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