Wikidata as a semantic framework for the Gene Wiki initiative - PubMed (original) (raw)

Wikidata as a semantic framework for the Gene Wiki initiative

Sebastian Burgstaller-Muehlbacher et al. Database (Oxford). 2016.

Abstract

Open biological data are distributed over many resources making them 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, 59,721 human genes and 73,355 mouse genes have been imported from NCBI and 27,306 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 these 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 are modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for usage of the data we imported in all 280 different language Wikipedias. Apart from the Gene Wiki infobox use case, a SPARQL endpoint and exporting functionality to several standard formats (e.g. JSON, XML) enable use of the data by scientists. In summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web. Database URL: https://www.wikidata.org/.

© The Author(s) 2016. Published by Oxford University Press.

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Figures

Figure 1

Figure 1

Wikidata item and data organization. Wikidata items can be added or edited by anyone manually. A Wikidata item consists of: (1) a language-specific label, (2) its unique identifier, (3) language specific aliases, (4) interwiki links to the different language Wikipedia articles or other Wikimedia projects and (5) a list of statements. For this specific example, the human protein Reelin was used (

https://www.wikidata.org/wiki/Q13569356

)

Figure 2

Figure 2

Gene Wiki data model in Wikidata. Each entity (human gene, human protein, mouse gene, mouse protein) is represented as a separate Wikidata item. Arrows represent direct links between Wikidata statements. The English language interwiki link on the human gene item points to the corresponding Gene Wiki article on the English Wikipedia.

Figure 3

Figure 3

GeneWiki infobox populated with data from Wikidata, using data from Wikidata items Q414043 for the human gene, Q13561329 for human protein, Q14331135 for the mouse gene and Q14331165 for the mouse protein. Three dots indicate that there is more information in the real Gene Wiki infobox for Reelin (

https://en.wikipedia.org/wiki/Reelin

).

Figure 4

Figure 4

An example SPARQL query, using the Wikidata SPARQL endpoint (query.wikidata.org). It retrieves all Wikidata (WD) items which are of subclass protein-coding gene (Q840604), which have a chromosomal start position (P644) according to human genome build GRCh38 and reside on human chromosome (P659) 9 (Q20966585) and a chromosomal end position (P645) also on chromosome 9. Furthermore, the region of interest is restricted to a chromosomal start position between 21 and 30 megabase pairs. Colors: Red indicates SPARQL commands, blue represents variable names, green represents URIs and brown are strings. Arrows point to the source code the description applies to.

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