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].
The OIIDDS workshop aims to:
We welcome the submission of published and unpublished work focusing on ontologies, knowledge graphs, and their applications related to the following topics: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.
Extended abstracts can be 1-2 pages excluding the references. Acception notification will be made 5 days after submission.
Manuscripts must be submitted as PDFs via this link.
Manuscripts should be formatted using the following ICBO 2024 template.
Please reach out to asiyah.linATaxleinfo.com for questions regarding submission.
Asiyah Yu Lin (Axle Research and Technology)
Alexander Diehl (University at Buffalo)
John Beverley (University at Buffalo)
Lindsay G. Cowell (UT Southwestern Medical Center)
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).
By participating in this workshop, attendees acknowledge and agree that the workshop will be recorded and that their participation, including any comments, questions, and visual/audio presence, may be captured during this recording. The recorded content may be edited, repurposed, or otherwise modified by the workshop organizers, who reserve the right to publish the content on platforms, including but not limited to YouTube. By participating, attendees grant the workshop organizers the irrevocable right to use the recorded content for promotional, educational, and other appropriate purposes without further notice or compensation. By continuing with participation, attendees confirm their understanding and agreement to these terms.
Playlists of the current and previous VDOS conference recordings will be made available on YouTube Biomedical Ontology World Channel.
(OIIDDS 2023 (inagural))[https://delaneycdmcnulty.wixsite.com/oiids-workshop]
Diehl AD, Lee JA, Scheuermann RH, Blake JA. Ontology development for biological systems: immunology. Bioinformatics. 2007 Apr 1;23(7):913-5. doi: 10.1093/bioinformatics/btm029. PMID: 17267433.
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform. 2011 Feb;44(1):75-9. doi: 10.1016/j.jbi.2010.01.006. PMID: 20123131 PMCID: PMC2892030.
Babcock S, Beverley J, Cowell LG, Smith B. The Infectious Disease Ontology in the age of COVID-19. J Biomed Semantics. 2021 Jul 18;12(1):13. doi: 10.1186/s13326-021-00245-1. PMID: 34275487; PMCID: PMC8286442.
He, Y., Yu, H., Huffman, A. et al. A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. J Biomed Semant 13, 25 (2022). https://doi.org/10.1186/s13326-022-00279-z.
Asiyah Yu Lin, Yuki Yamagata, William D. Duncan, Leigh C. Carmody, Tatsuya Kushida, Hiroshi Masuya, John Beverley, Biswanath Dutta, Michael DeBellis, Zoë May Pendlington, Paola Roncaglia, Yongqun He. A Community Effort for COVID-19 Ontology Harmonization. Proceedings of the International Conference on Biomedical Ontologies 2021 co-located with the Workshop on Ontologies for the Behavioural and Social Sciences (OntoBess 2021) as part of the Bolzano Summer of Knowledge (BOSK 2021), 2021