The 3rd International Workshop on Semantics-Powered Data Analytics (SEPDA 2018)

in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018)
to be held in Madrid, Spain
December 3 - 6, 2018


Biomedical ontologies and controlled terminologies provide structured domain knowledge to a variety of health information systems. The rich thesaurus with concepts linked by semantic relationships has been widely used in natural language processing, data mining, machine learning, semantic annotation, and automated reasoning. The dramatically increasing amount of health-related data poses unprecedented opportunities for mining previously unknown knowledge with semantics-powered data analytics methods. However, due to the heterogeneity of different data sources, it is a challenging problem to exploit multiple sources to solve real-world problems such as designing cost-effective treatment plan for patients, designing generalizable clinical trials, drug repurposing, and clinical phenotyping. The goal of this workshop is to bring people in the field of knowledge representation, knowledge management, and health data analytics to discuss innovative semantic methods, applications, and data analytics to address problems in healthcare, biomedicine, public health, and clinical research with biomedical, clinical, behavioral, and social web data.

We are inviting original research submissions (FULL 8 pages), work-in-progress (SHORT 4 pages), and poster abstracts (2 pages, NEW TYPE).

All the accepted submissions will be presented in SEPDA 2018 and published in the IEEE BIBM 2018 Proceedings (in IEEE Xplore Digital Library); Selected FULL/SHORT papers will be invited to publish an extended version in the supplement of BMC Medical Informatics & Decision Making (IF: 2.134; Indexed in SCIE, MEDLINE, and PMC; and subject to an article processing charge of $1,465). Selected high-quality SHORT papers will also be invited to submit an extended version to the journal supplement for consideration.

This is the third installment of the SEPDA workshop. The first SEPDA workshop (SEPDA 2016) was held in conjunction with IEEE BIBM 2016 in Shenzhen, China. SPEDA 2016 was a half-day workshop. Dr. Hua Xu, a leading expert in the field of Biomedical Informatics, gave the keynote speech on the bioCADDIE project. Eight quality papers were presented. Selected papers were invited to publish the extended version to the special issue on “Semantics-Powered Healthcare Engineering and Data Analytics” in the Journal of Healthcare Engineering (

The second SEPDA Workshop (SEPDA 2017) was held in conjunction with IEEE BIBM 2017 in Kansas City, Missouri, USA. SPEDA 2017 was a full day workshop. 17 high quality papers were presented in the workshop. Extended journal version of the papers was published in BMC Medical Informatics & Decision Making (IF: 2.134).


We are inviting original research submissions as well as work-in-progress.

Topics of interest include but not limited to:

  • Ontologies and Controlled Terminologies
    • Ontology development and enrichment
    • Quality assurance of ontologies and controlled terminologies
    • Semantic harmonization and ontology alignment
    • Knowledge representation and reasoning
  • Semantics-based Data Analytics
    • Ontology-based text mining and natural language processing
    • Ontology-based analysis on biomedical, clinical, or social web data
    • Information Extraction on biomedical, clinical, or social web data
    • Data mining or machine learning on biomedical, clinical or social web data
    • Semantic annotation on biomedical, clinical or social web data
  • Data Integration
    • Linked open data
    • Novel approaches for data integration of heterogenous data sources
    • Large scale data integration
  • Application
    • Novel tools and ontologies for data interpretation and visualization
    • Pharmacovigilance and drug repurposing using ontologies
    • Clinical trial generalizability assessment using ontologies
    • Algorithmic phenotyping and cohort identification using ontologies
    • Improving the literacy of health information consumers

Important Dates

Oct 7, 2018: Due date for full / work-in-progress workshop papers submission

Oct 27, 2018: Notification of paper acceptance to authors

Nov 15, 2018: Camera-ready of accepted papers

Dec 3, 2017: SEPDA 2018 Workshop

Journal submission deadline: TBD


Please submit a full-length paper (up to 8 page IEEE 2-column format) through the online submission system (you can download the format instruction here ). Electronic submissions (in PDF or Postscript format) are required. Selected participants will be asked to submit their revised papers in a format to be specified at the time of acceptance.

Submission site: Submit a New Paper


  • Organizing Committee
    • Zhe He, School of Information, Florida State University, USA
    • Cui Tao, School of Biomedical Informatics, University of Texas Health Center at Houston, USA
    • Rui Zhang, Institute for Health Informatics, University of Minnesota, USA
    • Jiang Bian, Health Outcomes & Biomedical Informatics, College of Medicine, University of Florida, USA
  • Program Committee
    • Praveen Chandar, Spotify Research, USA
    • James Cimino, University of Alabama Birmingham, USA
    • Licong Cui, University of Kentucky, USA
    • Yi Guo, University of Florida, USA
    • Zhengxing Huang, Zhejiang University, China
    • Guoqian Jiang, Mayo Clinic College of Medicine, USA
    • Xia Jing, Ohio University, USA
    • Juan Antonio Lossio-Ventura, University of Florida, USA
    • Jake Luo, University of Wisconsin at Milwaukee, USA
    • Riccardo Miotto, Icahn School of Medicine at Mount Sinai, USA
    • Fleur Mougin, University of Bordeaux, France
    • Neelufar Payrovnarizi, Florida State University, USA
    • Feichen Shen, Mayo Clinic, USA
    • Deyu Sun, Philips Research North America, USA
    • Buzhou Tang, Harbin Institute of Technology, China
    • Yonghui Wu, University of Florida, USA
    • GQ Zhang, University of Kentucky, USA
  • Student Program Committee
    • Hansi Zhang, Health Outcomes & Policy, University of Florida, USA
    • Jingcheng Du, UTHealth SBMI, USA
    • Yadan Fan, University of Minnesota, USA
    • Neelufar Payrovnarizi, Florida State University, USA



Accepted Papers

Workshop Schedule

The 3rd International Workshop on Semantics-Powered Data Analytics
Date, Time: December 3, 2018, 8:00 am – 5:10 pm; Room: To Be Determined
Workshop Chairs: Zhe He, Jiang Bian, Cui Tao, and Rui Zhang
Time Title Presenter/Author
8:00 am – 8:10 am Opening Remarks Zhe He
8:10 am – 9:00 am Keynote: TBA
9:00 am – 9:10 am Short Break
9:10 am – 10:10 am Session 1: Natural Language Processing & Text Mining
Analyzing Early Signals of Older Adult Cognitive Impairment in Electronic Health Records Somaieh Goudarzvand, Jennifer St. Sauver, Michelle Mielke, Paul Takahashi, and Sunghwan Sohn
Representing Knowledge for Radiation Therapy Planning with Markov Logic Networks Yi Zhen, Saugat Karki, Lulin Yuan, Jackie Wu, and Yaorong Ge
Automatic Relationship Verification in Online Medical Knowledge Base: a Large Scale Study in SemMedDB Danchen Zhang, Daqing He, Ning Zou, Xin Zhou, and Fen Pei
10:10 am -10:40 pm Coffee Break
10:40 am – 12:00 pm Session 2: Ontology and Knowledgebase
Extended Analysis of Topological-Pattern-Based Ontology Enrichment Zhe He, Vipina Kuttichi Keloth,,Yan Chen, and James Geller
A Methodology for Extracting Knowledge about Controlled Vocabularies from Textual Data using FCA-Based Ontology Engineering Simin Jabbari and Kilian Stoffel
OntoKeeper: A Semiotic-driven Ontology Evaluation Tool For Biomedical Ontologists Muhammad Amith, Frank Manion, Chen Liang, Marcelline Harris, Dennis Wang, Yongqun He, and Cui Tao
Prototyping an Interactive Visualization of Dietary Supplement Knowledge Graph Xing He, Rui Zhang, Rubina Rizvi, Jake Vasilakes, Xi Yang, Yi Guo, Zhe He, and Jiang Bian
12:10 pm – 2:00 pm Lunch Break
2:00 pm – 3:20 pm Session 3: Ontology-Based Data Analytics
Ontology-based Venous Thromboembolism Risk Factors Mining and Model Developing from Medical Records Yuqing Yang, Xin Wang, Yu Huang, Ning Chen, Juhong Shi, and Ting Chen
Constructing Biomedical Knowledge Graph based onSemMedDB and Linked Open Data Qing Cong, Zhiyong Feng, Fang Li, Li Zhang, Guozheng Rao, and Cui Tao
Comparing adverse effects of Hepatitis C drugs using FAERS data Jing Huang, Xinyuan Zhang, Jingcheng Du, Rui Duan, Liu Yang, Jason Moore, Yong Chen, and Cui Tao
Gene Family-led Meta-Analysis of Drug Target Data Qiong Cheng, Saurabh Mehta, Tudor Oprea, and Stephan Schurer
3:20 pm - 3:40 pm Coffee Break
3:40 pm - 4:40 pm Session 4: Deep Learning and Data Mining
Deep Convolution Neural Networks for Drug-Drug Interaction Extraction Xia Sun, Long Ma, Xiaodong Du, Jun Feng, and Ke Dong
X-A-BiLSTM: a Combinational Deep Learning Approach for Depression Detection in Imbalanced Data Qing Cong, Zhiyong Feng, Fang Li, Yang Xiang, Guozheng Rao, and Cui Tao
Formulation of FAIR Metrics for Primary Research Articles Adam Craig and Carl Taswell
4:40 pm – 5:00 pm Closing Remarks and Feedback


Please email Workshop co-chair, Zhe He (

Past Workshops