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

Abstract

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.

Authors:
 [1];  [1];  [1];  [2];  [3];  [4];  [4];  [1];  [1];  [1];  [1]
+ Show Author Affiliations
  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
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Inst. of Health (NIH) (United States)
OSTI Identifier:
1454673
Alternate Identifier(s):
OSTI ID: 1411647
Grant/Contract Number:  
AC02-05CH11231; R01GM089820; U54GM114833; U54DA036134; 5R01GM080203; 5R01HG004483
Resource Type:
Published Article
Journal Name:
Database
Additional Journal Information:
Journal Name: Database Journal Volume: 2017; Journal ID: ISSN 1758-0463
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English
Subject:
96 KNOWLEDGE MANAGEMENT AND PRESERVATION

Citation Formats

Putman, Tim E., Lelong, Sebastien, Burgstaller-Muehlbacher, Sebastian, Waagmeester, Andra, Diesh, Colin, Dunn, Nathan, Munoz-Torres, Monica, Stupp, Gregory S., Wu, Chunlei, Su, Andrew I., and Good, Benjamin M. WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. United Kingdom: N. p., 2017. Web. doi:10.1093/database/bax025.
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Putman, Tim E., Lelong, Sebastien, Burgstaller-Muehlbacher, Sebastian, Waagmeester, Andra, Diesh, Colin, Dunn, Nathan, Munoz-Torres, Monica, Stupp, Gregory S., Wu, Chunlei, Su, Andrew I., & Good, Benjamin M. WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. United Kingdom. https://doi.org/10.1093/database/bax025
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Putman, Tim E., Lelong, Sebastien, Burgstaller-Muehlbacher, Sebastian, Waagmeester, Andra, Diesh, Colin, Dunn, Nathan, Munoz-Torres, Monica, Stupp, Gregory S., Wu, Chunlei, Su, Andrew I., and Good, Benjamin M. Fri . "WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata". United Kingdom. https://doi.org/10.1093/database/bax025.
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@article{osti_1454673,
title = {WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata},
author = {Putman, Tim E. and Lelong, Sebastien and Burgstaller-Muehlbacher, Sebastian and Waagmeester, Andra and Diesh, Colin and Dunn, Nathan and Munoz-Torres, Monica and Stupp, Gregory S. and Wu, Chunlei and Su, Andrew I. and Good, Benjamin M.},
abstractNote = {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.},
doi = {10.1093/database/bax025},
journal = {Database},
number = ,
volume = 2017,
place = {United Kingdom},
year = {Fri Mar 24 00:00:00 EDT 2017},
month = {Fri Mar 24 00:00:00 EDT 2017}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1093/database/bax025
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