EMBL-EBIs Protein Data Bank in Europe

This section describes the mapping implemented to integrate metadata and links from EMBL-EBIs Protein Data Bank in Europe in the OpenAIRE Graph.

The Europe PMC RESTful Web Service gives the datalinks API to retrieve data-literature links in Scholix format.

How the data is collected

Starting from the Pubmed collection, the API below is used to obtain the bioentities related to publications for each PubMed identifier.

Example:

curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33024307/datalinks?format=json" | jq '.'
{
  "version": "6.8",
  "hitCount": 9,
  "request": {
    "id": "33024307",
    "source": "MED"
  },
  "dataLinkList": {
    "Category": [
      {
        "Name": "Nucleotide Sequences",
        "CategoryLinkCount": 5,
        "Section": [
          {
            "ObtainedBy": "tm_accession",
            "Tags": [
              "supporting_data"
            ],
            "SectionLinkCount": 5,
            "Linklist": {
              "Link": [
                {
                  "ObtainedBy": "tm_accession",
                  "PublicationDate": "04-11-2022",
                  "LinkProvider": {
                    "Name": "Europe PMC"
                  },
                  "RelationshipType": {
                    "Name": "References"
                  },
                  "Source": {
                    "Type": {
                      "Name": "literature"
                    },
                    "Identifier": {
                      "ID": "33024307",
                      "IDScheme": "MED"
                    }
                  },
                  "Target": {
                    "Type": {
                      "Name": "dataset"
                    },
                    "Identifier": {
                      "ID": "AY278488",
                      "IDScheme": "ENA",
                      "IDURL": "http://identifiers.org/ebi/ena.embl:AY278488"
                    },
                    "Title": "AY278488",
                    "Publisher": {
                      "Name": "Europe PMC"
                    }
                  },
            [...]

Mapping

The table below describes the mapping from the EBI links records to the OpenAIRE Graph Dataset format. We filter all the target links with pid type ena, pdb or uniprot For each target we construct a Bioentity with the following mapping

OpenAIRE Research Product field path	EBI record field xpath	Notes
id	target/identifier/ID and target/identifier/IDScheme	id in the form SCHEMA_________::md5(pid)
pid	target/identifier/ID and target/identifier/IDScheme	classid = classname = schema
publicationdate	target/PublicationDate	clean and normalize the format of the date to be YYYY-mm-dd
maintitle	target/Title
Instance Mapping
instance.type		Bioentity
type		Dataset
instance.pid	target/identifier/ID and target/identifier/IDScheme	classid = classname = schema
instance.url	target/identifier/IDURL	Copy the value as it is
instance.publicationdate	//PubmedPubDate	clean and normalize the format of the date to be YYYY-mm-dd
instance.accessright	OPEN	We consider the dataset is Open Access
instance.license	CC 0	According to https://www.ebi.ac.uk/pdbe/about/public-data-access-statement

Relation Mapping

OpenAIRE Relation Semantic and inverse	Source/Target type	Notes
IsRelatedTo	ResearchProduct/ResearchProduct	we create relationships between the BioEntity and the pubmed publication
IsSupplementTo/IsSupplementedBy	ResearchProduct/ResearchProduct	we create relationships between the BioEntity and the pubmed publication