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Genegames.org (poster ISMB2012)

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Structured gene annotations are a foundation on which many bioinformatics and statistical analyses are built, however their representation is quite sparse. As centralized biocuration efforts struggle …

Structured gene annotations are a foundation on which many bioinformatics and statistical analyses are built, however their representation is quite sparse. As centralized biocuration efforts struggle to keep up with the rate of biomedical data generation, new models for gene annotation need to be explored.
Recently, online games have emerged as an effective way to recruit, engage and organize contributors to help address difficult challenges like online image tagging (ESP Game), protein folding (Foldit), or multiple sequence alignment (Phylo).
We present here two online games - Dizeez and GenESP - aimed at identifying novel gene-disease annotations, i.e. gene-disease links well established in the literature, but not yet reflected as structured annotations. Preliminary results are provided from game play online and at scientific conferences. These data suggest that even after limited game play, novel gene-disease annotations can be mined from game playing logs.

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  • 1. Online games for human gene annotation Salvatore Loguercio, Benjamin M Good, Andrew I Su The Scripps Research Institute, La Jolla, California, USA ABSTRACT ABSTRACT Dizeez: gene – disease annotation quiz Community building and educational aspectsStructured gene annotations are a foundation on which many Select the disease related to the clue Game reviewbioinformatics and statistical analyses are built, however their gene. Guess as many as you can inrepresentation is quite sparse. As centralized biocuration one minute.efforts struggle to keep up with the rate of biomedical datageneration, new models for gene annotation need to be Every guess adds weight to a link Connect players withexplored. between a gene and a disease. published informationRecently, online games have emerged as an effective way to on genes and diseasesrecruit, engage and organize contributors to help addressdifficult challenges [1] like online image tagging (ESP Game), Preliminary Resultsprotein folding (Foldit) [2], or multiple sequence alignment 713 games, 180players;(Phylo) [3].We present here two online games - Dizeez and GenESP - aimed Overall: 4,585 unique gene-at identifying novel gene-disease annotations, i.e. gene- disease assertions.disease links well established in the literature, but not yet Training Gamereflected as structured annotations. Preliminary results are 224 assertions provided moreprovided from game play online and at scientific conferences. than once and not found inThese data suggest that even after limited game play, novel OMIM/PharmGKB.gene-disease annotations can be mined from game playing logs. Top associations provided four or more times and not found inPlay game prototypes at: http://genegames.org OMIM/PharmGKB. Even after limited game playing, the Dizeez game resulted in the identification of several novel gene-disease annotations. Game Objectives GeneESP: gene – concept association with a partner Use the Knowledge Powers! Powered by MyGene.Info and Phenotype • Capture general MyGeneInfo box community knowledge in a WordClouds gene pathway useful structure gene Community Gene Autocomplete Guess what genes your partner is thinking about when they see ‘neuroblastoma’ REFERENCES • Concentrate Improvements compared to Dizeez: 1. Good and Su (2011) Games with a Scientific Purpose. Genome Biology 2. Khatibet al (2011) Algorithm discovery by protein folding game players. PNAS community knowledge • Reward new, useful annotations with points 3. Kawrykowet al (2012) Phylo: A Citizen Science Approach for Improving Multiple Sequence Alignment. PLoS One and reasoning around • Add social interaction CONTACT predicting a particular • Enable gene-gene, gene-disease, gene-function Benjamin Good: bgood@scripps.eduSalvatore Loguercio: loguerci@scripps.eduAndrew Su: asu@scripps.edu phenotype games on the same platform • Increase scalability of annotation collection (does FUNDING See Poster A40, ‘Combo’ Phenotype 1 We acknowledge support from the National Institute of General Medical Sciences (GM089820 and not depend on a database of ‘right’ answers) GM083924) and the NIH through the FaceBase Consortium for a particular emphasis on Phenotype 2 craniofacial genes (DE-20057). .

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