float64
definition: 64-bit floating point.
type: Class
subclass of: ColumnTypeEnum

source_domain
type: DatatypeProperty
definition: Domain name of the upstream source.
in scheme: toxindex
range: string

ToolCall
definition: A persisted record of a tool invocation, capturing the input arguments, output, and the conversation it occurred in. Identified by (conversation_id, tool_call_id). Citations in flow documents resolve to these.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: string
  on property: arguments
subclass of: Restriction
  min cardinality: 0
  on property: arguments
subclass of: Restriction
  max cardinality: 1
  on property: arguments
subclass of: Restriction
  all values from: string
  on property: conversation_id
subclass of: Restriction
  min cardinality: 1
  on property: conversation_id
subclass of: Restriction
  max cardinality: 1
  on property: conversation_id
subclass of: Restriction
  all values from: boolean
  on property: is_error
subclass of: Restriction
  min cardinality: 0
  on property: is_error
subclass of: Restriction
  max cardinality: 1
  on property: is_error
subclass of: Restriction
  all values from: string
  on property: output
subclass of: Restriction
  min cardinality: 0
  on property: output
subclass of: Restriction
  max cardinality: 1
  on property: output
subclass of: Restriction
  all values from: string
  on property: tool_call_id
subclass of: Restriction
  min cardinality: 1
  on property: tool_call_id
subclass of: Restriction
  max cardinality: 1
  on property: tool_call_id
subclass of: Restriction
  all values from: string
  on property: tool_name
subclass of: Restriction
  min cardinality: 1
  on property: tool_name
subclass of: Restriction
  max cardinality: 1
  on property: tool_name

arguments
type: DatatypeProperty
definition: JSON-serialized input arguments to the tool.
in scheme: toxindex
range: string

Collection
definition: A curated group of documents sharing a common source or topic. Collections form a shallow hierarchy with one level of nesting.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  all values from: integer
  on property: document_count
subclass of: Restriction
  min cardinality: 0
  on property: document_count
subclass of: Restriction
  max cardinality: 1
  on property: document_count
subclass of: Restriction
  all values from: string
  on property: labels
subclass of: Restriction
  min cardinality: 0
  on property: labels
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 1
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: Collection
  on property: parent
subclass of: Restriction
  min cardinality: 0
  on property: parent
subclass of: Restriction
  max cardinality: 1
  on property: parent
subclass of: Restriction
  all values from: string
  on property: retrieval_notes
subclass of: Restriction
  min cardinality: 0
  on property: retrieval_notes
subclass of: Restriction
  max cardinality: 1
  on property: retrieval_notes
subclass of: Restriction
  all values from: string
  on property: slug
subclass of: Restriction
  min cardinality: 1
  on property: slug
subclass of: Restriction
  max cardinality: 1
  on property: slug
subclass of: Restriction
  all values from: string
  on property: source_domain
subclass of: Restriction
  min cardinality: 0
  on property: source_domain
subclass of: Restriction
  max cardinality: 1
  on property: source_domain
subclass of: Restriction
  all values from: anyURI
  on property: upstream_url
subclass of: Restriction
  min cardinality: 0
  on property: upstream_url
subclass of: Restriction
  max cardinality: 1
  on property: upstream_url

tool_name
type: DatatypeProperty
in scheme: toxindex
range: string

document_id
type: DatatypeProperty
definition: Stable document identifier.
in scheme: toxindex
range: string

vocab_uri
type: DatatypeProperty
definition: Stable URI for this column's concept. A column whose convention has an established public-ontology term resolves to that external URI (e.g., cheminf:CHEMINF_000446 for cas_number); a convention without one resolves to a ToxIndex-minted vocabulary term; a column with no convention resolves to a term minted under the owning brick's instance namespace, scoped to that brick, table, and column.
in scheme: toxindex
range: anyURI

Brick
definition: A curated reference dataset, such as a regulatory list, a chemical property table, or a biological endpoint dataset. Each brick contains one or more typed tables with column-level vocabulary annotations.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: dateTime
  on property: built_at
subclass of: Restriction
  min cardinality: 0
  on property: built_at
subclass of: Restriction
  max cardinality: 1
  on property: built_at
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  all values from: string
  on property: domain
subclass of: Restriction
  min cardinality: 0
  on property: domain
subclass of: Restriction
  max cardinality: 1
  on property: domain
subclass of: Restriction
  all values from: string
  on property: license
subclass of: Restriction
  min cardinality: 0
  on property: license
subclass of: Restriction
  max cardinality: 1
  on property: license
subclass of: Restriction
  all values from: string
  on property: slug
subclass of: Restriction
  min cardinality: 1
  on property: slug
subclass of: Restriction
  max cardinality: 1
  on property: slug
subclass of: Restriction
  all values from: anyURI
  on property: source
subclass of: Restriction
  min cardinality: 0
  on property: source
subclass of: Restriction
  max cardinality: 1
  on property: source
subclass of: Restriction
  all values from: BrickTable
  on property: tables
subclass of: Restriction
  min cardinality: 0
  on property: tables
subclass of: Restriction
  all values from: string
  on property: tags
subclass of: Restriction
  min cardinality: 0
  on property: tags
subclass of: Restriction
  all values from: string
  on property: title
subclass of: Restriction
  min cardinality: 1
  on property: title
subclass of: Restriction
  max cardinality: 1
  on property: title

SectionStatusEnum
type: Class
definition: Completion state of a document section.
in scheme: toxindex
permissible values: empty
permissible values: active
permissible values: done
permissible values: blocked
union of: empty
union of: active
union of: done
union of: blocked

Section
definition: A node in a flow document tree. Sections are the structural building block: each has an identity, a kind (object, list, scalar, enum), a status, and optional citations linking its value back to tool calls. Workflow schemas define what sections exist; the ontology defines the shape they all share.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: Section
  on property: children
subclass of: Restriction
  min cardinality: 0
  on property: children
subclass of: Restriction
  all values from: Citation
  on property: citations
subclass of: Restriction
  min cardinality: 0
  on property: citations
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: string
  on property: node_id
subclass of: Restriction
  min cardinality: 1
  on property: node_id
subclass of: Restriction
  max cardinality: 1
  on property: node_id
subclass of: Restriction
  all values from: SectionKindEnum
  on property: section_kind
subclass of: Restriction
  min cardinality: 0
  on property: section_kind
subclass of: Restriction
  max cardinality: 1
  on property: section_kind
subclass of: Restriction
  all values from: SectionStatusEnum
  on property: section_status
subclass of: Restriction
  min cardinality: 0
  on property: section_status
subclass of: Restriction
  max cardinality: 1
  on property: section_status

SectionKindEnum
type: Class
definition: Structural type of a document section node.
in scheme: toxindex
permissible values: object
permissible values: list
permissible values: scalar
permissible values: enum
union of: object
union of: list
union of: scalar
union of: enum

tool_call_id
type: DatatypeProperty
definition: Identifier of a specific tool invocation within a conversation.
in scheme: toxindex
range: string

primary_key
type: DatatypeProperty
definition: Column names forming the table's primary key.
in scheme: toxindex
range: string

BrickColumn
definition: A column in a brick table. Carries a vocabulary annotation that resolves the column to a stable concept URI: a column whose annotation matches a known controlled-vocabulary convention resolves to a well-known chemical or biological term (e.g., CAS Registry Number, SMILES, InChIKey), and a column with no matching convention resolves to a term minted under the owning brick's instance namespace, scoped to that brick, table, and column.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: ColumnTypeEnum
  on property: column_type
subclass of: Restriction
  min cardinality: 1
  on property: column_type
subclass of: Restriction
  max cardinality: 1
  on property: column_type
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 1
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: boolean
  on property: nullable
subclass of: Restriction
  min cardinality: 0
  on property: nullable
subclass of: Restriction
  max cardinality: 1
  on property: nullable
subclass of: Restriction
  all values from: string
  on property: vocab_label
subclass of: Restriction
  min cardinality: 0
  on property: vocab_label
subclass of: Restriction
  max cardinality: 1
  on property: vocab_label
subclass of: Restriction
  all values from: anyURI
  on property: vocab_uri
subclass of: Restriction
  min cardinality: 0
  on property: vocab_uri
subclass of: Restriction
  max cardinality: 1
  on property: vocab_uri

Document
definition: An indexed document in the platform's regulatory and scientific corpus. Sourced by a crawler, optionally grouped into collections.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: Collection
  on property: collections
subclass of: Restriction
  min cardinality: 0
  on property: collections
subclass of: Restriction
  all values from: string
  on property: crawler_id
subclass of: Restriction
  min cardinality: 0
  on property: crawler_id
subclass of: Restriction
  max cardinality: 1
  on property: crawler_id
subclass of: Restriction
  all values from: dateTime
  on property: created_at
subclass of: Restriction
  min cardinality: 0
  on property: created_at
subclass of: Restriction
  max cardinality: 1
  on property: created_at
subclass of: Restriction
  all values from: string
  on property: document_id
subclass of: Restriction
  min cardinality: 1
  on property: document_id
subclass of: Restriction
  max cardinality: 1
  on property: document_id
subclass of: Restriction
  all values from: string
  on property: document_type
subclass of: Restriction
  min cardinality: 0
  on property: document_type
subclass of: Restriction
  max cardinality: 1
  on property: document_type
subclass of: Restriction
  all values from: string
  on property: source_domain
subclass of: Restriction
  min cardinality: 0
  on property: source_domain
subclass of: Restriction
  max cardinality: 1
  on property: source_domain
subclass of: Restriction
  all values from: anyURI
  on property: url
subclass of: Restriction
  min cardinality: 1
  on property: url
subclass of: Restriction
  max cardinality: 1
  on property: url

Flow
definition: An instance of a workflow execution. A structured, schema-conformant document being filled out (or completed) with provenance citations linking each section back to the tool call that produced it.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: dateTime
  on property: created_at
subclass of: Restriction
  min cardinality: 0
  on property: created_at
subclass of: Restriction
  max cardinality: 1
  on property: created_at
subclass of: Restriction
  all values from: dateTime
  on property: finished_at
subclass of: Restriction
  min cardinality: 0
  on property: finished_at
subclass of: Restriction
  max cardinality: 1
  on property: finished_at
subclass of: Restriction
  all values from: string
  on property: flow_id
subclass of: Restriction
  min cardinality: 1
  on property: flow_id
subclass of: Restriction
  max cardinality: 1
  on property: flow_id
subclass of: Restriction
  all values from: Section
  on property: sections
subclass of: Restriction
  min cardinality: 0
  on property: sections
subclass of: Restriction
  all values from: integer
  on property: sections_active
subclass of: Restriction
  min cardinality: 0
  on property: sections_active
subclass of: Restriction
  max cardinality: 1
  on property: sections_active
subclass of: Restriction
  all values from: integer
  on property: sections_done
subclass of: Restriction
  min cardinality: 0
  on property: sections_done
subclass of: Restriction
  max cardinality: 1
  on property: sections_done
subclass of: Restriction
  all values from: integer
  on property: sections_total
subclass of: Restriction
  min cardinality: 0
  on property: sections_total
subclass of: Restriction
  max cardinality: 1
  on property: sections_total
subclass of: Restriction
  all values from: StatusEnum
  on property: status
subclass of: Restriction
  min cardinality: 1
  on property: status
subclass of: Restriction
  max cardinality: 1
  on property: status
subclass of: Restriction
  all values from: Workflow
  on property: workflow
subclass of: Restriction
  min cardinality: 1
  on property: workflow
subclass of: Restriction
  max cardinality: 1
  on property: workflow

children
type: ObjectProperty
definition: Nested child sections.
in scheme: toxindex
range: Section

url
type: DatatypeProperty
in scheme: toxindex
range: anyURI

description
type: DatatypeProperty
in scheme: toxindex
range: string

output_schema
type: DatatypeProperty
definition: JSON Schema defining the tool's output.
in scheme: toxindex
range: string

Workflow
definition: A repeatable structured process that produces a document, such as a regulatory assessment or a technical evaluation report. Workflows define a schema that guides structured content generation with cited evidence.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  all values from: string
  on property: formats
subclass of: Restriction
  min cardinality: 0
  on property: formats
subclass of: Restriction
  all values from: string
  on property: param_schema
subclass of: Restriction
  min cardinality: 0
  on property: param_schema
subclass of: Restriction
  max cardinality: 1
  on property: param_schema
subclass of: Restriction
  all values from: string
  on property: title
subclass of: Restriction
  min cardinality: 0
  on property: title
subclass of: Restriction
  max cardinality: 1
  on property: title
subclass of: Restriction
  all values from: string
  on property: version
subclass of: Restriction
  min cardinality: 0
  on property: version
subclass of: Restriction
  max cardinality: 1
  on property: version
subclass of: Restriction
  all values from: string
  on property: workflow_id
subclass of: Restriction
  min cardinality: 1
  on property: workflow_id
subclass of: Restriction
  max cardinality: 1
  on property: workflow_id

section_kind
type: ObjectProperty
definition: Structural type of a document section.
in scheme: toxindex
range: SectionKindEnum

name
type: DatatypeProperty
in scheme: toxindex
range: string

formats
type: DatatypeProperty
definition: Available output formats (e.g., html, pdf, json).
in scheme: toxindex
range: string

Conversation
definition: A multi-turn question-and-answer session with the platform's agent.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: string
  on property: conversation_id
subclass of: Restriction
  min cardinality: 1
  on property: conversation_id
subclass of: Restriction
  max cardinality: 1
  on property: conversation_id
subclass of: Restriction
  all values from: string
  on property: title
subclass of: Restriction
  min cardinality: 0
  on property: title
subclass of: Restriction
  max cardinality: 1
  on property: title
subclass of: Restriction
  all values from: dateTime
  on property: updated_at
subclass of: Restriction
  min cardinality: 0
  on property: updated_at
subclass of: Restriction
  max cardinality: 1
  on property: updated_at

version
type: DatatypeProperty
in scheme: toxindex
range: string

source
type: DatatypeProperty
definition: Canonical source URL for a dataset or tool.
in scheme: toxindex
range: anyURI

row_count
type: DatatypeProperty
definition: Number of rows in a table.
in scheme: toxindex
range: integer

Citation
definition: A provenance link from a document section to the tool invocation that produced or supported its value.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: string
  on property: node_id
subclass of: Restriction
  min cardinality: 1
  on property: node_id
subclass of: Restriction
  max cardinality: 1
  on property: node_id
subclass of: Restriction
  all values from: ToolCall
  on property: tool_call
subclass of: Restriction
  min cardinality: 1
  on property: tool_call
subclass of: Restriction
  max cardinality: 1
  on property: tool_call

int64
definition: 64-bit integer.
type: Class
subclass of: ColumnTypeEnum

BrickTable
definition: A single table within a brick. Contains typed, described columns with optional mappings to external ontology terms.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: BrickColumn
  on property: columns
subclass of: Restriction
  min cardinality: 0
  on property: columns
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 1
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: string
  on property: primary_key
subclass of: Restriction
  min cardinality: 0
  on property: primary_key
subclass of: Restriction
  all values from: integer
  on property: row_count
subclass of: Restriction
  min cardinality: 0
  on property: row_count
subclass of: Restriction
  max cardinality: 1
  on property: row_count

done
definition: Written and validated.
type: Class
subclass of: SectionStatusEnum

labels
type: DatatypeProperty
definition: Classification labels (e.g., epa, echa).
in scheme: toxindex
range: string

param_schema
type: DatatypeProperty
definition: JSON Schema for workflow parameters.
in scheme: toxindex
range: string

updated_at
type: DatatypeProperty
in scheme: toxindex
range: dateTime

upstream_url
type: DatatypeProperty
in scheme: toxindex
range: anyURI

tables
type: ObjectProperty
in scheme: toxindex
range: BrickTable

retrieval_notes
type: DatatypeProperty
definition: Guidance on how to use this collection for retrieval.
in scheme: toxindex
range: string

license
type: DatatypeProperty
in scheme: toxindex
range: string

column_type
type: ObjectProperty
definition: Data type of the column.
in scheme: toxindex
range: ColumnTypeEnum

document_type
type: DatatypeProperty
in scheme: toxindex
range: string

nullable
type: DatatypeProperty
in scheme: toxindex
range: boolean

workflow_id
type: DatatypeProperty
definition: Workflow identifier.
in scheme: toxindex
range: string

Tool
definition: A computational capability available on the platform, such as a QSAR model, a descriptor calculator, or a metabolite predictor. Tools accept structured input (typically a SMILES string) and return structured output.
in scheme: toxindex
type: Class
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  all values from: string
  on property: input_schema
subclass of: Restriction
  min cardinality: 0
  on property: input_schema
subclass of: Restriction
  max cardinality: 1
  on property: input_schema
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 1
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: string
  on property: output_schema
subclass of: Restriction
  min cardinality: 0
  on property: output_schema
subclass of: Restriction
  max cardinality: 1
  on property: output_schema
subclass of: Restriction
  all values from: string
  on property: title
subclass of: Restriction
  min cardinality: 0
  on property: title
subclass of: Restriction
  max cardinality: 1
  on property: title

status
type: ObjectProperty
in scheme: toxindex
range: StatusEnum

columns
type: ObjectProperty
in scheme: toxindex
range: BrickColumn

output
type: DatatypeProperty
definition: JSON-serialized tool output.
in scheme: toxindex
range: string

active
definition: Activated, not yet written.
type: Class
subclass of: SectionStatusEnum

collections
type: ObjectProperty
definition: Collections this document belongs to.
in scheme: toxindex
range: Collection

ColumnTypeEnum
type: Class
in scheme: toxindex
permissible values: string
permissible values: int64
permissible values: float64
permissible values: boolean
union of: string
union of: int64
union of: float64
union of: boolean

citations
type: ObjectProperty
definition: Provenance links from this section to the tool calls that produced its value.
in scheme: toxindex
range: Citation

boolean
definition: Boolean value.
type: Class
subclass of: ColumnTypeEnum

tool_call
type: ObjectProperty
definition: The tool invocation that produced this section's value.
in scheme: toxindex
range: ToolCall

object
definition: Structured object with named child fields.
type: Class
subclass of: SectionKindEnum

domain
type: DatatypeProperty
definition: Scientific domain (e.g., Toxicology, Genomics).
in scheme: toxindex
range: string

string
definition: Text value.
type: Class
subclass of: ColumnTypeEnum

sections_active
type: DatatypeProperty
definition: Number of sections currently being worked on.
in scheme: toxindex
range: integer

node_id
type: DatatypeProperty
definition: Dot-delimited path to a node in a flow document tree.
in scheme: toxindex
range: string

slug
type: DatatypeProperty
definition: Stable URL-safe identifier.
in scheme: toxindex
range: string

section_status
type: ObjectProperty
definition: Completion state of a document section.
in scheme: toxindex
range: SectionStatusEnum

flow_id
type: DatatypeProperty
definition: Flow execution identifier.
in scheme: toxindex
range: string

parent
type: ObjectProperty
definition: Parent collection (one level of nesting).
in scheme: toxindex
range: Collection

sections
type: ObjectProperty
definition: The root-level sections of this flow's document tree.
in scheme: toxindex
range: Section

StatusEnum
type: Class
in scheme: toxindex
permissible values: running
permissible values: completed
permissible values: failed
union of: running
union of: completed
union of: failed

is_error
type: DatatypeProperty
definition: Whether the tool invocation resulted in an error.
in scheme: toxindex
range: boolean

created_at
type: DatatypeProperty
in scheme: toxindex
range: dateTime

conversation_id
type: DatatypeProperty
definition: Conversation identifier.
in scheme: toxindex
range: string

tags
type: DatatypeProperty
in scheme: toxindex
range: string

completed
type: Class
subclass of: StatusEnum

empty
definition: Not yet activated or read.
type: Class
subclass of: SectionStatusEnum

input_schema
type: DatatypeProperty
definition: JSON Schema defining the tool's accepted input.
in scheme: toxindex
range: string

vocab_label
type: DatatypeProperty
definition: Controlled-vocabulary annotation a brick column carries (e.g., CAS, SMILES, InChIKey). Backed by a stable convention that determines how vocab_uri resolves.
in scheme: toxindex
range: string

toxindex
type: Ontology
definition: User-facing domain ontology for ToxIndex. Defines the concepts that customers and integrations consume: curated reference data, document corpora, computational tools, structured workflows, and their provenance.
title: ToxIndex Ontology
version: 1.0.0
license: https://creativecommons.org/licenses/by/4.0/

list
definition: Array of items.
type: Class
subclass of: SectionKindEnum

built_at
type: DatatypeProperty
in scheme: toxindex
range: dateTime

running
type: Class
subclass of: StatusEnum

sections_done
type: DatatypeProperty
definition: Number of sections completed.
in scheme: toxindex
range: integer

workflow
type: ObjectProperty
definition: The workflow this flow is an instance of.
in scheme: toxindex
range: Workflow

enum
definition: Fixed set of allowed values.
type: Class
subclass of: SectionKindEnum

scalar
definition: Primitive value (string, number, etc.).
type: Class
subclass of: SectionKindEnum

document_count
type: DatatypeProperty
in scheme: toxindex
range: integer

title
type: DatatypeProperty
in scheme: toxindex
range: string

crawler_id
type: DatatypeProperty
definition: Identifier of the harvester that sourced a document.
in scheme: toxindex
range: string

finished_at
type: DatatypeProperty
in scheme: toxindex
range: dateTime

failed
type: Class
subclass of: StatusEnum

blocked
definition: Prerequisites not yet completed.
type: Class
subclass of: SectionStatusEnum

sections_total
type: DatatypeProperty
definition: Total number of sections in the document.
in scheme: toxindex
range: integer