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BED (version 1.6.2)

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. The method has been published by Godard and van Eyll (2018) .

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Version

Install

install.packages('BED')

Monthly Downloads

683

Version

1.6.2

License

GPL-3

Issues

Pull Requests

Stars

Forks

Maintainer

Patrice Godard

Last Published

June 3rd, 2025

Functions in BED (1.6.2)

dumpEnsCore

Feeding BED: Dump table from the Ensembl core database
checkBedConn

Check if there is a connection to a BED database
checkBedCache

Check BED cache
cleanDubiousXRef

Identify and remove dubious cross-references
convDfBeIds

Add BE ID conversion to a data frame
convBeIds

Converts BE IDs
convBeIdLists

Converts lists of BE IDs
connectToBed

Connect to a neo4j BED database
compareBedInstances

Compare 2 BED database instances
clearBedCache

Clear the BED cache SQLite database
exploreBe

Explore BE identifiers
filterByBEID

Filter an object to keep only a set of BEIDs
dumpUniprotDb

Feeding BED: Dump and preprocess flat data files from Uniprot
exploreConvPath

Explore the shortest convertion path between two identifiers
focusOnScope.BEIDList

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

First common upstream BE
dumpNcbiDb

Feeding BED: Dump tables from the NCBI gene DATA
forgetBedConnection

Forget a BED connection
focusOnScope

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

Construct CQL sub-query to map 2 biological entity
genProbePath

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

Find Biological Entity identifiers
getBeIdDescription

Get description of Biological Entity identifiers
findBe

Find Biological Entity
getBeIdConvTable

Get a conversion table between biological entity (BE) identifiers
getDirectOrigin

Get the direct origin of BE identifiers
getDirectProduct

Get the direct product of BE identifiers
dumpNcbiTax

Feeding BED: Dump tables with taxonomic information from NCBI
geneIDsToAllScopes

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

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

Check if two objects have the same BEID scope
is.BEIDList

Check if the provided object is a BEIDList
getEnsemblTranscriptIds

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

Get description of genes corresponding to Biological Entity identifiers
getHomTable

Get gene homologs between 2 organisms
getNcbiGeneTransPep

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

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

Get biological entities identifiers
getTaxId

Get taxonomy ID of an organism name
loadBE

Feeding BED: Load biological entities in BED
getTargetedBe

Identify the biological entity (BE) targeted by probes
loadBENames

Feeding BED: Load names associated to BEIDs
getBeIdNames

Get names of Biological Entity identifiers
getBeIdURL

Get reference URLs for BE IDs
getBeIdNameTable

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

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

Feeding BED: Load symbols associated to BEIDs
getBeIdSymbolTable

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

Feeding BED: Load history of BEIDs
loadIsHomologOf

Feeding BED: Load homology between BE IDs
loadIsTranslatedIn

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

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

Feeding BED: Load BE ID associations
loadBeAttribute

Feeding BED: Load attributes for biological entities in BED
lsBedConnections

List all registered BED connection
loadBedOtherIndexes

Feeding BED: Load additional indexes in neo4j
listBe

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

Autoselect source of biological entity identifiers
loadLuceneIndexes

Feeding BED: Create Lucene indexes in neo4j
getBeIdSymbols

Get symbols of Biological Entity identifiers
getUniprot

Feeding BED: Download Uniprot information in BED
loadOrganisms

Feeding BED: Load organisms in BED
listDBAttributes

List all attributes provided by a BEDB
listBeIdSources

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

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

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

Lists all the probe platforms available in the BED database
getEnsemblPeptideIds

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

Lists all the organisms available in the BED database
metadata<-

Set object metadata
getOrgNames

Get organism names from taxonomy IDs
lsBedCache

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

Get a BED query result from cache
loadProbes

Feeding BED: Load probes targeting BE IDs
loadPlf

Feeding BED: Load a probes platform
scope

Get the BEID scope of an object
scopes

Get the BEID scopes of an object
loadCodesFor

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

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

Feeding BED: Load taxonomic information from NCBI
loadCorrespondsTo

Feeding BED: Load correspondances between BE IDs
loadBedModel

Feeding BED: Load BED data model in neo4j
metadata

Get object metadata
registerBEDB

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

Search a BEID
searchId

Search identifier, symbol or name information
setBedVersion

Feeding BED: Set the BED version
showBedDataModel

Show the data model of BED
beidsServer

Shiny module for searching BEIDs
bedCall

Call a function on the BED graph
cacheBedCall

Cached neo4j call
BEIDs

Get the BEIDs from an object
checkBeIds

Check biological entities (BE) identifiers
bedImport

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

Find all BEID and ProbeID corresponding to a BE
BED

Biological Entity Dictionary (BED)
cacheBedResult

Put a BED query result in cache
BEIDList

Create a BEIDList