inst/doc/Enhancing_Chemical_Data_Access_with_PubChemR.R

In PubChemR: Interface to the 'PubChem' Database for Chemical Data Retrieval

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  class.output="scroll-100",
  cache.path = "cached/"
)
library(PubChemR)

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result <- get_pug_view(annotation = "data", identifier = "1234", domain = "compound", output = "JSON")

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result

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retrieve(object = result, .slot = "RecordType",  .to.data.frame = FALSE)

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retrieve(object = result, .slot = "RecordNumber",  .to.data.frame = FALSE)

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retrieve(object = result, .slot = "RecordTitle",  .to.data.frame = FALSE)

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section <- retrieve(object = result, .slot = "Section",  .to.data.frame = FALSE)
section

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sectionList(section)

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structures <- section(object = result, .id = "S1")

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structures

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retrieve(object = structures, .slot = "TOCHeading")

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retrieve(object = structures, .slot = "Description")

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retrieve(object = structures, .slot = "Section")

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result <- get_pug_view(annotation = "data", identifier = "2244", domain = "compound", output = "JSON", heading = "Experimental Properties")

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result

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s1 <- section(object = result, .id = "S1")

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s1

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s1_s1 <- section(object = s1, .id = "S1")

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s1_s1

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s1_s1_s10 <- section(object = s1_s1, .id = "S10")

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s1_s1_s10

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retrieve(object = s1_s1_s10, .slot = "Information", .to.data.frame = FALSE)

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result <- get_pug_view(annotation = "data", identifier = "1", domain = "assay", output = "JSON")

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result

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sectionList(object = result)

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record_description <- section(object = result, .id = "S10")
record_description

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record_description

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retrieve(object = record_description, .slot = "Information")

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result <- get_pug_view(annotation = "data", identifier = "1", domain = "gene", output = "JSON")

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result

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retrieve(object = result, .slot = "RecordTitle")

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sectionList(object = result)

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result <- get_pug_view(annotation = "annotations", identifier = "Viscosity", domain = "heading", output = "JSON")

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result

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annotations <- retrieve(object = result, .slot = "Annotation", .to.data.frame = FALSE)

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head(annotations)

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result <- get_pug_view(annotation = "annotations", identifier = NULL, domain = "heading", output = "JSON", heading = "Viscosity")
result

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result <- get_pug_view(annotation = "annotations", identifier = "Boiling Point", domain = "heading", output = "JSON", headingType = "Compound")

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result

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annotations <- retrieve(object = result, .slot = "Annotation", .to.data.frame = FALSE)

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head(annotations)

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result <- get_pug_view(annotation = "annotations", identifier = "CAS", domain = "heading", output = "JSON", page = "10")

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result

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annotations <- retrieve(object = result, .slot = "Annotation", .to.data.frame = FALSE)

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head(annotations)

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result <- get_pug_view(annotation = "categories", identifier = "1234", domain = "compound", output = "JSON")
result

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categories <- retrieve(object = result, .slot = "Categories", .to.data.frame = FALSE)

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head(categories)

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result <- get_pug_view(annotation = "neighbors", identifier = "1234", domain = "compound", output = "JSON")

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result

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retrieve(object = result, .slot = "NeighborsOfType", .to.data.frame = FALSE)

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result <- get_pug_view(annotation = "literature", identifier = "1234", domain = "compound", output = "JSON")

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result

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retrieve(object = result, .slot = "AllURL", .to.data.frame = FALSE)

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result <- get_pug_view(annotation = "linkout", identifier = "1234", domain = "compound", output = "JSON")
result

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retrieve(result, .slot = "ObjUrl", .to.data.frame = FALSE)

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result <- get_pug_view(annotation = "structure", identifier = "2244", domain = "compound", output = "JSON")
result

## -----------------------------------------------------------------------------
retrieve(object = result, .slot = "Structures", .to.data.frame = FALSE)