integrating Scholexplorer Bio Entity Datasource documentation (PR#48)
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@ -60,3 +60,6 @@ When tagging a new version, the document versioning mechanism will:
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* Copy the full `docs/` folder contents into a new `versioned_docs/version-<versionName>/` folder.
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* Create a versioned sidebars file based from your current sidebar configuration, saved as `versioned_sidebars/version-<versionName>-sidebars.json`.
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* Append the new version number to `versions.json`.
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Therefore, when previewing the compiled site locally with `npm run start`, ensure to visualise the `Next` version on the browser as it shows the changes under `/docs`.
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To change a version that was already versioned, the source files to be modified are in the `versioned_docs/version-<versionName>/` folder.
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@ -26,6 +26,9 @@ _Start Date: 2023-02-13 • Release Date: 2023-03-01 • Dump release: **n
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- Revised SDG classification: improved coverage (+600K classified DOIs)
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- General increase of the funded scientific outputs, thanks to the full text mining scanning new OpenAccess publications
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- Integrated contents from
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- [EMBL-EBIs Protein Data Bank in Europe](/data-provision/aggregation/non-compatible-sources/ebi)
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- [UniProtKB/Swiss-Prot](/data-provision/aggregation/non-compatible-sources/uniprot)
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#### Changed
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@ -1,32 +1,31 @@
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# UniProtKB/Swiss-Prot
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this section describes the mapping implemented for [UniProtKB/Swiss-Prot](https://www.uniprot.org/).
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The whole dump can be downloaded by [here](https://www.uniprot.org/help/downloadss) the Reviewed (Swiss-Prot).
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From this Dump we extract only the protein linked to a pubmed Publication.
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This section describes the mapping implemented to integrate metadata and links from [UniProtKB/Swiss-Prot](https://www.uniprot.org/).
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The complete data dump "Reviewed (Swiss-Prot)" can be downloaded from [here](https://www.uniprot.org/help/downloads).
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From this dataset, only the protein records linked to a PubMed publication are extracted.
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## Entity Mapping
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The table below describes the mapping from the TEXT metadata format to the OpenAIRE Graph dump format.
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You can check an example of the text metadata [here](https://rest.uniprot.org/uniprotkb/A0A0C5B5G6.txt)
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| OpenAIRE Result field path | FASTA record field xpath| Notes|
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|--------------------------------|----------------------|---------|
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| **BIOEntity Mapping** | | |
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| `id` | `LINE Starts with AC` | id in the form `uniprot_____::md5(id)`|
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| `pid` | `LINE Starts with AC` | example `AC A0A0C5B5G6;` classid=classname=`uniprot` the vaue is the text after `AC` |
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| `publicationdate` | `LINE START WITH DT containg text integrated into UniProtKB/Swiss-Prot` | clean and normalize the format of the date to be `YYYY-mm-dd` |
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| `maintitle` | `LINE START WITH GN`|main 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` | `LINE Starts with AC` | `classid = classname = uniprot` |
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| `instance.url` | `pid` | prepend to the value `https://www.uniprot.org/uniprot/`|
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| `instance.publicationdate` | `LINE START WITH DT containg text integrated into UniProtKB/Swiss-Prot` | clean and normalize the format of the date to be YYYY-mm-dd |
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| OpenAIRE Result field path | FASTA record field xpath | Notes |
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|------------------------------|--------------------------------------------------------------------------|------------------------------------------------------------------------------------------|
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| **BIOEntity Mapping** | | |
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| `id` | `LINE Starts with AC` | id in the form `uniprot_____::md5(id)` |
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| `pid` | `LINE Starts with AC` | example `AC A0A0C5B5G6;` classid=classname=`uniprot` the vaue is the text after `AC` |
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| `publicationdate` | `LINE START WITH DT containg text integrated into UniProtKB/Swiss-Prot` | clean and normalize the format of the date to be `YYYY-mm-dd` |
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| `maintitle` | `LINE START WITH GN` | main 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` | `LINE Starts with AC` | `classid = classname = uniprot` |
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| `instance.url` | `pid` | prepend to the value `https://www.uniprot.org/uniprot/` |
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| `instance.publicationdate` | `LINE START WITH DT containg text integrated into UniProtKB/Swiss-Prot` | 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` | `LINE START WITH RX` | we create relationships between the BioEntity and the pubmed or DOI generating an unresolved target identifier |
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| OpenAIRE Relation Semantic and inverse | Source/Target type | Notes |
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|----------------------------------------|----------------------|--------------------------------------------------------------------------------------------------------------------------|
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| `IsRelatedTo` | `LINE START WITH RX` | the mapping creates relationships between the BioEntity and the PubMed or DOI generating an unresolved target identifier |
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@ -88,8 +88,7 @@ const sidebars = {
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{ type: 'doc', id: 'data-provision/aggregation/non-compatible-sources/pubmed' },
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{ type: 'doc', id: 'data-provision/aggregation/non-compatible-sources/datacite' },
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{ type: 'doc', id: 'data-provision/aggregation/non-compatible-sources/ebi', label: 'EMBL-EBI' },
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{ type: 'doc', id: 'data-provision/aggregation/non-compatible-sources/uniprot', label: 'UniProtKB/Swiss-Prot' },
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{ type: 'doc', id: 'data-provision/aggregation/non-compatible-sources/uniprot', label: 'UniProtKB/Swiss-Prot' }
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]
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}
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]
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@ -26,6 +26,9 @@ _Start Date: 2023-02-13 • Release Date: 2023-03-01 • Dump release: **n
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- Revised SDG classification: improved coverage (+600K classified DOIs)
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- General increase of the funded scientific outputs, thanks to the full text mining scanning new OpenAccess publications
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- Integrated contents from
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- [EMBL-EBIs Protein Data Bank in Europe](/data-provision/aggregation/non-compatible-sources/ebi)
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- [UniProtKB/Swiss-Prot](/data-provision/aggregation/non-compatible-sources/uniprot)
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#### Changed
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@ -18,6 +18,10 @@ Such a policy defines a list of data sources that are considered authoritative f
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| doi | [Crossref](https://www.crossref.org), [Datacite](https://datacite.org) |
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| pmc, pmid | [Europe PubMed Central](https://europepmc.org/), [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc) |
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| arXiv | [arXiv.org e-Print Archive](https://arxiv.org/) |
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| uniprot | [Protein Data Bank](http://www.pdb.org/) |
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| ena | [Protein Data Bank](http://www.pdb.org/) |
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| pdb | [Protein Data Bank](http://www.pdb.org/) |
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There is an exception though: Handle(s) are minted by several repositories; as listing them all would not be a viable option, to avoid losing them as PIDs, Handles bypass the PID authority filtering rule.
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In all other cases, PIDs are be included in the graph as alternate Identifiers.
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@ -63,12 +67,15 @@ When the record is collected from a source which is not authoritative for any ty
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Currently, the following data sources are used as "PID authorities":
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| PID Type | Prefix (12 chars) | Authority |
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|-----------|------------------------|-----------------------------------------|
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|-----------|------------------------|-------------------------------------------|
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| doi | `doi_________` | Crossref, Datacite, Zenodo |
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| pmc | `pmc_________` | Europe PubMed Central, PubMed Central |
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| pmid | `pmid________` | Europe PubMed Central, PubMed Central |
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| arXiv | `arXiv_______` | arXiv.org e-Print Archive |
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| handle | `handle______` | any repository |
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| ena | `ena_________` | EMBL-EBI |
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| pdb | `pdb_________` | EMBL-EBI |
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| uniprot | `uniprot_____` | EMBL-EBI |
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OpenAIRE also perform duplicate identification (see the [dedicated section for details](/data-provision/deduplication)).
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All duplicates are **merged** together in a **representative record** which must be assigned a dedicated OpenAIRE identifier (i.e. it cannot have the identifier of one of the aggregated record).
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@ -0,0 +1,31 @@
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# UniProtKB/Swiss-Prot
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This section describes the mapping implemented to integrate metadata and links from [UniProtKB/Swiss-Prot](https://www.uniprot.org/).
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The complete data dump "Reviewed (Swiss-Prot)" can be downloaded from [here](https://www.uniprot.org/help/downloads).
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From this dataset, only the protein records linked to a PubMed publication are extracted.
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## Entity Mapping
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The table below describes the mapping from the TEXT metadata format to the OpenAIRE Graph dump format.
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You can check an example of the text metadata [here](https://rest.uniprot.org/uniprotkb/A0A0C5B5G6.txt)
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| OpenAIRE Result field path | FASTA record field xpath | Notes |
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|------------------------------|--------------------------------------------------------------------------|------------------------------------------------------------------------------------------|
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| **BIOEntity Mapping** | | |
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| `id` | `LINE Starts with AC` | id in the form `uniprot_____::md5(id)` |
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| `pid` | `LINE Starts with AC` | example `AC A0A0C5B5G6;` classid=classname=`uniprot` the vaue is the text after `AC` |
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| `publicationdate` | `LINE START WITH DT containg text integrated into UniProtKB/Swiss-Prot` | clean and normalize the format of the date to be `YYYY-mm-dd` |
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| `maintitle` | `LINE START WITH GN` | main 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` | `LINE Starts with AC` | `classid = classname = uniprot` |
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| `instance.url` | `pid` | prepend to the value `https://www.uniprot.org/uniprot/` |
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| `instance.publicationdate` | `LINE START WITH DT containg text integrated into UniProtKB/Swiss-Prot` | 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` | `LINE START WITH RX` | the mapping creates relationships between the BioEntity and the PubMed or DOI generating an unresolved target identifier |
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@ -128,6 +128,11 @@
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"type": "doc",
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"id": "data-provision/aggregation/non-compatible-sources/ebi",
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"label": "EMBL-EBI"
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},
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{
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"type": "doc",
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"id": "data-provision/aggregation/non-compatible-sources/uniprot",
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"label": "UniProtKB/Swiss-Prot"
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}
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]
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}
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