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openaire-graph-docs/docs/data-provision/aggregation/pubmed.md

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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 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
  • \attributes\types\resourceType
  • \attributes\types\resourceTypeGeneral
  • attributes\types\schemaOrg
 Using the dnet:result_typologies vocabulary, we look up the instance.type synonym to generate one of the following main entities:
  • publication
  • dataset
  • software
  • otherresearchproduct
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