Introduction to the Gene Ontology and GO Annotation Resources
Games for Human Gene Annotation
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Transcript of Games for Human Gene Annotation
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Salvatore)Loguercio*,)Benjamin)Good,)Andrew)Su)
Department)of)Molecular)and)Experimental)Medicine)The)Scripps)Research)InsDtute)
ISMB)BioEOntologies)SIG)
July)13,)2012)
Games)for)Human)Gene)AnnotaDon)
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Growth of potential annotations 2
500000 550000 600000 650000 700000 750000 800000 850000 900000 950000
1000000
Number of articles
added to PubMed
PubMed in 2012: > 21 million articles.
Approaching 1 million new articles per year (>1/minute)
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3
0
10
20
1979 1984 1989 1994 1999 2004 2009
Average capacity of human scientist Number of articles read by typical scientist
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1.5%)of)PubMed*)cited)by)GO)annotaDons)
*311,696)arDcles)(2011)))
PubMed)
GO)
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5
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Sooner or later, the research community will
need to be involved in the annotation effort to scale
up to the rate of data generation.
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How)to)involve)the)community)in)gene)annotaDon?)
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Crowdsourcing)Biology)
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Gene)Wiki:)Comprehensively)organize)knowledge)of)all)human)genes)
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Gene)annotaDon)portal)for)aggregaDng)geneEcentric)online)content)
h]p://biogps.org))
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Biological)games)Build)scienDfic)knowledge)through)game)play)
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Why)games?)
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It)is)esDmated)that)9)billion)hours)are)spent)playing)Solitaire)every)year)
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13)
h]p://www.flickr.com/photos/archana3k1/4124330493/)
Seven million human hours
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14)
Twenty million human hours
h]p://www.flickr.com/photos/ableman/2171326385/)
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E)15)
150 billion human hours
h]p://www.flickr.com/photos/rvpEcw/6243289302/)
per year
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Can)we)harness)some)of)this)Dme)and)energy?))
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Games)with)a)purpose)
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Devise)protein)folding)algorithms)
Fix)mulDple)sequence)alignments)Design)RNA)molecules)
Label)all)images)on)the)Web)
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Annotate)all)human)genes)
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Record)the)relevant)properDes)of)each)gene)in)a)manner)that)facilitates)computaDon)
• biological)process)• molecular)funcDon)• cellular)localizaDon)• interacDon)partners)• disease)relevance)• genomic)locaDon)• geneDc)variaDons)• post)translaDonal)
modificaDons)• related)drugs)• related)publicaDons)• ...)
Gene)
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Dizeez:)geneEdisease)associaDon)quiz)
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DIZEEZ:)geneEdisease)associaDon)quiz)
If its ‘right’, you get points
then on to the next question
Click the related disease
hurry!
h]p://genegames.org)
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• AdverDsed)with)a)blog)post,)a)few)tweets)and)conference)poster)
• Results)since)Dec.)2011:)
– 180)people)have)played)it)– 713)one)minute)game)rounds)have)been)completed)– 5,282)disDnct)geneEdisease)associaDons)collected)
Gameplay)
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Quality)through)replicaDon)
5,282)DisDnct)geneEdisease)pairs)collected)
example:)ABCB5))Acute)myeloid)leukemia))
collected)more)than)once)482))PotenDal)new)annotaDons)
(do)not)appear)in)OMIM,)PharmGKB))223))
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Novel)annotaDons)E)I)
#&Occurrences& Gene& Disease&
7) GAST% gastrinoma)
7) RBP3% reDnoblastoma)
7) SSX1% synovial)sarcoma)
6) TG% Graves')disease)
6) CRYGC%% Cataract)
6) SOX8% mental)retardaDon)
6) WRN%% Werner)syndrome)
6) ABL1%% leukemia)
6) MLL3%% leukemia)
6) SNAI2%% breast)carcinoma)
Pubmed) OMIM) PharmGKB) Gene&Wiki)
2010)or)later)
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Novel)annotaDons)E)II)
#&Occurrences& Gene& Disease&
2) ABCB5) acute)myeloid)leukemia)
2) HOXB7) leukemia)
2) SULF1) carcinoma)
2) ALPP) reDnoblastoma)
2) FOXM1) Melanoma)
Pubmed) OMIM) PharmGKB) Gene&Wiki)
2009)or)later)
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Current)limitaDons))
• Dizeez)actually)punishes)desired)behavior)(adding)new,)unknown)associaDons))by)not)awarding)points)
• Does)not)allow)player)to)enter)associaDons)other)than)those)in)the)provided)list)
• GenESP)fixes)both)problems)
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GenESP:)gene)E)concept)associaDon)with)a)partner)
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(modeled)amer)the)ESP)Game).)See:)Ahn)and)Dabbish)(2004))Labeling)images)with)a)computer)game,)SIGCHI)
h]p://genegames.org)
Gene)–)concept)associaDon)with)a)partner)
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A)reEusable)pa]ern)
Gene) Disease)
Gene) FuncDon)
Gene) Gene)
Gene) Gene)relaDonship)
The Gene Wiki Hairball!
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)Geong)players))
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Social)gaming)
EducaDng)players)Building)a)community))
Arena)mode)labs)vs.)labs)
MulDplayer)Online)E)“Farmville)for)gene)annotaDon”)
SOX2!)TP53!)
Dizeez&
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Epilogue)Crowdsourcing)for)knowledge)acquisiDon)
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Data)and)contributors)
Crowdsourced)model)TradiDonal)model)
Knowledge)
Small)expert)group)
Knowledge)
Data)
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Crowdsourced)model)TradiDonal)model)
ComputaDon)
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Annotate)all)human)genes)
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Erik)Clarke)Max)Nanis)
Ian)Macleod)Chunlei)Wu)
Su)Lab)@)TSRI)
Funding&and&Support&
(BioGPS:)GM83924,)Gene)Wiki:)GM089820))
Interwebs&h]p://sulab.org)
[email protected])@sal999)
+Salvatore)Loguercio)
Crowdsourcing)Biology)@)GSoC)2012!)
Special)thanks)to:)
Ben)Good)Andrew)Su)
Students:)Clarence)Leung)Carolina)Lidstrom)