31 lines
3.7 KiB
Markdown
31 lines
3.7 KiB
Markdown
# 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 Dataset 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 Research Product 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 | |