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WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata [article]

Tim E Putman, Sebastien Lelong, Sebastian Burgstaller-Muelhbacher, Andra Waagmeester, Colin Diesh, Nathan Dunn, Monica Munoz-Torres, Gregory Stupp, Andrew Su, Benjamin M Good
2017 bioRxiv   pre-print
Here we describe WikiGenomes (wikigenomes.org), a web application that facilitates the consumption and curation of genomic data by the entire scientific community.  ...  WikiGenomes empowers community curation of genomic and biomedical knowledge through a domain-specific application built on top of Wikidata, bringing that curated knowledge to the public domain.  ...  It facilitates both the consumption and community curation 88 of genomic data in Wikidata, extending the reach of the biocuration effort deeper into the long 89 tail of sequenced genomes. 90 Results  ... 
doi:10.1101/102046 fatcat:bingqzpta5c73cdxoo5rvt3giu

WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata [article]

Timothy Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin Diesh, Nathan Dunn, Monica Munoz-Torres, Gregory S. Stupp, Chunlei Wu, Andrew I. Su, Benjamin M. Good
2017 Figshare  
Slideshow of the Wikidata backed web application WikiGenomes.org, presented at the Biocuration 2017 conference at Stanford University.  ...  pattern for using a public, open and shared database • Technical layer that allows users to integrate data into the underlying schema • Data that comes from WikiGenomes becomes available to any application  ...  analysis than eukaryotes GO Annotations GO annotations manually approved by a human curator. • Close to half of human annotations • Close to 2% of the most studied bacteria; • Application development  ... 
doi:10.6084/m9.figshare.5150065 fatcat:o5enmw7awfciffrdd4oxeegsdq

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

Tim E. Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin Diesh, Nathan Dunn, Monica Munoz-Torres, Gregory S. Stupp, Chunlei Wu, Andrew I. Su, Benjamin M. Good
2017 Database: The Journal of Biological Databases and Curation  
Acknowledgements We would like to thank the Wikimedia foundation for supporting the Wikidata project, and especially the Wikidata community for their efforts in populating it. Conflict of interest.  ...  It facilitates both the consumption and community curation of genomic data in Wikidata, extending the reach of the biocuration effort deeper into the long tail of sequenced genomes.  ...  (F) Annotations The annotations that have been curated in Wikidata for the currently loaded Gene/Protein are displayed in the content window in the bottom right corner of the application, separated and  ... 
doi:10.1093/database/bax025 pmid:28365742 pmcid:PMC5467579 fatcat:o3tyj5golfhv3kuwa4m3sra6zq

GeneDB and Wikidata

Magnus Manske, Ulrike Böhme, Christoph Püthe, Matt Berriman
2019 Wellcome Open Research  
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.  ...  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.  ...  To integrate GeneDB data into Wikidata, the authors wrote bots (robots/database clients) using the language Rust and imported GeneDB genes, proteins and Gene Ontology annotations into Wikidata.  ... 
doi:10.12688/wellcomeopenres.15355.2 fatcat:3mna644b3fgbtiycec7cndod4y

Wikidata as a FAIR knowledge graph for the life sciences [article]

Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M Good, Malachi Griffith, Obi Griffith, Kristina Hanspers, Henning Hermjakob, Kevin Hybiske, Sarah M. Keating, Magnus Manske, Michael Mayers (+12 others)
2019 bioRxiv   pre-print
We built a collection of open-source tools that simplify the addition and synchronization of Wikidata with source databases.  ...  Wikidata is a well-suited infrastructure for creating, editing, integrating, and accessing biomedical knowledge.  ...  WikiGenomes: an open web application for 11 community consumption and curation of gene annotation data in Wikidata. Internet]. Zenodo; 2020 [cited 2020 Jan 15].  ... 
doi:10.1101/799684 fatcat:inurqfmvv5cbxhoucg5grj6srm

11,000 researchers gave their views on data sharing, here's what we learned

Mithu Lucraft, Samuel Winthrop
2019 Septentrio Conference Series  
Data sharing and planning is currently suboptimal: The majority of the research community are not yet managing or sharing data in ways that make it findable, accessible or reusable.  ...  The majority of researchers see data sharing as important: across three surveys, when asked about the importance of making data discoverable, researchers gave an average rating of 7.5 out of 10.  ...  WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata, Database, 1 January 2017, bax025, https://doi.org/10.1093/database/bax025 https://web.archive.org  ... 
doi:10.7557/5.4917 fatcat:lbj5yyjetzekbnc3d54u65sfce