diff --git a/docs/data-provision/aggregation/datacite.md b/docs/data-provision/aggregation/datacite.md
index b268e14..0de7b98 100644
--- a/docs/data-provision/aggregation/datacite.md
+++ b/docs/data-provision/aggregation/datacite.md
@@ -32,46 +32,45 @@ The metadata collection process identifies the most recent record date available
## Datacite Mapping
The table below describes the mapping from the XML baseline records to the OpenAIRE Graph dump format.
-
-| OpenAIRE Result field path | Datacite record JSON path | # Notes |
-|--------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| `id` | `\attributes\doi` | id in the form `doi_________::md5(doi)` |
-| - `instance`
- `instance.type`
| - `\attributes\types\resourceType`
- `\attributes\types\resourceTypeGeneral`
- `attributes\types\schemaOrg`
| Use the vocabulary **_dnet:publication_resource_** to find a synonym to one of these terms and get the `instance.type`. |
-|`type` | - `\attributes\types\resourceType`
- `\attributes\types\resourceTypeGeneral`
- `attributes\types\schemaOrg`
| Using the **_dnet:result_typologies_** vocabulary, we look up the `instance.type` synonym to generate one of the following main entities: - `publication`
- `dataset`
- `software`
- `otherresearchproduct`
|
-| `pid` | `\attributes\doi` | `scheme = doi` |
-| `originalid` | `\attributes\doi` | |
-| `dateofcollection` | `attributes\updated` | the timestamp is defined in milliseconds we convert to "yyyy-MM-dd'T'HH:mm:ssZ" format |
-| `author` | `\attributes\creators` | Each creator field will be mapped in the author entity below the subfield. **If the record has no Creator it will be skipped** |
-| `author.fullname` | `\attributes\creators\name` | if name is not defined, we construct from given and family name |
-| `author.rank` | | Incremental index starting from 1 |
-| `author.name` | `\attributes\creators\givenName` | |
-| `author.surname` | `\attributes\creators\familyName` | |
-| `author.pid` | `\attributes\creators\nameIdentifiers` | this is a list of pids associated to the creator |
-| `author.pid.scheme` | `\attributes\creators\nameIdentifiers` | mapping with vocabulary **dnet:pid_types** |
-| `author.pid.value` | `\attributes\creators\nameIdentifiers/nameIdentifier` | the pid value |
-| `maintitle` | `\attributes\titles` | Titles whose title type is null or title type is Main |
-| `subtitle` | `\attributes\titles` | Titles whose title type is Subtitle since the title type vocabulary in OpenAIRE use the datacite title type vocabulary |
-| **date section** | | for each date in particular for DOI starting with _10.14457_ we Apply a fix thai date convert a date to ThaiBuddhistDate and reformat to local one see ticket [#6791](https://support.openaire.eu/issues/6791) |
-| `publicationdate` | `\attributes\dates` | where `dateType` is **issued** |
-| `publicationdate` | `\attributes\publicationYear` | we create this date format `01-01-publicationYear` |
-| `embargoenddate` | `\attributes\dates` | where `dateType` is **available** |
-| `subjects` | `\attributes\subject` | `scheme=keywords` |
-| `description` | `\attributes\descriptions` | |
-| `publisher` | `\attributes\publisher` | |
-| `language` | `\attributes\language` | cleaned by using vocabulary `dnet:languages` |
-| `publisher` | `\attributes\publisher` | |
-| `instance.license` | `\attributes\rightsList` | if right value starts with http and matches a particular regex |
-| `instance.accessright` | `\attributes\rightsList` | - if not present :`unknown`
- if datasource is _figshare_:`open`
- If `embargo_date < today()`: _OPEN_
|
+| OpenAIRE Result field path | Datacite record JSON path | # Notes |
+|--------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| `id` | `\attributes\doi` | id in the form `doi_________::md5(doi)` |
+| - `instance`
- `instance.type`
| - `\attributes\types\resourceType`
- `\attributes\types\resourceTypeGeneral`
- `attributes\types\schemaOrg`
| Use the vocabulary **_dnet:publication_resource_** to find a synonym to one of these terms and get the `instance.type`. |
+| `type` | - `\attributes\types\resourceType`
- `\attributes\types\resourceTypeGeneral`
- `attributes\types\schemaOrg`
| Using the **_dnet:result_typologies_** vocabulary, we look up the `instance.type` synonym to generate one of the following main entities: - `publication`
- `dataset`
- `software`
- `otherresearchproduct`
|
+| `pid` | `\attributes\doi` | `scheme = doi` |
+| `originalid` | `\attributes\doi` | |
+| `dateofcollection` | `attributes\updated` | the timestamp is defined in milliseconds we convert to "yyyy-MM-dd'T'HH:mm:ssZ" format |
+| `author` | `\attributes\creators` | Each creator field will be mapped in the author entity below the subfield. **If the record has no Creator it will be skipped** |
+| `author.fullname` | `\attributes\creators\name` | if name is not defined, we construct from given and family name |
+| `author.rank` | | Incremental index starting from 1 |
+| `author.name` | `\attributes\creators\givenName` | |
+| `author.surname` | `\attributes\creators\familyName` | |
+| `author.pid` | `\attributes\creators\nameIdentifiers` | this is a list of pids associated to the creator |
+| `author.pid.scheme` | `\attributes\creators\nameIdentifiers` | mapping with vocabulary **dnet:pid_types** |
+| `author.pid.value` | `\attributes\creators\nameIdentifiers/nameIdentifier` | the pid value |
+| `maintitle` | `\attributes\titles` | Titles whose title type is null or title type is Main |
+| `subtitle` | `\attributes\titles` | Titles whose title type is Subtitle since the title type vocabulary in OpenAIRE use the datacite title type vocabulary |
+| **date section** | | for each date in particular for DOI starting with _10.14457_ we Apply a fix thai date convert a date to ThaiBuddhistDate and reformat to local one see ticket [#6791](https://support.openaire.eu/issues/6791) |
+| `publicationdate` | `\attributes\dates` | where `dateType` is **issued** |
+| `publicationdate` | `\attributes\publicationYear` | we create this date format `01-01-publicationYear` |
+| `embargoenddate` | `\attributes\dates` | where `dateType` is **available** |
+| `subjects` | `\attributes\subject` | `scheme=keywords` |
+| `description` | `\attributes\descriptions` | |
+| `publisher` | `\attributes\publisher` | |
+| `language` | `\attributes\language` | cleaned by using vocabulary `dnet:languages` |
+| `publisher` | `\attributes\publisher` | |
+| `instance.license` | `\attributes\rightsList` | if the rights value starts with http and matches a particular regex |
+| `instance.accessright` | `\attributes\rightsList` | - if not present :`unknown`
- if datasource is Figshare:`open`
- If `embargo_date < today()`: OPEN
|
### Mapping Relation
-| 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_ |
+| 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
diff --git a/docs/data-provision/aggregation/ebi.md b/docs/data-provision/aggregation/ebi.md
index 11a8507..fdbcc7a 100644
--- a/docs/data-provision/aggregation/ebi.md
+++ b/docs/data-provision/aggregation/ebi.md
@@ -2,13 +2,403 @@
This section describes the mapping implemented for [EMBL-EBIs Protein Data Bank in Europe](https://www.ebi.ac.uk/).
-The Europe PMC RESTful Web Service gives the [datalinks API](https://europepmc.org/RestfulWebService#!/Europe32PMC32Articles32RESTful32API)to retrieve data-literature links in Scholix format .
+The Europe PMC RESTful Web Service gives the [datalinks API](https://europepmc.org/RestfulWebService#!/Europe32PMC32Articles32RESTful32API) to retrieve data-literature links in Scholix format.
-## how data is collected
-Starting from the Pubmed collection, we exploit this API to get all the related bioentities related to a Publication with a specific PubMed identifier.
+## How the data is collected
-Following this request: `https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json` we store for each pubmedID the links related.
+Starting from the Pubmed collection, the API below is used to obtain the bioentities related to publications for each PubMed identifier.
+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"
+ }
+ }
+ }
+ ]
+ }
+ }
+ ]
+ }
+ ]
+ }
+}
+```
## Mapping
The table below describes the mapping from the EBI links records to the OpenAIRE Graph dump format.