Nov 18, 2015

Wikidata as a semantic framework for the Gene Wiki initiative

BioRxiv : the Preprint Server for Biology
Sebastian Burgstaller-MuehlbacherAndrew I Su

Abstract

Open biological data is distributed over many resources making it challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia. In order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata. In total, 59,530 human genes and 73,130 mouse genes have been imported from NCBI and 27,662 human proteins and 16,728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike. The first use case for this data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata is modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for a usage of the data we imported in a...Continue Reading

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Mentioned in this Paper

Genes
Genes and Gene Therapy
Ncbi Taxonomy
Body of Uterus
Universal Protein Resource
Human gene
Mouse Embryonic Stem Cells
Disease Management
NR4A2 protein, human
Molecular Biology

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