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

To align the different sources in Wikidata, a common data schema is needed. We have created a collection of schema's that represent the structure of the items added 11 . 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 It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 to wikidata. Input to the workflow is the NCBI taxon identifier, which is input to mygene.info (see Figure 3 ). Taxon information is obtained and added to Wikidata according to a set of linked Entity Schemas ( E170 : virus, E174 : strain, E69 : disease). Gene annotations are obtained and added to WIkidata following the Schemas ( E165 : virus gene, E169 : virus protein) and protein annotations are obtained and added to Wikidata following the two schemas. The last two schemas are an extension from more generic schemas for proteins ( E167 ) and genes ( E75 ). Table 1 . The copyright holder for this preprint (which was not peer-reviewed) is the .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 Wikidata identifiers, 69 NCBI Gene identifiers, 42 UniProt identifiers, and 55 RefSeq identifiers. The mapping file has been released on the BridgeDb website ( https://bridgedb.github.io/data/gene_database/ ). The mapping database has also been loaded on the BridgeDb webservice at http://webservice.bridgedb.org/ which means it can be used in the next use case: providing links out for WikiPathways. The copyright holder for this preprint (which was not peer-reviewed) is the .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 gene and protein, two Wikidata identifiers with links may be given. In that case, one is for the gene and one for the protein.