2022-10-06 11:37:33 +02:00
# PubMed
This section describes the mapping implemented for [MEDLINE/PubMed ](https://pubmed.ncbi.nlm.nih.gov/ ).
## Input
The native data is collected from the [ftp baseline ](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/ ) site.
It contains XML records compliant with the schema available at https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html.
## 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` | ?? | ?? |
| `pid` | `//PMID` | `classid = classname = pmid` |
| `publicationdate` | `//PubmedPubDate` | apply the function GraphCleaningFunctions.cleanDate before assign it |
| `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` | ?? |
| `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 |
| `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` | |
| *OpenAIRE Relation field path* | PubMed record field xpath | Notes |
|--------------------------------|---------------------------|-------|
| | | |
#TODO
Missing item mapped
