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2.4 KiB
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#Pubmed Mapping This section describes the mapping implemented for MEDLINE/PubMed.
Collection
The native data is collected from ftp baseline containing XML with the following schema
Parsing
The resposible class of parsing is PMParser that generates an intermediate mapping of PubMed Article defined here
Mapping
The table below describes the mapping from the XML Native to the OAF mapping
| Xpath Source | Oaf Field | Notes |
|---|---|---|
| //PMID | pid | classid = classname = pmid |
| Instance Mapping | ||
| //PublicationType | InstanceType | 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 |
| //PMID | instance/PID | Map the pmid also in the pid in the instance |
| //ArticleId[./@IdType="doi" | instance/alternateIdentifier | classid = classname = doi |
| //PMID | instance/URL | prepend to the PMId the base url https://pubmed.ncbi.nlm.nih.gov/ |
| //PubmedPubDate | instance/Dateofacceptance | apply the function GraphCleaningFunctions.cleanDate before assign it |
| FOR ALL INSTANCE | CollectedFrom | datasourceName: Europe PubMed Central DatasourceId: |
| Journal Mapping | ||
| //Journal/PubDate | Journal/Conferencedate | map the date of the Journal |
| //Journal/Title | Journal/Name | |
| //Journal/Volume | Journal/Vol | |
| //Journal/ISSN | Journal/issPrinted | |
| //Journal/Issue | Journal/Iss | |
| Publication Mapping | ||
| //PubmedPubDate | Dateofacceptance | apply the function GraphCleaningFunctions.cleanDate before assign it |
| //Title | title | with qualifier ModelConstants.MAIN_TITLE_QUALIFIER |
| //AbstractText | Description | |
| //Language | Language | cleaning vocabulary -> dnet:languages |
| //DescriptorName | Subject | classId, className = keyword |
| Author Mapping | ||
| //Author/LastName | author.Surname | |
| //Author/ForeName | author.Forename | |
| //Author/FullName | author.Forename | Concatenation of forname + lastName if exist |
| FOR ALL AUTHOR | author.rank | sequential number starting from 1 |
#TODO
Missing item mapped