# Biological Entity Dictionary (BED)

## Documentation for package ‘BED’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

BED | Biological Entity Dictionary (BED)
bedCall | Call a function on the BED graph
bedImport | Feeding BED: Imports a data.frame in the BED graph database
BEIDList | Create a BEIDList
BEIDs | Get the BEIDs from an object
beidsServer | Shiny module for searching BEIDs
beIDsToAllScopes | Find all BEID and ProbeID corresponding to a BE
beidsUI | Shiny module for searching BEIDs
cacheBedCall | Cached neo4j call
cacheBedResult | Put a BED query result in cache
checkBedCache | Check BED cache
checkBedConn | Check if there is a connection to a BED database
checkBeIds | Check biological entities (BE) identifiers
cleanDubiousXRef | Identify and remove dubious cross-references
clearBedCache | Clear the BED cache SQLite database
compareBedInstances | Compare 2 BED database instances
connectToBed | Connect to a neo4j BED database
convBeIdLists | Converts lists of BE IDs
convBeIds | Converts BE IDs
convDfBeIds | Add BE ID conversion to a data frame
dumpEnsCore | Feeding BED: Dump table from the Ensembl core database
dumpNcbiDb | Feeding BED: Dump tables from the NCBI gene DATA
dumpNcbiTax | Feeding BED: Dump tables with taxonomic information from NCBI
dumpUniprotDb | Feeding BED: Dump and preprocess flat dat files fro Uniprot
exploreBe | Explore BE identifiers
exploreConvPath | Explore the shortest convertion path between two identifiers
filterByBEID | Filter an object to keep only a set of BEIDs
findBe | Find Biological Entity
findBeids | Find Biological Entity identifiers
firstCommonUpstreamBe | First common upstream BE
focusOnScope | Focus a BE related object on a specific identifier (BEID) scope
focusOnScope.BEIDList | Convert a BEIDList object in a specific identifier (BEID) scope
forgetBedConnection | Forget a BED connection
genBePath | Construct CQL sub-query to map 2 biological entity
geneIDsToAllScopes | Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresponding to a Gene in any organism
genProbePath | Identify the biological entity (BE) targeted by probes and construct the CQL sub-query to map probes to the BE
getAllBeIdSources | List all the source databases of BE identifiers whatever the BE type
getBeIdConvTable | Get a conversion table between biological entity (BE) identifiers
getBeIdDescription | Get description of Biological Entity identifiers
getBeIdNames | Get names of Biological Entity identifiers
getBeIdNameTable | Get a table of biological entity (BE) identifiers and names
getBeIds | Get biological entities identifiers
getBeIdSymbols | Get symbols of Biological Entity identifiers
getBeIdSymbolTable | Get a table of biological entity (BE) identifiers and symbols
getBeIdURL | Get reference URLs for BE IDs
getDirectOrigin | Get the direct origin of BE identifiers
getDirectProduct | Get the direct product of BE identifiers
getEnsemblGeneIds | Feeding BED: Download Ensembl DB and load gene information in BED
getEnsemblPeptideIds | Feeding BED: Download Ensembl DB and load peptide information in BED
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
getOrgNames | Get organism names from taxonomy IDs
getRelevantIds | Get relevant IDs for a formerly identified BE in a context of interest
getTargetedBe | Identify the biological entity (BE) targeted by probes
getTaxId | Get taxonomy ID of an organism name
getUniprot | Feeding BED: Download Uniprot information in BED
guessIdOrigin | Guess biological entity (BE), database source and organism of a vector of identifiers.
guessIdScope | Guess biological entity (BE), database source and organism of a vector of identifiers.
identicalScopes | Check if two objects have the same BEID scope
is.BEIDList | Check if the provided object is a BEIDList
largestBeSource | Autoselect source of biological entity identifiers
listBe | Lists all the biological entities (BE) available in the BED database
listBeIdSources | Lists all the databases taken into account in the BED database for a biological entity (BE)
listDBAttributes | List all attributes provided by a BEDB
listOrganisms | Lists all the organisms available in the BED database
listPlatforms | Lists all the probe platforms available in the BED database
loadBE | Feeding BED: Load biological entities in BED
loadBeAttribute | Feeding BED: Load attributes for biological entities in BED
loadBedModel | Feeding BED: Load BED data model in neo4j
loadBedOtherIndexes | Feeding BED: Load additional indexes in neo4j
loadBedResult | Get a BED query result from cache
loadBENames | Feeding BED: Load names associated to BEIDs
loadBESymbols | Feeding BED: Load symbols associated to BEIDs
loadBEVersion | Feeding BED: Load biological entities in BED with information about DB version
loadCodesFor | Feeding BED: Load correspondance between genes and objects as coding events
loadCorrespondsTo | Feeding BED: Load correspondances between BE IDs
loadHistory | Feeding BED: Load history of BEIDs
loadIsAssociatedTo | Feeding BED: Load BE ID associations
loadIsExpressedAs | Feeding BED: Load correspondance between genes and transcripts as expression events
loadIsHomologOf | Feeding BED: Load homology between BE IDs
loadIsTranslatedIn | Feeding BED: Load correspondance between transcripts and peptides as translation events
loadLuceneIndexes | Feeding BED: Create Lucene indexes in neo4j
loadNCBIEntrezGOFunctions | Feeding BED: Load in BED GO functions associated to Entrez gene IDs from NCBI
loadNcbiTax | Feeding BED: Load taxonomic information from NCBI
loadOrganisms | Feeding BED: Load organisms in BED
loadPlf | Feeding BED: Load a probes platform
loadProbes | Feeding BED: Load probes targeting BE IDs
lsBedCache | List all the BED queries in cache and the total size of the cache
lsBedConnections | List all registered BED connection
metadata | Get object metadata
metadata<- | Set object metadata
registerBEDB | Feeding BED: Register a database of biological entities in BED DB
scope | Get the BEID scope of an object
scopes | Get the BEID scopes of an object
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