Hong Cui

Interests

Research

information and knowledge organization, machine learning, natural language processing, biodiversity informatics

Teaching

information and knowledge organization

Courses

Scholarly Contributions

Chapters

• Blank, C., Cui, H., Jin, M., Moore, L., Thacker, R., & Walls, R. (2018). Accelerating the Large-Scale Study of Prokaryotic Phenotypes and Niche Space Evolution Through Time Using the MicrO Ontology, MicroPIE, and MicroPIEDigester Software. In Application of Semantic Technologies in Biodiversity Science.
• Cui, H. -., Sai, D., & Tang, X. (2007). Chapter 3: Information Representation.
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  Written for Chinese readers in Chinese.;Your Role: First author. Authored 1/3 of the sections in the chapter. Organized the entire chapter. Edited and revised the entire chapter to make it more coherent. Verified references.;Full Citation: Cui, H., Sai, D., & Tang, X. (2007). Chapter 3: Information Representation. In Heting Chu & Yin Zhang. (Eds.), Research Fronts in Library and Information Science in the West. Beijing: Renmin University Press. (Series on Research Fronts in the Humanities and Social Sciences in the West).;Other collaborative: Yes;Specify other collaborative: collaborative with faculty members of other universities. ;

Journals/Publications

• Cui, H., Thessen, A., Endara, L., Cole, H., & Cao, Y. (2018). Modifier Ontologies for freqency, certainty, degree and coverage pheontoype modifiers.. Biodiversity Data Journal. doi:https://doi.org/10.3897/BDJ.6.e29232
• Endara, L., Cui, H., & Burleigh, G. (2018). Semiautomatic extraction of phenotypic traits from taxonomic descriptions using a Natural Language Processing approach.. Applications in Plant Sciences..
• Manda, P., Cui, H., Balhoff, J., Dahdul, W., Dececchi, A., Ibrhim, N., Lapp, H., Mabee, P., & Vision, T. (2018). Annotating phenotypes using ontological concepts: Inter-curator consistency as a baseline for evaluating the performance of a natural language processing system. Database (Oxford).
• Mao, J., & Cui, H. (2018). Identifying bacterial biotope entities using sequence labeling: performance and feature analysis. Journal of the Association for Information Science and Technology.
• Pender, J., Sachs, J., Macklin, J., Cui, H., Vallance, A., Lujan-Toro, B., Rodenhausen, T., Belisle-Leclerc, M., & Levin, G. (2018). Bringing a Semantic MediaWiki Flora to Life. Biodiversity Information Science and Standards. doi:https://doi.org/10.3897/biss.2.25885
• Xu, D., Chong, S., Cui, H., & Rodenhausen, T. (2018). Resolving “orphaned” parts using machine learning and natural language processing methods. Biodiversity Data Journal. doi:https://doi.org/10.3897/BDJ.6.e26659
• Cui, H., Macklin, J., Starr, J., Reznicek, A., Ford, B., & Chen, H. (2018). Incentivizing use of structured language in biological descriptions: author-driven phenotype data and ontology production. Biodiversity Data Journal. doi:https://doi.org/10.3897/BDJ.6.e29616
• Endara, L., Cole, H., Burleigh, G., Nagalingum, N., Macklin, J., Liu, J., & Cui, H. (2017). Building the “Plant Glossary”—A controlled botanical vocabulary using terms extracted from the Floras of North America and China.. TAXON, 66(4). doi:DOI: 10.12705/664.9
• Blank, C., Cui, H., Moore, L., & Wells, R. (2016). MicrO - an ontology of prokaryotic phenotypic and metabolic characters. Journal of Biomedical Semantics.
• Cui, H. (2016). Introducing Explorer of Taxon Concepts with a Case Study on Spider Measurement Matrix Building. BMC Bioinformatics.
• Mao, J., Moore, L., Blank, C., Wu, E., Ackerman, M., Ranade, S., & Cui, H. (2016). Microbial Phenomics Information Extractor (MicroPIE): A Natural Language Processing Tool for the Automated Acquisition of Prokaryotic Phenotypic Characters from Text Sources.. MBC Bioinformatics.
• Cui, H. (2016). Using taxonomic descriptions to build and evaluate a standardized Plant Glossary.. Taxon.
• Deans, A., Lewis, S. E., Huala, E., authors..., .. o., Cui, H., & authors, .. o. (2015). Finding Our Way through Phenotypes. PLoS Biology, 13(1).
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  This is a Perspective paper with 74 authors, too many to list The paper represents the current view of those who are actively working on the intelligent extraction, representation, connection, and usage of organism phenotypes at the life level (not just limited to a taxon or a group of taxa).
• Huang, F., Cui, H., Macklin, J. A., Cole, H. A., & Endara, L. (2015). OTO: Ontology Term Organizer. BMC Bioinformatics., 16(47).
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  OTO was developed by Huang, supervised by Cui, in collaboration with Mackline. Post-Doc Cole and Endara used the tool and provided constructive suggestions that helped improve the usability and efficiency of the tool. Within the week the paper is published, six new users have registered on OTO, suggesting the need for lower-barrier tools for ontology development.
• Manda, P., & Cui, H. -. (2015). Annotating phenotypes using ontological concepts: Inter-curator consistency as a baseline for evaluating the performance of a natural language processing system. to be determined.
• Dahdul, W. M., Cui, H., Mabee, P. M., Mungall, C. J., Osumi-Sutherland, D., Walls, R., & Haendel, M. A. (2014). The Biological Spatial Ontology: anatomical descriptors for spatial and topological aspects of biological structures. Journal of Biomedical Semantics. Journal of Biomedical Semantics, 5(34), 13.
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  Contribution:All authors contributed to the ontology and the manuscript. WD, MAH, PM, and RLW developed the figures. All authors read and approved the final manuscript.
• Arighi, C. N., Carterette, B., Cohen, K. B., Krallinger, M., Wilbur, W. J., Fey, P., Dodson, R., Cooper, L., Van Slyke, C. E., Dahdul, W., Mabee, P., Li, D., Harris, B., Gillespie, M., Jimenez, S., Roberts, P., Matthews, L., Becker, K., Drabkin, H., , Bello, S., et al. (2013). An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. Database : the journal of biological databases and curation, 2013, bas056.
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  In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have developed tools for text mining from a computer science/linguistics perspective, and there are many initiatives to curate some aspect of biology from the literature. Some biocuration efforts already make use of a text mining tool, but there have not been many broad-based systematic efforts to study which aspects of a text mining tool contribute to its usefulness for a curation task. Here, we report on an effort to bring together text mining tool developers and database biocurators to test the utility and usability of tools. Six text mining systems presenting diverse biocuration tasks participated in a formal evaluation, and appropriate biocurators were recruited for testing. The performance results from this evaluation indicate that some of the systems were able to improve efficiency of curation by speeding up the curation task significantly (∼1.7- to 2.5-fold) over manual curation. In addition, some of the systems were able to improve annotation accuracy when compared with the performance on the manually curated set. In terms of inter-annotator agreement, the factors that contributed to significant differences for some of the systems included the expertise of the biocurator on the given curation task, the inherent difficulty of the curation and attention to annotation guidelines. After the task, annotators were asked to complete a survey to help identify strengths and weaknesses of the various systems. The analysis of this survey highlights how important task completion is to the biocurators' overall experience of a system, regardless of the system's high score on design, learnability and usability. In addition, strategies to refine the annotation guidelines and systems documentation, to adapt the tools to the needs and query types the end user might have and to evaluate performance in terms of efficiency, user interface, result export and traditional evaluation metrics have been analyzed during this task. This analysis will help to plan for a more intense study in BioCreative IV.
• Burleigh, G., Alphonse, K., Cui, H., & et al., . (2013). Next generation phenomics for the Tree of Life.. PLOS Currents.
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  Complete author list:J. Gordon BurleighKenzley AlphonseAndrew J AlversonHolly M BikCarrine BlankAndrea L CirranelloHong CuiMarymegan DalyThomas G DietterichGail GasparichJed IrvineMatthew JuliusSeth KaufmanEdith LawJing LiuLisa MooreMaureen A O'LearyMaria PassarottiSonali RanadeNancy B SimmonsDennis W. StevensonRobert W ThackerEdward C TheriotSinisa TodorovicPaúl M. VelazcoRamona L WallsJoanna M WolfeMengjie Yu
• Burleigh, J. G., Alphonse, K., Alverson, A. J., Bik, H. M., Blank, C., Cirranello, A. L., Cui, H., Daly, M., Dietterich, T. G., Gasparich, G., Irvine, J., Julius, M., Kaufman, S., Law, E., Liu, J., Moore, L., O'Leary, M. A., Passarotti, M., Ranade, S., , Simmons, N. B., et al. (2013). Next-generation phenomics for the Tree of Life. PLoS currents, 5.
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  The phenotype represents a critical interface between the genome and the environment in which organisms live and evolve. Phenotypic characters also are a rich source of biodiversity data for tree building, and they enable scientists to reconstruct the evolutionary history of organisms, including most fossil taxa, for which genetic data are unavailable. Therefore, phenotypic data are necessary for building a comprehensive Tree of Life. In contrast to recent advances in molecular sequencing, which has become faster and cheaper through recent technological advances, phenotypic data collection remains often prohibitively slow and expensive. The next-generation phenomics project is a collaborative, multidisciplinary effort to leverage advances in image analysis, crowdsourcing, and natural language processing to develop and implement novel approaches for discovering and scoring the phenome, the collection of phentotypic characters for a species. This research represents a new approach to data collection that has the potential to transform phylogenetics research and to enable rapid advances in constructing the Tree of Life. Our goal is to assemble large phenomic datasets built using new methods and to provide the public and scientific community with tools for phenomic data assembly that will enable rapid and automated study of phenotypes across the Tree of Life.
• Cui, H. -. (2009). Evaluating Plant Character Ontologies Against Domain Literature.. Journal of American Society of Information Science and Technology.
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  ;Your Role: sole author;
• Cui, H. -. (2011). CharaParser for Fine-Grained Semantic Annotation of Taxonomic Descriptions. Journal of American Society of Information Science and Technology.
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  Cui, H. (In press, 2012). CharaParser for Fine-Grained Semantic Annotation of Taxonomic Descriptions. Journal of American Society of Information Science and Technology;
• Cui, H. -., Arighi, C., & Cohen, e. a. (2012). An Overview of the BioCreative 2012 Workshop Track III: Interactive Text Mining Task.. Database.
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  ;Your Role: This paper describe all the 7 text mining systems participated in BioCreative 2012 Track III. Arighi was the organizer of the events. I was the team leader and developer of one of the 7 systems. Contributed to the paper by providing all information related to our system, including system evaluation. Contributed to the revisions.;Other collaborative: Yes;Specify other collaborative: Collaborative with researchers/faculty from other institutes.;
• Cui, H. -., Boufford, D., & Selden, P. (2009). Semantic Annotation of Biosystematics Literature without Training Examples.. Journal of American Society of Information Science and Technology..
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  This is an interdisciplinary collaboration between an information scientist and biologists.;Your Role: I was the leading author of the paper. I originated the algorithm and implemented it. The algorithm had been tested on small data sets before. ;Other collaborative: Yes;Specify other collaborative: Boufford and Selden are editors of Flora of North America and Treatises on Invertebrate Paleontology resp. They are a botanist and paleontologist. They helped in creating the evaluation data collections, which were used to evaluate the performance of the semantic annotation system reported in the paper.;
• Duan, Y., Hei, Z., Jiu, F., & Cui, H. (2013). Heuristics based semantic annotation of biodiversity documents in Chinese. Chinese Journal of Library and Information Science (English)., 6(2), 33-46.
• Duan, Y., Hei, Z., Jiu, F., & Cui, H. (2013). Heuristics based semantic annotation of biodiversity documents in Chinese.. Chinese Journal of Library and Information Science (English)., 6(2), 33-46.
• Cui, H. -., & Cui, H. -. (2012). CharaParser for fine-grained semantic annotation of organism morphological descriptions.. Journal of American Society of Information Science and Technology..
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  ;Your Role: solo author, responsible for all aspects of the work and the writing.;Full Citation: Cui, H. (2012). CharaParser for fine-grained semantic annotation of organism morphological descriptions. Journal of American Society of Information Science and Technology. 63(4) DOI: 10.1002/asi.22618 http://onlinelibrary.wiley.com/doi/10.1002/asi.22618/pdf;
• Cui, H. -., &amp, T., & Dmitry, . (2012). Applications of Natural Language Processing in Biodiversity Science. Advances in Bioinformatics.
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  ;Your Role: Planned and wrote significant chunks of the paper and responded to sections of reviewers comments;Full Citation: Thessen, A., Cui, H., & Mozzherin Dmitry. (2012). Applications of Natural Language Processing in Biodiversity Science. Advances in Bioinformatics.Volume 2012. doi:10.1155/2012/391574. http://www.hindawi.com/journals/abi/2012/391574/;Other collaborative: Yes;Specify other collaborative: Collaborative with researchers from other institutes.;
• Cui, H. -., Duan, Y., Hei, Z., & Ju, F. (2012). Semantic Annotation of Species Description Text in Chinese Literature by Naive Bayes Classifier.. Journal of the China Society for Scientific and Technical Information.
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  ;Your Role: Provided the idea and base source code for the computer program.;Full Citation: Duan, Y, Hei, Z, Ju, F., Cui, H. (2012). Semantic Annotation of Species Description Text in Chinese Literature by Naive Bayes Classifier. Journal of the China Society for Scientific and Technical Information (Chinese). 31, (8), 805-812.;Other collaborative: Yes;Specify other collaborative: collaborative with international collaborators.;
• Cui, H. -., Duan, Y., Hei, Z., & Ju, F. (2012). Study on Semantic Markup of Species Description Text in Chinese Based on Auto-Learned Rules. New Techonology of Library and Information Services.
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  ;Your Role: Provided the idea and base source code for the computer program.;Full Citation: Duan, Y, Hei, Z, Ju, F., Cui, H. (2012). Study on Semantic Markup of Species Description Text in Chinese Based on Auto-Learned Rules. New Techonology of Library and Information Services (Chinese). 2012 (5).;Other collaborative: Yes;Specify other collaborative: collaborative with international collaborators.;
• Cui, H. -., Duan, Y., Li, ., & Fang, . (2011). Machine learning based semantic markup of biodiversity literature in English. Document, Information, & Knowledge (Chinese).
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  ;Your Role: This work is a derived work of Cui's research for Chinese audience. The paper is a review of semantic markup research conducted by Cui and collaborators.;Full Citation: Cui, H., Duan, Y. & Li, F. (2011). Machine learning based semantic markup of biodiversity literature in English. Document, Information, & Knowledge, 2 (Chinese).;Other collaborative: Yes;Specify other collaborative: International collaborators.;
• Cui, H. -. (2010). Evaluating Plant Character Ontologies Against Domain Literature. Journal of American Society of Information Science and Technology.
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  ;Your Role: solo author;Full Citation: Cui, H. (2010). Evaluating Plant Character Ontologies Against Domain Literature. Journal of American Society of Information Science and Technology. 61(6):1144-1165. http://www3.interscience.wiley.com/cgi-bin/fulltext/123319711/PDFSTART;
• Cui, H. -., & Cui, H. -. (2010). Semantic Annotation of Morphological Descriptions: An Overall Strategye. BMC Bioinformatics.
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  BMC Bioinformatics ranked #3 in ISI bioinformatics category.The paper is 11 pages long.;Your Role: solo author;Full Citation: Cui, H. (2010). Semantic Annotation of Morphological Descriptions: An Overall Strategy. BMC Bioinformatics.11:278. DOI:10.1186/1471-2105-11-278.http://www.biomedcentral.com/1471-2105/11/278;Electronic: Yes;
• Cui, H. -., Boufford, D., & Selden, P. (2010). Semantic Annotation of Biosystematics Literature without Training Examples.
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  ;Your Role: Leading author. Designed and carried out the research. Two co-authors are biologists who provide most valuable assistance in evaluate machine-generated annotations. ;Full Citation: Cui, H., Boufford, D., & Selden, P. (2010). Semantic Annotation of Biosystematics Literature without Training Examples. Journal of American Society of Information Science and Technology. 61 (3): 522-542.http://www3.interscience.wiley.com/cgi-bin/fulltext/123319711/PDFSTART;Other collaborative: Yes;Specify other collaborative: collaborators are domain scientists from Harvard U. and U. of Kansas ;
• Cui, H., & Cui, H. -. (2010). Semantic annotation of morphological descriptions: an overall strategy. BMC bioinformatics, 11.
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  Large volumes of morphological descriptions of whole organisms have been created as print or electronic text in a human-readable format. Converting the descriptions into computer- readable formats gives a new life to the valuable knowledge on biodiversity. Research in this area started 20 years ago, yet not sufficient progress has been made to produce an automated system that requires only minimal human intervention but works on descriptions of various plant and animal groups. This paper attempts to examine the hindering factors by identifying the mismatches between existing research and the characteristics of morphological descriptions.
• Cui, H. -. (2008). Converting Taxonomic Descriptions to New Digital Formats. Biodiversity Informatics.
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  Biodiversity Informatics is the only peer-reviewed journal publishing research on biodiversity informatics.The research is interdisciplinary as it applies and advances methodologies of machine learning, computational linguistics, and information science for semantic-based access of biodiversity information.;Your Role: Sole authorship;Full Citation: Biodiversity Informatics. 5, 2008. pp. 20-40. https://journals.ku.edu/index.php/jbi/article/view/46/1551;Electronic: Yes;
• Cui, H. -., & Heidorn, B. P. (2007). The reusability of induced knowledge for the automatic semantic markup of taxonomic descriptions. Journal of the American Society for Information Science and Technology / Wiley InterScience.
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  Based on Ph.D dissertation. The 2nd author was the dissertation director, who was on sabbatical leave at the time of the dissertation research but offered valuable comments. ;Your Role: First author. Designed and carried out the research, which benefited from the constructive comments provided by the 2nd author and used data sets obtained with help of the 2nd author.;Full Citation: Cui, H. & Heidorn, P.B. (2007). The reusability of induced knowledge for the automatic semantic markup of taxonomic descriptions. Journal of the American Society for Information Science and Technology. 58(1), 133-149.;Other collaborative: Yes;Specify other collaborative: Collaborative with faculty member of University of Illinois at Urbana-Champaign;
• Cui, H. -., & Nickerson, G. (2007). Use Server2Go to Teach IT Courses for LIS Students. Journal of Association for Library and Information Science Education.
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  ;Your Role: Initiated the paper and written the first draft.;Full Citation: Cui, H. & Nickerson, G. (2007). Use Server2Go to Teach IT Courses for LIS Students. Journal of Association for Library and Information Science Education. 48 (4);Other collaborative: Yes;Specify other collaborative: with faculty member of the University of Western Ontario, Canada;

Proceedings Publications

• Endara, L., Burleigh, G., Cooper, L., Jaiswal, P., Laporte, M., & Cui, H. (2018, Fall). A Natural Language Processing Pipeline to Extract Phenotypic Data from Formal Taxonomic Descriptions with a Focus on Flagellate Plants.. In 2018 International Conference on Biomedical Ontologies.
• Vikas, Y., Sadeque, F., Heidorn, B., & Cui, H. (2018, march). Where are iSchools heading?. In iConferece.
• Zhang, Y., Burkell, J., Cui, H., & Mercer, R. (2018, Summer). An automated approach for rating the content quality of Web healthcare information: A case study on depression treatment Web pages.. In of the 2018 International Conference on Health Informatics & Medical Systems.
• Zhang, Y., Mercer, R., Burkell, J., & Cui, H. (2018, Spring). Using shallow semantic analysis to implement automated quality assessment of web health care information.. In The 19th International Conference on Computational Linguistics and Intelligent Text Processing, CICLing 2018, Selected for publication in Springer LNCS..
• Dahdul, W., Manda, P., Cui, H., Balhoff, J., Dececchi, A., Ibrahim, N., Mabee, P., & Vision, T. (2017, Fall). Gold standard evaluation of machine- and human-generated annotations of biodiverse phenotypes. In Biocuration 2017.
• T, D., Cui, H., & A. G., F. (2016, Jun). MultiLayerMatrix: Visualizing large taxonomic datasets [full paper]. In EuroVis Workshop on Visual Analytics (EuroVA).
• Cui, H. (2015, Nov). CharaPaser+EQ: Performance Evaluation Without Gold Standard. Nov 6-10, St Louis, Missouri, 2015. (Full paper, acceptance rate: 36.%). In Annual Meeting of American Society for Information Science and Technology,.
• Zhang, Y., Cui, H., Burkell, J., & Mercer, R. (2014, March). A machine learning approach for rating the quality of depression treatment web pages.. In iConference 2014.
• Zhang, Y., Cui, H., Burkell, J., & Mercer, R. E. (2014, March). A machine learning approach for rating the quality of depression treatment web pages.. In iConference, 2014.
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  The paper is based on Zhang's dissertation, supervised by Cui, Burkell, and Mercer. The paper was drafted by Zhang & Cui.
• Cui, H. -., & Janning, A. (2012). Evaluating the botanical coverage of PATO using an unsupervised learning algorithm.
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  short paper and poster;Your Role: Corresponding author. Designed the study, supervised student author to complete the study, helped finalizing the pub.;Full Citation: Janning, A. & Cui, H. (2012). Evaluating the botanical coverage of PATO using an unsupervised learning algorithm. iConference 2012, Feb 7-10, 2012, Toronto, Canada.;Collaborative with graduate student: Yes;
• Cui, H. -., Balhoff, D., Lapp, M., & Vision., C. (2012). PCS for Phylogenetic Systematic Literature Curation.
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  ;Your Role: First and corresponding author.;Full Citation: Cui, H., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Chang, Z. (2012). PCS for Phylogenetic Systematic Literature Curation. Proceedings of the BioCreative workshop 2012 (pp.137-144). [full paper];Collaborative with graduate student: Yes;Other collaborative: Yes;Specify other collaborative: and collaborative with researchers/faculty from other institutes;
• Cui, H. -., Huang, M., Morris, S., & Morris, C. (2012). OTO: Ontology Term Organizer.
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  short paper and poster.;Your Role: Corresponding author. Supervised student author Huang (first author), reviewed and edited the submissions/poster.;Full Citation: Huang, F.Q.,Macklin, J, Morris, P., Sanyal, P.P., Morris, R.A. , Cole, H. & Cui, H (2012) OTO: Ontology Term Organizer. Annual Conference of American Society for Information Science and Technology. [poster];Collaborative with graduate student: Yes;
• Cui, H. -., Walls, C., & Jaiswal, . (2012). Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources.
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  ;Your Role: One of the main contributors of the work reported in the poster. Helped editing the submission.;Full Citation: Walls, R., Cui, H., Macklin J., Mungall, C., Cooper, L., Stevenson, D.W., & Jaiswal, P.(2012) Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources. Proceedings of the 3rd International Conference on Biomedical Ontology, June 2012 Austria.;Other collaborative: Yes;Specify other collaborative: collaborative with faculty/researchers from other institutes.;
• Cui, H. -., Z., C., J., B., W., D., H., L., P., M., & T., V. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements.
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  ;Your Role: Corresponding author. Supervised student author (Chang, first author).;Full Citation: Chang Z., Balhoff J., Dahdul W., Lapp H., Mabee P., Vision T., & Cui, H. (2012). Workflow of CharaParser and Phenex: Turning character descriptions to EQ statements. BioCreative workshop 2012, Washington, D.C. [poster and software demo];Collaborative with graduate student: Yes;Other collaborative: Yes;Specify other collaborative: and collaborative with researchers/faculty from other institutes;
• Cui, H. -. (2011). Fine-Grained Semantic Markup of Descriptive Data.
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  ;Your Role: solo author;Full Citation: Cui, H. (2011). Fine-Grained Semantic Markup of Descriptive Data. Panelist in Informatics Tools for the SEmantic Enhancement of Taxonomic Literature Symposium, XVIII International Botanical Congress, 2011. Melbbourn, Australia, July 23-30. [Abstract and oral presentation];
• Cui, H. -., Macklin, J., ,, M., Robert., M., & Paul., . (2011). Floras in the 21st Century: The Flora of North America saga.
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  ;Your Role: Conducted research presented. Review/revised the abstract.;Full Citation: Macklin, J., Cui, H., Morris, R., Morris, P. (2011). Floras in the 21st Century: The Flora of North America saga. In Creating Next Generation Floras Symposium, International Botanical Congress, Australia, July 22-30 2011 [abstract];Other collaborative: Yes;Specify other collaborative: Collaborative with faculty member and researcher of US and Canada.;
• Cui, H. -., Singaram, S. &., & Janning, A. (2011). Combine Unsupervised Learning and Heuristic Rules to Annotate Morphological Characters.
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  ;Your Role: conducted research, prepared manuscript, supervised student co-authors.;Full Citation: Cui, H.,Singaram, S., & Janning, A. (2011). Combine Unsupervised Learning and Heuristic Rules to Annotate Morphological Characters. 2011 Annual Meeting of American Society of Information Science and Technology, New Orleans, Oct 9-12, 2011. [Full Paper];Collaborative with graduate student: Yes;
• Cui, H. -. (2010). Linking Corpus Characteristics to Performance of Semantic Annotation Systems for Biosystematic Descriptions.
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  ;Your Role: sole author;Full Citation: Cui, H. (2010). Linking Corpus Characteristics to Performance of Semantic Annotation Systems for Biosystematic Descriptions. Proceedings of the 2nd International Conference On Bioinformatics and Biomedical Technology. Chengdu, China. April 16-18, 2010.;
• Cui, H. -., & none, . (2010). Unsupervised Extraction of Text Segments from Heterogeneous Document Collections.
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  ;Your Role: solo author;Full Citation: Cui, H. (2010). Unsupervised Extraction of Text Segments from Heterogeneous Document Collections[Poster]. Proceedings of the 73rd ASIS&T Annual Meeting v. 47. Oct 22-27, 2010. Pittsburg, PA. http://www.asis.org/asist2010/proceedings/proceedings/ASIST_AM10/openpage.html;
• Cui, H. -., Jiang, Y., & Sanyal, P. (2010). From Text to RDF Triple Store: An Application for Biodiversity Literature.
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  ;Your Role: leading author. Designed the study and supervised the graduate students. Implemented part of the software. Write the paper.;Full Citation: Cui, H., Jiang, Y, & Sanyal P.P. (2010). From Text to RDF Triple Store: An Application for Biodiversity Literature[Demo]. Proceedings of the 73rd ASIS&T Annual Meeting v. 47. Oct 22-27, 2010. Pittsburg, PA. http://www.asis.org/asist2010/proceedings/proceedings/ASIST_AM10/openpage.html;Collaborative with graduate student: Yes;
• Cui, H. -., P.P., S., & C., Y. (2010). Tools for Semantic Annotation of Taxonomic Descriptions.
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  ;Your Role: leading author. Designed the study, carried out part of the study, supervised the graduate students, and write the paper.;Full Citation: Cui, H., Sanyal P.P., & Yu C. (2010). Tools for Semantic Annotation of Taxonomic Descriptions. In R. Setchi et al. (Eds.): Proceedings of 14th International Conference on Knowledge-Based and Intelligent Information and Engineering Systems., Part IV, Lecture Notes in Artificial Intelligence 6279, pp. 506--516. Springer Heidelberg. Sept 8-10, 2010, Cardiff, Wales, UK.;Collaborative with graduate student: Yes;
• Cui, H. -., C., Y., & Macklin, . (2009). Application of Semantic Annotation for Quality Insurance in Biosystematics Publishing.
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  This is a poster and 2-page short paper.;Your Role: I was the leading author of the paper. I originated the research and wrote the paper. Chunshui Yu was a graduate student, who implemented my ideas in Java. ;Full Citation: Cui, H., Yu C., & Macklin, J. (2009). Application of Semantic Annotation for Quality Insurance in Biosystematics Publishing. Proceedings of the Annual Meeting of American Society of Information Science and Technology 2009.;Collaborative with graduate student: Yes;Other collaborative: Yes;Specify other collaborative: James Macklin is with Harvard University Herbaria, University of Harvard. James is also with the Flora of North America Project, who provided the funds for the project, part of which was reported in the paper.;
• Cui, H. -., Macklin, J., Chunshu, Y. u., & Sanyal, P. (2009). Fine-Grained Semantic Annotation of Descriptive Data for Knowledge Application in Biodiversity.
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  This is an oral presentation and a system demonstration.;Your Role: I was the leading author of the paper. I originated the research and wrote the paper. Chunshui Yu was a graduate student, who implemented my ideas in Java. Sanyal made minor improvements to the system.;Full Citation: Cui, H. et al. (2009). "Fine-Grained Semantic Annotation of Descriptive Data for Knowledge Application in Biodiversity". TDWG Annual Meeting 09. France.;Collaborative with graduate student: Yes;Other collaborative: Yes;Specify other collaborative: Yu and Sanyal were UA graduate students.James Macklin with Harvard University Herbaria, University of Harvard. James is also with the Flora of North America Project, who provided the funds for the project, part of which was reported in the paper.;
• Cui, H. -. (2008). Approaches to Semantic Mark up for Natural Heritage Literature.
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  The research is interdisciplinary as it applies and advances methodologies of machine learning, computational linguistics, and information science for semantic-based access of biodiversity information.;Your Role: Sole authorship;Full Citation: Proceedings of the iConference 2008. http://www.ischools.org/oc/conference08/pc/PA5-2_iconf08.doc;Electronic: Yes;
• Cui, H. -. (2008). Unsupervised Learning for Semantic Markup of Biodiversity Literature.
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  The research is interdisciplinary as it applies and advances methodologies of machine learning, computational linguistics, and information science for semantic-based access of biodiversity information.;Your Role: sole authorship;Full Citation: Proceedings of the 8th ACM/IEEE-CS Joint Conference on Digital Libraries (JCDL), (pp. 25-28);Electronic: Yes;

Presentations

• Cui, H. (2019, April). Reporting from the Author's Project. Semantic Data Models in Anatomy Workshop. Zoological Research Museum. Bonn, Germany: Museum of Alexander Koenig.
• Cui, H., & Reznicek, A. (2019, July 30). Authors in the driver’s seat: Evaluating phenotypes data authoring tools. [Workshop]. Botany 2019.. Tucson.
• Cui, H. (2017, July). Bottom-up ontology building. International Botany Congress XIX. Shen Zhen, China.
• Cui, H. (2017, Jun). Authors in the Driver’s Seat.. Evolution 2017.
• Cui, H. (2016, Dec). Bottom up, pattern-based ontology building for phenotype characters.. TDWG 2016 Annual Conference. Costa Rica: TDWG.
• Endara, L., Burleigh, J., & Cui, H. (2016, July). Using natural language processing tools to facilitate learning taxonomy, nomenclature, and botany in the classroom.. Botany 2016.
• Burleigh, G., Nathalie, N., Endara, L., & Cui, H. (2015, July). Semi-automated approaches for extracting phylogenetically informative phenomic datasets from the taxonomic descriptions. Botany 2015.
• Cui, H. (2015, Jan). From Text to Matrices: Using Natural Language Processing (NLP) to Facilitate Assembling Taxon-Character Matrices. Next Generation Phonemics Project Annual Meeting 2015.
• Cui, H. (2015, Spring). Phylogenetic relationships and classification of Cycas. CYCAD 2015: The 10th International Conference on Cycad Biology..
• Blank, C. E., Wu, H., Cui, H., Moore, L. R., Burleigh, G. J., Liu, J., & Gasparich, G. (2014, June). AVAToL microbial phenomics: an ontology and natural language processing tools to facilitate trait evolution stdueis for the archaeal domain of life.. Evolution 2014. Raleigh, NC, June 20-24..
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  The material presented were developed by Blank, Wu (Cui's post doc), and Cui, with assistance from other others.
• Endara, L., Liu, J., Burleigh, G. J., Nagalingum, N., & Cui, H. (2014, June). Transformation of Taxonomic Literature to a Taxon-Character Matrix for Phylogenetics.. Evolution 2014. Raleigh, North Carolina.
• Endara, L., authors..., .., Cui, .., & authors.., o. (2014, Nov). Next-generation phenomics for the Tree of Life.. TWDG 2014. Berlin, Germany.
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  complete list of authors: Carmen Lorena Endara, Carrine E. Blank, John Gordon Burleigh, Andrea Cirranello, Hong Cui, Marymegan Daly, Gail Gasparich, Mariangeles Arce Hernandez, Jed Irvine, Lisa Moore, Thomas G. Dietterich, Jing Liu, Seth Kaufman, Michael Lam, Maureen O'Leary, Maria Passaroti, Javier Robalino, Nancy Simmons, Joan Slonczewski, Dennis Wm. Stevenson, Robert W. Thacker, Edward Theriot, Sinisa Todorovic, Ramona Walls, Paul M. Velazco, Elvis H. Wu, Anna Yu
• Macklin, J., Cole, H., Cui, H., & Sachs, J. (2014, Jun). Prototyping a botanical knowledge portal.. Canadian Botanical Association Annual Meeting..
• Cui, H. (2013, Feb). CharaParser and Associated Software. pro-iBiosphere workshop I.
• Cui, H. (2013, Feb). MarkupTools: CharaParser. pro-iBiosphere workshop III.
• Cui, H. (2013, Feb). Parsing Morphological Descriptions to Support Semantic-based Access. pro-iBiosphere workshop II.
• Cui, H. -. (2013, Feburary). CharaParser and Associated Software.. pro-iBiosphere workshop I. Leiden, the Netherlands.: pro-iBiosphere project.
• Cui, H. -. (2013, Feburary). MarkupTools: CharaParser.. pro-iBiosphere workshop III. Leiden, the Netherlands.: pro-iBiosphere project (EU).
• Cui, H. -. (2013, Feburary). Parsing Morphological Descriptions to Support Semantic-based Access.. pro-iBiosphere workshop II. Leiden, the Netherlands: pro-iBiosphere project (EU).
• Cui, H. -. (2013, November). Literature Markup Pilot. pro-iBiosphere workshop Nov 2013. Berlin Germany: pro-iBiosphere project (EU).
• Cui, H., Huang, F., Rodenhausen, T., & et al., . (2013, June). Semantic annotation of organism morphological descriptions using CharaParser along with a web-based ontology term organizer (OTO) [Software Demo]. IEvoBio 2013.. Utah.
• Cui, H., Randade, S., & Moore, L. (2013, May). A preliminary analysis of application of Stanford Parser and OSCAR4 for parsing and annotating microbial descriptions. IEvoBio 2013.
• Macklin, J., Sachs, J., Cui, H., & Cole, H. (2013, Oct). Prototyping a botanical knowledge portal. TDWG 2013. Florence, Italy.
• Ranade, S., Cui, H., Moore, L., Blank, C., & et al., . (2013, June). A preliminary analysis of application of Stanford Parser and OSCAR4 for parsing and annotating microbial descriptions.. IEvoBio 2013. Utah.
• Cui, H. -., Dusenbery, M., & Huang, . (2012, 2012-10-01). Semantic Annotation, Ontology Building, and Interactive Key Generation from Morphological Descriptions. Botany Institute of Chinese Academy of Sciences, Beijing, China.
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  ;Invited: Yes;Collaborative with graduate student: Yes;Other collaborative: Yes;Specify other collaborative: collaborative with researchers/faculty from other institutes;Type of Presentation: Professional Organization;
• Cui, H. -., Dusenbery, M., & Huang, . (2012, 2012-10-01). Semantic Annotation, Ontology Building, and Interactive Key Generation from Morphological Descriptions. TDWG 2012 Annual Meeting. Beijing, China.
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  ;Invited: Yes;Refereed: Yes;Collaborative with graduate student: Yes;Other collaborative: Yes;Specify other collaborative: and with researchers/faculty from other institutes;Type of Presentation: Invited/Plenary Speaker;
• Cui, H. -. (2011, 2011-04-01). Fine-Grained Semantic Annotation of Taxonomic Descriptions: Progress and Challenges. the Marine Biology Laboratory, Woods Hole, Boston.
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  ;Invited: Yes;Interdisciplinary: Yes;Type of Presentation: University;
• Cui, H. -. (2011, 2011-05-01). Fine-Grained Semantic Annotation of Taxonomic Descriptions: Progress and Challenges. Phenotype Research Collaboration Network. Boulder, Colorado.
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  ;Invited: Yes;Interdisciplinary: Yes;Type of Presentation: Academic Conference/Workshop;
• Cui, H. -. (2011, 2011-08-01). Text Mining in Taxonomic Literature. Virtual to the audience at Natural History Museum, Bogota Colombia..
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  ;Invited: Yes;Interdisciplinary: Yes;Type of Presentation: University;
• Cui, H. -. (2011, 2011-10-01). Fine-Grained Semantic Annotation of Taxonomic Descriptions: Progress and Challenges. Florida State University.
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  ;Invited: Yes;Type of Presentation: University;
• Cui, H. -. (2011, 2011-11-01). Fine-Grained Semantic Markup of Morphological Descriptions in Biodiversity Domains. SIRLS Research Brown Bag.
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  ;Submitted: Yes;Interdisciplinary: Yes;Type of Presentation: University;
• Cui, H. -. (2011, 2012-03-01). Fine-Grained Semantic Markup of Descriptive Data. XVIII International Botanical Congress. Melbbourn, Australia,.
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  ;Invited: Yes;Refereed: Yes;Interdisciplinary: Yes;Type of Presentation: Invited/Plenary Speaker;
• Cui, H. -. (2010, 2010-04-01). Biomedical Informatics and NLP. Department of Medical Information Management, Tongji Medical College, Huazhong Science and Technology University, Wuhai, China.
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  ;Invited: Yes;Interdisciplinary: Yes;Type of Presentation: University;
• Cui, H. -. (2010, 2010-04-01). Linking Corpus Characteristics to Performance of Semantic Annotation Systems for Biosystematic Descriptions.. the 2nd International Conference On Bioinformatics and Biomedical Technology. Chengdu, China.
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  ;Submitted: Yes;Refereed: Yes;Interdisciplinary: Yes;Type of Presentation: Academic Conference/Workshop;
• Cui, H. -. (2010, 2011-02-01). Natural Language Processing for Biodiversity Literature. School of Management Information Systems, East China Normal University, Shanghai, China..
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  ;Invited: Yes;Interdisciplinary: Yes;Type of Presentation: University;
• Cui, H. -., P.P., S., & C., Y. (2010, 2010-09-01). Tools for Semantic Annotation of Taxonomic Descriptions.. 14th International Conference on Knowledge-Based and Intelligent Information and Engineering Systems.. Cardiff, Wales, UK.
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  The paper also appears in Lecture Notes in Artificial Intelligence 6279, pp. 506--516. Springer Heidelberg;Your Role: Planed and carried out the research with assistance from co-authors. Supervised student co-authors. Presented the paper.;Submitted: Yes;Refereed: Yes;Interdisciplinary: Yes;Collaborative with graduate student: Yes;Type of Presentation: Academic Conference/Workshop;
• Cui, H. -., Singaram, S., Snyal, P., & Yang, J. (2010, 2010-10-01). SIRLS research brownbag: unsupervised learning, ontology construction, and semantic annotation. SIRLS.
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  ;Your Role: developed the presentation, carried out the research, supervised student co-authors.;Collaborative with graduate student: Yes;Type of Presentation: University;
• Cui, H. -. (2009, 2009-11-01). Fine-Grained Semantic Annotation of Biosystematics Documents for Knowledge Applications. CSC296H/496H Research Topics in Computer Science (Honors Students Seminor).
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  ;Invited: Yes;Interdisciplinary: Yes;Type of Presentation: University;
• Cui, H. -. (2008, 2008-02-01). Approaches to Semantic Markup for Natural Heritage Literature. iConference 2008. University of California, Los Angeles.
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  ;Submitted: Yes;Refereed: Yes;Type of Presentation: Academic Conference;
• Cui, H. -. (2008, 2008-04-01). Approaches to Semantic Markup for Natural Heritage Literature. Flora of North America: Digital Flora Workshop. Harvard University Herbaria.
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  Invited to present machine learning approaches to semantic markup of Flora of North America to FNA project board members, FNA editors, related IT personnel, efloras.org, and Flora of China representatives. The goal of the workshop was to set the short-term and mid-term plan for semantic-based access to flora data and evaluate the feasibility of Dr. Cui's unsupervised learning methods in meeting the identified needs. A detailed specification for a collaborative project between FNA and Dr. Cui to be carried out in Summer 2008 was also discussed. ;Invited: Yes;Type of Presentation: Academic Conference/Workshop;
• Cui, H. -. (2008, 2008-05-01). Simple Machine Learning Methods for Semantic Markup of Taxonomic Treatments. Paleontology Institute, University of Kansas.
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  The presentation was given to paleontologists and IT personnel of Paleontology Institute, University of Kansas, during a four-day visit of the Institute upon the invitation of the Director Paul Seldon. The purpose of the visit was to start a collaborative digitization program for the Treatise of Invertebrate Paleontology. Collaborators involved were the Institute, Prof. Richard Connor of Computer Science, University of Strathclyde, Scotland and myself. ;Invited: Yes;Interdisciplinary: Yes;Type of Presentation: Professional Organization;
• Cui, H. -. (2008, 2008-09-01). Approaches to Semantic Markup of Natural Heritage Literature. Cognative Sciences Colloquium. University of Arizona.
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  ;Invited: Yes;Type of Presentation: University;
• Cui, H. -. (2008, 2008-11-01). Semantic Markup of Biodiversity Literature & Its Real World Implications. SIRLS Research Brownbag. University of Arizona.
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  ;Interdisciplinary: Yes;Type of Presentation: University;

Poster Presentations

• Zhang, L., Cota, Z., Cui, H., & et al, e. a. (2019, Oct 19-23). Developing Community Phenotype Ontologies: Understanding Users’ Preferences... The 82nd ASIST Annual Meeting. Melbourne, Australia.
• Cao, Y., Franz, N., Macklin, J., Mao, J., & Cui, H. (2018, March). Resolving Taxonomic Names using Evidence Extracted from Text.. iConference. UK.
• Cao, Y., Franz, N., Macklin, J., Mao, J., & Cui, H. (2018, Spring). Resolving Taxonomic Names using Evidence Extracted from Text. iConference 2018.
• Chong, S., Xu, D., Rodenhausen, T., & Cui, H. (2018, Jun). Resolving Orphaned Parts in Taxonomic Descriptions with Machine Learning and Natural Language Processing Methods. The Second Annual Digital Data in Biodiversity Research Conference,.
• Cui, H. (2017, Summer). ETC Toolkit: Extract, Discover and Use Taxon Morphological Characters Documented in the Literature.. Evolution 2017. Portland, Oregon.
• Cui, H. (2016, Feb). Semantic Media Wiki as a Phenotype Browser and Knowledge Base.. Phenotype RCN 2016.
• Joseph, C., Stadelmann, K., Endara, L., & Cui, H. (2016, July). The New Language of Science: A novel approach to generating a phenomic matrix of gymnosperms.. Botany 2016.
• Mao, J., & Cui, H. (2016, March). MicroPIE. iConference.
• Endara, L., Burleigh, G., & Cui, H. (2015, Oct). Semi-automated extraction of phenomic characters from taxonomic descriptions: Natural Language Processing Approaches for the Tree of Life. [Best Post Award]. The SouthEastern Ecology and Evolutionary Genetics (SEPEEG) meeting.
• Thessen, A., & Cui, H. (2015, April). Building Machine-Readable Species Descriptions for Protists.. Research Data Alliance Meeting.
• Thessen, A., & Cui, H. (2015, March 9-11). Building Machine-Readable Species Descriptions for Protists. Research Date Alliance (RDA) Fifth Plenary. San Diego.
• Blank, C. E., Moore, L. R., Cui, H., Wu, H., Burleigh, G. J., Liu, J., Slonczewski, J. L., Barich, D., & Gasparich, G. (2014, May 18-23.). AVAToL microbial phenomics: developing a microbial ontology and natural language processing tools to automate the study of the evolution of microbial traits.. Joint Aquatic Sciences Meeting,. Portland, OR,.
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  The work presented in the poster was created by Blank, Moore, Cui, Wu, Barich with assistance with others.
• Moore, L., Blank, C., Burleigh, J., Cui, H., Gasparich, G., Liu, J., & Ranade, S. (2013, Fall). Next Generation Microbial Phenomics. Australian Association for Microbiology Annual Scientific Meeting.

Creative Productions

• Endara, L., Cui, H., Burleigh, J., & Nagalingum, N. (2016. Constructing morphological character matrices from taxonomic descriptions using new software approaches [training workshop]. Botany 2016.
• Cui, H., & Rodenhausen, T. (2015. Explorer of Taxon Concepts Toolkit Website. http://etc-dev.cs.umb.edu/etcsite/: NSF. http://etc-dev.cs.umb.edu/etcsite/
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  The toolkit website consists of a set of software applications for organism trait extraction, ontology building, and taxon concept alignment. In 2015, one new tool, identification tool, was developed.
• Cui, H., Huang, F., & Rodenhausen, T. (2013. Semantic annotation of organism morphological descriptions using CharaParser along with a web-based ontology term organizer (OTO) [software demo].

Others

• Manda, P., Cui, H., Balhoff, J., Dahdul, W., Dececchi, A., Ibrhim, N., Lapp, H., Mabee, P., & Vision, T. (2018, Fall). Analysis source code for "Annotating phenotypes using ontological concepts: Inter-curator consistency as a baseline for evaluating the performance of a natural language processing system". Zenodo. https://doi.org/10.5281/zenodo.1218010
• Manda, P., Cui, H., Balhoff, J., Dahdul, W., Dececchi, A., Ibrhim, N., Lapp, H., Mabee, P., & Vision, T. (2018, Fall). Data for Annotating phenotypes using ontological concepts: Inter-curator consistency as a baseline for evaluating the performance of a natural language processing system. Zenodo. https://doi.org/10.5281/zenodo.1217594
• Manda, P., Cui, H., Balhoff, J., Dahdul, W., Dececchi, A., Ibrhim, N., Lapp, H., Mabee, P., & Vision, T. (2018, Fall). Software source code for "Annotating phenotypes using ontological concepts: Inter-curator consistency as a baseline for evaluating the performance of a natural language processing system". Zenodo. https://doi. org/10.5281/zenodo.1246698
• Rodenhausen, T., & Cui, H. -. (2013, Fall). ETC web appllication [Software]. http://etc.cs.umb.edu/etcsite/start.html
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  NSF project.
• Rodenhausen, T., Cui, H., Huang, F., Ludäscher, B., Macklin, J., Morris, R., & Yu, S. (2014, Nov). ETC: From description to matrix and beyond in a web-based toolbox [software demo]. TWDG 2014.
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  software demo.Software developed by Rodenhausen under Cui's supervision, with assistance from other authors.
• Cui, H. (2008). Attended The Training Course by Barry Smith on BIOMEDICAL ONTOLOGY, April 12-13, 2008 at the Univers.
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  Attended The Training Course by Barry Smith on BIOMEDICAL ONTOLOGY, April 12-13, 2008 at the University of Buffalo.
• Cui, H. (2008). Provided a support letter for Klemens Böhm and Guido Sautter (of Institut fuer Programmstrukturen.
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  Provided a support letter for Klemens Böhm and Guido Sautter (of Institut fuer Programmstrukturen und Datenorganisation (IPD), Universitaet Karlsruhe (TH), Germany)'s research proposal to DFG (German NSF).
• Cui, H. (2008). Provided a support letter for Prof. Richard Connor (Computer Science at University of Strathclyde, U.
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  Provided a support letter for Prof. Richard Connor (Computer Science at University of Strathclyde, UK)'s research proposal of the UK Research Council.
• Cui, H. (2010). Organizing a presentation given by a panel of 5 experts from US and Germany who attended the project.
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  Organizing a presentation given by a panel of 5 experts from US and Germany who attended the project meeting in Feb 2010. Researchers from several U of A academic units attended the presentation, including BIO5.
• Cui, H. (2010). Organizing all-hands meeting for the "Fine-Grained" project in Feb 2010..
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  Organizing all-hands meeting for the "Fine-Grained" project in Feb 2010.
• Cui, H. (2011). Helped Prof. Yufeng Duan to secure two research grants from Chinese government to adapt Cui's text m.
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  Helped Prof. Yufeng Duan to secure two research grants from Chinese government to adapt Cui's text mining systems for biodiversity literature in Chinese.
• Cui, H. (2012). 1. Wrote quarterly and annual reports to NSF on the "Fine-Grained Semantic Markup" project.
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  1. Wrote quarterly and annual reports to NSF on the "Fine-Grained Semantic Markup" project. 2. Hosted one annual project meeting (March 2012, 3 days) and one workshop (Dec 2012, 2 days) for "Fine-Grained Semantic Markup" project in SIRLS.3. Participated as the PI in the annual project meeting for "ETC" project hosted by co-PI at UC-Davis (2 days in Sept 2012)4. Participated as a Co-PI in the annual project meeting for "Tree Of Life" project in Stonybrook, NY (2 days in Sept 2012).5. Adviser of a Chinese government funded project led by Prof. Yufeng Duan.6. A member of the Art of Life Project Advisory Board (NEH [National Endowment for the Humanities] funded project). "The Art of Life: Data Mining and Crowdsourcing the Identification and Description of Natural History Illustrations from the Biodiversity Heritage Library" is a NEH funded project (Grant Number: PW-51041-12). The advisory board consists 7 members.
• Cui, H. -. (2008). Application of Semantic Annotation for Quality Insurance in Biosystematics Publishing.
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  ;Collaborative with graduate student: Yes;Other collaborative: Yes;Please specify if you select "Other collaborative" : Also collaborative with a biodiversity informatist of Harvard University and the Flora of North America (FNA) Project. FNA provided funding for the graduate student to program the software under the guidance of the first author for this research. The research ideas were from both the first author and the FNA project. ;Full Citation: Proceedings of the Annual Meeting of the American Society of Information Science and Technology, 2009.;Status: Submitted But Not Yet Accepted;
• Cui, H. -. (2008). Semantic Annotation of Scientific Literature without Training Examples.
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  ;Other collaborative: Yes;Please specify if you select "Other collaborative" : collaborative with a botanist of Harvard University and a paleontologist of Kansas University. The two domain scientists will appear as the 2nd and 3rd author on the paper. They ensure the benchmarks used in evaluating the machine learning algorithms created by the first author are accurately prepared and confirm to their domain conventions. ;Full Citation: To be submit to the Journal of American Society of Information Science and Technology (JASIST) ;Status: Paper in Preparation;
• Cui, H. -. (2009). Semantic Annotation of Morphological Descriptions: An Overall Strategy..
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  ;Full Citation: Cui, H. (2009). Semantic Annotation of Morphological Descriptions: An Overall Strategy. BMC Bioinformatics. Submitted.;Status: Submitted But Not Yet Accepted;
• Cui, H. -. (2010). Extract morphological descriptions from heterogeneous documents.
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  the publication of this paper is delayed because more time is needed to test the algorithm on several more collections.;Collaborative with graduate student: Yes;Full Citation: to be determined;Status: Paper in Preparation;
• Cui, H. -. (2010). Heuristic-based semantic annotation of taxonomic descriptions.
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  ;Collaborative with graduate student: Yes;Full Citation: place of publication to be determined;Status: Paper in Preparation;
• Cui, H. -. (2010). Towards Trait-based Search of Digital Floras/Faunas.
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  ;Other collaborative: Yes;Please specify if you select "Other collaborative" : with researchers of UMass-Boston and from Canada ;Full Citation: place of publication to be determined;Status: Paper in Preparation;
• Cui, H. -. (2010). Using Unsupervised Learning and Standard Syntactic Parser for Semantic Annotation of Biodiversity Descriptions.
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  ;Collaborative with graduate student: Yes;Full Citation: place of publication to be determined;Status: Paper in Preparation;
• Cui, H. -. (2011). Applications of Natural Language Processing in Biodiversity Science.
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  ;Please specify if you select "Other collaborative" : Collaborative with researchers of the US.;Full Citation: Thessen, A., Cui, H., & Mozzherin Dmitry. (submitted) Applications of Natural Language Processing in Biodiversity Science. Advances in Bioinformatics.;Status: Submitted But Not Yet Accepted;
• Rodenhausen, T., & Cui, H. (2013, Nov). CharaParser in iPlant DE [Software].
• Cui, H. -. (2008). An Application for Semantic Markup of Biodiversity Documents (System Demonstration)..
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  The research is interdisciplinary as it applies and advances methodologies of machine learning, computational linguistics, and information science for semantic-based access of biodiversity information.;Your Role: sole authorship;Full Citation: Proceedings of the 8th ACM/IEEE-CS joint conference on Digital libraries, (pp.421) ;Electronic: Yes;