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"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

Request:

"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"None
  • language in which the article was published
    • "PublicationType"None
  • type of material the article represents (e.g. "Review", "Clinical Trial", "Retracted Publication", "Letter")
    • MaxItems20
  • maximum results to return
    • "Elements""Data"data elements to return
    "StartIndex"0
  • index of first search result to return
    • "SortBy"Nonefield to sort by ("MostRecent", "Relevance", "PublicationDate", "Author", "Journal", "Title")

    • List Publication Types

    Request:

    "PublicationTypes" — a List of publication types

    Publication Abstract

    Request:

    "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

    Basic Examples  (1)Summary of the most common use cases

    Create a new connection by launching an authentication dialog:

    In[1]:=1
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-cqb8bi
    Out[1]=1

    Search publications by author and title:

    In[2]:=2
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-i84u70
    Out[2]=2

    Paginate over long lists of results:

    In[3]:=3
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-9l4cvv
    Out[3]=3

    Sort results by publication date:

    In[4]:=4
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-n3ryvm
    Out[4]=4

    Retrieve information for a specific publication:

    In[5]:=5
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-zbxkv1
    Out[6]=6

    Filter publications by type:

    In[7]:=7
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-7atjcj
    Out[8]=8
    In[9]:=9
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-zpdt7d
    Out[10]=10

    Use dates to filter search results:

    In[11]:=11
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-0pbr3f
    Out[11]=11
    In[12]:=12
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-7xrrct
    Out[12]=12

    Filter publications by language:

    In[13]:=13
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-uqta19
    Out[13]=13

    Retrieve an abstract for a given publication:

    In[14]:=14
    ✖
    https://wolfram.com/xid/0vvz0val55ftth5gysq-2k46f7
    Out[14]=14