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. 2019 Oct 14:4:114.
doi: 10.12688/wellcomeopenres.15355.2. eCollection 2019.

GeneDB and Wikidata

Magnus Manske  1 , Ulrike Böhme  1 , Christoph Püthe  1 , Matt Berriman  1
Affiliations

GeneDB and Wikidata

Magnus Manske et al. Wellcome Open Res. .

Abstract

Publishing authoritative genomic annotation data, keeping it up to date, linking it to related information, and allowing community annotation is difficult and hard to support with limited resources. Here, we show how importing GeneDB annotation data into Wikidata allows for leveraging existing resources, integrating volunteer and scientific communities, and enriching the original information.

Keywords: GeneDB; MediaWiki; Wikibase; Wikidata; annotation; curation; genome; reference.

PubMed Disclaimer

Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Part of the Scholia tool website about the PfCRT gene ( https://tools.wmflabs.org/scholia/topic/Q19044775).
These figures show connected topics, connected locations on a map, and the most prolific authors for this topic, respectively. All figures are generated live from Wikidata via its various APIs. All this information, and more, results from linking scientific publications to the genes in Wikidata.
Figure 2.
Figure 2.. Gene information on GeneDB ( https://www.genedb.org/gene/PF3D7_0709000).
All information comes exclusively from Wikidata.
Figure 3.
Figure 3.. GO term ontology ( https://www.genedb.org/gene/PF3D7_1135600), with sources.
Figure 4.
Figure 4.. Species page for Plasmodium gallinaceum, using information and image from Wikidata.
Figure 5.
Figure 5.. Genes for proteins with a specific GO term ( https://www.genedb.org/#/go/GO:0000799), in all species.
Results from Wikidata, limited to genes with a GeneDB ID.
See this image and copyright information in PMC

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