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Large expert-curateddatabase forbenchmarking documentsimilarity detectionin biomedicalliterature search Peter BrownAik-Choon TanMohamed A El-Esawi2019 год

Large expert-curated database for benchmarking document similarity detection in biomedical literature search
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Аннотация: Abstract Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
Год издания: 2019
Авторы: Peter Brown, Aik-Choon Tan, Mohamed A El-Esawi, Thomas Liehr, Oliver Blanck, Douglas P. Gladue, Gabriel Magno de Freitas Almeida, Tomislav Cernava, Carlos Óscar S. Sorzano, Andy Wai Kan Yeung, Michael S. Engel, Arun Richard Chandrasekaran, Thilo Muth, Martin S. Staege, Swapna Vidhur Daulatabad, Darius Widera, Junpeng Zhang, Adrian Meule, Ken Honjo, Olivier Pourret, Cong-Cong Yin, Zhongheng Zhang, Marco Cascella, Willy A. Flegel, Carl S. Goodyear, Mark J. van Raaij, Zuzanna Bukowy‐Bieryłło, L Campana, Nicholas A. Kurniawan, David Lalaouna, Felix J. Hüttner, Brooke A. Ammerman, Felix Ehret, Paul A Cobine, Ene‐Choo Tan, Hyemin Han, Wenfeng Xia, Christopher McCrum, Ruud P.M. Dings, Francesco Marinello, R. Henrik Nilsson, Brett Nixon, Konstantinos Voskarides, Long Yang, Vincent D. Costa, Johan Bengtsson‐Palme, W.J. Bradshaw, Dominik G. Grimm, Nitin Kumar, Elvis A. F. Martis, Daniel Prieto, Sandeep C. Sabnis, Said E D R Amer, Alan Wee‐Chung Liew, Paul Perco, Farid Rahimi, Giuseppe Riva, Chongxing Zhang, Hari Prasad Devkota, Koichi Ogami, Zarrin Basharat, Walter Fierz, Robert Siebers, Kok Hian Tan, Karen A. Boehme, Peter Brenneisen, James A. L. Brown, Brian P. Dalrymple, David J. Harvey, Grace Ng, Sebastiaan Werten, Mark Bleackley, Zhanwu Dai, Raman Dhariwal, Yael Gelfer, M.D. Hartmann, Paweł Miotła, Radu Tamaian, Pragashnie Govender, Oliver J. Gurney‐Champion, Joonas H. Kauppila, Xiaolei Zhang, Natalia Echeverría, Santhilal Subhash, Hannes Sallmon, Marco Tofani, Taeok Bae, Oliver J. Bosch, Páraic O Cuív, Antoine Danchin, B Diouf, Tuomas Eerola, Evangelos Evangelou, Fabian V. Filipp, Hannes Klump, Lukasz Kurgan, Simon S Smith, Olivier Terrier, Neil Tuttle, David B. Ascher, Sarath Chandra Janga, Leon N. Schulte, Daniel J. Becker, Christopher M. Browngardt, Stephen J. Bush, Guillaume Gaullier, Kazuki Ide, Clement Meseko, Gijsbert D. A. Werner, Jan Zaucha, Abd Al-Bar Al-Farha, Noah F. 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Patil, Sansoa A Pedro, Samuel R Perry, Jessica Peter, Brent M Peterson, Andrea Pezzuolo, Ilya Pozdnyakov, Siyu Qian, Lei Qin, Ali Rafe, Ishier Raote, Ali S. Raza, Henrike Rebl, Osama Refai, Tim Regan, Richa Tambi, Mark P. Richardson, Katie Robinson, Luca Rossoni, Romain Rouet, Soroush Safaei, Pierre H. H. Schneeberger, Daniela Schwotzer, Agata Sebastian, Jennifer Selinski, Stefanie Seltmann, Feng Sha, Nir Shalev, Jin-Long Shang, Josef Singer, Mandeep Singh, Taylor Smith, Emma Solomon-Moore, Lijuan Song, Samuele Soraggi, Ryan R. E. Stanley, Nico Steckhan, Frederic Strobl, Lorenzo Subissi, Irwan Supriyanto, Chinmay R. Surve, Tomo Suzuki, Caitlin Syme, Karl Sörelius, Young Tang, Marwa Tantawy, Sumudu Tennakoon, Serafino Teseo, Christine Toelzer, Nikola Tomov, Miguel Tovar, Linh Tran, Sushil Tripathi, Anil Man Tuladhar, Azubuike Christian Ukubuiwe, Carolina Oi Lam Ung, Kaspar Valgepea, Hamid Vatanparast, Arnau Vidal, Fang Wang, Qing Wang, Ricky Watari, Rebecca Webster, Ruth Webster, Junnian Wei, David Wibowo, Tanja S H Wingenbach, Rose Mary Xavier, Shumin Xiao, Peng Xiong, Shicai Xu, Shilin Xu, Ruifeng Yao, Wen Yao, Qinan Yin, Yongbo Yu, Masayoshi Zaitsu, Zeineb Zian, Xiao-Yong Zhan, Jilei Zhang, Rongqiang Zhang, Wei Zhang, Xianglilan Zhang, Shan Zheng, Bailing Zhou, Xiaoyan Zhou, Haroon Ahmad, Sayo A Akinwumi, Gregory F. Albery, Ahmed Alhowimel, Junaid Ali, Mansour Abdullah Alshehri, Mohammed Alsuhaibani, Andrey Anikin, Samuel O. Azubuike, Anders Malthe Bach‐Mortensen, Lior Baltiansky, Martin Bartas, Kiflemariam Y Belachew, Vivek Bhardwaj, Karin Binder, Nicholas S. Bland, Michael Boah, Benjamin Bullen, Giovanna Elisa Calabró, Tiffany J Callahan, Bing Cao, Kelsey Chalmers, Wei Chang, Zhengping Che, Andrew T Y Chen, Haimin Chen, Huaming Chen, Youning Chen, Zhao Chen, YoungRok Choi, Mohiuddin Ahsanul Kabir Chowdhury, Martin R Christensen, Rob Cooke, Marzia Cottini, Natalie V. Covington, Catriona Cunningham, Julien Delarocque, Lucie Devos, Aurup Ratan Dhar, Kefeng Ding, Kexian Dong, Zheng Dong, Niklas Dreyer, Chelsea Ekstrand, Tanguy Fardet, Berhanu Elfu Feleke, Thomas Feurer, Ângela Freitas, Tian Gao, N G Asefa, Francesco Giganti, Piotr Grabowski, José R Guerra-Mora, Chengying Guo, Xinyi Guo, Himanshu Gupta, Shuonan He, Marloes Heijne, Stephanie Heinemann, Alexander Hogrebe, Zhengping Huang, Sophinese Iskander-Rizk, Lavanya M Iyer, Yasmin Jahan, Ameh S James, Emmanuel S. Joel, Bastian Joffroy, Clara Jégousse, George Kambondo, Priyanka Karnati, Cihan Kaya, An Ke, Daniel P. Kelly, Rob Kickert, Peter Elias Kidibule, Jennifer P. Kieselmann, Hyeon Jin Kim, Takeshi Kitazawa, Aniek Lamberts, You Li, Huakang Liang, Sabrina N Linn, Thomas Litfin, Wang Liusuo, Vasiliki Lygirou, Ajay Kumar Mahato, Zhi-Ming Mai, Rupert Major, Samira Mali, Panagiotis Mallis, Leanda Denise Mason, Leanda Denise Mason, Katie Marvin‐Dowle, Leanda D Mason, Ben Merideth, Maria J Merino-Plaza, Britt Merlaen, Rossella Messina, Anand Mishra, Muhammad Junaid, Conrad Musinguzi, Afroditi Nanou, Amreen Naqash, Joe Nguyen, Thi Tuyet Hanh Nguyen, Duan Ni, Nida Nida, Shirli Notcovich, Barnabas Ohst, Quinn R. Ollivier, Daniël F. Osses, Xiangda Peng, Arnoud Plantinga, Michael S. Pulia, Muhammad Rafiq, Ayush T. Raman, Delphine Raucher‐Chéné, Rafał Rawski, Asit Ray, Lubna Abdul Razak, Kevin Rudolf, Peter Rusch, Margaux L. Sadoine, Axel Schmidt, Roey Schurr, Stephen Searles, Saurab Sharma, Barry Sheehan, Chunhu Shi, Belal Shohayeb, Andrew Sommerlad, Jan Strehlow, Xianbao Sun, Raghav Sundar, Ghazaleh Taherzadeh, Nur D M Tahir, Jun Tang, Jean Testa, Zhiqi Tian, Qian Tingting, Geert P. Verheijen, Casey Vickstrom, Teng Wang, Xiaomin Wang, Zhenxing Wang, Pan Wei, Alex Wilson, Wyart, Abdul‐Amir Yassine, Abbas Yousefzadeh, Asma Zare, Zhen Zeng, Cheng-Rong Zhang, Haowen Zhang, Linxing Zhang, Tongchuan Zhang, Weijia Zhang, Zhe Zhang, Jianyu Zhou, Dongjie Zhu, Vincenzo Adamo, Adebolajo A. Adeyemo, Maria Aggelidou, Adi Mohammed Al Owaifeer, Arwa Z. Al‐Riyami, Saeed K Alzghari, Vibeke Andersen, Kathryn Angus, Muhammad Asaduzzaman, Hadi Asady, Dai Ato, Xiaoyong Bai, Rebecca L Baines, Maghan Ballantyne, Bo Ban, Jill Beck, Walid Ben-Nafa, Emma Black, Antoine Blancher, Ron Blankstein, Neil Bodagh, Paulo A. V. Borges, Anastasia Brooks, Josué Brox-Ponce, Arturo Brunetti, Colin D Canham, Piero Carninci, Richard D. Carvajal, Shun C Chang, Jie Chao, Pranab Chatterjee, He Chen, Yi‐Chun Chen, Adnan K. Chhatriwalla, Ibrahim Chikowe, Trees‐Juen Chuang, Rosane G. Collevatti, Diego Valera-Cornejo, Ana Cuenda, Myriam Dao, Delphine Dauga, Zaian Deng, Kiran Devkota, Lisa Doan, Yaser H A Elewa, Dongsheng Fan, Mohammed Faruk, Feifei Shi, Trevor S. Ferguson, Francesco Fleres, Emma Foster, C. Stephen Foster, Tzvi Furer, Yibo Gao, Enid J García-Rivera, Adi Gazdar, Ronald B. George, Sayantan Ghosh, Elena Gianchecchi, Joshua Gleason, Allan Hackshaw, Adam Hall, Richard Hall, Paul Harper, William Hogg, Guangqun Huang, Kylie E Hunter, Adriaan P. IJzerman, Carlos Márcio Nóbrega de Jesus, Jian Gao, James S. Lewis, Souha S. Kanj, Harsheen Kaur, Shona Kelly, Fayez Kheir, Vera S. Kichatova, Musa Kiyani, Reinhild Klein, Thomas Kovesi, Jennifer L. Kraschnewski, Addanki P Kumar, Dmitry Labutin, Alejandro Lazo‐Langner, Guy Leclercq, Maoteng Li, Qingchun Li, Tangliang Li, Yongzhe Li, Wei-Ting Liao, Zheng-yin Liao, Jessica Lin, J Lizer, Giambattista Lobreglio, Cher Lowies, Cheng Lü, Haroon Majeed, Adam Martin, Luis Martínez‐Sobrido, Edwin Meresh, Marianne Middelveen, Alireza Mohebbi, Jorge Mota, Zahra Mozaheb, Ley Muyaya, Amar Nandhakumar, Sheryl Hui-Xian Ng, Monther Obeidat, Deog-Hwan Oh, Mohammed Owais, Pia Pace‐Asciak, Ajay Panwar, Caroline Park, Christopher Patterson, Felipe Penagos-Tabaree, Paolo T Pianosi, Valentina Pinzi, Clare Pridans, Anna Psaroulaki, Ravi Kumar Pujala, Leonardo Pulido-Arjona, Peng-Fei Qi, Proton Rahman, K Nayanjot, Tienush Rassaf, Julie Refardt, Walter Ricciardi, Olaf Riess, Alexandros Rovas, Frank M. Sacks, Sherif Saleh, Christopher Sampson, Axel Schmutz, Robert J. Sepanski, Neeraj Sharma, Manisha Singh, Paul Spearman, Mehala Subramaniapillai, Ritu Swali, Cher M Tan, Juan Ignacio Tellechea, Lisa-Marie Thomas, Xin Tong, Demetrios G. Vavvas, Ralf Veys, Veronica Vitriol, Horng‐Dar Wang, Jinhui Wang, Jiucun Wang, J M Waugh, S. Webb, Brendan A. Williams, Alan D. Workman, Tingxiu Xiang, Lixin Xie, Jun Xu, Taosheng Xu, Chongjun Yang, Jihoon G Yoon, Christina M. Yuan, Arno Zaritsky, Yao Zhang, Haochen Zhao, Hannah Zuckerman, Ran Lyu, Wayne Pullan, Yaoqi Zhou
Издательство: University of Oxford
Источник: Database
Ключевые слова: Biomedical Text Mining and Ontologies, Topic Modeling, Advanced Text Analysis Techniques
Другие ссылки: Database (HTML)
HAL (Le Centre pour la Communication Scientifique Directe) (PDF)
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HAL (Le Centre pour la Communication Scientifique Directe) (HTML)
HAL (Le Centre pour la Communication Scientifique Directe) (HTML)
PubliCatt (Università Cattolica del Sacro Cuore) (PDF)
PubliCatt (Università Cattolica del Sacro Cuore) (HTML)
USC Research Bank (University of the Sunshine Coast) (PDF)
USC Research Bank (University of the Sunshine Coast) (HTML)
Spiral (Imperial College London) (PDF)
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BORIS (University Library Bern) (PDF)
BORIS (University Library Bern) (HTML)
Discovery Research Portal (University of Dundee) (PDF)
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HAL (Le Centre pour la Communication Scientifique Directe) (HTML)
pure.tue.nl (HTML)
Data Archiving and Networked Services (DANS) (PDF)
Data Archiving and Networked Services (DANS) (HTML)
HAL (Le Centre pour la Communication Scientifique Directe) (HTML)
KTH Publication Database DiVA (KTH Royal Institute of Technology) (PDF)
KTH Publication Database DiVA (KTH Royal Institute of Technology) (HTML)
KU ScholarWorks (University of Kansas) (PDF)
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ANU Open Research (Australian National University) (PDF)
ANU Open Research (Australian National University) (HTML)
Open Publications Of UTS Scholars (University of Technology Sydney) (PDF)
Open Publications Of UTS Scholars (University of Technology Sydney) (HTML)
Minerva Access (University of Melbourne) (PDF)
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King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) (PDF)
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ABACUS. Repositorio de Producción Científica (Universidad Europea) (PDF)
ABACUS. Repositorio de Producción Científica (Universidad Europea) (HTML)
CINECA IRIS Institutial research information system (University of Pisa) (PDF)
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Ghent University Academic Bibliography (Ghent University) (PDF)
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EspaceINRS (National Institute for Scientific Research (Canada)) (HTML)
University of Southern Denmark Research Portal (University of Southern Denmark) (HTML)
HAL (Le Centre pour la Communication Scientifique Directe) (HTML)
Institutional Research Information System University of Turin (University of Turin) (PDF)
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Lirias (KU Leuven) (PDF)
Lirias (KU Leuven) (HTML)
University of Southern Denmark Research Portal (University of Southern Denmark) (PDF)
University of Southern Denmark Research Portal (University of Southern Denmark) (HTML)
PubliCatt (Università Cattolica del Sacro Cuore) (PDF)
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MPG.PuRe (Max Planck Society) (PDF)
MPG.PuRe (Max Planck Society) (HTML)
University of Groningen research database (University of Groningen / Centre for Information Technology) (HTML)
Data Archiving and Networked Services (DANS) (PDF)
Data Archiving and Networked Services (DANS) (HTML)
Radboud Repository (Radboud University) (HTML)
Radboud Repository (Radboud University) (PDF)
Radboud Repository (Radboud University) (HTML)
UpSpace Institutional Repository (University of Pretoria) (PDF)
UpSpace Institutional Repository (University of Pretoria) (HTML)
Chalmers Research (Chalmers University of Technology) (PDF)
Chalmers Research (Chalmers University of Technology) (HTML)
University of Groningen research database (University of Groningen / Centre for Information Technology) (PDF)
University of Groningen research database (University of Groningen / Centre for Information Technology) (HTML)
research.utwente.nl (PDF)
research.utwente.nl (HTML)
DORA Empa (Swiss Federal Laboratories for Materials Science and Technology (Empa)) (PDF)
DORA Empa (Swiss Federal Laboratories for Materials Science and Technology (Empa)) (HTML)
Research Padua Archive (University of Padua) (PDF)
Research Padua Archive (University of Padua) (HTML)
Repositori digital de la UPF (Universitat Pompeu Fabra) (PDF)
Repositori digital de la UPF (Universitat Pompeu Fabra) (HTML)
Griffith Research Online (Griffith University) (PDF)
Griffith Research Online (Griffith University) (HTML)
Research at the University of Copenhagen (University of Copenhagen) (HTML)
Institutional Repository of the University of Granada (University of Granada) (PDF)
Institutional Repository of the University of Granada (University of Granada) (HTML)
Discovery Research Portal (University of Dundee) (HTML)
CINECA IRIS Institutial Research Information System (University of Genoa) (PDF)
CINECA IRIS Institutial Research Information System (University of Genoa) (HTML)
IRIS Research product catalog (Sapienza University of Rome) (PDF)
IRIS Research product catalog (Sapienza University of Rome) (HTML)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (PDF)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (HTML)
Ghent University Academic Bibliography (Ghent University) (HTML)
Tampere University Institutional Repository (Tampere University) (PDF)
Tampere University Institutional Repository (Tampere University) (HTML)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (PDF)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (HTML)
PubMed Central (HTML)
Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (HTML)
ResearchOnline - JCU (James Cook University) (HTML)
SHURA (Sheffield Hallam University Research Archive) (Sheffield Hallam University) (HTML)
LSHTM Research Online (London School of Hygiene & Tropical Medicine) (HTML)
RVC Research Online (Royal Veterinary College) (PDF)
RVC Research Online (Royal Veterinary College) (HTML)
UA Campus Repository (The University of Arizona) (PDF)
UA Campus Repository (The University of Arizona) (HTML)
UEA Digital Repository (University of East Anglia) (HTML)
ePrints Soton (University of Southampton) (HTML)
Liverpool John Moores University (HTML)
CentAUR (University of Reading) (HTML)
Northumbria Research Link (Northumbria University) (HTML)
Stirling Online Research Repository (University of Stirling) (PDF)
Stirling Online Research Repository (University of Stirling) (HTML)
Deakin Research Online (Deakin University) (PDF)
Deakin Research Online (Deakin University) (HTML)
RePub (Erasmus University, Rotterdam) (PDF)
RePub (Erasmus University, Rotterdam) (HTML)
Open Publications Of UTS Scholars (University of Technology Sydney) (PDF)
Open Publications Of UTS Scholars (University of Technology Sydney) (HTML)
Lund University Publications (Lund University) (PDF)
Lund University Publications (Lund University) (HTML)
Data Archiving and Networked Services (DANS) (PDF)
Data Archiving and Networked Services (DANS) (HTML)
EUR Research Repository (Erasmus University Rotterdam) (HTML)
KTH Publication Database DiVA (KTH Royal Institute of Technology) (PDF)
KTH Publication Database DiVA (KTH Royal Institute of Technology) (HTML)
Lund University Publications (Lund University) (HTML)
PubMed (HTML)