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EMBL-EBIs Protein Data Bank in Europe
This section describes the mapping implemented for EMBL-EBIs Protein Data Bank in Europe.
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"
}
},
"Frequency": 1
},
{
"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": "MT121216",
"IDScheme": "ENA",
"IDURL": "http://identifiers.org/ebi/ena.embl:MT121216"
},
"Title": "MT121216",
"Publisher": {
"Name": "Europe PMC"
}
},
"Frequency": 1
},
{
"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": "KF367457",
"IDScheme": "ENA",
"IDURL": "http://identifiers.org/ebi/ena.embl:KF367457"
},
"Title": "KF367457",
"Publisher": {
"Name": "Europe PMC"
}
},
"Frequency": 1
},
{
"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": "MN996532",
"IDScheme": "ENA",
"IDURL": "http://identifiers.org/ebi/ena.embl:MN996532"
},
"Title": "MN996532",
"Publisher": {
"Name": "Europe PMC"
}
},
"Frequency": 1
},
{
"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": "MT072864",
"IDScheme": "ENA",
"IDURL": "http://identifiers.org/ebi/ena.embl:MT072864"
},
"Title": "MT072864",
"Publisher": {
"Name": "Europe PMC"
}
},
"Frequency": 1
}
]
}
}
]
},
{
"Name": "Protein Structures",
"NameLong": "Protein structures in PDBe",
"CategoryLinkCount": 2,
"Section": [
{
"ObtainedBy": "tm_accession",
"Tags": [
"supporting_data"
],
"SectionLinkCount": 2,
"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": "6VW1",
"IDScheme": "PDB",
"IDURL": "http://identifiers.org/pdbe/pdb:6VW1"
},
"Title": "6VW1",
"Publisher": {
"Name": "Europe PMC"
}
},
"Frequency": 1
},
{
"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": "2AJF",
"IDScheme": "PDB",
"IDURL": "http://identifiers.org/pdbe/pdb:2AJF"
},
"Title": "2AJF",
"Publisher": {
"Name": "Europe PMC"
}
},
"Frequency": 1
}
]
}
}
]
},
{
"Name": "Altmetric",
"CategoryLinkCount": 1,
"Section": [
{
"ObtainedBy": "ext_links",
"Tags": [
"altmetrics"
],
"SectionLinkCount": 1,
"Linklist": {
"Link": [
{
"ObtainedBy": "ext_links",
"PublicationDate": "15-10-2020",
"LinkProvider": {
"Name": "Europe PMC"
},
"RelationshipType": {
"Name": "IsReferencedBy"
},
"Source": {
"Type": {
"Name": "literature"
},
"Identifier": {
"ID": "33024307",
"IDScheme": "PMID"
}
},
"Target": {
"Type": {
"Name": "dataset"
},
"Identifier": {
"ID": "https://www.altmetric.com/details/91880755",
"IDScheme": "URL",
"IDURL": "https://www.altmetric.com/details/91880755"
},
"Title": "Characteristics of SARS-CoV-2 and COVID-19",
"Publisher": {
"Name": "Altmetric"
},
"ImageURL": "https://api.altmetric.com/v1/donut/91880755_64.png"
}
}
]
}
}
]
},
{
"Name": "BioStudies: supplemental material and supporting data",
"CategoryLinkCount": 1,
"Section": [
{
"ObtainedBy": "ext_links",
"Tags": [
"supporting_data"
],
"SectionLinkCount": 1,
"Linklist": {
"Link": [
{
"ObtainedBy": "ext_links",
"PublicationDate": "11-03-2021",
"LinkProvider": {
"Name": "Europe PMC"
},
"RelationshipType": {
"Name": "IsReferencedBy"
},
"Source": {
"Type": {
"Name": "literature"
},
"Identifier": {
"ID": "33024307",
"IDScheme": "PMID"
}
},
"Target": {
"Type": {
"Name": "dataset"
},
"Identifier": {
"ID": "http://www.ebi.ac.uk/biostudies/studies/S-EPMC7537588?xr=true",
"IDScheme": "URL",
"IDURL": "http://www.ebi.ac.uk/biostudies/studies/S-EPMC7537588?xr=true"
},
"Title": "Characteristics of SARS-CoV-2 and COVID-19.",
"Publisher": {
"Name": "BioStudies: supplemental material and supporting data"
}
}
}
]
}
}
]
}
]
}
}
Mapping
The table below describes the mapping from the EBI links records to the OpenAIRE Graph dump format.
| OpenAIRE Result field path | PubMed record field xpath | Notes |
|---|