The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Naihui ZhouYuxiang JiangTimothy R BergquistAlexandra J LeeBalint Z KacsohAlex W CrockerKimberley A LewisGeorge GeorghiouHuy N NguyenMd Nafiz HamidLarry DavisTunca DoganVolkan AtalayAhmet S RifaiogluAlperen DalkıranRengul Cetin AtalayChengxin ZhangRebecca L HurtoPeter L FreddolinoYang ZhangPrajwal BhatFran SupekJosé M FernándezBranislava GemovicVladimir R PerovicRadoslav S DavidovićNeven SumonjaNevena VeljkovicEhsaneddin AsgariMohammad R K MofradGiuseppe ProfitiCastrense SavojardoPier Luigi MartelliRita CasadioFlorian BoeckerHeiko SchoofIndika KahandaNatalie ThurlbyAlice C McHardyAlexandre RenauxRabie SaidiJulian GoughAlex A FreitasMagdalena AntczakFabio FabrisMark N WassJie HouJianlin ChengZheng WangAlfonso E RomeroAlberto PaccanaroHaixuan YangTatyana GoldbergChenguang ZhaoLiisa HolmPetri TörönenAlan J MedlarElaine ZosaItamar BorukhovIlya NovikovAngela WilkinsOlivier LichtargePo-Han ChiWei-Cheng TsengMichal LinialPeter W RoseChristophe DessimozVedrana VidulinSaso DzeroskiIan SillitoeSayoni DasJonathan Gill LeesDavid T JonesCen WanDomenico CozzettoRui FaMateo TorresAlex Warwick VesztrocyJose Manuel RodriguezMichael L TressMarco FrascaMarco NotaroGiuliano GrossiAlessandro PetriniMatteo ReGiorgio ValentiniMarco MesitiDaniel B RocheJonas ReebDavid W RitchieSabeur AridhiSeyed Ziaeddin AlborziMarie-Dominique DevignesDa Chen Emily KooRichard BonneauVladimir GligorijevićMeet BarotHai FangStefano ToppoEnrico LavezzoMarco FaldaMichele BerselliSilvio C E TosattoMarco CarraroDamiano PiovesanHafeez Ur RehmanQizhong MaoShanshan ZhangSlobodan VuceticGage S BlackDane JoErica SuhJonathan B DaytonDallas J LarsenAshton R OmdahlLiam J McGuffinDanielle A BrackenridgePatricia C BabbittJeffrey M YunesPaolo FontanaFeng ZhangShanfeng ZhuRonghui YouZihan ZhangSuyang DaiShuwei YaoWeidong TianRenzhi CaoCaleb ChandlerMiguel AmezolaDevon JohnsonJia-Ming ChangWen-Hung LiaoYi-Wei LiuStefano PascarelliYotam FrankRobert HoehndorfMaxat KulmanovImane BoudelliouaGianfranco PolitanoStefano Di CarloAlfredo BensoKai HakalaFilip GinterFarrokh MehryarySuwisa KaewphanJari BjörneHans MoenMartti E E TolvanenTapio SalakoskiDaisuke KiharaAashish JainTomislav ŠmucAdrian AltenhoffAsa Ben-HurBurkhard RostSteven E BrennerChristine A OrengoConstance J JefferyGiovanni BoscoDeborah A HoganMaria J MartinClaire O'DonovanSean D MooneyCasey S GreenePredrag RadivojacIddo FriedbergPublished in: Genome biology (2019)
We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.