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

# 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 [www.nlm.nih.gov](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html).

## Incremental harvesting
Pubmed exposes an entry point FTP with all the updates for each one. [ftp baseline update](https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/). 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`                         | <ul><li>`\attributes\types\resourceType`</li>  <li> `\attributes\types\resourceTypeGeneral` </li>  <li>`attributes\types\schemaOrg`</li></ul> | Using the **_dnet:result_typologies_** vocabulary, we look up the `instance.type` synonym to  generate one of the following main entities: <ul><li>`publication`</li>  <li>`dataset`</li> <li> `software`</li>  <li>`otherresearchproduct`</li></ul>  | 
| `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                                                                                                                                                                                           |