forked from D-Net/openaire-graph-docs
408 lines
13 KiB
Markdown
408 lines
13 KiB
Markdown
# EMBL-EBIs Protein Data Bank in Europe
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This section describes the mapping implemented for [EMBL-EBIs Protein Data Bank in Europe](https://www.ebi.ac.uk/).
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The Europe PMC RESTful Web Service gives the [datalinks API](https://europepmc.org/RestfulWebService#!/Europe32PMC32Articles32RESTful32API) to retrieve data-literature links in Scholix format.
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## How the data is collected
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Starting from the Pubmed collection, the API below is used to obtain the bioentities related to publications for each PubMed identifier.
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Example:
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```commandline
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curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33024307/datalinks?format=json" | jq '.'
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{
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"version": "6.8",
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"hitCount": 9,
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"request": {
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"id": "33024307",
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"source": "MED"
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},
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"dataLinkList": {
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"Category": [
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{
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"Name": "Nucleotide Sequences",
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"CategoryLinkCount": 5,
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"Section": [
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{
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"ObtainedBy": "tm_accession",
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"Tags": [
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"supporting_data"
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],
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"SectionLinkCount": 5,
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"Linklist": {
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"Link": [
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{
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"ObtainedBy": "tm_accession",
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"PublicationDate": "04-11-2022",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "References"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "MED"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "AY278488",
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"IDScheme": "ENA",
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"IDURL": "http://identifiers.org/ebi/ena.embl:AY278488"
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},
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"Title": "AY278488",
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"Publisher": {
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"Name": "Europe PMC"
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}
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},
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"Frequency": 1
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},
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{
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"ObtainedBy": "tm_accession",
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"PublicationDate": "04-11-2022",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "References"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "MED"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "MT121216",
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"IDScheme": "ENA",
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"IDURL": "http://identifiers.org/ebi/ena.embl:MT121216"
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},
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"Title": "MT121216",
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"Publisher": {
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"Name": "Europe PMC"
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}
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},
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"Frequency": 1
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},
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{
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"ObtainedBy": "tm_accession",
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"PublicationDate": "04-11-2022",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "References"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "MED"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "KF367457",
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"IDScheme": "ENA",
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"IDURL": "http://identifiers.org/ebi/ena.embl:KF367457"
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},
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"Title": "KF367457",
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"Publisher": {
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"Name": "Europe PMC"
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}
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},
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"Frequency": 1
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},
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{
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"ObtainedBy": "tm_accession",
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"PublicationDate": "04-11-2022",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "References"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "MED"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "MN996532",
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"IDScheme": "ENA",
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"IDURL": "http://identifiers.org/ebi/ena.embl:MN996532"
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},
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"Title": "MN996532",
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"Publisher": {
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"Name": "Europe PMC"
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}
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},
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"Frequency": 1
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},
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{
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"ObtainedBy": "tm_accession",
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"PublicationDate": "04-11-2022",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "References"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "MED"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "MT072864",
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"IDScheme": "ENA",
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"IDURL": "http://identifiers.org/ebi/ena.embl:MT072864"
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},
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"Title": "MT072864",
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"Publisher": {
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"Name": "Europe PMC"
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}
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},
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"Frequency": 1
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}
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]
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}
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}
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]
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},
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{
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"Name": "Protein Structures",
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"NameLong": "Protein structures in PDBe",
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"CategoryLinkCount": 2,
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"Section": [
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{
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"ObtainedBy": "tm_accession",
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"Tags": [
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"supporting_data"
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],
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"SectionLinkCount": 2,
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"Linklist": {
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"Link": [
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{
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"ObtainedBy": "tm_accession",
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"PublicationDate": "04-11-2022",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "References"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "MED"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "6VW1",
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"IDScheme": "PDB",
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"IDURL": "http://identifiers.org/pdbe/pdb:6VW1"
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},
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"Title": "6VW1",
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"Publisher": {
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"Name": "Europe PMC"
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}
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},
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"Frequency": 1
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},
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{
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"ObtainedBy": "tm_accession",
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"PublicationDate": "04-11-2022",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "References"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "MED"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "2AJF",
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"IDScheme": "PDB",
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"IDURL": "http://identifiers.org/pdbe/pdb:2AJF"
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},
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"Title": "2AJF",
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"Publisher": {
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"Name": "Europe PMC"
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}
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},
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"Frequency": 1
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}
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]
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}
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}
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]
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},
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{
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"Name": "Altmetric",
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"CategoryLinkCount": 1,
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"Section": [
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{
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"ObtainedBy": "ext_links",
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"Tags": [
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"altmetrics"
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],
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"SectionLinkCount": 1,
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"Linklist": {
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"Link": [
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{
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"ObtainedBy": "ext_links",
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"PublicationDate": "15-10-2020",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "IsReferencedBy"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "PMID"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "https://www.altmetric.com/details/91880755",
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"IDScheme": "URL",
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"IDURL": "https://www.altmetric.com/details/91880755"
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},
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"Title": "Characteristics of SARS-CoV-2 and COVID-19",
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"Publisher": {
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"Name": "Altmetric"
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},
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"ImageURL": "https://api.altmetric.com/v1/donut/91880755_64.png"
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}
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}
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]
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}
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}
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]
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},
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{
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"Name": "BioStudies: supplemental material and supporting data",
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"CategoryLinkCount": 1,
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"Section": [
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{
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"ObtainedBy": "ext_links",
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"Tags": [
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"supporting_data"
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],
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"SectionLinkCount": 1,
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"Linklist": {
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"Link": [
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{
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"ObtainedBy": "ext_links",
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"PublicationDate": "11-03-2021",
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"LinkProvider": {
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"Name": "Europe PMC"
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},
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"RelationshipType": {
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"Name": "IsReferencedBy"
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},
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"Source": {
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"Type": {
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"Name": "literature"
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},
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"Identifier": {
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"ID": "33024307",
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"IDScheme": "PMID"
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}
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},
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"Target": {
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"Type": {
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"Name": "dataset"
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},
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"Identifier": {
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"ID": "http://www.ebi.ac.uk/biostudies/studies/S-EPMC7537588?xr=true",
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"IDScheme": "URL",
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"IDURL": "http://www.ebi.ac.uk/biostudies/studies/S-EPMC7537588?xr=true"
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},
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"Title": "Characteristics of SARS-CoV-2 and COVID-19.",
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"Publisher": {
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"Name": "BioStudies: supplemental material and supporting data"
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}
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}
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}
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]
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}
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}
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]
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}
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]
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}
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}
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```
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## Mapping
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The table below describes the mapping from the EBI links records to the OpenAIRE Graph dump format.
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| *OpenAIRE Result field path* | PubMed record field xpath | Notes |
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|--------------------------------|--------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------| |