BioCADDIE Virtual Issue
The goal of the BioCaddie project is to build a unified ecosystem for discovering biomedical datasets. A major component of the project is a search engine capable of finding relevant datasets for a given query. Because the query result is datasets (as opposed to documents), it presents some interesting challenges for information retrieval systems.
The articles in this virtual issue have been curated to assess the challenges that can occur for information retrieval systems when working with datasets.
BioCADDIE VI
Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge
Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Trevor Cohen and Hua Xu
Database, Volume 2017, 1 January 2017, bax068, doi:10.1093/database/bax068
Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge
Wei Wei, Zhanglong Ji, Yupeng He, Kai Zhang, Yuanchi Ha, Qi Li and Lucila Ohno-Machado
Database, Volume 2018, 1 January 2018, bay017, doi:10.1093/database/bay017
Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval
Payam Karisani, Zhaohui S Qin and Eugene Agichtein
Database, Volume 2018, 1 January 2018, bax104, doi:10.1093/database/bax104
Baseline and extensions approach to information retrieval of complex medical data: Poznan's approach to the bioCADDIE 2016
Artur Cieslewicz, Jakub Dutkiewicz and Czeslaw Jedrzejek
Database, Volume 2018, 1 January 2018, bax103, doi:10.1093/database/bax103
Improving average ranking precision in user searches for biomedical research datasets
Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon and Patrick Ruch
Database, Volume 2017, 1 January 2017, bax083, doi:10.1093/database/bax083
Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy
Nai-Wen Chang, Hong-Jie Dai, Yung-Yu Shih, Chi-Yang Wu, Mira Anne C Dela Rosa, Rofeamor P Obena, Yu-Ju Chen, Wen-Lian Hsu and Yen-Jen Oyang
Database, Volume 2017, 1 January 2017, bax082, doi:10.1093/database/bax082
Query expansion using MeSH terms for dataset retrieval: OHSU at the bioCADDIE 2016 dataset retrieval challenge
Theodore B Wright, David Ball and William Hersh
Database, Volume 2017, 1 January 2017, bax065, doi:10.1093/database/bax065
Multi-field query expansion is effective for biomedical dataset retrieval
Mohamed Reda Bouadjenek and Karin Verspoor
Database, Volume 2017, 1 January 2017, bax062, doi:10.1093/database/bax062
A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge
Trevor Cohen, Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, George Alter, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado and Hua Xu
Database, Volume 2017, 1 January 2017, bax061, doi:10.1093/database/bax061
Elsevier’s approach to the bioCADDIE 2016 Dataset Retrieval Challenge
Antony Scerri, John Kuriakose, Amit Ajit Deshmane, Mark Stanger, Peter Cotroneo, Rebekah Moore, Raj Naik and Anita de Waard
Database, Volume 2017, 1 January 2017, bax056, doi:10.1093/database/bax056
GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species
Richard J. Challis, Sujai Kumar, Lewis Stevens and Mark Blaxter
Database, Volume 2017, 1 January 2017, bax039, doi:10.1093/database/bax039
