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

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