Overview

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 mining and 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 ontologies, data mining, knowledge representation, knowledge management, and 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.

In the past three years, SEPDA has been established as a key venue for disseminating research on health data analytics using semantic web technologies such as ontologies. In the past few years, we have seen an increasing interest in using semantic web technologies for health data analysis with more and more submissions that present novel methods and applications for linked open data, information extraction, semantic-web-based knowledge bases, and deep learning. The NIH Data Science Strategic Plan released in June 2018 explicitly commits to ensuring that all data-science activities and products supported by the agency adhere to the FAIR principles, meaning that data be Findable, Accessible, Interoperable, and Reusable. Semantic web technologies play a crucial role to address the FAIR principles. With the infrastructure support such as NCBO’s BioPortal for ontology maintenance, the CEDAR software for metadata creation and validation, more and more researchers are using ontologies and semantic web technologies for knowledge representation, semantic inference, natural language processing, and data analytics. Meanwhile, we received submissions that use semantic-based methods to tackle critical problems in biomedical informatics such as extracting drug-drug interaction, drug repurposing, adverse drug reaction, detecting early signals for cognitive impairment, and visualizing dietary supplement knowledge. It is thus critical for SEPDA to continue our momentum and allow researchers to present and discuss novel methods and applications in this fast growing field. This year, we will hold SEPDA in ISWC, the premier conference in semantic web.

Topics

Topics of interest include but not limited to:

• Semantics-based Data Mining and Analytics
  • Ontology-based text mining and natural language processing
  • Semantics-powered data mining and machine learning from biomedical, clinical, or social web data
  • Information Extraction from biomedical, clinical, or social web data
  • Semantic annotation on biomedical, clinical or social web data
• 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 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
  • Drug repurposing
  • Clinical trial generalizability assessment using ontologies
  • Algorithmic phenotyping and cohort identification using ontologies
  • Improving the literacy of health information consumers

Important Dates

June 28, 2019: Due date for full / work-in-progress workshop papers submission

July 24, 2019: Notification of paper acceptance to authors

August 10, 2019: Camera-ready of accepted papers

October 26, 2019: SEPDA 2019 Workshop

Submission

We are inviting original research submissions (FULL 12 pages), work-in-progress (SHORT 4 pages), and poster abstracts (2 pages).

All the accepted submissions will be presented in SEPDA 2019. The abstracts of full papers (2 pages) and the short papers (4 pages) will be published in CEUR Workshop Proceedings.

The full papers will be published in a mainstream journal in semantic web / biomedical informatics (TBA).

Submission site: Submit a New Paper

Submissions must be in English formatted in the style of the Springer Publications format for Lecture Notes in Computer Science (LNCS). For details on the LNCS style, see Springer’s Author Instructions.

Organizing

• Organizing Committee
  • Zhe He, PhD, School of Information, Florida State University, USA
  • Cui Tao, PhD, School of Biomedical Informatics, University of Texas Health Science Center at Houston, USA
  • Jiang Bian, PhD, Biomedical Informatics, Health Outcomes & Policy, College of Medicine, University of Florida, USA
  • Rui Zhang, PhD, Institute for Health Informatics, University of Minnesota, USA
• Program Committee Members
  • James Cimino, PhD, University of Alabama, Birmingham, USA
  • Yi Guo, PhD, University of Florida, USA
  • Xia Jing, PhD, Ohio University, USA
  • Jake Luo, PhD, University of Wisconsin–Milwaukee, USA
  • Yonghui Wu, PhD, University of Florida, USA
  • Licong Cui, PhD, School of Biomedical Informatics, University of Texas Health Science Center at Houston, USA
  • Feichen Shen, PhD, Mayo Clinic, USA
  • Fleur Mougin, PhD, University of Bordeaux, USA
  • Yuji Zhang, University of Maryland School of Medicine, USA
  • Zhengxing Huang, Zhejiang University, China
  • Guoqian Jiang, Mayo Clinic College of Medicine, USA
• Student Program Committee Members
  • Jingcheng Du, University of Texas Health Science Center at Houston, USA
  • Hansi Zhang, University of Florida, USA
  • Yunpeng Zhao, University of Florida, USA
  • Seyedeh Neelufar Payrovnaziri, Florida State University, USA
  • Xi Yang, University of Florida, USA
  • Xing He, University of Florida, USA
  • Xinyuan Zhang, University of Texas Health Science Center at Houston, USA

Accepted Papers

• Nur Hafieza Ismail, Mengnan Du, Ninghao Liu, Zhe He and Xia Hu. Using Deep Neural Network to Identify Cancer Survivors Living with Post-Traumatic Stress Disorder on Social Media
• Gilles Vandewiele, Bram Steenwinckel, Femke Ongenae and Filip De Turck. Inducing a decision tree with discriminative paths to classify entities in a knowledge graph
• Jiebin Chu, Wei Dong and Zhengxing Huang. Treatment Effect Prediction with Generative Adversarial Networks Using Electronic Health Records
• Hansi Zhang, Xing He, Tyler Harrison and Bian Jiang. Aero: An Evidence-based Semantic Web Knowledge Base of Cancer Behavioral Risk Factors
• Muhammad Amith, Rebecca Lin, Licong Cui, Dennis Wang, Anna Zhu, Grace Xiong, Hua Xu, Kirk Roberts and Cui Tao. An Ontology-Powered Dialogue Engine For Patient Communication of Vaccines
• Hansi Zhang, Yi Guo and Jiang Bian. Ontology for Documentation of Variable and Data Source Selection Process to Support Integrative Data Analysis in Cancer Outcomes Research
• Alyssa Lees, Chris Welty, Jacek Korycki and Shubin Zhao. Taxonomy Embeddings on PubMed Article Subject Headings
• Guocai Chen, Xiaoqian Jiang and Wenjin Zheng. Feature compression for predicting effective drug combination
• Guozheng Rao, Wenwen Li, Xiaowang Zhang, Li Zhang and Cui Tao. A multi-source linked open data fusion method for gene-disorder-drug relationship mining
• Anderson Rossanez and Julio Cesar dos Reis. Generating Knowledge Graphs from Scientific Literature of Degenerative Diseases
• Keyuan Jiang, Tingyu Chen, Liyuan Huang, Gelareh Karbaschi and Gordon Bernard. Semantic Similarity of Medication-Effect Relations Inferred from Neural Embedding

CEUR Proceedings

Links: http://ceur-ws.org/Vol-2427/

Workshop Schedule

Past Workshops

• The 1st 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 2nd 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).
• The 3rd SEPDA Workshop (SEPDA 2018) was held in conjunction with IEEE BIBM 2018 in Madrid, Spain. SPEDA 2018 was a full day workshop. 14 high quality papers were presented in the workshop. Extended journal version of the papers will be published in BMC Medical Informatics & Decision Making (IF: 2.134).