The 1st International Workshop on Semantics-Powered Data Analytics (SEPDA 2016)

in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016)
to be held at Shenzhen, China
on December 15, 2016


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 leverage 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 (8 pages) as well as work-in-progress (4 pages). All the accepted papers will be published in the main conference proceedings of BIBM 2016. Selected full papers will be invited to submit an extended version of the paper to Journal of Healthcare Engineering (Impact Factor: 0.925 according to the 2015 Journal Citation Reports released by Thomson Reuters in 2016; and are indexed by major databases such as MEDLINE, PubMed and Science Citation Index Expanded) Special Issue on "Semantics-Powered Healthcare Engineering and Data Analytics". We accept general submissions to the special issue beyond accepted workshop papers as well. Further, the special issue has an expanded scope. We welcome submissions related to semantics-powered healthcare engineering as well.

Camera ready paper submission is due: 11/20

Conference Hotel:
This year the conference will be hosted at the Kylin Villa resort, a 5-star resort in Shenzhen, China.
A block of rooms have been reserved for December 14, 2016 – December 20, 2016 for this Conference. To book a room at the discounted rate (the cut off date is November 15), please follow the instruction at


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
  • Data Analytics
    • Ontology-based literature mining
    • Ontology-based analysis on biomedical, clinical, or social web data
    • Named entity recognition and relation extraction on biomedical, clinical, or social web data
    • Data mining or machine learning on biomedical, clinical, multimedia 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
    • Drug repurposing using semantic web technologies
    • Clinical trial generalizability assessment using semantic web technologies
    • Algorithmic phenotyping and cohort identification using ontologies
    • Improving the literacy of health information consumers

Important Dates

Oct 25, 2016: Due date for full / work-in-progress workshop papers submission

Oct 31, 2016: Due date for work-in-progress paper submissions

Nov 10, 2016: Notification of paper acceptance to authors

Nov 20, 2016: Camera-ready of accepted papers

Dec 15, 2016: Workshops

Journal submission deadline: January 15, 2017


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
    • Michel Dumontier, Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University, USA
    • Jiang Bian, Biomedical Informatics, Health Outcomes & Policy, College of Medicine, University of Florida, USA
  • Program Committee
    • William Hogan, University of Florida, USA
    • Rui Zhang, University of Minnesota, USA
    • GQ Zhang, University of Kentucky, USA
    • James Geller, New Jersey Institute of Technology, USA
    • Guoqian Jiang, Mayo Clinic, USA
    • Jake Luo, University of Wisconsin, Milwaukee, USA
    • Tianyong Hao, Guangdong University of Foreign Studies, China
    • Amanda Hicks, University of Florida, USA
    • Hong Cui, University of Arizona, USA
    • Yongqun “Oliver” He, University of Michigan, USA
    • Fernando Martin-Sanchez, Weill Cornell College of Medicine, USA
    • Vasant Honavar, Pennsylvania State University, USA
    • James Cimino, University of Alabama at Birmingham, USA
    • Licong Cui, University of Kentucky, USA
    • Xia Jing, Ohio University, USA
    • Hongfang Liu, Mayo Clinic, USA
    • Riccardo Miotto, Icahn School of Medicine at Mount Sinai, USA
    • Olivier Bodenreider, US National Library of Medicine, USA
    • Dingcheng Li, Mayo Clinic, USA
    • Kin Wah Fung, US National Library of Medicine, USA
    • Fleur Mougin, University of Bordeaux, France
    • Praveen Chandar, IBM Research, USA
    • Samson Tu, Stanford University, USA
    • Kevin Cohen, University of Colorado, USA
    • Hua Xu, University of Texas Health Center at Houston, USA
    • Yonghui Wu, University of Texas Health Center at Houston, USA
    • Ronald Cornet, University of Amsterdam, Netherlands
    • Jingshan Huang, University of South Alabama
    • Yi Guo, University of Florida
    • Juan Antonio Lossio-Ventura, University of Florida


The workshop is scheduled in the morning of 12/15/2016 from 8:00 am to 12:00 pm. The conference program of BIBM 2016 is now available at

Accepted Papers

    Full Papers

  • Yadan Fan, Lu He, and Rui Zhang. Classification of Status for Supplement Use in Clinical Notes.
  • Jingshan Huang, Bi Liu, Yang Liu, and Ji Chen. The utilization of the OmniSearch semantic search tool to explore various microRNA regulation mechanisms in osteoarthritis.
  • Jingshan Huang, Dejing Dou, Jun She, Andrew Limper, Yanan Yang, and Ping Yang. A comprehensive (biological and computational) investigation on the role of microRNA::mRNA regulations performed in chronic obstructive pulmonary disease and lung cancer
  • Wenxin Ning and Ming Yu. Exploiting Distributional Semantics to Benefit Machine Learning in Automated Clinical Text Classification: An Initial Study.
  • Juan Antonio Lossio-Ventura, William Hogan, François Modave, Amanda Hicks, Josh Hanna, Yi Guo, Zhe He, and Jiang Bian. Towards an obesity-cancer knowledge base: biomedical entity identification and relation detection.
  • Shengyu Liu, Kai Chen, Qingcai Chen, and Buzhou Tang. Dependency-based convolutional neural network for drug-drug interaction extraction.
  • Mohcine Madkour, Hsing-yi Song, Jingcheng Du, and Cui Tao. A Representational Analysis of Temporal Uncertainty in Clinical Events.

    Short Papers

  • Lawrence Chan, Cesar Wong, and Keith Chiu. Ontological Features of Electronic Health Records Reveal Distinct Association Patterns in Hepatocellular Carcinoma and Liver Metastasis.


At least one author of an accepted paper needs to register as one full registration in order to have the paper published in the conference proceedings. The early registration deadline is November 20, 2016.

The URL of the registration is at


Please email Workshop co-chair, Zhe He (