type: has_many
    via: Data.process
- name: DescriptorSchema
  path: /api/descriptorschema
  relationships:
  - to: Data
    type: has_many
  - to: Collection
    type: has_many
  - to: Sample
    type: has_many
- name: AnnotationField
  path: /api/annotation_field
  relationships:
  - to: AnnotationGroup
    type: belongs_to
    via: group
  - to: AnnotationValue
    type: has_many
- name: AnnotationValue
  path: /api/annotation_value
  relationships:
  - to: AnnotationField
    type: belongs_to
    via: field
  - to: Sample
    type: belongs_to
    via: entity
- name: AnnotationPreset
  path: /api/annotation_preset
  relationships:
  - to: AnnotationField
    type: has_many
- name: PredictionField
  path: /api/prediction_field
  relationships:
  - to: PredictionGroup
    type: belongs_to
    via: group
- name: PredictionValue
  path: /api/prediction_value
  relationships:
  - to: PredictionField
    type: belongs_to
  - to: Sample
    type: belongs_to
- name: Variant
  path: /api/variant
  fields: [id, species, genome_assembly, chromosome, position, reference, alternative]
  relationships:
  - to: VariantAnnotation
    type: has_one
    via: annotation
  - to: VariantCall
    type: has_many
- name: VariantAnnotation
  path: /api/variant_annotations
  fields: [variant_id, type, clinical_diagnosis, clinical_significance, dbsnp_id, clinvar_id, transcripts]
  relationships:
  - to: Variant
    type: belongs_to
    via: variant_id
- name: VariantCall
  path: /api/variant_calls
  fields: [quality, genotype_quality, depth, alternative_allele_depth, filter, genotype]
  relationships:
  - to: Sample
    type: belongs_to
    via: sample
  - to: Variant
    type: belongs_to
    via: variant
  - to: VariantExperiment
    type: belongs_to
    via: experiment
  - to: Data
    type: belongs_to
    via: data
- name: VariantExperiment
  path: /api/variant_experiment
  relationships:
  - to: VariantCall
    type: has_many
  - to: User
    type: belongs_to
    via: contributor
- name: User
  path: /api/user
  relationships:
  - to: Group
    type: has_many
  - to: UserTag
    type: has_many
- name: Group
  path: /api/group
- name: BillingAccount
  path: /api/billingaccount
  relationships:
  - to: BillingStatistics
    type: has_many
  note: 'Usage estimation at /api/billingaccount/estimated_usage and /api/base/data_usage.'
- name: Basket
  path: /api/basket
  description: Ephemeral working set of samples/data used by the Expressions UI.
- name: Task
  path: /api/task
  description: Background task status.
- name: AccessToken
  path: /api/accesstoken/data
  description: Scoped access tokens for data objects.
- name: Storage
  path: /api/storage
- name: KnowledgeBase
  path: /api/kb
  description: Gene/feature knowledge base (features, mappings) used by search and gene lists.
permissions_model:
  style: per-object ACL
  endpoints:
  - /api/data/{id}/permissions
  - /api/collection/{id}/permissions
  - /api/sample/{id}/permissions
  - /api/process/{id}/permissions
  - /api/descriptorschema/{id}/permissions
  principals: [user, group, public]
counts:
  entities_documented: 24
  component_schemas: 205
  paths: 169
  operations: 254