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51
Chen Q, Zhang X, Wan Y, Zobel J, Verspoor K. Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions. J Comput Biol 2018;26:605-617. [PMID: 30585742 DOI: 10.1089/cmb.2018.0198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
52
Khumrin P, Ryan A, Juddy T, Verspoor K. DrKnow: A Diagnostic Learning Tool with Feedback from Automated Clinical Decision Support. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018;2018:1348-1357. [PMID: 30815179 PMCID: PMC6371235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
53
Pang PCI, Chang S, Verspoor K, Clavisi O. The Use of Web-Based Technologies in Health Research Participation: Qualitative Study of Consumer and Researcher Experiences. J Med Internet Res 2018;20:e12094. [PMID: 30377139 PMCID: PMC6234342 DOI: 10.2196/12094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/08/2018] [Accepted: 10/08/2018] [Indexed: 01/23/2023]  Open
54
Downie LE, Makrai E, Bonggotgetsakul Y, Dirito LJ, Kristo K, Pham MAN, You M, Verspoor K, Pianta MJ. Appraising the Quality of Systematic Reviews for Age-Related Macular Degeneration Interventions: A Systematic Review. JAMA Ophthalmol 2018;136:1051-1061. [PMID: 29978192 DOI: 10.1001/jamaophthalmol.2018.2620] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
55
Hameed PN, Verspoor K, Kusljic S, Halgamuge S. A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration. BMC Bioinformatics 2018;19:129. [PMID: 29642848 PMCID: PMC5896044 DOI: 10.1186/s12859-018-2123-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 03/21/2018] [Indexed: 01/02/2023]  Open
56
Panyam NC, Verspoor K, Cohn T, Ramamohanarao K. Exploiting graph kernels for high performance biomedical relation extraction. J Biomed Semantics 2018;9:7. [PMID: 29382397 PMCID: PMC5791373 DOI: 10.1186/s13326-017-0168-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 12/01/2017] [Indexed: 11/30/2022]  Open
57
Chen Q, Panyam NC, Elangovan A, Verspoor K. BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics. Database (Oxford) 2018;2018:5255181. [PMID: 30576491 PMCID: PMC6301335 DOI: 10.1093/database/bay122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/24/2018] [Accepted: 10/16/2018] [Indexed: 01/01/2023]
58
Bouadjenek MR, Verspoor K, Zobel J. Literature consistency of bioinformatics sequence databases is effective for assessing record quality. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017;2017:3074790. [PMID: 28365737 PMCID: PMC5467556 DOI: 10.1093/database/bax021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/20/2017] [Indexed: 11/18/2022]
59
Chen Q, Wan Y, Zhang X, Lei Y, Zobel J, Verspoor K. Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. ACM JOURNAL OF DATA AND INFORMATION QUALITY 2017. [DOI: 10.1145/3131611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
60
Cohen KB, Lanfranchi A, Choi MJY, Bada M, Baumgartner WA, Panteleyeva N, Verspoor K, Palmer M, Hunter LE. Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. BMC Bioinformatics 2017;18:372. [PMID: 28818042 PMCID: PMC5561560 DOI: 10.1186/s12859-017-1775-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 07/31/2017] [Indexed: 11/10/2022]  Open
61
Bouadjenek MR, Verspoor K, Zobel J. Automated detection of records in biological sequence databases that are inconsistent with the literature. J Biomed Inform 2017. [PMID: 28624643 DOI: 10.1016/j.jbi.2017.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
62
Hameed PN, Verspoor K, Kusljic S, Halgamuge S. Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes. BMC Bioinformatics 2017;18:140. [PMID: 28249566 PMCID: PMC5333429 DOI: 10.1186/s12859-017-1546-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/13/2017] [Indexed: 12/16/2022]  Open
63
Chen Q, Zobel J, Verspoor K. Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017;2017:baw163. [PMID: 28077566 PMCID: PMC5225397 DOI: 10.1093/database/baw163] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/22/2023]
64
Chen Q, Zobel J, Verspoor K. Benchmarks for measurement of duplicate detection methods in nucleotide databases. Database (Oxford) 2017;2023:2870676. [PMID: 28334741 PMCID: PMC10755258 DOI: 10.1093/database/baw164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/01/2023]
65
Lu Y, Sinnott RO, Verspoor K. A Semantic-Based K-Anonymity Scheme for Health Record Linkage. Stud Health Technol Inform 2017;239:84-90. [PMID: 28756441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
66
Pitson G, Banks P, Cavedon L, Verspoor K. Developing a Manually Annotated Corpus of Clinical Letters for Breast Cancer Patients on Routine Follow-Up. Stud Health Technol Inform 2017;235:196-200. [PMID: 28423782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
67
Li X, Verspoor K, Gray K, Barnett S. Understanding Health Professionals' Informal Learning in Online Social Networks: A Cross-Sectional Survey. Stud Health Technol Inform 2017;239:77-83. [PMID: 28756440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
68
Li X, Gray K, Verspoor K, Barnett S. Understanding the Context of Learning in an Online Social Network for Health Professionals' Informal Learning. Stud Health Technol Inform 2017;235:353-357. [PMID: 28423813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
69
Kiossoglou P, Borda A, Gray K, Martin-Sanchez F, Verspoor K, Lopez-Campos G. Characterising the Scope of Exposome Research: A Generalisable Approach. Stud Health Technol Inform 2017;245:457-461. [PMID: 29295136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
70
Khumrin P, Ryan A, Judd T, Verspoor K. Diagnostic Machine Learning Models for Acute Abdominal Pain: Towards an e-Learning Tool for Medical Students. Stud Health Technol Inform 2017;245:447-451. [PMID: 29295134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
71
Bouadjenek MR, Verspoor K. Multi-field query expansion is effective for biomedical dataset retrieval. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017;2017:4107606. [PMID: 29220457 PMCID: PMC5737205 DOI: 10.1093/database/bax062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/31/2017] [Indexed: 01/01/2023]
72
Verspoor K, Oellrich A, Collier N, Groza T, Rocca-Serra P, Soldatova L, Dumontier M, Shah N. Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop. J Biomed Semantics 2016;7:66. [PMID: 27955708 PMCID: PMC5154111 DOI: 10.1186/s13326-016-0108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 11/18/2016] [Indexed: 12/04/2022]  Open
73
Sun Y, Hameed PN, Verspoor K, Halgamuge S. A physarum-inspired prize-collecting steiner tree approach to identify subnetworks for drug repositioning. BMC SYSTEMS BIOLOGY 2016;10:128. [PMID: 28105946 PMCID: PMC5249043 DOI: 10.1186/s12918-016-0371-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
74
Mizuno S, Ogishima S, Nishigori H, Jamieson DG, Verspoor K, Tanaka H, Yaegashi N, Nakaya J. The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia. PLoS One 2016;11:e0162828. [PMID: 27788142 PMCID: PMC5082890 DOI: 10.1371/journal.pone.0162828] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 08/29/2016] [Indexed: 11/24/2022]  Open
75
Kocbek S, Cavedon L, Martinez D, Bain C, Manus CM, Haffari G, Zukerman I, Verspoor K. Text mining electronic hospital records to automatically classify admissions against disease: Measuring the impact of linking data sources. J Biomed Inform 2016;64:158-167. [PMID: 27742349 DOI: 10.1016/j.jbi.2016.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/20/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
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