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PubMedPubMed

Contains more than 19 million records from MEDLINE and from medical scientific journals, dating back from 1948. PubMed contains links to full-texts, either from other databases or the journals' publishers. Content must be "E-pub ahead of print", before imported into Pure.

 

Overview

Content type  License / subscription Available for Automated search Integrated with Available Updates
Research output No (though an API key gives some enhanced performance. See set up below).

Persons: Yes

Organisations: No

Yes

 

Set up online source

Go to Administrator > Research outputs > Online sources > PubMed

Setting Description Notes
Enabled Toggles it available for users or not.  
Connection timeout The read/connection timeout used when talking with the PubMed servers, value is in seconds.  
API key With an API key, PubMed will accept more queries per second, and provide a faster response and import. An API key is not mandatory, but recommended. Information can be found here: https://www.ncbi.nlm.nih.gov/books/NBK25497  
Intelligent organisation parsing The organisation field from PubMed is unstructured, however, Pure can try parsing the field and look for proper organisation names.
 
 
Only import root organisation This toggle requires the "Intelligent organisation parsing" to be enabled. If both are enabled, Pure will try and determine the root organisation and 
only import that organisation
 
Filter person match results by affiliation Defines if person matching should also take organisational unit affiliation in the source into account. If set to NONE, person matching during import is done on name only. If set to AGAINST_INDEX, the indexed organisational unit names is included in the filtering. If set to AGAINST_CONFIGURED_ADDRESSES is chosen, the person affiliation in the source must match one of the postal codes or organisational unit names configured on this screen.  
Organisational unit names to match Defines one or more valid organisational unit names as they appear in the import source(s). Used if person matching is set to use AGAINST_CONFIGURED_ADDRESSES. Multiple values are separated with commas or semi-colon
 
 
Valid postal codes Defines one or more valid organisational unit postal codes as they appear in the import source(s). Used if person matching is set to use AGAINST_CONFIGURED_ADDRESSES. Multiple values are separated with commas or semi-colon  

 

Mapping of document types from PubMed

All publications from PubMed is imported as Contribution to Journal > Article. 

Only exception to this rule is if publication type has the ID D016454 (In imported data), then it will be > Review.

  • (<PublicationType UI="D016454">Review</PublicationType>)

 

medRxiv to Pure data mapping

Table with mapping of fields to Pure.

Field in PubMed

Field in Pure

Base UK

Field in Pure

Base DK

Field in Pure

Base FI

Fields in Pure

Base BE

Note
MedlineCitation Status X X X X  
Owner X X X X  
PMID Version X X X X  
DateCreated X X X X  
Article PubModel X X X X  
JournalIssue CitedMedium X X X X  
ISSN ISSN or ISSN (Electronic) on the related journal ISSN på tilknyttet tidsskrift ISSN on the related journal ISSN on the related journal  
Volume Volume Vol/bind Volume Volume  
Issue Issue number Nummer

Journal number

Journal number  
PubDate Journal publication date Tidsskriftets publikationsdato

Publication date

Publication date

If this date is not available, we use the first provided date from this list

  • pubmed publication date
  • medline publication date
  • journal publication period from tha MedlineDate tag
Title Title of the related journal Titel på relateret tidsskrift Title of the related journal Title of the related journal Matched to an existing journal or a new is created
ISOAbbreviation X X X X  
CopyrightInformation X X Publisher's Copyright Statement X  
ArticleTitle Title of the contribution in original language Bidragets titel på originalsprog Title of the contribution in original language Title of the contribution in original language Article title and subtitle is divided by the first :
MedlinePgn Pages (from-to) Sider (fra-til) Pages (from-to) Pages (from-to) total pages is calculated
AbstractText Abstract Abstract (engelsk) X Abstract  
Author - LastName Related author Last name Relateret forfatters efternavn Related author Last name Related author Last name Matched to an existing or a new external person is created
Author - ForeName Related author First name Relateret forfatters fornavn Related author First name Related author First name Matched to an existing or a new external person is created
Author - Initials X X X X  
Author - Suffix X X X X  
CollectiveName
Group author Forfattergruppering Group author Group author When group author is added, author will as default be set to "hidden"
Language Original language Originalsprog Original language Original language  
PublicationType X X X X  
ArticleDate DateType X X X X  
MedlineTA X X X X  
NlmUniqueID X X X X  
ISSNLinking X X X X  
MeshHeading - DescriptorName X X Keywords X  

PubMedPubDate

PubStatus="received"

X X X X  

PubMedPubDate

PubStatus="accepted"

X X X X  

PubMedPubDate

PubStatus="aheadofprint"

X X X X  

PubMedPubDate

PubStatus="entrez"

X X X X  

PubMedPubDate

PubStatus="pubmed"

X X X X  

PubMedPubDate

PubStatus="medline"

X X X X  
ArticleId IdType="pii" X X X X  
ArticleId IdType="doi" DOIs DOI DOIs DOIs  
ArticleId IdType="pubmed" Source-ID Kilde ID Source-ID Source-ID  
 
 

 

 

Published at July 15, 2025

Download
Table of Contents
  1. Overview
  2. Set up online source
  3. Mapping of document types from PubMed
  4. medRxiv to Pure data mapping
  5. Table with mapping of fields to Pure.
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