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Introducing biocViews

Source: vignettes/biocviews.Rmd
biocviews.Rmd

Basic concepts

Introduction to biocViews

“biocViews” is the name of a package in Bioconductor that performs many roles

  • it was initially proposed to emulate CRAN task views, but did not achieve the levels of curation and narration present there
  • it was implemented as an instance of Bioconductor’s “graph” class
    • every vocabulary element is node in the biocViews graph
    • “is a” conceptual relationships are expressed using directed edges

Illustration using R:

library(biocViews)
library(graph)
data(biocViewsVocab)
biocViewsVocab
## A graphNEL graph with directed edges
## Number of Nodes = 497 
## Number of Edges = 496
head(nodes(biocViewsVocab),12)
##  [1] "BiocViews"          "Software"           "AnnotationData"    
##  [4] "ExperimentData"     "Workflow"           "AssayDomain"       
##  [7] "Technology"         "ResearchField"      "BiologicalQuestion"
## [10] "WorkflowStep"       "WorkflowManagement" "StatisticalMethod"
head(edges(biocViewsVocab),3)
## $BiocViews
## [1] "Software"       "AnnotationData" "ExperimentData" "Workflow"      
## 
## $Software
## [1] "AssayDomain"        "Technology"         "ResearchField"     
## [4] "BiologicalQuestion" "WorkflowStep"       "WorkflowManagement"
## [7] "StatisticalMethod"  "Infrastructure"     "ShinyApps"         
## 
## $AnnotationData
## [1] "Organism"             "ChipManufacturer"     "CustomCDF"           
## [4] "CustomArray"          "CustomDBSchema"       "FunctionalAnnotation"
## [7] "SequenceAnnotation"   "ChipName"             "PackageType"

Quick view of EDAM in R

The following has a one-time startup cost of introducing infrastructure for working with owlready2 (python) in R.

library(ontoProc) # must use Bioc 3.20
## Loading required package: ontologyIndex
ed = setup_entities2("https://edamontology.org/EDAM_1.25.owl")
head(ed$name, 12)
##           data_0006         format_1915      operation_0004           data_0842 
##              "Data"            "Format"         "Operation"        "Identifier" 
##          topic_0003           data_0005     DeprecatedClass           data_2337 
##             "Topic"     "Resource type"                  NA "Resource metadata" 
##           data_0007           data_0958           data_0581           data_0957 
##              "Tool"     "Tool metadata"          "Database" "Database metadata"
onto_plot2(ed, names(ed$name[ed$children$format_1915]))