About Hong Cui
Areas of Study
Information Organization, Natural Language Processing Applications, Machine Learning Applications, Biodiversity Informatics, Ontology Development, Software Development
Federal research grants:
• PI, "The Value of Automated Semantic Annotation for Biodiversity Informatics," NSERC, Canada, $75,000. Awarded. 2007. PI moved in 2007.
• PI, "Fine-Grained Semantic Markup of Descriptive Data for Knowledge Applications in Biodiversity Domains," NSF, $700,452.00, Awarded (EF-0849982). 9/2009-8/2012.
• Subcontractor, "Collaborative research: ABI Development: Ontology-enabled reasoning across phenotypes from evolution and model organisms" (NSF DBI-1062542), $49,596. Awarded. 7/2011-6/2013.
• Co-PI, “Collaborative Research: Next Generation Phenomics for the Tree of Life,” NSF, $335,000. Awarded (DEB-1208567). 5/2012-4/2015.
• PI, “BCSP: Collaborative Research: ABI Development: Exploring Taxon Concepts (ETC) through analyzing fine-grained semantic markup of descriptive literature,” NSF, $1,095,946.00. Awarded (DBI-1147266). 7/2012-6/2016
• Senior Personnel. “La SCALA: Latino Scholars Cambio Leadership Academy” Type: Training Grant. Institute for Museum and Library Studies, $173,000. Awarded
• PI: Research Experience for Undergraudate Students (REU) supplement to "Collaborative Research: AVATOL - Next Generation Phenomics for the Tree of Life” $7,500. Awarded (DEB-1208567). 5/2014-5/2017.
• Co-PI: Special Creativity Extension to "Collaborative Research: AVATOL - Next Generation Phenomics for the Tree of Life” $117,422. Awarded (DEB-1208567). 5/2015-5/2017.
• Co-PI: “Collaborative Research: Building a Comprehensive Evolutionary History of Flagellate Plants” $53,198. Awarded (DEB 1541509) 1/2016-12/2019.
• “Collaborative Research: ABI innovation: Authors in the driver's seat: fast, consistent, computable phenotype data and ontology production”, 7/1/2017-6/30/2020. $640,000.
Capstone/Directed Research Projects available for MS and Ph.D students (Fall 2017 and Spring 2018):
1. Capstone projects for MS students
1.1 Content fetcher: Design and develop of a software module that interactively and efficiently fetches digital content from public websites (e.g. an open access journal site) for the use as input to the ETC toolkit. Required skills: programming skill in any language.
1.2 Google Drive Extension: Extends Google Drive with a new ontology add-on. The main functions include highlight text that matches terms in an ontology, and show snippets of ontology in Google Doc view. Required skills: programming skill in any language.
1.3 Ontology visualization: Design and implement visualization modules using gwt-d3-api to visualize segements of an ontology in a larger GWT application.
2. Directed Research topics for Ph.D students
2.1 Deep learning for biodiversity Name Entitiy Recoganization tasks, including free phrases to ontology term mapping.
Email firstname.lastname@example.org if you are interested in any of the projects/topics.
Selected 10 Peer Reviewed Journal Publications (See the CV for a fuller list)
• Arighi, C.N., Carterette, B., Cohen K.B. et al. (2013). An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task. Database. doi: 10.1093/database/bas056
• Burleigh, G, et al. (2013). Next generation phenomics for the Tree of Life. Plos Current. http://currents.plos.org/treeoflife/article/next-generation-phenomics-fo...
• Duan, YF., Hei ZZ., Jiu, F., & Cui, H.(2013) Heuristics based semantic annotation of biodiversity documents in Chinese. Chinese Journal of Library and Information Science (English). 2013,6(2):33-46. http://ir.las.ac.cn/handle/12502/6238?mode=full&submit_simple=Show+full+...
• Dahdul, W.M., Cui, H., Mabee, P. et al. (2014) The Biological Spatial Ontology: anatomical descriptors for spatial and topological aspects of biological structures. Journal of Biomedical Semantics. 5:34. doi:10.1186/2041-1480-5-34 [13 pages]
• Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, et al. (2015) Finding Our Way through Phenotypes. PLoS Biology 13(1): e1002033. doi:10.1371/journal.pbio.1002033 [perspective paper].
• Huang, F, Macklin, J.A., Cui, H.*, Cole, H.A., & Endara, L. (2015). OTO: Ontology Term Organizer. BMC Bioinformatics. 16:47 doi:10.1186/s12859-015-0488-1
• Carrine, B., Cui, H., Moore, L., Ramona, W. (2016). MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions. Journal of Biomedical Semantics, 7:18, DOI: 10.1186/s13326-016-0060-6, http://www.jbiomedsem.com/content/7/1/18
• Cui, H.*, Xu, D., Chong, S.S., Ramirez, M.J., Rodenhausen, T., Macklin, J.A., Ludascher, B., Morris, R.A., Soto, E. M., & Koch, N.M. (2017). Introducing Explorer of Taxon Concepts with a Case Study on Spider Measurement Matrix Building. BMC Bioinformatics.
• Mao, J. Moore, L., Blank, C. Wu, E.H-H, Ackerman, M., Ranade, S., & Cui, H* (2017). Microbial Phenomics Information Extractor (MicroPIE): A Natural Language Processing Tool for the Automated Acquisition of Prokaryotic Phenotypic Characters from Text Sources. BMC Bioinformatics.
• Endara, L. Cole, H.A., Burleigh, J.G., Nagalingum, N., Macklin, J.A., Liu, J., Cui, H*. (2017) Using taxonomic descriptions to build a standardized Plant Glossary, Taxon.
672: Introduction to Applied Technology
515: Organization of Information
630: Controlled Vocabularies
588 special topic: XML and Semantic Web Standards
Doctoral seminar: Text Mining