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Session Workshop Report
Duration 1 hour
Date/Time 02 Mar 2022 17:00 GMT
9:00am PST/12:00pm EST
5:00pm GMT/6:00pm CET
Convener Ravi Sharma
Track Pandemics

Ontology Summit 2022 Workshop Report

Dealing with Disasters

The COVID-19 pandemic as well as other pandemics and disasters have prompted an impressive, worldwide response by governments, industry, and the academic community. Ontologies can play a significant role in search, data description, interoperability and harmonization of the increasingly large data sources that are relevant to disasters such as the COVID-19 pandemic. The Ontology Summit 2022 examined the overall landscape of disasters and related ontologies. A framework consisting of a set of dimensions was developed to characterize this landscape. The framework was applied to health-related disasters, environmental disasters, as well as aerospace and cyberspace disasters. It was found that there are many cross-domain linkages between different kinds of disasters and that ontologies developed for one kind of disaster can be repurposed for other kinds. A representative sample of projects that have been developing and using ontologies for disaster monitoring and response management is presented to illustrate best practices and lessons learned. The Communiqué ends by presenting the findings and recommendations of the summit.

Agenda

  • Kenneth Baclawski Overview of the Pandemics Track Slides
  • Asiyah Lin Post-workshop Report of WCO-2020: Workshop on COVID-19 Ontologies Slides
    • Dr. Asiyah Yu Lin has an Interdisciplinary background in medicine, immunology, molecular biology, medical informatics, and e-commerce entrepreneurship with a focus in ontology-based data, information and knowledge management and integration solutions for bio and health data. She is a knowledgeable ontologist with expertise in a wide variety of artificial intelligence (AI) semantic technologies, strategic design, business analysis, process development, and project control and coordination in the medicinal product regulation and biomedical research space. Asiyah advocates leveraging ontologies for data interoperability and establishing a knowledge eco-system for science and regulatory communities. She initiated and manages the OHDSI Medical Device Working Group, COVID-19 ontology harmonization group, and the FDA-NIH ontology round table discussion group. Currently, with the NIH’s Data and Technology Advancement National Service Scholar program, Asiyah coordinates NIH internal and external stakeholders for the NIH Cloud Platform Interoperability (NCPI) to build the genomics data ecosystem. More about her on LinkedIn https://www.linkedin.com/in/dryulin/ .
  • Video Recording

Conference Call Information

  • Date: Wednesday, 02 Mar 2022
  • Start Time: 9:00am PST / 12:00pm EST / 6:00pm CET / 5:00pm GMT / 1700 UTC
  • Expected Call Duration: 1 hour
  • The Video Conference URL is https://bit.ly/3rTKSGQ
    • Meeting ID: 881 4427 2329
    • Passcode: 553714
  • Chat Room: https://bit.ly/37g93pC
    • If the chat room is not available, then use the Zoom chat room.
  • One tap mobile

Attendees

Discussion

[11:55] RaviSharma: Hello and welcome

[12:09] RaviSharma: Asiyah Lin is reporting on a 2-day workshop

[12:11] RaviSharma: Speakers included Yamagata, Asiyah and members of the Jackson Lab

[12:12] RaviSharma: Ontologies included Covoc, Codo and Cido

[12:13] RaviSharma: Harmonization and standardization were the main issues

[12:15] RaviSharma: One purpose of harmonization was to find protein targets and drug candidates for treating COVID-19.

[12:17] RaviSharma: Data was in semantically connected property graphs and Knowledge graphs

[12:17] RaviSharma: Asiyah is reviewing the workshop

[12:19] Leia Dickerson: What language are semantic labeled property graphs written and which graph platform is used? (is it Cypher or something else)

[12:19] RaviSharma: Health Canada, N3C and others participated in the workshop.

[12:20] RaviSharma: Workshop activities included

  • Libraries and tools
  • Ontobridge and bioharmony for integration and harmonization
  • Seven ontologies were shown and collaboration discussed
  • Integration was discussed
  • Alignment with BFO
  • Discussing different tiers of harmonization

[12:24] RaviSharma: DeBellis and Dutta will be discussing CODO from India next week.

[12:29] RaviSharma: There will be a Mini Hackathon on March 15, 2022.

[12:30] RaviSharma: Testing

[12:30] RaviSharma: FDA EUA

[12:33] RaviSharma: FDA NIH Health Canada and Univ collaborations (Miami) focussing on tools

[12:33] RaviSharma: FDA Data standards work

[12:36] RaviSharma: Data are being used by communities, FAIR ontologies, data challenges,

[12:43] RaviSharma: Answer to Gary Berg-Cross's request for examples: Biomedical ontology is a small community, Alpha reuses a lot of OBO and is harmonizable.

[12:44] RaviSharma: Gary - roles, ENVO, ES, hierarchies were to be consistent

[12:46] RaviSharma: OBO foundry needs to better align, BFO is old 20 years?

[12:46] RaviSharma: Not yet productive level, a lot of work TBD on OBO foundries.

[12:47] RaviSharma: Asiyah's portfolio work is to improve ontologies

[12:51] RaviSharma: Asiyah's email addresses are available on request.

[12:57] Robert Rovetto: Top level ontologies are not necessary and are often not desired. There are technical reasons not to use them. In any case, anyone can make their own.

[12:58] RaviSharma: Asiyah agreed and showed interest in data sharing models

[13:01] RaviSharma: Gary contact gbergcross@gmail.com

[13:01] RaviSharma: Asiyah made request for Workshop proposal

[13:02] RaviSharma: End of Sept is new data after ICBO meeting

[13:03] RaviSharma: Ram - on validation of BFO What is possible

[13:03] RaviSharma: OBO foundry is somewhat using BFO

[13:06] Gary Berg-Cross: Trojahn, Cassia, et al. "Foundational ontologies meet ontology matching: A survey." Semantic Web Preprint (2021): 1-20.

[13:07] Robert Rovetto: There are and have been other top level ontologies, such as DOLCE, GFO, UFO, SUMO, Cyc, YAMATO

[13:07] Gary Berg-Cross: Matching BFO, DOLCE, GFO and SUMO: an evaluation of OAEI 2018 matching systems see https://www.researchgate.net/profile/Daniela-Schmidt-3/publication/338935334_Matching_BFO_DOLCE_GFO_and_SUMO_an_evaluation_of_OAEI_2018_matching_systems/links/5e339b5392851c7f7f0eb36d/Matching-BFO-DOLCE-GFO-and-SUMO-an-evaluation-of-OAEI-2018-matching-systems.pdf

[13:09] Gary Berg-Cross: see also "BFO and DOLCE: So Far, So Close... NICOLA GUARINO"

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