Type:	Package
Title:	Biological Entity Dictionary (BED)
Version:	1.6.2
Description:	An interface for the 'Neo4j' database providing mapping between different identifiers of biological entities. This Biological Entity Dictionary (BED) has been developed to address three main challenges. The first one is related to the completeness of identifier mappings. Indeed, direct mapping information provided by the different systems are not always complete and can be enriched by mappings provided by other resources. More interestingly, direct mappings not identified by any of these resources can be indirectly inferred by using mappings to a third reference. For example, many human Ensembl gene ID are not directly mapped to any Entrez gene ID but such mappings can be inferred using respective mappings to HGNC ID. The second challenge is related to the mapping of deprecated identifiers. Indeed, entity identifiers can change from one resource release to another. The identifier history is provided by some resources, such as Ensembl or the NCBI, but it is generally not used by mapping tools. The third challenge is related to the automation of the mapping process according to the relationships between the biological entities of interest. Indeed, mapping between gene and protein ID scopes should not be done the same way than between two scopes regarding gene ID. Also, converting identifiers from different organisms should be possible using gene orthologs information. The method has been published by Godard and van Eyll (2018) <doi:10.12688/f1000research.13925.3>.
URL:	https://patzaw.github.io/BED/, https://github.com/patzaw/BED
BugReports:	https://github.com/patzaw/BED/issues
License:	GPL-3
Depends:	R (≥ 3.6), neo2R (≥ 2.4.1), visNetwork
Imports:	dplyr, readr, stringr, utils, shiny (≥ 0.13), htmltools, DT, miniUI (≥ 0.1.1), rstudioapi (≥ 0.5)
Suggests:	knitr, rmarkdown, biomaRt, GEOquery, base64enc, webshot2, RCurl
Encoding:	UTF-8
VignetteBuilder:	knitr
RoxygenNote:	7.3.2
NeedsCompilation:	yes
Packaged:	2025-06-03 07:53:52 UTC; pgodard
Author:	Patrice Godard [aut, cre, cph]
Maintainer:	Patrice Godard <patrice.godard@gmail.com>
Repository:	CRAN
Date/Publication:	2025-06-03 09:50:05 UTC

Biological Entity Dictionary (BED)

Description

An interface for the neo4j database providing mapping between different identifiers of biological entities. This Biological Entity Dictionary (BED) has been developed to address three main challenges. The first one is related to the completeness of identifier mappings. Indeed, direct mapping information provided by the different systems are not always complete and can be enriched by mappings provided by other resources. More interestingly, direct mappings not identified by any of these resources can be indirectly inferred by using mappings to a third reference. For example, many human Ensembl gene ID are not directly mapped to any Entrez gene ID but such mappings can be inferred using respective mappings to HGNC ID. The second challenge is related to the mapping of deprecated identifiers. Indeed, entity identifiers can change from one resource release to another. The identifier history is provided by some resources, such as Ensembl or the NCBI, but it is generally not used by mapping tools. The third challenge is related to the automation of the mapping process according to the relationships between the biological entities of interest. Indeed, mapping between gene and protein ID scopes should not be done the same way than between two scopes regarding gene ID. Also, converting identifiers from different organisms should be possible using gene orthologs information.

• Vignette

• Available database instance: https://github.com/patzaw/BED#bed-database-instance-available-as-a-docker-image

• Building a database instance: https://github.com/patzaw/BED#build-a-bed-database-instance

• Repository: https://github.com/patzaw/BED

• Bug reports: https://github.com/patzaw/BED/issues

Author(s)

Patrice Godard

Create a BEIDList

Description

Create a BEIDList

Usage

BEIDList(l, metadata, scope)

Arguments

Value

A BEIDList object which is a list of BEID vectors with 2 additional attributes:

• metadata: a data.frame with metadata about list elements. The ".lname" column correspond to the names of the BEIDList.

• scope: the BEID scope ("be", "source" and "organism")

Examples

## Not run: 
bel <- BEIDList(
   l=list(
      kinases=c("117283", "3706", "3707", "51447", "80271", "9807"),
      phosphatases=c(
         "130367", "249", "283871", "493911", "57026", "5723", "81537"
      )
   ),
   scope=list(be="Gene", source="EntrezGene", organism="Homo sapiens")
)
scope(bel)
metadata(bel)
metadata(bel) <- dplyr::mutate(
   metadata(bel),
   "description"=c("A few kinases", "A few phosphatases")
)
metadata(bel)

## End(Not run)

Get the BEIDs from an object

Description

Get the BEIDs from an object

Usage

BEIDs(x, ...)

Arguments

Value

A tibble with at least 4 columns:

• value

• be

• source

• organism

• ...

Find all BEID and ProbeID corresponding to a BE

Description

Find all BEID and ProbeID corresponding to a BE

Usage

beIDsToAllScopes(
  beids,
  be,
  source,
  organism,
  entities = NULL,
  canonical_symbols = TRUE
)

Arguments

Value

A data.frame with the following fields:

• value: the identifier

• be: the type of BE

• source: the source of the identifier

• organism: the BE organism

• symbol: canonical symbol of the identifier

• BE_entity: the BE entity input

• BEID (optional): the BE ID input

• BE_source (optional): the BE source input

Call a function on the BED graph

Description

Call a function on the BED graph

Usage

bedCall(f, ..., bedCheck = FALSE)

Arguments

Value

The output of the called function.

See Also

checkBedConn

Examples

## Not run: 
result <- bedCall(
   cypher,
   query=prepCql(
      'MATCH (n:BEID)',
      'WHERE n.value IN $values',
      'RETURN n.value AS value, n.labels, n.database'
   ),
   parameters=list(values=c("10", "100"))
)

## End(Not run)

Feeding BED: Imports a data.frame in the BED graph database

Description

Not exported to avoid unintended modifications of the DB.

Usage

bedImport(cql, toImport, periodicCommit = 10000, ...)

Arguments

Value

the results of the query

See Also

bedCall, neo2R::import_from_df

Shiny module for searching BEIDs

Description

Shiny module for searching BEIDs

Usage

beidsServer(
  id,
  toGene = TRUE,
  excludeTechID = FALSE,
  multiple = FALSE,
  beOfInt = NULL,
  selectBe = TRUE,
  orgOfInt = NULL,
  selectOrg = TRUE,
  groupBySymbol = FALSE,
  searchLabel = "Search a gene",
  matchColname = "Match",
  selectFirst = FALSE,
  oneColumn = FALSE,
  withId = FALSE,
  maxHits = 75,
  compact = FALSE,
  tableHeight = 150,
  highlightStyle = "",
  highlightClass = "bed-search"
)

beidsUI(id)

Arguments

Value

A reactive data.frame with the following columns:

• beid: the BE identifier

• preferred: preferred identifier for the same BE in the same scope

• be: the type of biological entity

• source: the source of the identifier

• organism: the BE organism

• entity: internal identifier of the BE

• match: the matching character string

Functions

• beidsUI():

Examples

## Not run: 
library(shiny)
library(BED)
library(DT)

ui <- fluidPage(
   beidsUI("be"),
   fluidRow(
      column(
         12,
         tags$br(),
         h3("Selected gene entities"),
         DTOutput("result")
      )
   )
)

server <- function(input, output){
   found <- beidsServer("be", toGene=TRUE, multiple=TRUE, tableHeight=250)
   output$result <- renderDT({
      req(found())
      toRet <- found()
      datatable(toRet, rownames=FALSE)
   })
}

shinyApp(ui = ui, server = server)

## End(Not run)

Cached neo4j call

Description

This function calls neo4j DB the first time a query is sent and puts the result in the cache SQLite database. The next time the same query is called, it loads the results directly from cache SQLite database.

Usage

cacheBedCall(..., tn, recache = FALSE)

Arguments

Details

Use only with "row" result returned by DB request.

Internal use.

Value

The results of the bedCall.

See Also

cacheBedResult, bedCall

Put a BED query result in cache

Description

Internal use

Usage

cacheBedResult(value, name)

Arguments

See Also

cacheBedCall, loadBedResult

Check biological entities (BE) identifiers

Description

This function takes a vector of identifiers and verify if they can be found in the provided source database according to the BE type and the organism of interest. If an ID is in the DB but not linked directly nor indirectly to any entity then it is considered as not found.

Usage

checkBeIds(ids, be, source, organism, stopThr = 1, caseSensitive = FALSE)

Arguments

Value

invisible(TRUE). Stop if too many (see stopThr parameter) ids are not found. Warning if any id is not found.

See Also

getBeIds, listBeIdSources, getAllBeIdSources

Examples

## Not run: 
checkBeIds(
   ids=c("10", "100"), be="Gene", source="EntrezGene", organism="human"
)
checkBeIds(
   ids=c("10", "100"), be="Gene", source="Ens_gene", organism="human"
)

## End(Not run)

Check BED cache

Description

This function checks information recorded into BED cache and resets it if not relevant.

Usage

checkBedCache(newCon = FALSE)

Arguments

Details

Internal use.

See Also

clearBedCache, lsBedCache

Check if there is a connection to a BED database

Description

Check if there is a connection to a BED database

Usage

checkBedConn(verbose = FALSE)

Arguments

Value

• TRUE if the connection can be established

• Or FALSE if the connection cannot be established or the "System" node does not exist or does not have "BED" as name or any version recorded.

See Also

connectToBed

Identify and remove dubious cross-references

Description

Not exported to avoid unintended modifications of the DB.

Usage

cleanDubiousXRef(d, strict = TRUE)

Arguments

Value

This function returns d without dubious cross-references. Issues are reported in attr(d, "issues").

Clear the BED cache SQLite database

Description

Clear the BED cache SQLite database

Usage

clearBedCache(queries = NULL, force = FALSE, hard = FALSE, verbose = FALSE)

Arguments

See Also

lsBedCache

Compare 2 BED database instances

Description

Compare 2 BED database instances

Usage

compareBedInstances(connections)

Arguments

Details

The current connection is restored when exiting this function.

Value

If only one connection is provided, the function returns a list with information about BEID and platforms available for the connection along with DB version information. If two connections are provided the same information as above is provided for the 2 connection named V1 and V2 in that order. In addition, differences observed between the 2 instances are reported for BEID and platforms.

Connect to a neo4j BED database

Description

Connect to a neo4j BED database

Usage

connectToBed(
  url = NULL,
  username = NULL,
  password = NULL,
  connection = 1,
  remember = FALSE,
  useCache = NA,
  importPath = NULL,
  .opts = list()
)

Arguments

Details

Be careful that you should reconnect to BED database each time the environment is reloaded. It is done automatically if remember is set to TRUE.

Information about how to get an instance of the BED 'Neo4j' database is provided here:

• https://github.com/patzaw/BED#bed-database-instance-available-as-a-docker-image

• https://github.com/patzaw/BED#build-a-bed-database-instance

Value

This function does not return any value. It prepares the BED environment to allow transparent DB calls.

See Also

checkBedConn, lsBedConnections, forgetBedConnection

Converts lists of BE IDs

Description

Converts lists of BE IDs

Usage

convBeIdLists(idList, entity = FALSE, ...)

Arguments

Value

A list of convBeIds ouput ids. Scope ("be", "source" "organism" and "entity" (see Arguments)) is provided as a named list in the "scope" attributes: attr(x, "scope")

See Also

convBeIds, convDfBeIds

Examples

## Not run: 
convBeIdLists(
   idList=list(a=c("10", "100"), b=c("1000")),
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to.source="Ens_gene"
)

## End(Not run)

Converts BE IDs

Description

Converts BE IDs

Usage

convBeIds(
  ids,
  from,
  from.source,
  from.org,
  to,
  to.source,
  to.org,
  caseSensitive = FALSE,
  canonical = FALSE,
  prefFilter = FALSE,
  restricted = TRUE,
  recache = FALSE,
  limForCache = 2000
)

Arguments

Value

a data.frame with the following columns:

• from: the input IDs

• to: the corresponding IDs in to.source

• to.preferred: boolean indicating if the to ID is a preferred ID for the corresponding entity.

• to.entity: the entity technical ID of the to IDs

This data.frame can be filtered in order to remove duplicated from/to.entity associations which can lead information bias. Scope ("be", "source" and "organism") is provided as a named list in the "scope" attributes: attr(x, "scope")

See Also

getBeIdConvTable, convBeIdLists, convDfBeIds

Examples

## Not run: 
oriId <- c("10", "100")
convBeIds(
   ids=oriId,
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to.source="Ens_gene"
)
convBeIds(
   ids=oriId,
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to="Peptide",
   to.source="Ens_translation"
)
convBeIds(
   ids=oriId,
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to="Peptide",
   to.source="Ens_translation",
   to.org="mouse"
)

## End(Not run)

Add BE ID conversion to a data frame

Description

Add BE ID conversion to a data frame

Usage

convDfBeIds(df, idCol = NULL, entity = FALSE, ...)

Arguments

Value

A data.frame with converted IDs. Scope ("be", "source", "organism" and "entity" (see Arguments)) is provided as a named list in the "scope" attributes: attr(x, "scope").

See Also

convBeIds, convBeIdLists

Examples

## Not run: 
toConv <- data.frame(a=1:2, b=3:4)
rownames(toConv) <- c("10", "100")
convDfBeIds(
   df=toConv,
   from="Gene",
   from.source="EntrezGene",
   from.org="human",
   to.source="Ens_gene"
)

## End(Not run)

Feeding BED: Dump table from the Ensembl core database

Description

Not exported to avoid unintended modifications of the DB.

Usage

dumpEnsCore(
  organism,
  release,
  gv,
  ddir,
  toDump = c("attrib_type", "gene_attrib", "transcript", "external_db", "gene",
    "translation", "external_synonym", "object_xref", "xref", "stable_id_event"),
  env = parent.frame(n = 1)
)

Arguments

Feeding BED: Dump tables from the NCBI gene DATA

Description

Not exported to avoid unintended modifications of the DB.

Usage

dumpNcbiDb(
  taxOfInt,
  reDumpThr,
  ddir,
  toLoad = c("gene_info", "gene2ensembl", "gene_group", "gene_orthologs", "gene_history",
    "gene2refseq"),
  env = parent.frame(n = 1),
  curDate
)

Arguments

Feeding BED: Dump tables with taxonomic information from NCBI

Description

Not exported to avoid unintended modifications of the DB.

Usage

dumpNcbiTax(
  reDumpThr,
  ddir,
  toDump = c("names.dmp"),
  env = parent.frame(n = 1),
  curDate
)

Arguments

Feeding BED: Dump and preprocess flat data files from Uniprot

Description

Not exported to avoid unintended modifications of the DB.

Usage

dumpUniprotDb(
  taxOfInt,
  divOfInt,
  release,
  ddir,
  ftp = "ftp://ftp.expasy.org/databases/uniprot",
  env = parent.frame(n = 1)
)

Arguments

Explore BE identifiers

Description

This function uses visNetwork to draw all the identifiers corresponding to one BE (including ProbeID and BESymbol)

Usage

exploreBe(
  id,
  source,
  be,
  showBE = FALSE,
  showProbes = FALSE,
  showLegend = TRUE
)

Arguments

Examples

## Not run: 
exploreBe("Gene", "100", "EntrezGene")

## End(Not run)

Explore the shortest convertion path between two identifiers

Description

This function uses visNetwork to draw all the shortest convertion paths between two identifiers (including ProbeID).

Usage

exploreConvPath(
  from.id,
  to.id,
  from,
  from.source,
  to,
  to.source,
  edgeDirection = FALSE,
  showLegend = TRUE,
  verbose = FALSE
)

Arguments

Examples

## Not run: 
exploreConvPath(
   from.id="ENST00000413465",
   from="Transcript", from.source="Ens_transcript",
   to.id="ENSMUST00000108658",
   to="Transcript", to.source="Ens_transcript"
)

## End(Not run)

Filter an object to keep only a set of BEIDs

Description

Filter an object to keep only a set of BEIDs

Usage

filterByBEID(x, toKeep, ...)

Arguments

Find Biological Entity

Description

Find Biological Entity in BED based on their IDs, symbols and names

Usage

findBe(
  be = NULL,
  organism = NULL,
  ncharSymb = 4,
  ncharName = 8,
  restricted = TRUE,
  by = 20,
  exclude = c("BEDTech_gene", "BEDTech_transcript")
)

Arguments

Value

A data frame with the following fields:

• found: the element found in BED corresponding to the searched term

• be: the type of the element

• source: the source of the element

• organism: the related organism

• entity: the related entity internal ID

• ebe: the BE of the related entity

• canonical: if the symbol is canonical

• Relevant ID: the seeked element id

• Symbol: the symbol(s) of the corresponding gene(s)

• Name: the symbol(s) of the corresponding gene(s)

Scope ("be", "source" and "organism") is provided as a named list in the "scope" attributes: 'attr(x, "scope")“

Find Biological Entity identifiers

Description

Find Biological Entity identifiers

Usage

findBeids(toGene = TRUE, ...)

Arguments

Value

NULL if not any result, or a data.frame with the selected values and the following column:

• value: the BE identifier

• preferred: preferred identifier for the same BE in the same scope

• be: the type of biological entity

• source: the source of the identifier

• organism: the organism of the BE

• canonical (if toGene==TRUE): canonical gene product? (if known)

• symbol: the symbol of the identifier (if any)

First common upstream BE

Description

Returns the first common Biological Entity (BE) upstream a set of BE.

Usage

firstCommonUpstreamBe(beList = listBe(), uniqueOrg = TRUE)

Arguments

Details

This function is used to identified the level at which different BE should be compared. Peptides and transcripts should be compared at the level of transcripts whereas transcripts and objects should be compared at the level of genes. BE from different organism should be compared at the level of genes using homologs.

See Also

listBe

Examples

## Not run: 
firstCommonUpstreamBe(c("Object", "Transcript"))
firstCommonUpstreamBe(c("Peptide", "Transcript"))
firstCommonUpstreamBe(c("Peptide", "Transcript"), uniqueOrg=FALSE)

## End(Not run)

Focus a BE related object on a specific identifier (BEID) scope

Description

Focus a BE related object on a specific identifier (BEID) scope

Usage

focusOnScope(
  x,
  be,
  source,
  organism,
  scope,
  force,
  restricted,
  prefFilter,
  ...
)

Arguments

Value

Depends on the class of x

Convert a BEIDList object in a specific identifier (BEID) scope

Description

Convert a BEIDList object in a specific identifier (BEID) scope

Usage

## S3 method for class 'BEIDList'
focusOnScope(
  x,
  be = NULL,
  source = NULL,
  organism = NULL,
  scope = NULL,
  force = FALSE,
  restricted = TRUE,
  prefFilter = TRUE,
  ...
)

Arguments

Value

A BEIDList

Forget a BED connection

Description

Forget a BED connection

Usage

forgetBedConnection(connection, save = FALSE)

Arguments

See Also

lsBedConnections, checkBedConn, connectToBed

Construct CQL sub-query to map 2 biological entity

Description

Internal use

Usage

genBePath(from, to, onlyR = FALSE)

Arguments

Value

A character value corresponding to the sub-query. Or, if onlyR, a character vector with the names of the relationships.

See Also

genProbePath, listBe

Identify the biological entity (BE) targeted by probes and construct the CQL sub-query to map probes to the BE

Description

Internal use

Usage

genProbePath(platform)

Arguments

Value

A character value corresponding to the sub-query. The attr(,"be") correspond to the BE targeted by probes

See Also

genBePath, listPlatforms

Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresponding to a Gene in any organism

Description

Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresponding to a Gene in any organism

Usage

geneIDsToAllScopes(
  geneids,
  source,
  organism,
  entities = NULL,
  orthologs = TRUE,
  canonical_symbols = TRUE
)

Arguments

Value

A data.frame with the following fields:

• value: the identifier

• preferred: preferred identifier for the same BE in the same scope

• be: the type of BE

• organism: the BE organism

• source: the source of the identifier

• canonical: canonical gene product (logical)

• symbol: canonical symbol of the identifier

• Gene_entity: the gene entity input

• GeneID (optional): the gene ID input

• Gene_source (optional): the gene source input

• Gene_organism (optional): the gene organism input

List all the source databases of BE identifiers whatever the BE type

Description

List all the source databases of BE identifiers whatever the BE type

Usage

getAllBeIdSources(recache = FALSE)

Arguments

Value

A data.frame indicating the BE related to the ID source (database).

See Also

listBeIdSources, listPlatforms

Get a conversion table between biological entity (BE) identifiers

Description

Get a conversion table between biological entity (BE) identifiers

Usage

getBeIdConvTable(
  from,
  to = from,
  from.source,
  to.source,
  organism,
  caseSensitive = FALSE,
  canonical = FALSE,
  restricted = TRUE,
  entity = TRUE,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL,
  limForCache = 100
)

Arguments

Value

a data.frame mapping BE IDs with the following fields:

• from: the from BE ID

• to: the to BE ID

• entity: (optional) the technical ID of to BE

• preferred: true if "to" is the preferred identifier for the entity

See Also

getHomTable, listBe, listPlatforms, listBeIdSources

Examples

## Not run: 
getBeIdConvTable(
    from="Gene", from.source="EntrezGene",
    to.source="Ens_gene",
    organism="human"
)

## End(Not run)

Get description of Biological Entity identifiers

Description

This description can be used for annotating tables or graph based on BE IDs.

Usage

getBeIdDescription(ids, be, source, organism, ...)

Arguments

Value

a data.frame providing for each BE IDs (row.names are provided BE IDs):

• id: the BE ID

• symbol: the BE symbol

• name: the corresponding name

See Also

getBeIdNames, getBeIdSymbols

Examples

## Not run: 
getBeIdDescription(
   ids=c("10", "100"),
   be="Gene",
   source="EntrezGene",
   organism="human"
)

## End(Not run)

Get a table of biological entity (BE) identifiers and names

Description

Get a table of biological entity (BE) identifiers and names

Usage

getBeIdNameTable(
  be,
  source,
  organism,
  restricted,
  entity = TRUE,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL
)

Arguments

Value

a data.frame with the following fields:

• id: the from BE ID

• name: the BE name

• direct: false if the symbol is not directly associated to the BE ID

• preferred: true if the id is the preferred identifier for the BE

• entity: (optional) the technical ID of to BE

See Also

getBeIdNames, getBeIdSymbolTable

Examples

## Not run: 
getBeIdNameTable(
   be="Gene",
   source="EntrezGene",
   organism="human"
)

## End(Not run)

Get names of Biological Entity identifiers

Description

Get names of Biological Entity identifiers

Usage

getBeIdNames(ids, be, source, organism, limForCache = 4000, ...)

Arguments

Value

a data.frame mapping BE IDs and names with the following fields:

• id: the BE ID

• name: the corresponding name

• canonical: true if the name is canonical for the direct BE ID (often FALSE for backward compatibility)

• direct: true if the name is directly related to the BE ID

• preferred: true if the id is the preferred identifier for the BE

• entity: (optional) the technical ID of to BE

See Also

getBeIdNameTable, getBeIdSymbols

Examples

## Not run: 
getBeIdNames(
   ids=c("10", "100"),
   be="Gene",
   source="EntrezGene",
   organism="human"
)

## End(Not run)

Get a table of biological entity (BE) identifiers and symbols

Description

Get a table of biological entity (BE) identifiers and symbols

Usage

getBeIdSymbolTable(
  be,
  source,
  organism,
  restricted,
  entity = TRUE,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL
)

Arguments

Value

a data.frame with the following fields:

• id: the from BE ID

• symbol: the BE symbol

• canonical: true if the symbol is canonical for the direct BE ID

• direct: false if the symbol is not directly associated to the BE ID

• preferred: true if the id is the preferred identifier for the BE

• entity: (optional) the technical ID of to BE

See Also

getBeIdSymbols, getBeIdNameTable

Examples

## Not run: 
getBeIdSymbolTable(
   be="Gene",
   source="EntrezGene",
   organism="human"
)

## End(Not run)

Get symbols of Biological Entity identifiers

Description

Get symbols of Biological Entity identifiers

Usage

getBeIdSymbols(ids, be, source, organism, limForCache = 4000, ...)

Arguments

Value

a data.frame with the following fields:

• id: the from BE ID

• symbol: the BE symbol

• canonical: true if the symbol is canonical for the direct BE ID

• direct: false if the symbol is not directly associated to the BE ID

• preferred: true if the id is the preferred identifier for the BE

• entity: (optional) the technical ID of to BE

See Also

getBeIdSymbolTable, getBeIdNames

Examples

## Not run: 
getBeIdSymbols(
   ids=c("10", "100"),
   be="Gene",
   source="EntrezGene",
   organism="human"
)

## End(Not run)

Get reference URLs for BE IDs

Description

Get reference URLs for BE IDs

Usage

getBeIdURL(ids, databases)

Arguments

Value

A character vector of the same length than ids corresponding to the relevant URLs. NA is returned is there is no URL corresponding to the provided database.

Examples

## Not run: 
getBeIdURL(c("100", "ENSG00000145335"), c("EntrezGene", "Ens_gene"))

## End(Not run)

Get biological entities identifiers

Description

Get biological entities identifiers

Usage

getBeIds(
  be = c(listBe(), "Probe"),
  source,
  organism = NA,
  restricted,
  entity = TRUE,
  attributes = NULL,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL,
  caseSensitive = FALSE,
  limForCache = 100,
  bef = NULL
)

Arguments

Value

a data.frame mapping BE IDs with the following fields:

• id: the BE ID

• preferred: true if the id is the preferred identifier for the BE

• BE: IF entity is TRUE the technical ID of BE

• db.version: IF be is not "Probe" and source not "Symbol" the version of the DB

• db.deprecated: IF be is not "Probe" and source not "Symbol" a value if the BE ID is deprecated or FALSE if it's not

• canonical: IF source is "Symbol" TRUE if the symbol is canonical

• organism: IF be is "Probe" the organism of the targeted BE

If attributes are part of the query, additional columns for each of them. Scope ("be", "source" and "organism") is provided as a named list in the "scope" attributes: attr(x, "scope")

See Also

listPlatforms, listBeIdSources

Examples

## Not run: 
beids <- getBeIds(be="Gene", source="EntrezGene", organism="human", restricted=TRUE)

## End(Not run)

Get the direct origin of BE identifiers

Description

The origin is directly taken as provided by the original database. This function does not return indirect relationships.

Usage

getDirectOrigin(
  ids,
  sources = NULL,
  process = c("is_expressed_as", "is_translated_in", "codes_for")
)

Arguments

Value

a data.frame with the following columns:

• origin: the origin BE identifiers

• osource: the origin database

• product: the product BE identifiers

• psource: the production database

• canonical: whether the production process is canonical or not

The process is also returned as an attribute of the data.frame.

See Also

getDirectOrigin, convBeIds

Examples

## Not run: 
oriId <- c("XP_016868427", "NP_001308979")
res <- getDirectOrigin(
   ids=oriId,
   source="RefSeq_peptide",
   process="is_translated_in"
)
attr(res, "process")

## End(Not run)

Get the direct product of BE identifiers

Description

The product is directly taken as provided by the original database. This function does not return indirect relationships.

Usage

getDirectProduct(
  ids,
  sources = NULL,
  process = c("is_expressed_as", "is_translated_in", "codes_for"),
  canonical = NA
)

Arguments

Value

a data.frame with the following columns:

• origin: the origin BE identifiers

• osource: the origin database

• product: the product BE identifiers

• psource: the production database

• canonical: whether the production process is canonical or not

The process is also returned as an attribute of the data.frame.

See Also

getDirectOrigin, convBeIds

Examples

## Not run: 
oriId <- c("10", "100")
res <- getDirectProduct(
   ids=oriId,
   source="EntrezGene",
   process="is_expressed_as",
   canonical=NA
)
attr(res, "process")

## End(Not run)

Feeding BED: Download Ensembl DB and load gene information in BED

Description

Not exported to avoid unintended modifications of the DB.

Usage

getEnsemblGeneIds(organism, release, gv, ddir, dbCref, dbAss, canChromosomes)

Arguments

Feeding BED: Download Ensembl DB and load peptide information in BED

Description

Not exported to avoid unintended modifications of the DB.

Usage

getEnsemblPeptideIds(organism, release, gv, ddir, dbCref, canChromosomes)

Arguments

Feeding BED: Download Ensembl DB and load transcript information in BED

Description

Not exported to avoid unintended modifications of the DB.

Usage

getEnsemblTranscriptIds(organism, release, gv, ddir, dbCref, canChromosomes)

Arguments

Get description of genes corresponding to Biological Entity identifiers

Description

This description can be used for annotating tables or graph based on BE IDs.

Usage

getGeneDescription(
  ids,
  be,
  source,
  organism,
  gsource = largestBeSource(be = "Gene", organism = organism, rel = "is_known_as",
    restricted = TRUE),
  limForCache = 2000
)

Arguments

Value

a data.frame providing for each BE IDs (row.names are provided BE IDs):

• id: the BE ID

• gsource: the Gene ID the column name provides the source of the used identifier

• symbol: the associated gene symbols

• name: the associated gene names

See Also

getBeIdDescription, getBeIdNames, getBeIdSymbols

Examples

## Not run: 
getGeneDescription(
   ids=c("1438_at", "1552335_at"),
   be="Probe",
   source="GPL570",
   organism="human"
)

## End(Not run)

Get gene homologs between 2 organisms

Description

Get gene homologs between 2 organisms

Usage

getHomTable(
  from.org,
  to.org,
  from.source = "Ens_gene",
  to.source = from.source,
  restricted = TRUE,
  verbose = FALSE,
  recache = FALSE,
  filter = NULL,
  limForCache = 100
)

Arguments

Value

a data.frame mapping gene IDs with the following fields:

• from: the from gene ID

• to: the to gene ID

See Also

getBeIdConvTable

Examples

## Not run: 
getHomTable(
   from.org="human",
   to.org="mouse"
)

## End(Not run)

Feeding BED: Download NCBI gene DATA and load gene, transcript and peptide information in BED

Description

Not exported to avoid unintended modifications of the DB.

Usage

getNcbiGeneTransPep(organism, reDumpThr = 1e+05, ddir, curDate)

Arguments

Get organism names from taxonomy IDs

Description

Get organism names from taxonomy IDs

Usage

getOrgNames(taxID = NULL)

Arguments

Value

A data.frame mapping taxonomy IDs to organism names with the following fields:

• taxID: the taxonomy ID

• name: the organism name

• nameClass: the class of the name

See Also

getTaxId, listOrganisms

Examples

## Not run: 
getOrgNames(c("9606", "10090"))
getOrgNames("9606")

## End(Not run)

Get relevant IDs for a formerly identified BE in a context of interest

Description

DEPRECATED: use searchBeid and geneIDsToAllScopes instead. This function is meant to be used with searchId in order to implement a dictonary of identifiers of interest. First the searchId function is used to search a term. Then the getRelevantIds function is used to find the corresponding IDs in a context of interest.

Usage

getRelevantIds(
  d,
  selected = 1,
  be = c(listBe(), "Probe"),
  source,
  organism,
  restricted = TRUE,
  simplify = TRUE,
  verbose = FALSE
)

Arguments

Value

The d data.frame with a new column providing the relevant ID in the context of interest and without the gene field. Scope ("be", "source" and "organism") is provided as a named list in the "scope" attributes: attr(x, "scope")

See Also

searchId

Identify the biological entity (BE) targeted by probes

Description

Identify the biological entity (BE) targeted by probes

Usage

getTargetedBe(platform)

Arguments

Value

The BE targeted by the platform

See Also

listPlatforms

Examples

## Not run: 
getTargetedBe("GPL570")

## End(Not run)

Get taxonomy ID of an organism name

Description

Get taxonomy ID of an organism name

Usage

getTaxId(name)

Arguments

Value

A vector of taxonomy ID

See Also

getOrgNames, listOrganisms

Examples

## Not run: 
getTaxId("human")

## End(Not run)

Feeding BED: Download Uniprot information in BED

Description

Not exported to avoid unintended modifications of the DB.

Usage

getUniprot(organism, taxDiv, release, ddir)

Arguments

Guess biological entity (BE), database source and organism of a vector of identifiers.

Description

Guess biological entity (BE), database source and organism of a vector of identifiers.

Usage

guessIdScope(ids, be, source, organism, tcLim = 100)

guessIdOrigin(...)

Arguments

Value

A list (NULL if no match):

• be: a character vector of length 1 providing the best BE guess (NA if inconsistent with user input: be, source or organism)

• source: a character vector of length 1 providing the best source guess (NA if inconsistent with user input: be, source or organism)

• *organism$: a character vector of length 1 providing the best organism guess (NA if inconsistent with user input: be, source or organism)

The "details" attribute ('attr(x, "details")“) is a data frame providing numbers supporting the guess

Functions

• guessIdOrigin(): Deprecated version of guessIdScope

Examples

## Not run: 
guessIdScope(ids=c("10", "100"))

## End(Not run)

Check if two objects have the same BEID scope

Description

Check if two objects have the same BEID scope

Usage

identicalScopes(x, y)

Arguments

Value

A logical indicating if the 2 scopes are identical

Check if the provided object is a BEIDList

Description

Check if the provided object is a BEIDList

Usage

is.BEIDList(x)

Arguments

Value

A logical value

Autoselect source of biological entity identifiers

Description

The selection is based on direct identifiers

Usage

largestBeSource(
  be,
  organism,
  rel = NA,
  restricted = TRUE,
  exclude = c("BEDTech_gene", "BEDTech_transcript")
)

Arguments

Value

The name of the selected source. The selected source will be the one providing the largest number of current identifiers.

See Also

listBeIdSources

Examples

## Not run: 
largestBeSource(be="Gene", "Mus musculus")

## End(Not run)

Lists all the biological entities (BE) available in the BED database

Description

Lists all the biological entities (BE) available in the BED database

Usage

listBe()

Value

A character vector of biological entities (BE)

See Also

listPlatforms, listBeIdSources, listOrganisms

Lists all the databases taken into account in the BED database for a biological entity (BE)

Description

Lists all the databases taken into account in the BED database for a biological entity (BE)

Usage

listBeIdSources(
  be = listBe(),
  organism,
  direct = FALSE,
  rel = NA,
  restricted = FALSE,
  recache = FALSE,
  verbose = FALSE,
  exclude = c()
)

Arguments

Value

A data.frame indicating the number of ID in each available database with the following fields:

• database: the database name

• nbBe: number of distinct entities

• nbId: number of identifiers

• be: the BE under focus

See Also

listBe, largestBeSource

Examples

## Not run: 
listBeIdSources(be="Transcript", organism="mouse")

## End(Not run)

List all attributes provided by a BEDB

Description

List all attributes provided by a BEDB

Usage

listDBAttributes(dbname)

Arguments

Value

A character vector of attribute names

Lists all the organisms available in the BED database

Description

Lists all the organisms available in the BED database

Usage

listOrganisms()

Value

A character vector of organism scientific names

See Also

listPlatforms, listBeIdSources, listBe, getTaxId, getOrgNames

Lists all the probe platforms available in the BED database

Description

Lists all the probe platforms available in the BED database

Usage

listPlatforms(be = c(NA, listBe()))

Arguments

Value

A data.frame mapping platforms to BE with the following fields:

• name: the platform nam

• description: platform description

• focus: Targeted BE

See Also

listBe, listBeIdSources, listOrganisms, getTargetedBe

Examples

## Not run: 
listPlatforms(be="Gene")
listPlatforms()

## End(Not run)

Feeding BED: Load biological entities in BED

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadBE(
  d,
  be = "Gene",
  dbname,
  version = NA,
  deprecated = NA,
  taxId = NA,
  onlyId = FALSE
)

Arguments

Feeding BED: Load names associated to BEIDs

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadBENames(d, be = "Gene", dbname)

Arguments

Feeding BED: Load symbols associated to BEIDs

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadBESymbols(d, be = "Gene", dbname)

Arguments

Feeding BED: Load biological entities in BED with information about DB version

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadBEVersion(d, be = "Gene", dbname, taxId = NA, onlyId = FALSE)

Arguments

Feeding BED: Load attributes for biological entities in BED

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadBeAttribute(d, be = "Gene", dbname, attribute)

Arguments

Feeding BED: Load BED data model in neo4j

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadBedModel()

Feeding BED: Load additional indexes in neo4j

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadBedOtherIndexes()

Get a BED query result from cache

Description

Internal use

Usage

loadBedResult(name)

Arguments

See Also

cacheBedCall, cacheBedResult

Feeding BED: Load correspondance between genes and objects as coding events

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadCodesFor(d, gdb, odb)

Arguments

Feeding BED: Load correspondances between BE IDs

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadCorrespondsTo(d, db1, db2, be = "Gene")

Arguments

Feeding BED: Load history of BEIDs

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadHistory(d, dbname, be = "Gene")

Arguments

Feeding BED: Load BE ID associations

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadIsAssociatedTo(d, db1, db2, be = "Gene")

Arguments

Details

When associating one id1 to id2, the BE identified by id1 is deleted after that its production edges have been transferred to the BE identified by id2. After this operation all id "corresponding_to" id1 do not directly identify any BE as they are supposed to do. Thus, to run this function with id1 involved in "corresponds_to" edges.

Feeding BED: Load correspondance between genes and transcripts as expression events

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadIsExpressedAs(d, gdb, tdb)

Arguments

Feeding BED: Load homology between BE IDs

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadIsHomologOf(d, db1, db2, be = "Gene")

Arguments

Feeding BED: Load correspondance between transcripts and peptides as translation events

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadIsTranslatedIn(d, tdb, pdb)

Arguments

Feeding BED: Create Lucene indexes in neo4j

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadLuceneIndexes()

Feeding BED: Load in BED GO functions associated to Entrez gene IDs from NCBI

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadNCBIEntrezGOFunctions(organism, reDumpThr = 1e+05, ddir, curDate)

Arguments

Feeding BED: Load taxonomic information from NCBI

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadNcbiTax(reDumpThr, ddir, orgOfInt = c("human", "rat", "mouse"), curDate)

Arguments

Feeding BED: Load organisms in BED

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadOrganisms(d)

Arguments

Feeding BED: Load a probes platform

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadPlf(name, description, be)

Arguments

Feeding BED: Load probes targeting BE IDs

Description

Not exported to avoid unintended modifications of the DB.

Usage

loadProbes(d, be = "Transcript", platform, dbname)

Arguments

List all the BED queries in cache and the total size of the cache

Description

List all the BED queries in cache and the total size of the cache

Usage

lsBedCache(verbose = TRUE)

Arguments

Value

A data.frame giving for each query (row names) its size in Bytes (column "size") and in human readable format (column "hr"). The attribute "Total" corresponds to the sum of all the file size.

See Also

clearBedCache

List all registered BED connection

Description

List all registered BED connection

Usage

lsBedConnections()

See Also

connectToBed, forgetBedConnection, checkBedConn

Get object metadata

Description

Get object metadata

Usage

metadata(x, ...)

Arguments

Set object metadata

Description

Set object metadata

Usage

metadata(x) <- value

Arguments

Feeding BED: Register a database of biological entities in BED DB

Description

Not exported to avoid unintended modifications of the DB.

Usage

registerBEDB(name, description = NA, currentVersion = NA, idURL = NA)

Arguments

Get the BEID scope of an object

Description

Get the BEID scope of an object

Usage

scope(x, ...)

Arguments

Get the BEID scopes of an object

Description

Get the BEID scopes of an object

Usage

scopes(x, ...)

Arguments

Value

A tibble with 4 columns:

• be

• source

• organism

• Freq

Search a BEID

Description

Search a BEID

Usage

searchBeid(x, maxHits = 75, clean_id_search = TRUE, clean_name_search = TRUE)

Arguments

Value

NULL if there is not any match or a data.frame with the following columns:

• value: the matching term

• from: the type of the matched term (e.g. BESymbol, GeneID...)

• be: the matching biological entity (BE)

• beid: the BE identifier

• source: the BEID reference database

• preferred: TRUE if the BEID is considered as a preferred identifier

• symbol: BEID canonical symbol

• name: BEID name

• entity: technical BE identifier

• GeneID: Corresponding gene identifier

• Gene_source: Gene ID database

• preferred_gene: TRUE if the GeneID is considered as a preferred identifier

• Gene_symbol: Gene symbol

• Gene_name: Gene name

• Gene_entity: technical gene identifier

• organism: gene organism (scientific name)

• score: score of the fuzzy search

• included: is the search term fully included in the value

• exact: is the value an exact match of the term

Search identifier, symbol or name information

Description

DEPRECATED: use searchBeid and geneIDsToAllScopes instead. This function is meant to be used with getRelevantIds in order to implement a dictonary of identifiers of interest. First the searchId function is used to search a term. Then the getRelevantIds function is used to find the corresponding ID in a context of interest.

Usage

searchId(
  searched,
  be = NULL,
  organism = NULL,
  ncharSymb = 4,
  ncharName = 8,
  verbose = FALSE
)

Arguments

Value

A data frame with the following fields:

• found: the element found in BED corresponding to the searched term

• be: the type of the element

• source: the source of the element

• organism: the related organism

• entity: the related entity internal ID

• ebe: the BE of the related entity

• canonical: if the symbol is canonical

• gene: list of the related genes BE internal ID

Exact matches are returned first folowed by the shortest elements.

See Also

getRelevantIds

Feeding BED: Set the BED version

Description

Not exported to avoid unintended modifications of the DB. This function is used when modifying the BED content.

Usage

setBedVersion(bedInstance, bedVersion)

Arguments

Show the data model of BED

Description

Show the shema of the BED data model.

Usage

showBedDataModel()