Wolfram Function Repository

Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 SpeciesGenomeSummary

Source Notebook

Find genome information for a given taxonomic species

Contributed by: Keiko Hirayama

ResourceFunction["SpeciesGenomeSummary"][species]

gives genomic summary information for a specified species entity.

ResourceFunction["SpeciesGenomeSummary"][species,property]

gives the value of the specified genomic property for the given species.

ResourceFunction["SpeciesGenomeSummary"][species,property,format]

gives the summary information in a specified format.

ResourceFunction["SpeciesGenomeSummary"][species,format]

gives all information in the specified format.

Details

ResourceFunction["SpeciesGenomeSummary"] returns the latest genomics information reported by NCBI (National Center for Biotechnology Information).
Selected "TaxonomicSpecies" entities can be used.
More than one species can be given as a list ResourceFunction["SpeciesGenomeSummary"][{s1,s2,…},…], in which case the result is returned as tabular data.
Supported values of property include the following:
"AnnotationName"name of the genome annotation
"ReleaseDate"date of release for the genome asssembly
"RefSeqAssemblyAccession"ExternalIdentifier object representing a RefSeq assebly accession number
"TotalNumberOfChromosomes"total number of chromosomes in the primary assembly
"TotalSequenceLength"total length of sequences including bases and gaps in the primary assembly
"TotalUngappedLength"total length of all top‐level sequences ignoring gaps in the primary assembly; any stretch of 10 or more ambiguous bases (Ns) in a sequence is treated like a gap
"NumberOfContigs"total number of sequence contigs in the primary assembly; any stretch of 10 or more ambiguous bases (Ns) in a sequence is treated as a gap between two contigs in a scaffold when counting contigs and calculating contig N50 & L50 values
"ContigN50"length such that sequence contigs of this length or longer include half the bases of the primary assembly
"ContigL50"number of sequence contigs that are longer than, or equal to, the N50 length and therefore include half the bases of the primary assembly
"NumberOfScaffolds"number of scaffolds including placed, unlocalized, unplaced, alternate loci and patch scaffolds in the primary assembly
"ScaffoldN50"length such that scaffolds of this length or longer include half the bases of the primary assembly
"ScaffoldL50"number of scaffolds that are longer than, or equal to, the N50 length and therefore include half the bases of the primary assembly
"NumberOfComponentSequences"total number of component Whole Genome Shotgun (WGS) or clone sequences in the primary assembly
"GCCount"number of guanine (G) or cytosine (C) bases in the primary assembly
"PercentageOfGC"percentage of guanine (G) or cytosine (C) bases in the primary assembly
"TotalNumberOfGenes"total number of reported genes in the primary assembly
"TotalNumberOfProteinCodingGenes"total number of protein coding genes in the primary assembly
"TotalNumberOfNonCodingGenes"total number of non‐coding genes in the primary assembly
"TotalNumberOfPseudogenes"total number of pseudogene in the primary assembly
"TotalNumberOfOtherGenes"total number of genes other than protein coding, non‐coding, and pseudo‐ genes in the primary assembly
Supported values of format include the following:
"Association"Association of species entities and entity-property values
"Dataset"Dataset in which the specified species entities are keys, and values are an Association of property names and entity-property values
SpeciesGenomeSummary[species] is equivalent to SpeciesGenomeSummary[species, "Dataset"].

Examples

Basic Examples (1) 

Get the genome report for lions:

In[1]:=
ResourceFunction["SpeciesGenomeSummary"][ Entity["TaxonomicSpecies", "PantheraLeo::d7933"]]

Scope (2) 

Explore a specific genomic property:

In[2]:=
ResourceFunction["SpeciesGenomeSummary"][ Entity["TaxonomicSpecies", "CaenorhabditisElegans::93m45"], "TotalNumberOfChromosomes"]
Out[2]=

Get gene information as an Association:

In[3]:=
ResourceFunction["SpeciesGenomeSummary"][ Entity["TaxonomicSpecies", "GorillaGorilla::57mg3"], {"TotalNumberOfGenes", "TotalNumberOfProteinCodingGenes", "TotalNumberOfNonCodingGenes"}, "Association"]
Out[3]=

Applications (2) 

Compare genomic characteristics for common fruit plants:

In[4]:=
fruit = {Entity["TaxonomicSpecies", "PrunusPersica::76q6r"], Entity["TaxonomicSpecies", "MalusDomestica::k7rps"], Entity["TaxonomicSpecies", "AnanasComosus::7524s"], Entity["TaxonomicSpecies", "CitrusSinensis::fdd23"], Entity["TaxonomicSpecies", "VitisVinifera::v8884"], Entity["TaxonomicSpecies", "MusaAcuminata::35k78"]};
In[5]:=
genome = ResourceFunction["SpeciesGenomeSummary"][ fruit, {"TotalNumberOfChromosomes", "TotalSequenceLength", "TotalNumberOfGenes"}]
Out[5]=

Plot the total genome length against the number of chromosomes:

In[6]:=
ListPlot[ genome[All, {"TotalNumberOfChromosomes", "TotalSequenceLength"}]]
Out[6]=

Possible Issues (1) 

Genome information is available for selected species only. Trying to visualize a higher rank taxon returns Missing:

In[7]:=
ResourceFunction["SpeciesGenomeSummary"][ Entity["TaxonomicSpecies", "Mammalia::5448z"]]
Out[7]=

Requirements

Wolfram Language 13.0 (December 2021) or above

Version History

  • 1.0.0 – 05 January 2024

Related Resources

License Information