From b007a67a3cc95f7d7245bc3456fd795c4b3badef Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 8 Nov 2022 15:58:21 +0100 Subject: [PATCH] added EBI mapping --- docs/data-provision/aggregation/datacite.md | 12 ----------- docs/data-provision/aggregation/ebi.md | 23 +++++++++++++++++++-- 2 files changed, 21 insertions(+), 14 deletions(-) diff --git a/docs/data-provision/aggregation/datacite.md b/docs/data-provision/aggregation/datacite.md index 64d3cdb..722f393 100644 --- a/docs/data-provision/aggregation/datacite.md +++ b/docs/data-provision/aggregation/datacite.md @@ -69,23 +69,11 @@ The table below describes the mapping from the XML baseline records to the OpenA ### Relation Mapping -<<<<<<< HEAD | OpenAIRE Relation Semantic and inverse | Datacite record JSON path | Source/Tartget type | #Notes | |-------------------------------------------|-------------------------------|-------------------------------|---------| | `isProducedBy` |`attributes\fundingReferences` | `Result/Project`| we must identifi if match this pattern `(info:eu-repo/grantagreement/ec/h2020/)(\d{6})(.*)`| | `IsProvidedBy` | | `Result/DataSource` | Datasource is always Datacite| | `IsHostedBy` | `\attributes\relationships\client\id` | `Result/DataSource` |we defined a curated map clientId/Datasource if we found a match we create an _hostedBy Relation_ | | | `\attribute\relatedIdentifiers` | result/result | we create relationships whenever the pid of the target is resolved on the Research Graph | -======= -| OpenAIRE Relation Semantic and inverse | Datacite record JSON path | Source/Tartget type | #Notes | -|----------------------------------------|---------------------------------------|----------------------|---------------------------------------------------------------------------------------------------| -| `isProducedBy` | `attributes\fundingReferences` | `Result/Project` | we must identifi if match this pattern `(info:eu-repo/grantagreement/ec/h2020/)(\d{6})(.*)` | -| `IsProvidedBy` | | `Result/DataSource` | Datasource is always Datacite | -| `IsHostedBy` | `\attributes\relationships\client\id` | `Result/DataSource` | we defined a curated map clientId/Datasource if we found a match we create an _hostedBy Relation_ | - - -### Relation Resolution - ->>>>>>> 92baad5acb3ecfb774510b48fee6aeeba92738df diff --git a/docs/data-provision/aggregation/ebi.md b/docs/data-provision/aggregation/ebi.md index fdbcc7a..f03d49d 100644 --- a/docs/data-provision/aggregation/ebi.md +++ b/docs/data-provision/aggregation/ebi.md @@ -402,7 +402,26 @@ curl -s "https://www.ebi.ac.uk/europepmc/webservices/rest/MED/33024307/datalinks ## Mapping The table below describes the mapping from the EBI links records to the OpenAIRE Graph dump 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 Result field path* | PubMed record field xpath | Notes | -|--------------------------------|--------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------| \ No newline at end of file +| *OpenAIRE Result 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 + + +### Relation Mapping +| OpenAIRE Relation Semantic and inverse | Datacite record JSON path | Source/Tartget type | #Notes | +|-------------------------------------------|-------------------------------|-------------------------------|---------| +| `IsRelatedTo` | | result/result | we create relationships between the BioEntity and the pubmed publication |