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 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 2017 and published in the IEEE BIBM 2017 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: 1.643; Indexed in SCIE, MEDLINE, and PMC; and subject to an article processing charge of £1,122). Selected high-quality SHORT papers will also be invited to submit an extended version to the journal supplement for consideration.

Note: If a paper is selected for possible journal publication, the authors will be asked to shorten their workshop paper to be published in the BIBM 2017 Proceedings and then submit the journal version after the workshop. The authors can still choose to publish their full papers in the conference proceedings, in which case however, the authors will NOT be eligible to publish in the journal supplement due to the journal's self-plagiarism concern.

A new review process: To mitigate the biases and reduce the burden of the reviewer community, we will employ a hybrid approach in the review process of this workshop. We will invite external reviewers (in the Cyberchair system) as well as contributing authors to review the submissions (in the Pevals system). The final decision will be made based on the review reports from both systems. As such, the organizers, the external reviewers, as well as contributing authors will have a shared responsibility to maintain a high standard for the review process and ensure the quality of the workshop papers. To accommodate the busy schedule of the authors, you can choose the number of submission to review or not to participate in the peer-review in Pevals. In such a case, the decision will be made based on the external reviewers' review reports. (More details about the new review process)

The journal articles have been published in BMC Medical Informatics & Decision Making

Scope

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

Sept 27, 2017: Due date for full / work-in-progress workshop papers submission

Oct 15, 2017: Notification of paper acceptance to authors

Oct 25, 2017: Camera-ready of accepted papers

Nov 13, 2017: SEPDA 2017 Workshop

Journal submission deadline: TBD

Submission

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 (https://wi-lab.com/cyberchair/2017/bibm17/scripts/submit.php?subarea=S03&undisplay_detail=1&wh=/cyberchair/2017/bibm17/scripts/ws_submit.php)

Organizing

• 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
  • Jingshan Huang, School of Computing, University of South Alabama, USA
  • Jiang Bian, Biomedical Informatics, Health Outcomes & Policy, College of Medicine, University of Florida, USA
• Program Committee
  • GQ Zhang, University of Kentucky, USA
  • James Geller, New Jersey Institute of Technology, USA
  • Guoqian Jiang, Mayo Clinic, USA
  • Zhihui Luo, University of Wisconsin, Milwaukee, USA
  • Tianyong Hao, The cisco School of Informatics, Guangdong University of Foreign Studies, China
  • Amanda Hicks, University of Florida, USA
  • Yongqun “Oliver” He, University of Michigan, USA
  • Fernando Martin-Sanchez, Weill Cornell College of Medicine, USA
  • James Cimino, University of Alabama at Birmingham, USA
  • Licong Cui, University of Kentucky, USA
  • Xia Jing, Ohio University, USA
  • Riccardo Miotto, Icahn School of Medicine at Mount Sinai, USA
  • Olivier Bodenreider, US National Library of Medicine, USA
  • Fleur Mougin, University of Bordeaux, France
  • Praveen Chandar, IBM Research, USA
  • Yonghui Wu, University of Florida, USA
  • Ronald Cornet, University of Amsterdam, Netherlands
  • Yi Guo, University of Florida
  • Juan Antonio Lossio-Ventura, University of Florida
  • Buzhou Tang, Intelligent Computing Research Center, Harbin Institute of Technology Shenzhen, China
  • Zhengxing Huang, Zhejiang University, China
  • Gang Feng, Northwestern University
  • Hua Li, School of Medicine, Washington University
  • Han Wu, Rutgers University
  • Yang Xiang, University of Texas Health Science Center at Houston
  • Ryan Benton, University of South Alabama
  • Ankur Agrawal, Manhattan College

Review Process of Pevals

Introduction to the new peer-review system – Pevals (Participant-engaged evaluation system)

The review process consists of the following steps:

Step 1: Each contact author will claim organizational or individual conflicts-of-interest with all the other submissions. (10/1/2017 - 10/2/2017)

Step 2: Each contact author will be assigned to review and rank three other papers. Review assignments will be made so as to avoid organizational or individual conflicts-of-interest. All authors must complete their review and ranking of the assigned papers within 10 days of the date of their assignment. (10/3/2017 - 10/13/2017)

Step 3: A composite ranking of all papers will be determined, and each author’s paper ranking will be adjusted based on a measure of the “quality” of the reviews provided by the author. The adjustment is designed to provide an incentive to all authors to do an honest and thorough job of reviewing the papers to which they are assigned.

Step 4: Final acceptance/rejection decision making will be done by the workshop organizer based on the review results in both Pevals and Cyberchair (BIBM 2017 official review system).

Note: failure to complete this review and ranking within the allotted times will result in the disqualification of the author’s own paper.

Anonymity of reviewers will be preserved as authors will not know which of the other authors review their papers.

The advantages of adopting the new peer-review system are the following:

1. As you will commit significant time and efforts in reviewing the papers assigned to you, you would expect other authors who review your papers more committed than the reviewers of the current system.

2. Potential review bias will be minimized since biases will have serious consequences, which is lacking in current review system.

Program

TBD

Accepted Papers

• Rebecca Lin, Muhammad Amith, Chen Liang, and Cui Tao, "Designing an Ontology for Emotion-driven Visual Representations"
• Rui Zhang, Sisi Ma, Liesa Shanahan, Jessica Munroe, Sarah Horn, and Stuart Speedie, "Automatic Methods to Extract New York Heart Association Classification from Clinical Notes"
• Zhiwei Chen, Zhe He, Xiuwen Liu, and Jiang Bian, "An Exploration of Semantic Relations in Neural Word Embeddings Using Extrinsic Knowledge"
• Rashmie Abeysinghe and Licong Cui, "Query-constraint-based Association Rule Mining from Diverse Clinical Datasets in the National Sleep Research Resource"
• Biyang Yu and Zhe He, "Exploratory Textual Analysis of Consumer Health Languages for People who are D/deaf and Hard of Hearing"
• Yadan Fan, Lu He, and Rui Zhang, "Evaluating Automatic Methods to Extract Patients’ Supplement Use from Clinical Reports"
• Hee-Jin Lee, Yaoyun Zhang, Min Jiang, Jun Xu, Cui Tao, and Hua Xu, "Towards practical temporal relation extraction from clinical notes: an analysis of direct temporal relations"
• Juan Antonio Lossio-Ventura, William Hogan, Francois Modave, Yi Guo, Zhe He, Amanda Hicks, and Jiang Bian, "OC-2-KB: A software pipeline to build an evidence-based obesity and cancer knowledge base"
• Hansi Zhang, Yi Guo, Qian Li, Thomas George, Elizabeth Shenkman, and Jiang Bian, "Ontology-guided Semantic Data Integration to Support Integrative Data Analysis: A Case Study of Cancer Survival"
• Xinyuan Zhang, Shiqi Wang, Jie Liu, and Cui Tao, "Computer-aided Diagnosis of Four Common Cutaneous Diseases Using Deep Learning Algorithm"
• Huiqin Chen, Dihua Zhang, Guoping Zhang, Xiaofeng Li, Ying Liang, Mohan Kasukurthi, Glen Borchert, and Jingshan Huang, "MeSH term-based semantic analysis of microRNA regulation on glucocorticoid resistance in pediatric acute lymphoblastic leukemia"
• Kaixian Yu, Tingting Zhao, Peixiang Zhao, and Jinfeng Zhang, "Extraction of protein-protein interactions using natural language processing based pattern matching"
• Huawei Jin, Zhenhua Yu, Xiaodan Wang, Weian Chen, Shaolei Guo, Mohan Kasukurthi, Glen Borchert, and Jingshan Huang, "Computational analysis to discover microRNA biomarkers in glioblastoma"
• Jingcheng Du, Yaoyun Zhang, Cui Tao, and Hua Xu, "A pilot study of mining association between psychiatric stressors and symptoms in tweets"
• Zhe He, Yehoshua Perl, Gai Elhanan, Yan Chen, James Geller, and Jiang Bian, "Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts"
• Haodi Li, Qingcai Chen, Buzhou Tang, and Xiaolong Wang, "Chemical-induced Disease Extraction via Convolutional Neural Networks"
• Rashmie Abeysinghe, Eugene W. Hinderer III, Hunter N.B. Moseley, and Licong Cui, "Auditing Subtype Inconsistencies among Gene Ontology Concepts"

Registration

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.

Contact

Please email Workshop co-chair, Zhe He (Zhe.He@cci.fsu.edu)

Past Workshops

• The 1st International Workshop on Semantics-Powered Data Analytics (SEPDA 2016), in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), Shenzhen, China, December 15, 2016