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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
|
| 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