PubMed
This section describes the mapping implemented for MEDLINE/PubMed.
Input
The native data is collected from the ftp baseline site. It contains XML records compliant with the schema available at www.nlm.nih.gov.
Incremental harvesting
Pubmed exposes an entry point FTP with all the updates for each one. ftp baseline update. We collect the new file and generate the new dataset by upserting the existing item.
Entity Mapping
The table below describes the mapping from the XML baseline records to the OpenAIRE Research Graph dump format.
| OpenAIRE Result field path | PubMed record field xpath | Notes |
|---|---|---|
| Publication Mapping | ||
id | //PMID | id in the form pmid_________::md5(pmid) |
pid | //PMID | classid = classname = pmid |
publicationdate | //PubmedPubDate | clean and normalize the format of the date to be YYYY-mm-dd |
maintitle | //Title | |
description | //AbstractText | |
language | //Language | cleaning vocabulary -> dnet:languages |
subjects | //DescriptorName | classId, className = keyword |
| Author Mapping | ||
author.surname | //Author/LastName | |
author.name | //Author/ForeName | |
author.fullname | //Author/FullName | Concatenation of forename + lastName if exist |
author.rank | FOR ALL AUTHORS | sequential number starting from 1 |
| Journal Mapping | ||
container.conferencedate | //Journal/PubDate | map the date of the Journal |
container.name | //Journal/Title | name of the journal |
container.vol | //Journal/Volume | journal volume |
container.issPrinted | //Journal/ISSN | the journal issn |
container.iss | //Journal/Issue | The journal issue |
| Instance Mapping | ||
instance.type | //PublicationType | if the article contains the typology Journal Article then we apply this type else We have to find a terms that match the vocabulary otherwise we discard it |
type |
| Using the dnet:result_typologies vocabulary, we look up the instance.type synonym to generate one of the following main entities:
|
instance.pid | //PMID | map the pmid in the pid in the instance |
instance.url | //PMID | creates the URL by prepending https://pubmed.ncbi.nlm.nih.gov/ to the PMId |
instance.alternateIdentifier | //ArticleId[./@IdType="doi"] | |
instance.publicationdate | //PubmedPubDate | clean and normalize the format of the date to be YYYY-mm-dd |