95 lines
4.7 KiB
Markdown
95 lines
4.7 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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[...]
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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 Dataset format.
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We filter all the target links with pid type **ena**, **pdb** or **uniprot**
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For each target we construct a Bioentity with the following mapping
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| OpenAIRE Research Product field path | EBI record field xpath | Notes |
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|-----------------------------|----------------------------------------------------------|---------------------------------------------------------------|
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| `id` | `target/identifier/ID` and `target/identifier/IDScheme` | id in the form `SCHEMA_________::md5(pid)` |
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| `pid` | `target/identifier/ID` and `target/identifier/IDScheme` | `classid = classname = schema` |
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| `publicationdate` | `target/PublicationDate` | clean and normalize the format of the date to be `YYYY-mm-dd` |
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| `maintitle` | `target/Title` | |
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| **Instance Mapping** | | |
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| `instance.type` | | `Bioentity` |
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| `type` | | `Dataset` |
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| `instance.pid` | `target/identifier/ID` and `target/identifier/IDScheme` | `classid = classname = schema` |
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| `instance.url` | `target/identifier/IDURL` | Copy the value as it is |
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| `instance.publicationdate` | `//PubmedPubDate` | clean and normalize the format of the date to be YYYY-mm-dd |
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### Relation Mapping
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| OpenAIRE Relation Semantic and inverse | Source/Target type | Notes |
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|----------------------------------------|---------------------|--------------------------------------------------------------------------|
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| `IsRelatedTo` | `ResearchProduct/ResearchProduct` | we create relationships between the BioEntity and the pubmed publication |
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