Biological Entity Dictionary

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.

Installation

From CRAN

install.packages("BED")

Dependencies

The following R packages available on CRAN are required:

neo2R: Neo4j to R
visNetwork: Network Visualization using ‘vis.js’ Library
dplyr: A Grammar of Data Manipulation
readr: Read Rectangular Text Data
stringr: Simple, Consistent Wrappers for Common String Operations
utils: The R Utils Package
shiny: Web Application Framework for R
DT: A Wrapper of the JavaScript Library ‘DataTables’
miniUI: Shiny UI Widgets for Small Screens
rstudioapi: Safely Access the RStudio API

And those are suggested:

knitr: A General-Purpose Package for Dynamic Report Generation in R
rmarkdown: Dynamic Documents for R
biomaRt: Interface to BioMart databases (i.e. Ensembl)
GEOquery: Get data from NCBI Gene Expression Omnibus (GEO)
base64enc: Tools for base64 encoding
htmltools: Tools for HTML
webshot2: Take Screenshots of Web Pages
RCurl: General Network (HTTP/FTP/…) Client Interface for R

Installation from github

devtools::install_github("patzaw/BED")

Possible issue when updating from releases <= 1.3.0

If you get an error like the following…

Error: package or namespace load failed for ‘BED’:
 .onLoad failed in loadNamespace() for 'BED', details:
  call: connections[[connection]][["cache"]]
  error: subscript out of bounds

… remove the BED folder located here:

file.exists(file.path(Sys.getenv("HOME"), "R", "BED"))

Documentation

Documentation is provided in the BED vignette.

A public instance of the BED Neo4j database is provided for convenience and can be reached as follows:

library(BED)
connectToBed("https://genodesy.org/BED/", remember=TRUE, useCache=TRUE)
findBeids()

Citing BED

This package and the underlying research has been published in this peer reviewed article:

Patrice Godard and Jonathan van Eyll (2018). BED: a Biological Entity Dictionary based on a graph data model (version 3; peer review: 2 approved). F1000Research, 7:195.

Available BED database instance

An instance of the BED database (UCB-Human) has been built using the script provided in the BED R package.

This instance is focused on Homo sapiens, Mus musculus, Rattus norvegicus, Sus scrofa and Danio rerio organisms. It has been built from the following resources:

Ensembl
NCBI
Uniprot
HGNC
GEOquery

The Neo4j graph database is available as a dump file shared in Zenodo.

The following shell commands can be adapted according to user needs and called to get a running Neo4j container with a BED database instance.

#!/bin/sh

####################################################@
## Check folders ----
if test -e ~/.cache/BED/neo4jData; then
   echo "~/.cache/BED/neo4jData directory exists ==> abort - Remove it before proceeding" >&2
   exit
fi
mkdir -p ~/.cache/BED/neo4jData

if test -e ~/.cache/BED/neo4jDump; then
   echo "~/.cache/BED/neo4jDump directory exists ==> abort - Remove it before proceeding" >&2
   exit
fi
mkdir -p ~/.cache/BED/neo4jDump

####################################################@
## Download data ----
export BED_REP_URL=https://zenodo.org/records/14048653/files/
wget $BED_REP_URL/dump_bed_Genodesy-Human_2024.11.07.dump -O ~/.cache/BED/neo4jDump/neo4j.dump

####################################################@
## Import data ----
docker run --interactive --tty --rm \
   --volume=~/.cache/BED/neo4jData/data:/data \
   --volume=~/.cache/BED/neo4jDump:/backups \
    neo4j:5.25.1 \
neo4j-admin database load neo4j --from-path=/backups

####################################################@
## Start neo4j ----
docker run -d \
   --name bed_2024.11.07 \
   --publish=5454:7474 \
   --publish=5687:7687 \
   --env=NEO4J_dbms_memory_heap_initial__size=4G \
   --env=NEO4J_dbms_memory_heap_max__size=4G \
   --env=NEO4J_dbms_memory_pagecache_size=4G \
   --env=NEO4J_dbms_read__only=true \
   --env=NEO4J_AUTH=none \
   --volume ~/.cache/BED/neo4jData/data:/data \
   --volume ~/.cache/BED/neo4jData/logs:/var/lib/neo4j/logs \
   --restart=always \
   neo4j:5.25.1

Build a BED database instance

Building and feeding a BED database instance is achieved using scripts available in the “supp/Build” folder.

Run a neo4j docker images

Using the S01-NewBED-Container.sh script.

Build and feed BED

Using the S02-Rebuild-BED.sh script which compile the Rebuild-BED.Rmd document.

Using the S03-Dump-BED.sh script

Docker notes

Sergio Espeso-Gil has reported stability issues with Docker images in Windows. It’s mainly solved by checking the “Use the WSL2 based engine” options in docker settings. More information is provided here: https://docs.docker.com/docker-for-windows/wsl/

README