D-Net
/
openaire-graph-docs
6
1
Fork 5
Code Issues 5 Pull Requests 2 Packages Projects Releases 67 Wiki Activity
openaire-graph-docs/docs/data-provision/aggregation/ebi.md

408 lines
13 KiB
Markdown
Raw Normal View History

Added EBI
2022-11-02 14:42:56 +01:00
# EMBL-EBIs Protein Data Bank in Europe
This section describes the mapping implemented for [EMBL-EBIs Protein Data Bank in Europe](https://www.ebi.ac.uk/).
datacite tables and EBI texts
2022-11-08 09:18:04 +01:00
The Europe PMC RESTful Web Service gives the [datalinks API](https://europepmc.org/RestfulWebService#!/Europe32PMC32Articles32RESTful32API) to retrieve data-literature links in Scholix format.
Added EBI
2022-11-02 14:42:56 +01:00
datacite tables and EBI texts
2022-11-08 09:18:04 +01:00
## How the data is collected
Added EBI
2022-11-02 14:42:56 +01:00
datacite tables and EBI texts
2022-11-08 09:18:04 +01:00
Starting from the Pubmed collection, the API below is used to obtain the bioentities related to publications for each PubMed identifier.
Added EBI
2022-11-02 14:42:56 +01:00
datacite tables and EBI texts
2022-11-08 09:18:04 +01:00
Example:
```commandline
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"
}
}
}
]
}
}
]
}
]
}
}
```
Added EBI
2022-11-02 14:42:56 +01:00
## 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 |
|--------------------------------|--------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------|