pubMedAbst-class: Class pubMedAbst, a class to handle PubMed abstracts, and...

In Bioconductor/annotate: Annotation for microarrays

Class pubMedAbst, a class to handle PubMed abstracts, and methods for processing them.

Description

This is a class representation for PubMed abstracts.

Creating Objects

new('pubMedAbst',
authors = ...., # Object of class vector
pmid = ...., # Object of class character
abstText = ...., # Object of class character
articleTitle = ...., # object of class character
journal = ...., # Object of class character
pubDate = ...., # Object of class character
)

Slots

pmid:

Object of class "character" The PubMed ID for this paper.

authors:

Object of class "vector" The authors of the paper.

abstText:

Object of class "character" The contained text of the abstract.

articleTitle:

Object of class "character" The title of the article the abstract pertains to.

journal:

Object of class "character" The journal the article was published in.

pubDate:

Object of class "character" The date the journal was published.

Methods

pmid

signature(object = "pmid"): An accessor function for pmid

abstText

signature(object = "pubMedAbst"): An accessor function for abstText

articleTitle

signature(object = "pubMedAbst"): An accessor function for articleTitle

authors

signature(object = "pubMedAbst"): An accessor function for authors

journal

signature(object = "pubMedAbst"): An accessor function for journal

pubDate

signature(object = "pubMedAbst"): An accessor function for pubDate

Author(s)

Jeff Gentry

See Also

pubmed, genbank

Examples

   x <- pubmed("9695952","8325638","8422497")
   a <- xmlRoot(x)
   numAbst <- length(xmlChildren(a))
   absts <- list()
   for (i in 1:numAbst) {
      absts[[i]] <- buildPubMedAbst(a[[i]])
   }

Bioconductor/annotate documentation built on July 4, 2025, 1:58 a.m.