Package 'R4AOP'

Title: Access the AOP-Wiki Through Its REST API
Description: Provides functions to retrieve Adverse Outcome Pathways (AOPs), Key Events, Key Event Relationships, stressors, chemicals and genes from the AOP-Wiki through its REST API, without writing SPARQL queries. Each exported function corresponds to one API endpoint, and results are returned as tibbles that fit directly into an R workflow. Pagination, input validation and session caching are handled internally, and every result carries the version of the AOP-Wiki data it came from, so that analyses can be reported reproducibly.
Authors: Sidra Adil [aut, cre] (ORCID: <https://orcid.org/0000-0002-3044-3561>), Egon Willighagen [ctb] (ORCID: <https://orcid.org/0000-0001-7542-0286>), Tooba Abbassi-Daloii [ctb] (ORCID: <https://orcid.org/0000-0002-4904-3269>), Marvin Martens [aut] (ORCID: <https://orcid.org/0000-0003-2230-0840>)
Maintainer: Sidra Adil <[email protected]>
License: MIT + file LICENSE
Version: 0.99.0
Built: 2026-11-03 19:49:40 UTC
Source: https://github.com/BiocStaging/R4AOP

Help Index

List Adverse Outcomes

Description

List Adverse Outcomes

Usage

ao_list(
  q = NULL,
  level = NULL,
  aop = NULL,
  taxon = NULL,
  organ = NULL,
  cell_type = NULL,
  gene = NULL
)

Arguments

q

Free-text search term.
level

Biological level of organisation.
aop

Only Key Events belonging to this AOP id.
taxon, organ, cell_type

Biological context filters.
gene

Only Key Events linked to this gene.

Value

A tibble with one row per Adverse Outcome.

Examples

ao_list(q = "carcinoma")

Clear the R4AOP response cache

Description

Responses are cached for the current R session. Clear the cache to force fresh requests, for example after the AOP-Wiki data has been updated.

Usage

aop_cache_clear()

Value

Invisibly TRUE.

Examples

aop_cache_clear()

Chemicals of an AOP

Description

Chemicals of an AOP

Usage

aop_chemicals(aop_id)

Arguments

aop_id

AOP identifier.

Value

A tibble of chemicals.

Examples

aop_chemicals(1)

Key Event Components of every Key Event in an AOP

Description

Retrieves the Key Event Components of each Key Event of an AOP and returns them in a single table. One request is made per Key Event, so the first call for a large AOP takes a few seconds. Responses are cached for the session.

Usage

aop_components(aop_id)

Arguments

aop_id

AOP identifier.

Value

A tibble as returned by ke_components(), with the columns ke_title and role added.

Examples

aop_components(38)

Data version of a result

Description

Reports which version of the AOP-Wiki dataset a result came from. Use it when reporting results, so an analysis can be reproduced later.

Usage

aop_data_version(x = NULL)

Arguments

x

A tibble returned by an R4AOP function. If missing, the current version is fetched from the API.

Value

A version string, e.g. "2026.09.12".

Examples

aops <- aop_list(q = "liver")
aop_data_version(aops)
aop_data_version()

Dataset information

Description

Version, license, data dumps and entity counts of the AOP-Wiki RDF dataset.

Usage

aop_dataset_info()

Value

A tibble with one row.

Examples

aop_dataset_info()

Summarise the genes of an AOP per Key Event

Description

Counts the distinct genes linked to each Key Event of an AOP, separately for each detection method (regex, ner or both).

Usage

aop_gene_summary(aop_id)

Arguments

aop_id

AOP identifier.

Value

A tibble with the columns ke_id, ke_title, role, detected_by and n_genes.

Examples

aop_gene_summary(38)

Genes linked to an AOP

Description

Genes linked to an AOP

Usage

aop_genes(aop_id, method = NULL)

Arguments

aop_id

AOP identifier.
method

How genes were linked: one of "any", "regex", "ner" or "both".

Value

A tibble of genes.

Examples

aop_genes(1)

Get a single Adverse Outcome Pathway

Description

Get a single Adverse Outcome Pathway

Usage

aop_get(aop_id, include = NULL)

Arguments

aop_id

AOP identifier, e.g. 1.
include

Optional extra content to request from the API.

Value

A tibble with one row.

Examples

aop_get(1)

Key Event Relationships of an AOP

Description

Key Event Relationships of an AOP

Usage

aop_kers(aop_id)

Arguments

aop_id

AOP identifier.

Value

A tibble of KERs.

Examples

aop_kers(1)

Key Events of an AOP

Description

Key Events of an AOP

Usage

aop_key_events(aop_id, role = NULL)

Arguments

aop_id

AOP identifier.
role

Optional filter: one of "mie", "ke" or "ao".

Value

A tibble of Key Events.

Examples

aop_key_events(1)
aop_key_events(1, role = "mie")

List Adverse Outcome Pathways

Description

Retrieve AOPs from the AOP-Wiki, optionally filtered. All filters are optional; unused ones are not sent to the API.

Usage

aop_list(
  q = NULL,
  status = NULL,
  taxon = NULL,
  ke = NULL,
  mie = NULL,
  ao = NULL,
  stressor = NULL,
  chemical = NULL,
  modified_since = NULL,
  resolve_titles = FALSE
)

Arguments

q

Free-text search term, e.g. "liver".
status

OECD status of the AOP.
taxon

Taxon filter.
ke, mie, ao

Identifier of a Key Event, Molecular Initiating Event or Adverse Outcome that the AOP must contain.
stressor

Stressor identifier.
chemical

Chemical identifier (CAS number).
modified_since

Only AOPs modified after this date ("YYYY-MM-DD").
resolve_titles

If TRUE, add the list-columns mie_titles and ao_titles holding the titles of the Molecular Initiating Events and Adverse Outcomes named in mie_ids and ao_ids. The titles are looked up with a single additional request for all Key Events, which is cached for the session.

Value

A tibble with one row per AOP.

Examples

aop_list(q = "liver")
aop_list(q = "liver fibrosis", resolve_titles = TRUE)

Measurement methods used in an AOP

Description

Methods described for measuring the Key Events of an AOP.

Usage

aop_methods(aop_id)

Arguments

aop_id

AOP identifier.

Value

A tibble of measurement methods.

Examples

aop_methods(1)

Plot the Key Event Components of an AOP

Description

Shows, for every Key Event of an AOP, the biological process, the biological object and the action that describe it, together with their ontology identifiers. Key Events are ordered from the molecular initiating event to the adverse outcome, and those two are marked in their titles, coloured green and red when the marquee package is installed. Components that AOP-Wiki does not record are left blank.

Usage

aop_plot_components(aop_id, wrap = 26)

Arguments

aop_id

AOP identifier.
wrap

Width in characters at which long terms are wrapped.

Value

A ggplot object.

Examples

aop_plot_components(38)

Plot the genes of an AOP per Key Event

Description

Draws a bar chart of the distinct genes linked to each Key Event of an AOP, coloured by detection method. Every Key Event of the AOP is shown, so a Key Event without gene links appears with an empty bar. The molecular initiating event and the adverse outcome are marked in the Key Event titles, and coloured green and red when the marquee package is installed. Requires the ggplot2 package.

Usage

aop_plot_genes(aop_id)

Arguments

aop_id

AOP identifier.

Value

A ggplot object, which can be further modified in the usual way.

Examples

aop_plot_genes(38)

Search across AOP-Wiki entities

Description

Free-text search over AOPs, Key Events, KERs, stressors and chemicals at once.

Usage

aop_search(q, types = NULL, limit = 100)

Arguments

q

Search term (1 to 200 characters).
types

Restrict to certain entity types, e.g. "aop" or "key_event".
limit

Maximum number of results.

Value

A tibble of matches, with a type column and a relevance score.

Examples

aop_search("liver")

Stressors of an AOP

Description

Stressors of an AOP

Usage

aop_stressors(aop_id)

Arguments

aop_id

AOP identifier.

Value

A tibble of stressors.

Examples

aop_stressors(1)

Overview of an AOP

Description

Returns the Key Events of an AOP in causal order, from the molecular initiating event to the adverse outcome, with the biological level of organisation and the role of each event. The title of the AOP, its OECD status, its taxonomic applicability, its stressors and the version of the data are attached as attributes and shown when the result is printed.

Usage

aop_summary(aop_id)

Arguments

aop_id

AOP identifier.

Details

The order is computed from the Key Event Relationships, since the Key Events themselves are not stored in sequence. An AOP that branches has no single chain, so the order is then one valid sequence among several, and the printed output says so.

Value

A tibble with the columns step, ke_id, ke_title, level and role, of class aop_summary.

Examples

aop_summary(38)

AOPs linked to a chemical

Description

AOPs linked to a chemical

Usage

chemical_aops(cas)

Arguments

cas

CAS registry number, e.g. "56-23-5".

Value

A tibble of AOPs.

Examples

chemical_aops("56-23-5")

Get a single chemical

Description

Get a single chemical

Usage

chemical_get(cas)

Arguments

cas

CAS registry number, e.g. "56-23-5".

Value

A tibble with one row.

Examples

chemical_get("56-23-5")

Key Events linked to a chemical

Description

Key Events linked to a chemical

Usage

chemical_key_events(cas, role = NULL)

Arguments

cas

CAS registry number, e.g. "56-23-5".
role

Optional filter: one of "mie", "ke" or "ao".

Value

A tibble of Key Events.

Examples

chemical_key_events("56-23-5")

List or search chemicals

Description

List or search chemicals

Usage

chemical_list(
  q = NULL,
  aop = NULL,
  stressor = NULL,
  inchikey = NULL,
  chebi = NULL,
  pubchem = NULL,
  chemspider = NULL,
  wikidata = NULL,
  chembl = NULL,
  drugbank = NULL,
  kegg = NULL,
  hmdb = NULL,
  lipidmaps = NULL
)

Arguments

q

Free-text search term.
aop

Only chemicals used in this AOP id.
stressor

Only chemicals linked to this stressor id.
inchikey, chebi, pubchem, chemspider, wikidata

Identifier filters.
chembl, drugbank, kegg, hmdb, lipidmaps

Further identifier filters. Look the chemical up by an identifier in that database.

Value

A tibble with one row per chemical.

Examples

chemical_list(q = "benzene")

WikiPathways containing a chemical

Description

WikiPathways containing a chemical

Usage

chemical_pathways(cas)

Arguments

cas

CAS registry number, e.g. "56-23-5".

Value

A tibble of pathways.

Examples

chemical_pathways("56-23-5")

Get a single gene

Description

Get a single gene

Usage

gene_get(gene)

Arguments

gene

Gene symbol or HGNC identifier, e.g. "TP53".

Value

A tibble with one row.

Examples

gene_get("TP53")

List genes

Description

List genes

Usage

gene_list(q = NULL, aop = NULL, ke = NULL, method = NULL)

Arguments

q

Free-text search term, e.g. a gene symbol.
aop

Only genes linked to this AOP id.
ke

Only genes linked to this Key Event id.
method

How genes were linked: "any", "regex", "ner" or "both".

Value

A tibble with one row per gene.

Examples

gene_list(q = "TP53")
gene_list(aop = 37)

Adverse Outcomes linked to a Key Event

Description

Adverse Outcomes linked to a Key Event

Usage

ke_adverse_outcomes(ke_id, as = NULL)

Arguments

ke_id

Key Event identifier.
as

Which AOPs to consider: "mie" (only AOPs where this KE is the MIE) or "any" (every AOP containing it).

Value

A tibble of Adverse Outcomes.

Examples

ke_adverse_outcomes(334)

AOPs containing a Key Event

Description

AOPs containing a Key Event

Usage

ke_aops(ke_id, role = NULL)

Arguments

ke_id

Key Event identifier.
role

Optional filter: one of "mie", "ke" or "ao".

Value

A tibble of AOPs.

Examples

ke_aops(334)

Chemicals of a Key Event

Description

Chemicals of a Key Event

Usage

ke_chemicals(ke_id)

Arguments

ke_id

Key Event identifier.

Value

A tibble of chemicals.

Examples

ke_chemicals(334)

Key Event Components of a Key Event

Description

Key Event Components describe a Key Event in ontology terms: a biological process, an optional biological object, and the action that links them. The API returns them nested inside a single Key Event record, and this function returns them as one row per component.

Usage

ke_components(ke_id)

Arguments

ke_id

Key Event identifier.

Value

A tibble with the columns ke_id, action, process, process_id, object and object_id. The identifiers are ontology terms, for example "GO:0008219". Components that name no object have NA in object and object_id.

Examples

ke_components(55)

Key Events downstream of a Key Event

Description

Follows Key Event Relationships forwards.

Usage

ke_downstream(ke_id, depth = 1)

Arguments

ke_id

Key Event identifier.
depth

How many relationships to follow (1 to 3, default 1).

Value

A tibble of Key Events.

Examples

ke_downstream(334, depth = 2)

Key Event gene sets of an AOP as a GeneSetCollection

Description

Returns the genes linked to each Key Event of an AOP as a GSEABase::GeneSetCollection, with one gene set per Key Event. This is the form that Bioconductor enrichment tools expect, so the result can be passed straight to functions such as GSVA::gsva() or limma::camera() without reshaping.

Usage

ke_gene_sets(aop_id, method = NULL)

Arguments

aop_id

AOP identifier.
method

How genes were linked: one of "any", "regex", "ner" or "both".

Details

Each gene set is named ⁠KE_<id>⁠, carries the Key Event title as its short description, and records the Key Event role and the version of the AOP-Wiki data in its long description. Key Events without gene links are omitted, since an empty gene set is not useful for enrichment. Use aop_gene_summary() to see which Key Events those are.

Value

A GeneSetCollection with one GeneSet per Key Event that has linked genes.

See Also

aop_genes() for the same information as a tibble.

Examples

gsc <- ke_gene_sets(38)
names(gsc)

Get a single Key Event

Description

Get a single Key Event

Usage

ke_get(ke_id)

Arguments

ke_id

Key Event identifier.

Value

A tibble with one row.

Examples

ke_get(334)

List Key Events

Description

List Key Events

Usage

ke_list(
  q = NULL,
  role = NULL,
  level = NULL,
  aop = NULL,
  taxon = NULL,
  organ = NULL,
  cell_type = NULL,
  gene = NULL
)

Arguments

q

Free-text search term.
role

Optional filter: one of "mie", "ke" or "ao".
level

Biological level of organisation.
aop

Only Key Events belonging to this AOP id.
taxon, organ, cell_type

Biological context filters.
gene

Only Key Events linked to this gene.

Value

A tibble with one row per Key Event.

Examples

ke_list(q = "apoptosis")
ke_list(aop = 1)

Molecular Initiating Events linked to a Key Event

Description

Molecular Initiating Events linked to a Key Event

Usage

ke_mies(ke_id, as = NULL)

Arguments

ke_id

Key Event identifier.
as

Which AOPs to consider: "ao" (only AOPs where this KE is the AO) or "any" (every AOP containing it).

Value

A tibble of MIEs.

Examples

ke_mies(334)

Stressors of a Key Event

Description

Stressors of a Key Event

Usage

ke_stressors(ke_id)

Arguments

ke_id

Key Event identifier.

Value

A tibble of stressors.

Examples

ke_stressors(334)

Key Events upstream of a Key Event

Description

Follows Key Event Relationships backwards.

Usage

ke_upstream(ke_id, depth = 1)

Arguments

ke_id

Key Event identifier.
depth

How many relationships to follow (1 to 3, default 1).

Value

A tibble of Key Events.

Examples

ke_upstream(334, depth = 2)

Get a single Key Event Relationship

Description

Get a single Key Event Relationship

Usage

ker_get(ker_id)

Arguments

ker_id

KER identifier.

Value

A tibble with one row.

Examples

ker_get(158)

List Key Event Relationships

Description

List Key Event Relationships

Usage

ker_list(
  aop = NULL,
  upstream = NULL,
  downstream = NULL,
  ke = NULL,
  gene = NULL
)

Arguments

aop

Only KERs belonging to this AOP id.
upstream

Only KERs starting at this Key Event id.
downstream

Only KERs ending at this Key Event id.
ke

Only KERs involving this Key Event id, in either position.
gene

Only KERs linked to this gene.

Value

A tibble with one row per KER.

Examples

ker_list(aop = 1)
ker_list(ke = 334)

List Molecular Initiating Events

Description

List Molecular Initiating Events

Usage

mie_list(
  q = NULL,
  level = NULL,
  aop = NULL,
  taxon = NULL,
  organ = NULL,
  cell_type = NULL,
  gene = NULL
)

Arguments

q

Free-text search term.
level

Biological level of organisation.
aop

Only Key Events belonging to this AOP id.
taxon, organ, cell_type

Biological context filters.
gene

Only Key Events linked to this gene.

Value

A tibble with one row per MIE.

Examples

mie_list(q = "receptor")

AOPs linked to a stressor, with their adverse outcomes

Description

Lists every AOP in which a stressor is used, together with the adverse outcomes those AOPs end in. The AOP identifiers come from the aop_ids field of the stressor record, and the titles and adverse outcomes are taken from the AOP list, which is cached for the session. The stressor may be given as an identifier or as a name, in which case the name is looked up with stressor_list().

Usage

stressor_aops(stressor)

Arguments

stressor

Stressor identifier, or a stressor name.

Value

A tibble with the columns stressor_id, stressor_title, aop_id, aop_title, ao_id and ao_title, with one row per AOP and adverse outcome. An AOP with no adverse outcome recorded keeps one row, with NA in the two ao columns. A stressor used in no AOP gives zero rows.

Examples

stressor_aops(150)
stressor_aops("hexachlorobenzene")

Get a single stressor

Description

Get a single stressor

Usage

stressor_get(stressor_id)

Arguments

stressor_id

Stressor identifier.

Value

A tibble with one row.

Examples

stressor_get(150)

List stressors

Description

List stressors

Usage

stressor_list(q = NULL, aop = NULL, chemical = NULL, has_chemical = NULL)

Arguments

q

Free-text search term.
aop

Only stressors used in this AOP id.
chemical

Only stressors linked to this chemical (CAS number).
has_chemical

If TRUE, only stressors that have a chemical mapping.

Value

A tibble with one row per stressor.

Examples

stressor_list(q = "benzene")
stressor_list(aop = 1)