UniProtKB/Swiss-Prot
This section describes the mapping implemented to integrate metadata and links from UniProtKB/Swiss-Prot. The complete data dump "Reviewed (Swiss-Prot)" can be downloaded from here.
From this dataset, only the protein records linked to a PubMed publication are extracted.
Entity Mapping
The table below describes the mapping from the TEXT metadata format to the OpenAIRE Graph Dataset format. You can check an example of the text metadata here
| OpenAIRE Research Product field path | FASTA record field xpath | Notes |
|---|---|---|
| BIOEntity Mapping | ||
id | LINE Starts with AC | id in the form uniprot_____::md5(id) |
pid | LINE Starts with AC | example AC A0A0C5B5G6; classid=classname=uniprot the vaue is the text after AC |
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 |
maintitle | LINE START WITH GN | main title |
| Instance Mapping | ||
instance.type | Bioentity | |
type | Dataset | |
instance.pid | LINE Starts with AC | classid = classname = uniprot |
instance.url | pid | prepend to the value https://www.uniprot.org/uniprot/ |
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 |
Relation Mapping
| OpenAIRE Relation Semantic and inverse | Source/Target type | Notes |
|---|---|---|
IsRelatedTo | LINE START WITH RX | the mapping creates relationships between the BioEntity and the PubMed or DOI generating an unresolved target identifier |