Literature DB >> 23782614

Crowdsourcing for bioinformatics.

Benjamin M Good1, Andrew I Su.   

Abstract

MOTIVATION: Bioinformatics is faced with a variety of problems that require human involvement. Tasks like genome annotation, image analysis, knowledge-base population and protein structure determination all benefit from human input. In some cases, people are needed in vast quantities, whereas in others, we need just a few with rare abilities. Crowdsourcing encompasses an emerging collection of approaches for harnessing such distributed human intelligence. Recently, the bioinformatics community has begun to apply crowdsourcing in a variety of contexts, yet few resources are available that describe how these human-powered systems work and how to use them effectively in scientific domains.
RESULTS: Here, we provide a framework for understanding and applying several different types of crowdsourcing. The framework considers two broad classes: systems for solving large-volume 'microtasks' and systems for solving high-difficulty 'megatasks'. Within these classes, we discuss system types, including volunteer labor, games with a purpose, microtask markets and open innovation contests. We illustrate each system type with successful examples in bioinformatics and conclude with a guide for matching problems to crowdsourcing solutions that highlights the positives and negatives of different approaches.

Entities:  

Mesh:

Year:  2013        PMID: 23782614      PMCID: PMC3722523          DOI: 10.1093/bioinformatics/btt333

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  28 in total

1.  Algorithm discovery by protein folding game players.

Authors:  Firas Khatib; Seth Cooper; Michael D Tyka; Kefan Xu; Ilya Makedon; Zoran Popovic; David Baker; Foldit Players
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-07       Impact factor: 11.205

2.  Development and evaluation of a crowdsourcing methodology for knowledge base construction: identifying relationships between clinical problems and medications.

Authors:  Allison B McCoy; Adam Wright; Archana Laxmisan; Madelene J Ottosen; Jacob A McCoy; David Butten; Dean F Sittig
Journal:  J Am Med Inform Assoc       Date:  2012-05-12       Impact factor: 4.497

3.  Galaxy evolution. Galaxy zoo volunteers share pain and glory of research.

Authors:  Daniel Clery
Journal:  Science       Date:  2011-07-08       Impact factor: 47.728

4.  Raising money for scientific research through crowdfunding.

Authors:  Rachel E Wheat; Yiwei Wang; Jarrett E Byrnes; Jai Ranganathan
Journal:  Trends Ecol Evol       Date:  2012-12-05       Impact factor: 17.712

5.  Knowledge acquisition for medical diagnosis using collective intelligence.

Authors:  G Hernández-Chan; A Rodríguez-González; G Alor-Hernández; J M Gómez-Berbís; M A Mayer-Pujadas; R Posada-Gómez
Journal:  J Med Syst       Date:  2012-10-23       Impact factor: 4.460

6.  Predicting protein structures with a multiplayer online game.

Authors:  Seth Cooper; Firas Khatib; Adrien Treuille; Janos Barbero; Jeehyung Lee; Michael Beenen; Andrew Leaver-Fay; David Baker; Zoran Popović; Foldit Players
Journal:  Nature       Date:  2010-08-05       Impact factor: 49.962

7.  Prize-based contests can provide solutions to computational biology problems.

Authors:  Karim R Lakhani; Kevin J Boudreau; Po-Ru Loh; Lars Backstrom; Carliss Baldwin; Eric Lonstein; Mike Lydon; Alan MacCormack; Ramy A Arnaout; Eva C Guinan
Journal:  Nat Biotechnol       Date:  2013-02       Impact factor: 54.908

8.  Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.

Authors:  Christopher B Eiben; Justin B Siegel; Jacob B Bale; Seth Cooper; Firas Khatib; Betty W Shen; Foldit Players; Barry L Stoddard; Zoran Popovic; David Baker
Journal:  Nat Biotechnol       Date:  2012-01-22       Impact factor: 54.908

9.  Efficient replication of over 180 genetic associations with self-reported medical data.

Authors:  Joyce Y Tung; Chuong B Do; David A Hinds; Amy K Kiefer; J Michael Macpherson; Arnab B Chowdry; Uta Francke; Brian T Naughton; Joanna L Mountain; Anne Wojcicki; Nicholas Eriksson
Journal:  PLoS One       Date:  2011-08-17       Impact factor: 3.240

10.  Crowdsourcing malaria parasite quantification: an online game for analyzing images of infected thick blood smears.

Authors:  Miguel Angel Luengo-Oroz; Asier Arranz; John Frean
Journal:  J Med Internet Res       Date:  2012-11-29       Impact factor: 5.428

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  42 in total

1.  Use of big data in drug development for precision medicine.

Authors:  Rosa S Kim; Nicolas Goossens; Yujin Hoshida
Journal:  Expert Rev Precis Med Drug Dev       Date:  2016-04-28

2.  GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.

Authors:  Gregory W Gundersen; Matthew R Jones; Andrew D Rouillard; Yan Kou; Caroline D Monteiro; Axel S Feldmann; Kevin S Hu; Avi Ma'ayan
Journal:  Bioinformatics       Date:  2015-05-13       Impact factor: 6.937

3.  Crowdsourcing and mining crowd data.

Authors:  Robert Leaman; Benjamin M Good; Andrew I Su; Zhiyong Lu
Journal:  Pac Symp Biocomput       Date:  2015

4.  Validation of a Crowdsourcing Methodology for Developing a Knowledge Base of Related Problem-Medication Pairs.

Authors:  A B McCoy; A Wright; M Krousel-Wood; E J Thomas; J A McCoy; D F Sittig
Journal:  Appl Clin Inform       Date:  2015-05-20       Impact factor: 2.342

Review 5.  Crowdsourcing in biomedicine: challenges and opportunities.

Authors:  Ritu Khare; Benjamin M Good; Robert Leaman; Andrew I Su; Zhiyong Lu
Journal:  Brief Bioinform       Date:  2015-04-17       Impact factor: 11.622

6.  Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.

Authors:  Kathleen M Jagodnik; Simon Koplev; Sherry L Jenkins; Lucila Ohno-Machado; Benedict Paten; Stephan C Schurer; Michel Dumontier; Ruben Verborgh; Alex Bui; Peipei Ping; Neil J McKenna; Ravi Madduri; Ajay Pillai; Avi Ma'ayan
Journal:  J Biomed Inform       Date:  2017-05-10       Impact factor: 6.317

7.  Scientific Discovery Games for Biomedical Research.

Authors:  Rhiju Das; Benjamin Keep; Peter Washington; Ingmar H Riedel-Kruse
Journal:  Annu Rev Biomed Data Sci       Date:  2019-07

8.  The potential of crowdsourcing to improve patient-centered care.

Authors:  Michael Weiner
Journal:  Patient       Date:  2014       Impact factor: 3.883

9.  Use of scientific social networking to improve the research strategies of PubMed readers.

Authors:  Pavel Evdokimov; Alexey Kudryavtsev; Ekaterina Ilgisonis; Elena Ponomarenko; Andrey Lisitsa
Journal:  BMC Res Notes       Date:  2016-02-18

10.  Bi-convex Optimization to Learn Classifiers from Multiple Biomedical Annotations.

Authors:  Xin Wang; Jinbo Bi
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2016-06-07       Impact factor: 3.710

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