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Inaugural Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science 

Important Information

Below you will find information about the Agenda for the Workshop

This is a link to a time zone converter:  https://www.worldtimebuddy.com/?pl=1&lid=3469058,12,2643743,5128581&h=3469058&hf=1 

Agenda

Part 1:  8:30- 10AM Brasilia / 7:30AM -9AM New York / 12PM -2PM London

8:45  - 9 AM opening by Dr. Asiyah Lin (virtual) & Dr. Alex Diehl (in-person)

9:00 - 9:45 AM Keynote by Dr. Lindsay Cowell : Creating the adaptive immune receptor repertoire knowledge commons: ontology-based large scale data integration and machine learning (virtual)

9:45 - 10:00 AM  Q&A and discussion

Part 2: 10:15AM - 11:45AM Brasilia / 9:15AM - 10:45AM New York / 2:15 PM - 3:45 PM London

10:15 - 10:45 AM  Tracking the functional effects of SARS-CoV-2 genomic variants: an ontology-driven approach (virtual) by Madeline Iseminger (25min and 5min Q&A)

10:45 - 11:15 AM  Modeling of vaccine-induced immune responses using the Vaccine Ontology (virtual) by Yongqun “Oliver” He  (25min and 5min Q&A)

11:15 - 11:45 AM  Interactive discussion

Part 3: 1:30PM - 3PM Brasilia / 12:30 - 2PM New York / 5:30 - 8PM London

1:30 - 2 PM Integrating Declarative and Procedural Knowledge in Infectious Disease Scenario for Epidemiological Monitoring (in-person) by Evellin Cardoso (25min and 5min Q&A)

2 - 2:30 PM Ontology development Methodologies in the Context of Infectious Disease Ontologies (virtual) by Giacomo De Colle (25min and 5min Q&A)

2:30 - 3PM Interactive discussion

Part 4: 3:15PM - 5:45PM Brasilia / 2:15 - 4:45 PM New York / 7:15 - 9:45 PM London

3:15 - 3:45 PM Standardizing terms to capture different types of in vivo administration in the Ontology for Biomedical Investigations (virtual) by Sebastian Duesing (25min & 5min Q&A)

3:15 - 3:45 PM Standardizing terms to capture different types of in vivo administration in the Ontology for Biomedical Investigations (virtual) by Sebastian Duesing (25min & 5min Q&A)

3:45 - 4:15 PM Harmonization of the Pathogenesis Gene Ontology (PathGO) (virtual)with GO by Gene D. Godbold (25min & 5min Q&A)

4:15 - 4:45 PM Classifying Dental Caries and Non-Carious lesions within the OBO Foundry (virtual) by Gopikrishnan M. Chandrasekharan  (25min & 5min Q&A)

4:45 - 5:15 PM Multi-Ontology framework of Maternal Milk for Immune Systems (MOMMIS) (virtual) by Emily Steliotes  (25min & 5min Q&A)

5:15 - 5:45 PM Interactive discussion & Closing remark

4:15 - 4:45 PM Classifying Dental Caries and Non-Carious lesions within the OBO Foundry (virtual) by Gopikrishnan M. Chandrasekharan  (25min & 5min Q&A)

4:45 - 5:15 PM Multi-Ontology framework of Maternal Milk for Immune Systems (MOMMIS) (virtual) by Emily Steliotes  (25min & 5min Q&A)

5:15 - 5:45 PM Interactive discussion & Closing remark

We are delighted to announce the first workshop on Ontologies for Infectious and Immune-mediated Disease Data Science (OIIDDS), as a part of the ICBO 2023 workshops & Tutorials. We invite you to join us for a hybrid and highly interactive workshop to discuss ontologies, data science, infectious disease, and immunology, at Brasilia University in Brazil. 

Important Dates

Extended Abstract Submission deadline: July 23, 2023, 11:59 PM EDT

Acceptance: July 30, 2023

Final Presentation Slides due: August 21, 2023

Workshop date: August 28, 2023

Extended Abstract or full-length paper for proceeding publish due: October 1, 2023

*If an early approval letter is needed for traveling purposes, please reach out to Dr. Asiyah Yu Lin at asiyah.lin@axleinfo.com 

Background: Infectious and immune-mediated disease (IID) research covers various disparate areas including autoimmune diseases, human inborn errors in immunity, infectious diseases and host-pathogen interactions, immunological studies, epidemiological studies, surveillance, clinical trials, and reagent and diagnostic method development. Rare immunological diseases, such as severe combined immunological deficiencies, remain a significant concern and focus for research. Ontologies and Knowledge Graphs (KG) serve as ideal tools for integrating such data to support innovations and decision-making. Over the last 15 years, the OBO Foundry community has developed multiple immunology and infectious disease ontologies [1][2][3][4]. There is, however, a growing need for better coordination and integration strategies across these and other efforts, as well as improved strategies for identifying gaps in existing domain coverage [5]. 

Hybrid experience

Objectives: 

  1. Evaluate the landscape of existing ontologies or KGs to support IID research and data science. 

  2. Demonstrate the successful use of existing ontologies or KGs in facilitating data integration in IID research.

  3. Identify gaps, challenges, and strategies for improving integration in IID research. 

  4. Provide education for and demonstrations of proper interface with ontology communities and existing ontologies (term reuse, requests, etc.)

  5. Strategize solutions to blockers for ontology reuse, including but not limited to: 

          Lack of awareness of existing ontologies
          Modification of ontology terms without considering user impact
          Excessive, regular, delayed responses to term request
          Academic incentives not aligned with user incentives

We welcome the submission of published and unpublished work focusing on ontologies, knowledge graphs, and their applications related to the following topics: 

  • Infectious and immune-mediated disease (IID).

  • Epidemiological surveillance and monitoring.

  • Big data-supported therapeutic discovery for IID.

  • Immunological data, pathways, and mechanisms.

  • Pathogen and host responses.

  • FAIR metadata for IID research.

  • Pandemic preparedness.

Submission Logistics

  • Extended abstracts can be 1-2 pages; short-length manuscripts for workshops are generally 5-6 pages.

  • Manuscripts must be submitted as PDFs via this link.

  • Manuscripts should be formatted using the following ICBO 2023 template.  

Organizing Committee

Open Science and FAIR Principle

Open Science and the FAIR principles are essential for advancing scientific research and promoting knowledge sharing.Our workshop embraces the practice of Open Science and FAIR principles. All material including submission, slides, and videos will be made publicly available after the workshop. We encourage authors to obtain DOIs for the submission and related material via a generalist repository (such as Zenodo, OSF, and more).

Information on other ICBO 2023 workshops and tutorials can be found here. 

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