Biological Entity Dictionary (BED)
Feeding BED: Download Ensembl DB and load gene information in BED
Feeding BED: Download Ensembl DB and load peptide information in BED
Feeding BED: Download Ensembl DB and load transcript information in BE...
Feeding BED: Load biological entities in BED
Feeding BED: Load attributes for biological entities in BED
Feeding BED: Load BED data model in neo4j
Feeding BED: Load additional indexes in neo4j
Get a BED query result from cache
Feeding BED: Load names associated to BEIDs
Feeding BED: Load symbols associated to BEIDs
Feeding BED: Load biological entities in BED with information about DB...
Feeding BED: Load correspondance between genes and objects as coding e...
Feeding BED: Load correspondances between BE IDs
Feeding BED: Load history of BEIDs
Feeding BED: Load BE ID associations
Feeding BED: Load correspondance between genes and transcripts as expr...
Feeding BED: Load homology between BE IDs
Feeding BED: Load correspondance between transcripts and peptides as t...
Feeding BED: Create Lucene indexes in neo4j
Feeding BED: Load in BED GO functions associated to Entrez gene IDs fr...
Feeding BED: Load taxonomic information from NCBI
Feeding BED: Load organisms in BED
Feeding BED: Load a probes platform
Feeding BED: Load probes targeting BE IDs
List all the BED queries in cache and the total size of the cache
List all registered BED connection
Set object metadata
Get object metadata
Feeding BED: Register a database of biological entities in BED DB
Get the BEID scope of an object
Get the BEID scopes of an object
Forget a BED connection
Clear the BED cache SQLite database
Construct CQL sub-query to map 2 biological entity
Compare 2 BED database instances
Feeding BED: Dump and preprocess flat data files from Uniprot
Get the BEIDs from an object
Explore BE identifiers
Biological Entity Dictionary (BED)
Call a function on the BED graph
Feeding BED: Imports a data.frame in the BED graph database
Create a BEIDList
Shiny module for searching BEIDs
Find all BEID and ProbeID corresponding to a BE
Cached neo4j call
Put a BED query result in cache
Check BED cache
Check if there is a connection to a BED database
Check biological entities (BE) identifiers
Identify and remove dubious cross-references
Connect to a neo4j BED database
Converts lists of BE IDs
Converts BE IDs
Add BE ID conversion to a data frame
Feeding BED: Dump table from the Ensembl core database
Feeding BED: Dump tables from the NCBI gene DATA
Feeding BED: Dump tables with taxonomic information from NCBI
Explore the shortest convertion path between two identifiers
Filter an object to keep only a set of BEIDs
Find Biological Entity
Find Biological Entity identifiers
First common upstream BE
Convert a BEIDList object in a specific identifier (BEID) scope
Focus a BE related object on a specific identifier (BEID) scope
Find all GeneID, ObjectID, TranscriptID, PeptideID and ProbeID corresp...
Identify the biological entity (BE) targeted by probes and construct t...
List all the source databases of BE identifiers whatever the BE type
Get a conversion table between biological entity (BE) identifiers
Get description of Biological Entity identifiers
Get names of Biological Entity identifiers
Get a table of biological entity (BE) identifiers and names
Get biological entities identifiers
Get symbols of Biological Entity identifiers
Get a table of biological entity (BE) identifiers and symbols
Get reference URLs for BE IDs
Get the direct origin of BE identifiers
Get the direct product of BE identifiers
Get description of genes corresponding to Biological Entity identifier...
Get gene homologs between 2 organisms
Feeding BED: Download NCBI gene DATA and load gene, transcript and pep...
Get organism names from taxonomy IDs
Get relevant IDs for a formerly identified BE in a context of interest
Identify the biological entity (BE) targeted by probes
Get taxonomy ID of an organism name
Feeding BED: Download Uniprot information in BED
Guess biological entity (BE), database source and organism of a vector...
Check if two objects have the same BEID scope
Check if the provided object is a BEIDList
Autoselect source of biological entity identifiers
Lists all the biological entities (BE) available in the BED database
Lists all the databases taken into account in the BED database for a b...
List all attributes provided by a BEDB
Lists all the organisms available in the BED database
Lists all the probe platforms available in the BED database
Search a BEID
Search identifier, symbol or name information
Feeding BED: Set the BED version
Show the data model of BED
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>.
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