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aggregation section #2

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schatz merged 27 commits from aggregation into main 2022-11-09 12:01:13 +01:00
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14
docs/data-provision/aggregation/datacite.md
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@ -65,15 +65,13 @@ The table below describes the mapping from the XML baseline records to the OpenA
| `instance.license` | `\attributes\rightsList` | if the rights value starts with http and matches a particular regex |
| `instance.accessright` | `\attributes\rightsList` | <ul><li>if not present :`unknown`</li><li>if datasource is Figshare:`open`</li><li>If `embargo_date < today()`: OPEN</li></ul> |
### Relation Mapping
| 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/Target type | #Notes |
|----------------------------------------|---------------------------------------|---------------------|------------------------------------------------------------------------------------------------------------|
| `isProducedBy/produces` | `attributes\fundingReferences` | `result/project` | only when the fundingReferences matches the pattern `(info:eu-repo/grantagreement/ec/h2020/)(\d{6})(.*)` |
| `IsProvidedBy/provides` | | `result/datasource` | Datasource is always set to `Datacite` |
| `isHostedBy/host` | `\attributes\relationships\client\id` | `result/datasource` | we defined a curated map clientId/Datasource if we found a match we create an _hostedBy Relation_ |
| `isRelatedTo` | `\attribute\relatedIdentifiers` | `result/result` | we create relationships whenever the pid of the target is resolved on the Research Graph |

31
docs/data-provision/aggregation/ebi.md
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@ -406,22 +406,21 @@ We filter all the target links with pid type **ena**, **pdb** or **uniprot**
For each target we construct a Bioentity with the following mapping
schatz commented 2022-11-08 12:57:54 +01:00
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This is empty. Remove it or add content. Also remove italics from the table header.

This is empty. Remove it or add content. Also remove italics from the table header.
claudio.atzori commented 2022-11-08 17:05:07 +01:00
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Fixed

Fixed
| *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
| *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 |
| OpenAIRE Relation Semantic and inverse | Source/Target type | #Notes |
|----------------------------------------|---------------------|--------------------------------------------------------------------------|
| `IsRelatedTo` | `result/result` | we create relationships between the BioEntity and the pubmed publication |