A protocol for adding knowledge to Wikidata, a case report

Andra Waagmeester; Egon L. Willighagen; Andrew I. Su; Martina Kutmon; Jose Emilio Labra Gayo; Daniel Fernández-Álvarez; Peter J. Schaap; Lisa M. Verhagen; Jasper J. Koehorst

The second step in our workflow is to add entries for all virus strains, genes and their gene products to Wikidata. This information is spread over different resources. Here, annotations were obtained from NCBI EUtils (33) , Mygene.info (34) , and UniProt, as 7 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.05.026336 doi: bioRxiv preprint outlined below. Input to the workflow is the NCBI Taxonomy identifier of a virus under scrutiny. ( e.g. 2697049 for SARS-CoV-2). The taxon annotations are extracted from NCBI EUtils. The gene and gene product annotations are extracted from mygene.info and the protein annotations are extracted from UniProt using the SPARQL endpoint at ( https://sparql.uniprot.org/ ). Genomic information from seven human coronaviruses (HCoVs) was obtained from literature including the NCBI Taxonomy identifiers. For six virus strains a reference genome was available and was used to populate Wikidata. For SARS-CoV-1, the NCBI Taxonomy identifier referred to various strains, though no reference strain was available. To overcome this issue, the species taxon for SARS-related coronaviruses (SARSr-CoV) was used instead, following the practices of NCBI Genes and UniProt.