WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

Journal Article · Fri Mar 24 00:00:00 EDT 2017 · Database

DOI:https://doi.org/10.1093/database/bax025· OSTI ID:1454673

Putman, Tim E. ^[1]; Lelong, Sebastien ^[1]; Burgstaller-Muehlbacher, Sebastian ^[1]; Waagmeester, Andra ^[2]; Diesh, Colin ^[3]; Dunn, Nathan ^[4]; Munoz-Torres, Monica ^[4]; Stupp, Gregory S. ^[1]; Wu, Chunlei ^[1]; Su, Andrew I. ^[1]; Good, Benjamin M. ^[1]

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1. Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037 USA
2. Micelio, Antwerp, Belgium
3. Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
4. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

With the advancement of genome-sequencing technologies, new genomes are being sequenced daily. Although these sequences are deposited in publicly available data warehouses, their functional and genomic annotations (beyond genes which are predicted automatically) mostly reside in the text of primary publications. Professional curators are hard at work extracting those annotations from the literature for the most studied organisms and depositing them in structured databases. However, the resources don’t exist to fund the comprehensive curation of the thousands of newly sequenced organisms in this manner. Here, we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomic data by the entire scientific community. WikiGenomes is based on Wikidata, an openly editable knowledge graph with the goal of aggregating published knowledge into a free and open database. WikiGenomes empowers the individual genomic researcher to contribute their expertise to the curation effort and integrates the knowledge into Wikidata, enabling it to be accessed by anyone without restriction.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Inst. of Health (NIH) (United States)
• Grant/Contract Number: AC02-05CH11231; R01GM089820; U54GM114833; U54DA036134; 5R01GM080203; 5R01HG004483
• OSTI ID: 1454673
• Alternate ID(s): OSTI ID: 1411647
• Journal Information: Database, Journal Name: Database Vol. 2017; ISSN 1758-0463
• Publisher: Oxford University Press
• Country of Publication: United Kingdom
• Language: English

Related Subjects

96 KNOWLEDGE MANAGEMENT AND PRESERVATION