avidaR: an R library to perform complex queries on a semantic database of digital organisms (avidaDB)

Introduction.

avidaR was born as part of a project focused on providing semantics to data resulting from experiments carried out in an Artificial Life software platform (Avida) for studying the evolution of self-replicating computer programs, known as digital organisms. This package provides users of the R programming language with an easy-to-use tools for performing complex queries on avidaDB, a semantic database that stores genomes and transcriptomes of more than a million digital organisms. The avidaR library was developed by the Computational Biology Lab of the Doñana Biological Station (EBD), a research institute of the Spanish National Research Council (CSIC) based in Seville (Spain).

Installation.

avidaR depends on the following packages: - base64enc - xml2 - httr - dplyr - readr - tidyr - tibble - circlize - RColorBrewer - R6 - curl - devtools: needed for the GitLab installation.

Please, first install those packages with install.packages. Then, install avidaR from GitLab using the following command:

devtools::install_gitlab("fortunalab/avidaR")

Usage.

avidaR is loaded as follows:

library(avidaR)

Connect to avidaDB.

avidaDB is a semantic database (or triple-store) on genomes and transcriptomes of more a million digital organisms stored as RDF data. It allows querying data using the SPARQL query language. The library avidaR can connect to triple-stores that support the RDF4J server REST API such as GraphDB. Since avidaDB is implemented in GraphDB, a basic connection (requiring no password or requiring basic HTTP user-pass authentication) or a connection secured with an API access token can be established.

avidaR provides a triplestore_access class to manage access options and retrieve data through the database server API. In order to get access to the entire database, you should first create the triplestore object and run the set_access_options() method as follows:

# create object of class triplestore_access
avidaDB <- triplestore_access$new()

# set access options to avidaDB
avidaDB$set_access_options(
    url = "https://graphdb.fortunalab.org",
    user = "public_avida",
    password = "public_avida",
    repository = "avidaDB"
  )

Get data from avidaDB.

The following function can be used to get the genome sequence of a single genome (e.g., genome_id = 1):

get_genome_seq_from_genome_id(genome_id = 1, triplestore = avidaDB)

or to get the genome sequences of multiple genomes at once:

get_genome_seq_from_genome_id(genome_id = c(1, 2, 3), triplestore = avidaDB)

Please, use the R help command to get more details about any specific function by writing the name of the function preceded by the symbol ?:

?get_genome_seq_from_genome_id

List of available functions grouped by the target entity:

Get the genome of a digital organism:

• get_genome_id_from_logic_operation()
• get_genome_id_from_phenotype_id()
• get_genome_id_from_transcriptome_id()
• get_genome_id_from_genome_seq()
• get_genome_seq_from_genome_id()

Get the phenotype encoded by the genome of a digital organism:

• get_phenotype_id_from_logic_operation()
• get_phenotype_id_from_genome_id()
• get_phenotype_id_from_genome_seq()
• get_phenotype_id_from_transcriptome_id()

Get the logic operations (i.e., traits) defining the phenotype of a digital organism:

• get_logic_operations_from_phenotype_id()

Get the transcriptome executed by a digital organism:

• get_transcriptome_id_from_logic_operation()
• get_transcriptome_id_from_genome_id()
• get_transcriptome_id_from_genome_seq()
• get_transcriptome_id_from_phenotype_id()
• get_transcriptome_seq_from_transcriptome_id()

Get the tandem repeat contained in the transcriptome of a digital organism:

• get_tandem_id_from_logic_operation()
• get_tandem_id_from_genome_id()
• get_tandem_id_from_genome_seq()
• get_tandem_id_from_phenotype_id()
• get_tandem_seq_from_tandem_id()

Get data provenance:

• get_experiment_id_from_organism_id()
• get_doi_from_experiment_id()
• get_docker_image_from_experiment_id()

Miscellaneous functions:

• get_db_summary()
• instruction_set()
• get_genome_id_of_wild_type_organisms()
• get_mutant_at_pos()
• convert_org_into_seq()
• convert_seq_into_org()
• plot_transcriptome()

Source code

avidaR was developed by Raúl Ortega.