DrugProt Large-Scale Text Mining corpus: Biocreative VII Track 1 - Text mining drug and chemical-protein interactions

Autor: Miranda-Escalada, Antonio, Jouni Luoma, Farrokh Mehryary, Sampo Pyysalo, Krallinger, Martin

This Zenodo contains the BioCreative VII Large scale DrugProt Additional Subtrackabstracts and entity annotations. Abstracts large_scale_abstracts.tsvThis filecontains plain-­text, UTF8-­encoded, NFC normalized DrugProt PubMed records in a tab­ �

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::25411c99fd25dfbf9c44bc99a6284dde

Neural network and random forest models in protein function prediction

Autor: Jari Björne, Suwisa Kaewphan, Martti Tolvanen, Tapio Salakoski, Hans Moen, Filip Ginter, Farrokh Mehryary, Kai Hakala

Over the past decade, the demand for automated protein function prediction has increased due to the volume of newly sequenced proteins. In this paper, we address the function prediction task by developing an ensemble system automatically assigning Ge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::664626b9707d778625bb59ba6f1947af

The Cafa Challenge Reports Improved Protein Function Prediction And New Functional Annotations For Hundreds Of Genes Through Experimental Screens

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

Publikováno v: Repisalud
Instituto de Salud Carlos III (ISCIII)
Genome Biology
Genome Biology, BioMed Central, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩
Zhou, N, Jiang, Y, Bergquist, T R, Lee, A J, Kacsoh, B Z, Crocker, A W, Lewis, K A, Georghiou, G, Nguyen, H N, Hamid, M N, Davis, L, Dogan, T, Atalay, V, Rifaioglu, A S, Dalklran, A, Cetin Atalay, R, Zhang, C, Hurto, R L, Freddolino, P L, Zhang, Y, Bhat, P, Supek, F, Fernández, J M, Gemovic, B, Perovic, V R, Davidović, R S, Sumonja, N, Veljkovic, N, Asgari, E, Mofrad, M R K, Profiti, G, Savojardo, C, Martelli, P L, Casadio, R, Boecker, F, Schoof, H, Kahanda, I, Thurlby, N, McHardy, A C, Renaux, A, Saidi, R, Gough, J, Freitas, A A, Antczak, M, Fabris, F, Wass, M N, Hou, J, Cheng, J, Wang, Z, Romero, A E, Paccanaro, A, Yang, H, Goldberg, T, Zhao, C, Holm, L, Törönen, P, Medlar, A J, Zosa, E, Borukhov, I, Novikov, I, Wilkins, A, Lichtarge, O, Chi, P H, Tseng, W C, Linial, M, Rose, P W, Dessimoz, C, Vidulin, V, Dzeroski, S, Sillitoe, I, Das, S, Lees, J G, Jones, D T, Wan, C, Cozzetto, D, Fa, R, Torres, M, Warwick Vesztrocy, A, Rodriguez, J M, Tress, M L, Frasca, M, Notaro, M, Grossi, G, Petrini, A, Re, M, Valentini, G, Mesiti, M, Roche, D B, Reeb, J, Ritchie, D W, Aridhi, S, Alborzi, S Z, Devignes, M D, Koo, D C E, Bonneau, R, Gligorijević, V, Barot, M, Fang, H, Toppo, S, Lavezzo, E, Falda, M, Berselli, M, Tosatto, S C E, Carraro, M, Piovesan, D, Ur Rehman, H, Mao, Q, Zhang, S, Vucetic, S, Black, G S, Jo, D, Suh, E, Dayton, J B, Larsen, D J, Omdahl, A R, McGuffin, L J, Brackenridge, D A, Babbitt, P C, Yunes, J M, Fontana, P, Zhang, F, Zhu, S, You, R, Zhang, Z, Dai, S, Yao, S, Tian, W, Cao, R, Chandler, C, Amezola, M, Johnson, D, Chang, J M, Liao, W H, Liu, Y W, Pascarelli, S, Frank, Y, Hoehndorf, R, Kulmanov, M, Boudellioua, I, Politano, G, Di Carlo, S, Benso, A, Hakala, K, Ginter, F, Mehryary, F, Kaewphan, S, Björne, J, Moen, H, Tolvanen, M E E, Salakoski, T, Kihara, D, Jain, A, Šmuc, T, Altenhoff, A, Ben-Hur, A, Rost, B, Brenner, S E, Orengo, C A, Jeffery, C J, Bosco, G, Hogan, D A, Martin, M J, O'Donovan, C, Mooney, S D, Greene, C S, Radivojac, P & Friedberg, I 2019, ' The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens ', Genome Biology, vol. 20, no. 1, 244 (2019) . https://doi.org/10.1186/s13059-019-1835-8
Genome biology
Genome Biology, Vol 20, Iss 1, Pp 1-23 (2019)
Genome Biology, 2019, 20 (1), ⟨10.1186/s13059-019-1835-8⟩

Tosatto, Silvio/0000-0003-4525-7793; Zhang, Feng/0000-0003-3447-897X; Gonzalez, Jose Maria Fernandez/0000-0002-4806-5140; Devignes, Marie-Dominique/0000-0002-0399-8713; Wass, Mark/0000-0001-5428-6479; Falda, Marco/0000-0003-2642-519X; Thurlby, Natali

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::99caa2a2ab2b36bdcf4f44143c8015a5
http://hdl.handle.net/11655/24591

Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction

Autor: Farrokh Mehryary, Jari Björne, Tapio Salakoski, Filip Ginter

Publikováno v: Database: The Journal of Biological Databases and Curation

Biomedical researchers regularly discover new interactions between chemical compounds/drugs and genes/proteins, and report them in research literature. Having knowledge about these interactions is crucially important in many research areas such as pr

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3ce4b527fe9c43cbdc073bc7186d167c
https://doi.org/10.1093/database/bay120

Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification

Autor: Farrokh Mehryary, Kai Hakala, Filip Ginter, Suwisa Kaewphan

Publikováno v: Journal of Biomedical Semantics

Background Biomedical event extraction is one of the key tasks in biomedical text mining, supporting various applications such as database curation and hypothesis generation. Several systems, some of which have been applied at a large scale, have bee

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::be304b18b031e71c728b8823fa1555b2
https://doi.org/10.1186/s13326-016-0070-4