Package 'ReactomeContentService4R' reference manual

Package 'ReactomeContentService4R'

Title:	Interface for the Reactome Content Service
Description:	Reactome is a free, open-source, open access, curated and peer-reviewed knowledgebase of bio-molecular pathways. This package is to interact with the Reactome Content Service API. Pre-built functions would allow users to retrieve data and images that consist of proteins, pathways, and other molecules related to a specific gene or entity in Reactome.
Authors:	Chi-Lam Poon [aut, cre] , Reactome [cph]
Maintainer:	Chi-Lam Poon <[email protected]>
License:	Apache License (>= 2.0) \| file LICENSE
Version:	1.13.0
Built:	2024-06-30 03:57:34 UTC
Source:	https://github.com/bioc/ReactomeContentService4R

Title:

Interface for the Reactome Content Service

Description:

Reactome is a free, open-source, open access, curated and peer-reviewed knowledgebase of bio-molecular pathways. This package is to interact with the Reactome Content Service API. Pre-built functions would allow users to retrieve data and images that consist of proteins, pathways, and other molecules related to a specific gene or entity in Reactome.

Authors:

Chi-Lam Poon [aut, cre]

, Reactome [cph]

Maintainer:

Chi-Lam Poon <[email protected]>

License:

Apache License (>= 2.0) | file LICENSE

Version:

1.13.0

Built:

2024-06-30 03:57:34 UTC

Source:

https://github.com/bioc/ReactomeContentService4R

Help Index

Search engines discovery schema

Description

Search engines discovery schema

Usage

discover(event.id)
discover(event.id)

Arguments

event.id

stable id or db id of an Event

Value

a list of the event schema

Examples

discover("R-HSA-73893")
discover("R-HSA-73893")

File exporter

Description

Export Reactome pathway diagrams in SBGN or SBML format.

Usage

exportEventFile(
  id,
  format = c("sbgn", "sbml"),
  writeToFile = TRUE,
  file = NULL
)
exportEventFile(
  id,
  format = c("sbgn", "sbml"),
  writeToFile = TRUE,
  file = NULL
)

Arguments

`id`	a stable or db id of an Event (Pathway or Reaction)
`format`	either in "sbgn" (SBGN, Systems Biology Graphical Notation) or "sbml" (SBML, Systems Biology Markup Language)
`writeToFile`	If set to `TRUE`, the returned data would be written into a file. If `file=NULL`, the output file will be automatically saved into the working directory and named based on the `id` and `format`
`file`	full path of the output file

Value

a character object with the content of SBGN/SBML for a given id, or a SBGN/SMBL file saved into the specified path. If the output is empty character or list, please check on ContentService or contact HelpDesk [email protected].

Examples

exportEventFile("R-HSA-432047", "sbgn", writeToFile=FALSE)
## Not run: exportEventFile("R-HSA-68616", "sbml", file="orc.assembly.sbml")
exportEventFile("R-HSA-432047", "sbgn", writeToFile=FALSE)
## Not run: exportEventFile("R-HSA-68616", "sbml", file="orc.assembly.sbml")

Image exporter

Description

The diagram exporter allows researchers to include images of their favorite pathway diagrams into their publications, posters or presentations. For details see Reactome diagram exporter guide.

Usage

exportImage(
  id = NULL,
  output = c("diagram", "fireworks", "reaction"),
  species = NULL,
  format = c("png", "jpg", "jpeg", "svg", "gif"),
  quality = 5,
  flg = NULL,
  flgInteractors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  ehld = TRUE,
  diagramProfile = "Modern",
  token = NULL,
  resource = "TOTAL",
  analysisProfile = "Standard",
  expColumn = NULL,
  fireworksCoverage = FALSE,
  file = NULL,
  ...
)
exportImage(
  id = NULL,
  output = c("diagram", "fireworks", "reaction"),
  species = NULL,
  format = c("png", "jpg", "jpeg", "svg", "gif"),
  quality = 5,
  flg = NULL,
  flgInteractors = TRUE,
  sel = NULL,
  title = TRUE,
  margin = 15,
  ehld = TRUE,
  diagramProfile = "Modern",
  token = NULL,
  resource = "TOTAL",
  analysisProfile = "Standard",
  expColumn = NULL,
  fireworksCoverage = FALSE,
  file = NULL,
  ...
)

Arguments

`id`	stable or db id of a ReactionLikeEvent for "reaction" output, or id of an Event for "diagram"
`output`	type of exported image including "diagram", "fireworks", "reaction"
`species`	name or db id or taxon id of a species. Used in "fireworks" output
`format`	output format including "png", "jpg", "jpeg", "svg", "gif"
`quality`	result image quality between 1-10, default is 5
`flg`	gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram
`flgInteractors`	defines whether to take into account interactors for the flagging
`sel`	highlight element(s) selection in the diagram
`title`	whether the name of the pathway is shown below
`margin`	defines the image margin between 0-20, default is 15
`ehld`	whether textbook-like illustration are taken into account
`diagramProfile`	color profile, "modern" or "standard"
`token`	token from Reactome Analysis Service
`resource`	the analysis resource for which the results will be overlaid on top of the given pathways overview
`analysisProfile`	analysis color profile including "Standard", "Strosobar", "Copper%20plus"
`expColumn`	the specific expression analysis results column to be overlaid. If it is not specified (null), the first one is selected. If it is not specified (null) and format is gif, then an animated gif is generated with all the columns.
`fireworksCoverage`	set `TRUE` to overlay analysis coverage values in a fireworks image
`file`	full path of the output file
`...`	additional parameters passed to `magick::image_write()`

Value

an image saved into the specified path or a magick image object. More magick processing see the package.

Examples

# fireworks
exportImage(species="9606", output="fireworks", 
            format="jpg", quality=7)

## Not run: 
# animated gifs of EHLDs
# can use your own token from your Reactome Analysis
gif <- exportImage(id="R-HSA-69278", output="diagram", format="gif",
                   sel="R-HSA-69242", token="MjAyMDA2MTcyMDM5NDBfMzU2")
print(gif)

# reaction
exportImage(id="R-HSA-6787403", output="reaction", format="svg",
       flg="MTO1", analysisProfile="Copper%20plus", file="R-HSA-6787403.svg")


## End(Not run)
# fireworks
exportImage(species="9606", output="fireworks", 
            format="jpg", quality=7)

## Not run: 
# animated gifs of EHLDs
# can use your own token from your Reactome Analysis
gif <- exportImage(id="R-HSA-69278", output="diagram", format="gif",
                   sel="R-HSA-69242", token="MjAyMDA2MTcyMDM5NDBfMzU2")
print(gif)

# reaction
exportImage(id="R-HSA-6787403", output="reaction", format="svg",
       flg="MTO1", analysisProfile="Copper%20plus", file="R-HSA-6787403.svg")


## End(Not run)

PhysicalEntity queries

Description

This method retrieves instances related to PhysicalEntity.

Usage

getEntities(
  id,
  retrieval = c("subunits", "complexes", "componentOf", "otherForms"),
  resource = "Reactome",
  subunitsExcludeStructures = FALSE
)
getEntities(
  id,
  retrieval = c("subunits", "complexes", "componentOf", "otherForms"),
  resource = "Reactome",
  subunitsExcludeStructures = FALSE
)

Arguments

`id`	stable or db id of a Reactome PhysicalEntity, or id from resources other than Reactome
`retrieval`	entities to be retrieved, including "subunits", "complexes", "componentOf", "otherForms"
`resource`	resource other than Reactome, e.g. UniProt, Ensembl
`subunitsExcludeStructures`	whether contained Complexes and EntitySets are excluded when retrieving "subunits"

Details

Details on options of retrieval arg:

subunits: retrieves subunits that constitute any given Complex
complexes: retrieves Complexes that contain the given id and resource
componentOf: retrieves structures (Complexes and Sets) that include the given Entity as their component
otherForms: retrieves Entities containing all other forms of the given PhysicalEntity

Value

a dataframe containing requested information

Examples

getEntities("R-HSA-5674003", retrieval="subunits")
getEntities("P00533", retrieval="complexes", resource="UniProt")
getEntities("R-HSA-5674003", retrieval="subunits")
getEntities("P00533", retrieval="complexes", resource="UniProt")

EventsHierarchy queries

Description

Events (Pathways and Reactions) in Reactome are organized in a hierarchical structure for every species. By following all hasEvent relationships, this method retrieves the full event hierarchy for any given main species.

Usage

getEventsHierarchy(main.species)
getEventsHierarchy(main.species)

Arguments

main.species

name or taxon/db id or abbreviation of main species in Reactome

Value

a nested dataframe containing full event hierarchy for a given main species

Examples

## Not run: 
getEventsHierarchy("chicken")
getEventsHierarchy("XTR")

## End(Not run)
## Not run: 
getEventsHierarchy("chicken")
getEventsHierarchy("XTR")

## End(Not run)

Orthology related queries

Description

This function retrieves the orthology for any given Event or Entity in the specified species. More information on inferred events see https://www.reactome.org/pages/documentation/electronically-inferred-events/.

Usage

getOrthology(id, species)
getOrthology(id, species)

Arguments

`id`	a stable or db id of an Event or Entity
`species`	name or taxon id or dbId or abbreviation of species

Value

a list containing the orthology for given Event or Entity in the specified species

Examples

getOrthology("R-HSA-5674003", "pig")
getOrthology("R-HSA-5674003", "pig")

Participants related queries

Description

Data in Reactome are organized in a hierarchical manner - Pathways contain Reactions, Reactions contain PhysicalEntities. This function is to get the participants of a given Event.

Usage

getParticipants(
  event.id,
  retrieval = c("AllInstances", "PhysicalEntities", "ReferenceEntities",
    "EventsInPathways")
)
getParticipants(
  event.id,
  retrieval = c("AllInstances", "PhysicalEntities", "ReferenceEntities",
    "EventsInPathways")
)

Arguments

`event.id`	a stable or db id of an Event (pathways and reactions)
`retrieval`	participants to be retrieved, including "AllInstances", "PhysicalEntities", "ReferenceEntities", "EventsInPathways"

Details

Details on options of retrieval arg:

AllInstances: retrieves all participants (PhysicalEntities) from a given Event and their ReferenceEntities
PhysicalEntities: retrieves all the PhysicalEntities that take part in a given Event
ReferenceEntities: retrieves the ReferenceEntities for all PhysicalEntities in every constituent Pathway/Reaction
EventsInPathways: recursively retrieves all the Events contained in any given Event

Value

a dataframe containing requested participants

Examples

getParticipants("R-HSA-6804741", "AllInstances")
getParticipants("R-HSA-69306", "EventsInPathways")
getParticipants("R-HSA-6804741", "AllInstances")
getParticipants("R-HSA-69306", "EventsInPathways")

Pathway related queries

Description

To get the Events that contain the given PhysicalEntity or Event (i.e. subpathway).

Usage

getPathways(id, species = NULL, allForms = FALSE, top.level = FALSE)
getPathways(id, species = NULL, allForms = FALSE, top.level = FALSE)

Arguments

`id`	a stable or db id of a PhysicalEntity or Event present in the pathways
`species`	name or taxon id or dbId or abbreviation of species
`allForms`	if set to `TRUE`, all low level pathways that contain the given PhysicalEntity (not Event) in all forms returned
`top.level`	if set to `TRUE`, only top-level pathways returned

Value

a dataframe containing requested pathways

Examples

getPathways("R-HSA-199420", "Homo sapiens")
getPathways("R-HSA-199420", "Homo sapiens")

Person queries

Description

Retrieves a specific person’s property by his/her name or OrcidId or dbId.

Usage

getPerson(name = NULL, id = NULL, attributes = NULL)
getPerson(name = NULL, id = NULL, attributes = NULL)

Arguments

`name`	Person’s first or/and last name
`id`	Person's Orcid Id or DbId
`attributes`	Property for a person. Return all available attributes if it is not specified.

Value

a list of requested information

Examples

getPerson(name="Robin Haw", attributes=c("displayName", "affiliation"))
getPerson(name="Robin Haw", attributes=c("displayName", "affiliation"))

Schema class queries

Description

Fetch instances by Class. All Classes see Reactome data schema.

Usage

getSchemaClass(
  class,
  species = NULL,
  all = FALSE,
  rows = 1000,
  minimised = FALSE,
  reference = FALSE
)
getSchemaClass(
  class,
  species = NULL,
  all = FALSE,
  rows = 1000,
  minimised = FALSE,
  reference = FALSE
)

Arguments

`class`	schema class name
`species`	name or taxon id or dbId or abbreviation of species. Only Event and PhysicalEntity classes can specify species
`all`	to return ALL entries or not, default is `FALSE`
`rows`	the number of entries retrieved, default is 1000
`minimised`	to retrieve simplified entries (db id, stable id, displayName, type) or not, default is `FALSE`
`reference`	to retrieve simplified reference objects (db id, external identifier, external database name) or not, default is `FALSE`. Only for ReferenceEntity or ExternalOntology class

Value

a sorted dataframe containing entries that belong to the specified schema class

Examples

## Not run: 
getSchemaClass(class="Drug", all=TRUE)

## End(Not run)
getSchemaClass(class="Regulation", rows=20, minimised=TRUE)
getSchemaClass(class="Complex", species="pig", rows=10)
## Not run: 
getSchemaClass(class="Drug", all=TRUE)

## End(Not run)
getSchemaClass(class="Regulation", rows=20, minimised=TRUE)
getSchemaClass(class="Complex", species="pig", rows=10)

Species queries

Description

This method retrieves the list of all or main species in Reactome knowledgebase.

Usage

getSpecies(main = FALSE)
getSpecies(main = FALSE)

Arguments

main

determine whether return main species, which are those have either manually curated or computationally inferred pathways

Value

a dataframe of species information

Examples

# get a list of main species
getSpecies(main=TRUE)
# get a list of main species
getSpecies(main=TRUE)

List filter items

Description

To list the available filtering options for searchQuery(), and their counts.

Usage

listSearchItems(
  items = c("all", "species", "types", "compartments", "keywords"),
  facet = FALSE
)
listSearchItems(
  items = c("all", "species", "types", "compartments", "keywords"),
  facet = FALSE
)

Arguments

`items`	categories of query, including "species", "types", "compartments", "keywords", or "all"
`facet`	return faceting information or not

Value

available search items

Examples

listSearchItems()
listSearchItems()

Non-Reactome id mappings

Description

Mappings between non-Reactome identifiers and Reactome objects.

Usage

map2RefEntities(external.id)

map2Events(external.id, resource, species, mapTo = c("pathways", "reactions"))

event2Ids(event.id)
map2RefEntities(external.id)

map2Events(external.id, resource, species, mapTo = c("pathways", "reactions"))

event2Ids(event.id)

Arguments

`external.id`	an id from external dabatases, e.g. ChEBI, UniProt
`resource`	database name other than Reactome (e.g. UniProt, GeneCards)
`species`	name or taxon id or dbId or abbreviation of species
`mapTo`	retrieve Pathways or Reactions where an identifier can be mapped to
`event.id`	a stable or db id of an Event (Pathways and Reactions)

Details

Descriptions of functions:

map2RefEntities maps a non-Reactome id to ReferenceEntities that store the given external id
map2Events fetches Events related to a given non-Reactome id
event2Ids gets all non-Reactome ids associated with a given Event

Value

a list of ReferenceEntity information

a dataframe of Events associated with the given id

non-Reactome ids associated with a given Event

Examples

## Not run: 
map2RefEntities("15377") #ChEBI id

## End(Not run)
map2Events("Q7Z569", resource="GeneCards", species="human", mapTo="reactions")
event2Ids("R-HSA-69541")
## Not run: 
map2RefEntities("15377") #ChEBI id

## End(Not run)
map2Events("Q7Z569", resource="GeneCards", species="human", mapTo="reactions")
event2Ids("R-HSA-69541")

Common data retrieval

Description

This function retrieves a Reactome Database object that has all its properties and direct relationships (relationships of depth 1) filled, while it also includes any second level relationships regarding regulations and catalysts.

Usage

query(id)
query(id)

Arguments

`id`	a stable or db id of any Reactome entry

Value

a list containing comprehensive information (all attributes) for a given id

Examples

query("R-HSA-60140")
query("R-HSA-60140")

Search query

Description

Search for Reactome objects by name or identifiers.

Usage

searchQuery(
  query,
  species = NULL,
  types = NULL,
  compartments = NULL,
  keywords = NULL,
  cluster = TRUE,
  range = NULL
)
searchQuery(
  query,
  species = NULL,
  types = NULL,
  compartments = NULL,
  keywords = NULL,
  cluster = TRUE,
  range = NULL
)

Arguments

`query`	name or dbId or stId of a search term from any class
`species`	name or taxon id or dbId or abbreviation of species
`types`	type filter, such as "Protein", "Complex", "Reaction", etc
`compartments`	compartment filter, such as "cytosol", "plasma membrane", "nucleoplasm", etc
`keywords`	keyword filter, such as "binds", "phosphorylates", "transports", etc
`cluster`	cluster returned data or not
`range`	start row and the number of rows to include, e.g. `range = c(0, 2)`

Value

a list of information about the search term

Examples

searchQuery(query="Biological oxidation", species="Mus musculus", types=c("Pathway", "Reaction"))
searchQuery(query="Biological oxidation", species="Mus musculus", types=c("Pathway", "Reaction"))

Spell-check suggestions for a given query

Description

Spell-check suggestions for a given query

Usage

spellCheck(query)
spellCheck(query)

Arguments

query

a search term

Value

spell-check suggestions for a given search term

Examples

spellCheck("intelukin")
spellCheck("intelukin")

Package 'ReactomeContentService4R'

Help Index

Search engines discovery schema

Description

Usage

Arguments

Value

Examples

File exporter

Description

Usage

Arguments

Value

See Also

Examples

Image exporter

Description

Usage

Arguments

Value

See Also

Examples

PhysicalEntity queries

Description

Usage

Arguments

Details

Value

See Also

Examples

EventsHierarchy queries

Description

Usage

Arguments

Value

See Also

Examples

Orthology related queries

Description

Usage

Arguments

Value

See Also

Examples

Participants related queries

Description

Usage

Arguments

Details

Value

See Also

Examples

Pathway related queries

Description

Usage

Arguments

Value

See Also

Examples

Person queries

Description

Usage

Arguments

Value

See Also

Examples

Schema class queries

Description

Usage

Arguments

Value

See Also

Examples

Species queries

Description

Usage

Arguments

Value

See Also

Examples