Andrew I. Su

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Andrew I. Su is an author.

Publications

Only those publications related to wikis are shown here.
Title Keyword(s) Published in Language DateThis property is a special property in this wiki. Abstract R C
The Gene Wiki in 2011: community intelligence applied to human gene annotation Nucleic Acids Research English 2012 The Gene Wiki is an open-access and openly editable collection of Wikipedia articles about human genes. Initiated in 2008, it has grown to include articles about more than 10 000 genes that, collectively, contain more than 1.4 million words of gene-centric text with extensive citations back to the primary scientific literature. This growing body of useful, gene-centric content is the result of the work of thousands of individuals throughout the scientific community. Here, we describe recent improvements to the automated system that keeps the structured data presented on Gene Wiki articles in sync with the data from trusted primary databases. We also describe the expanding contents, editors and users of the Gene Wiki. Finally, we introduce a new automated system, called WikiTrust, which can effectively compute the quality of Wikipedia articles, including Gene Wiki articles, at the word level. All articles in the Gene Wiki can be freely accessed and edited at Wikipedia, and additional links and information can be found at the project's Wikipedia portal page: http://en.wikipedia.org/wiki/Portal:Gene_Wiki. 0 0
Mining the Gene Wiki for functional genomic knowledge BMC genomics English 2011 Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology. RESULTS: Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses. The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses. 0 0
The Gene Wiki: community intelligence applied to human gene annotation Nucleic Acids Research
Nucleic Acids Research Pages Database issue
English 2010 Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it is increasingly clear that this approach does not scale with the rapid growth of the biomedical literature. The Gene Wiki utilizes an alternative and complementary model based on the principle of community intelligence. Directly integrated within the online encyclopedia, Wikipedia, the goal of this effort is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Previously, we described the creation of Gene Wiki ‘stubs’ for approximately 9000 human genes. Here, we describe ongoing systematic improvements to these articles to increase their utility. Moreover, we retrospectively examine the community usage and improvement of the Gene Wiki, providing evidence of a critical mass of users and editors. Gene Wiki articles are freely accessible within the Wikipedia web site, and additional links and information are available at http://en.wikipedia.org/wiki/Portal:Gene_Wiki.
Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it is increasingly clear that this approach does not scale with the rapid growth of the biomedical literature. The Gene Wiki utilizes an alternative and complementary model based on the principle of community intelligence. Directly integrated within the online encyclopedia, Wikipedia, the goal of this effort is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Previously, we described the creation of Gene Wiki 'stubs' for approximately 9000 human genes. Here, we describe ongoing systematic improvements to these articles to increase their utility. Moreover, we retrospectively examine the community usage and improvement of the Gene Wiki, providing evidence of a critical mass of users and editors. Gene Wiki articles are freely accessible within the Wikipedia web site, and additional links and information are available at http://en.wikipedia.org/wiki/Portal:Gene\_Wiki.
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A gene wiki for community annotation of gene function English 2008 This manuscript describes the creation of comprehensive gene wiki, seeded with data from public domain sources, which will enable and encourage community annotation of gene function. 0 5