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"PubMed" (Service Connection)

"PubMed" (Service Connection)

Connect to the PubMed API using the Wolfram Language to retrieve citations and abstracts for biomedical literature.

Connecting & Authenticating

ServiceConnect["PubMed"] creates a connection to the PubMed API. If a previously saved connection can be found, it will be used; otherwise, a new authentication request will be launched.

Requests

ServiceExecute["PubMed","request",params] sends a request to the PubMed API, using parameters params. The following gives possible requests.

Search Publications and Other Works

"PublicationSearch" — a Dataset with information about publications matching search criteria

Parameters:
  • "ID"NoneID or list of IDs
    "Query"Nonequery terms
    "Author"Noneauthor's name
    "Title"Nonetitle keywords
    "Publisher"Nonepublisher name
    "CreationDate"Nonedate the citation was first created
    "CompletionDate"Nonedate the National Library of Medicine finished processing the citation
    "ModificationDate"Nonedate of the most recent revision
    "EntrezDate"Nonedate the citation was added to PubMed
    "PublicationDate"Nonedate or date interval that the article was published
    "ISBN"NoneISBN for books or book chapters
    "Language"Nonelanguage in which the article was published
    "PublicationType"Nonetype of material the article represents (e.g. "Review", "Clinical Trial", "Retracted Publication", "Letter")
    MaxItems20maximum results to return
    "Elements""Data"data elements to return
    "StartIndex"0index of first search result to return
    "SortBy"Nonefield to sort by ("MostRecent", "Relevance", "PublicationDate", "Author", "Journal", "Title")

    • List Publication Types

    "PublicationTypes" — a List of publication types

    Publication Abstract

    "PublicationAbstract" — abstract for the specified PubMed ID

    Parameters:
  • "ID"(required)ID or list of IDs

    • Parameter details

    Possible values for "Elements" include:
  • "Data"return a dataset with a limited set of fields
    "FullData"return a dataset with all available fields

    • Examples

    open all close all

    Basic Examples  (2)

    Create a new connection to PubMed:

    Wolfram Language code: pubmed = ServiceConnect["PubMed"]

    Search publications by author and title:

    Wolfram Language code: pubmed["PublicationSearch", <|"Author" -> "smith", "Title" -> "healthcare"|>]

    Sort results by publication date:

    Wolfram Language code: ServiceExecute["PubMed", "PublicationSearch", <|"Query" -> "science", MaxItems -> 10, "SortBy" -> "PublicationDate"|>]

    Retrieve information for a specific publication:

    Wolfram Language code: ServiceExecute["PubMed", "PublicationSearch", <|"ID" -> "26671975", "Elements" -> "FullData"|>][1]

    Scope  (3)

    Paginate over long lists of results:

    Wolfram Language code: ServiceExecute["PubMed", "PublicationSearch", <|"Query" -> "science", MaxItems -> 5, "StartIndex" -> 5000|>]

    Filter publications by type:

    Wolfram Language code: publicationTypes = ServiceExecute["PubMed", "PublicationTypes"][[ ;; 10]]
    Wolfram Language code: ServiceExecute["PubMed", "PublicationSearch", <|"PublicationType" -> publicationTypes[[6]]|>][1]

    Use dates to filter search results:

    Wolfram Language code: ServiceExecute["PubMed", "PublicationSearch", <|"PublicationDate" -> {"25 october 1964", "1965"}|>]
    Wolfram Language code: ServiceExecute["PubMed", "PublicationSearch", <|"CreationDate" -> Today, MaxItems -> 5|>]

    Retrieve an abstract for a given publication:

    Wolfram Language code: ServiceExecute["PubMed", "PublicationAbstract", "ID" -> "26558272"]