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