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1. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Author

Zhou, Naihui, Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Zhou, Naihui, Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, and Lavezzo, Enrico

Abstract

BACKGROUND:The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. RESULTS:Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. CONCLUSION: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.

Published
2019

2. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author

Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemović, Branislava S., Perović, Vladimir R., Davidović, Radoslav S., Šumonja, Neven, Veljković, Nevena V., Asgari, Ehsaneddin, Mofrad, Mohammad R.K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C.E., Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S, Jo, Dane, Suh, Erica, Dayton, Jonathan B, Larsen, Dallas J, Omdahl, Ashton R, McGuffin, Liam J, Brackenridge, Danielle A, Babbitt, Patricia C, Yunes, Jeffrey M, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti E.E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E, Orengo, Christine A, Jeffery, Constance J, Bosco, Giovanni, Hogan, Deborah A, Martin, Maria J, O’Donovan, Claire, Mooney, Sean D, Greene, Casey S, Radivojac, Predrag, Friedberg, Iddo, Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemović, Branislava S., Perović, Vladimir R., Davidović, Radoslav S., Šumonja, Neven, Veljković, Nevena V., Asgari, Ehsaneddin, Mofrad, Mohammad R.K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C.E., Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S, Jo, Dane, Suh, Erica, Dayton, Jonathan B, Larsen, Dallas J, Omdahl, Ashton R, McGuffin, Liam J, Brackenridge, Danielle A, Babbitt, Patricia C, Yunes, Jeffrey M, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti E.E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E, Orengo, Christine A, Jeffery, Constance J, Bosco, Giovanni, Hogan, Deborah A, Martin, Maria J, O’Donovan, Claire, Mooney, Sean D, Greene, Casey S, Radivojac, Predrag, and Friedberg, Iddo

Abstract

Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-Term memory. Conclusion: 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. © 2019 The Author(s).

Published
2019

3. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Author

Zhou, Naihui, Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Zhou, Naihui, Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, and Lavezzo, Enrico

Abstract

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe 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.

Published
2019

4. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author

Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemović, Branislava S., Perović, Vladimir R., Davidović, Radoslav S., Šumonja, Neven, Veljković, Nevena V., Asgari, Ehsaneddin, Mofrad, Mohammad R.K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C.E., Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S, Jo, Dane, Suh, Erica, Dayton, Jonathan B, Larsen, Dallas J, Omdahl, Ashton R, McGuffin, Liam J, Brackenridge, Danielle A, Babbitt, Patricia C, Yunes, Jeffrey M, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti E.E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E, Orengo, Christine A, Jeffery, Constance J, Bosco, Giovanni, Hogan, Deborah A, Martin, Maria J, O’Donovan, Claire, Mooney, Sean D, Greene, Casey S, Radivojac, Predrag, Friedberg, Iddo, Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemović, Branislava S., Perović, Vladimir R., Davidović, Radoslav S., Šumonja, Neven, Veljković, Nevena V., Asgari, Ehsaneddin, Mofrad, Mohammad R.K., Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, Lavezzo, Enrico, Falda, Marco, Berselli, Michele, Tosatto, Silvio C.E., Carraro, Marco, Piovesan, Damiano, Ur Rehman, Hafeez, Mao, Qizhong, Zhang, Shanshan, Vucetic, Slobodan, Black, Gage S, Jo, Dane, Suh, Erica, Dayton, Jonathan B, Larsen, Dallas J, Omdahl, Ashton R, McGuffin, Liam J, Brackenridge, Danielle A, Babbitt, Patricia C, Yunes, Jeffrey M, Fontana, Paolo, Zhang, Feng, Zhu, Shanfeng, You, Ronghui, Zhang, Zihan, Dai, Suyang, Yao, Shuwei, Tian, Weidong, Cao, Renzhi, Chandler, Caleb, Amezola, Miguel, Johnson, Devon, Chang, Jia-Ming, Liao, Wen-Hung, Liu, Yi-Wei, Pascarelli, Stefano, Frank, Yotam, Hoehndorf, Robert, Kulmanov, Maxat, Boudellioua, Imane, Politano, Gianfranco, Di Carlo, Stefano, Benso, Alfredo, Hakala, Kai, Ginter, Filip, Mehryary, Farrokh, Kaewphan, Suwisa, Björne, Jari, Moen, Hans, Tolvanen, Martti E.E., Salakoski, Tapio, Kihara, Daisuke, Jain, Aashish, Šmuc, Tomislav, Altenhoff, Adrian, Ben-Hur, Asa, Rost, Burkhard, Brenner, Steven E, Orengo, Christine A, Jeffery, Constance J, Bosco, Giovanni, Hogan, Deborah A, Martin, Maria J, O’Donovan, Claire, Mooney, Sean D, Greene, Casey S, Radivojac, Predrag, and Friedberg, Iddo

Abstract

Background: The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results: Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-Term memory. Conclusion: 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. © 2019 The Author(s).

Published
2019

5. An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Author

Jiang, Yuxiang, Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, Bkc, Dukka, Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Jiang, Yuxiang, Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, Bkc, Dukka, Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, and Giollo, Manuel

Abstract

BackgroundA major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.ResultsWe conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2.ConclusionsThe top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

Published
2016

6. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C.E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C.E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

7. An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Author

Jiang, Yuxiang, Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, Bkc, Dukka, Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Jiang, Yuxiang, Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, Bkc, Dukka, Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, and Giollo, Manuel

Abstract

BackgroundA major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.ResultsWe conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2.ConclusionsThe top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

Published
2016

8. Tools and data services registry: a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C.E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C.E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

9. Tools and data services registry:a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans-Ioan, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans-Ioan, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

10. An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Author

Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T., Bankapur, Asma R., D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S., Kahanda, Indika, Verspoor, Karin M., Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed M.E., Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching Tai, Hsu, Wen Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T., Chapman, Samuel, BKC, Dukka, Khan, Ishita K., Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E., Hieta, Reija, Legge, Duncan, Lovering, Ruth C., Magrane, Michele, Melidoni, Anna N., Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon Charles, Das, Sayoni, Dawson, Natalie L., Lee, David, Lees, Jonathan G., Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E., Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E., Pavlidis, Paul, Feng, Shou, Cejuela, Juan M., Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio C.E., del Pozo, Angela, Fernández, José M., Maietta, Paolo, Valencia, Alfonso, Tress, Michael L., Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W., van Dijk, Aalt-Jan, Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C., Vencio, Ricardo Z.N., Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael J.E., Wass, Mark N., Huntley, Rachael P., Martin, Maria J., O'Donovan, Claire, Robinson, Peter N., Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C., Brenner, Steven E., Linial, Michal, Orengo, Christine A., Rost, Burkhard, Greene, Casey S., Mooney, Sean D., Friedberg, Iddo, Radivojac, Predrag, Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T., Bankapur, Asma R., D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S., Kahanda, Indika, Verspoor, Karin M., Ben-Hur, Asa, Koo, Da Chen Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed M.E., Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching Tai, Hsu, Wen Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T., Chapman, Samuel, BKC, Dukka, Khan, Ishita K., Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E., Hieta, Reija, Legge, Duncan, Lovering, Ruth C., Magrane, Michele, Melidoni, Anna N., Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon Charles, Das, Sayoni, Dawson, Natalie L., Lee, David, Lees, Jonathan G., Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E., Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E., Pavlidis, Paul, Feng, Shou, Cejuela, Juan M., Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio C.E., del Pozo, Angela, Fernández, José M., Maietta, Paolo, Valencia, Alfonso, Tress, Michael L., Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W., van Dijk, Aalt-Jan, Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C., Vencio, Ricardo Z.N., Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael J.E., Wass, Mark N., Huntley, Rachael P., Martin, Maria J., O'Donovan, Claire, Robinson, Peter N., Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C., Brenner, Steven E., Linial, Michal, Orengo, Christine A., Rost, Burkhard, Greene, Casey S., Mooney, Sean D., Friedberg, Iddo, and Radivojac, Predrag

Abstract

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.

Published
2016

11. Tools and data services registry:a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans-Ioan, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans-Ioan, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

12. Tools and data services registry:a community effort to document bioinformatics resources

Author

Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil Karol, Chmura, Piotr Jaroslaw, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, Brunak, Søren, Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil Karol, Chmura, Piotr Jaroslaw, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thomas, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Hans, Ioannidis, Vassilios, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chris, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C. E., de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of September 2015, the registry includes 1633 resources, with depositions from 91 individual registrations including 40 institutional providers and 51 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Published
2016

13. Graph algorithms for bioinformatics

Author

Casadio, Rita, Profiti, Giuseppe <1980>, Casadio, Rita, and Profiti, Giuseppe <1980>

Abstract

Biological data are inherently interconnected: protein sequences are connected to their annotations, the annotations are structured into ontologies, and so on. While protein-protein interactions are already represented by graphs, in this work I am presenting how a graph structure can be used to enrich the annotation of protein sequences thanks to algorithms that analyze the graph topology. We also describe a novel solution to restrict the data generation needed for building such a graph, thanks to constraints on the data and dynamic programming. The proposed algorithm ideally improves the generation time by a factor of 5. The graph representation is then exploited to build a comprehensive database, thanks to the rising technology of graph databases. While graph databases are widely used for other kind of data, from Twitter tweets to recommendation systems, their application to bioinformatics is new. A graph database is proposed, with a structure that can be easily expanded and queried.

Published
2015

14. Graph algorithms for bioinformatics

Author

Casadio, Rita, Profiti, Giuseppe <1980>, Casadio, Rita, and Profiti, Giuseppe <1980>

Abstract

Biological data are inherently interconnected: protein sequences are connected to their annotations, the annotations are structured into ontologies, and so on. While protein-protein interactions are already represented by graphs, in this work I am presenting how a graph structure can be used to enrich the annotation of protein sequences thanks to algorithms that analyze the graph topology. We also describe a novel solution to restrict the data generation needed for building such a graph, thanks to constraints on the data and dynamic programming. The proposed algorithm ideally improves the generation time by a factor of 5. The graph representation is then exploited to build a comprehensive database, thanks to the rising technology of graph databases. While graph databases are widely used for other kind of data, from Twitter tweets to recommendation systems, their application to bioinformatics is new. A graph database is proposed, with a structure that can be easily expanded and queried.

Published
2015

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