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Ontolog Forum

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| [[has date::09 Mar 2022 17:00 GMT]]
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| 9:00am PST/12:00pm EST
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== Agenda ==
== Agenda ==
* '''Michael DeBellis''' ''Semantic Technology and the COVID-19 Pandemic'' [https://bit.ly/3w5ZQ0X Slides]
* '''Kenneth Baclawski''' ''Overview of the Pandemics Track'' [https://bit.ly/3HuLFV9 Slides]  
** Michael DeBellis is an independent researcher and consultant. Previously he was a partner with Deloitte Consulting and their eBusiness Chief Technology Officer. He also ran the Deloitte Western Region solution center lab in San Francisco. Prior to that he was a scientist at Accenture's Center for Strategic Technology and Research (CSTaR) where he was principal investigator for Accenture's Knowledge Based Software Assistant (KBSA) program. Prior to that he was a research associate at the Information Sciences Institute (ISI) and a senior staff in Accenture's Artificial Intelligence group. He has an MS degree in Computer Science from the University of Southern California and a BS/BA degree in computer science, psychology, and philosophy from the University of IL. at Chicago. His research interests include the Semantic Web, Knowledge Graphs, Software Engineering methods, and Evolutionary Psychology.
* '''Asiyah Lin''' ''Post-workshop Report of WCO-2020: Workshop on COVID-19 Ontologies'' [https://bit.ly/3MqscZu Slides]
* '''Biswanath Dutta''' ''CODO: an ontology for collection and analysis of multiparadigm COVID-19 data'' [https://bit.ly/3tCltTD 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/ .
** Biswanath Dutta is an Associate Professor at the Documentation Research and Training Centre (DRTC) of Computer and Communication Sciences Division of the Indian Statistical Institute (ISI), Bangalore Centre, INDIA. He holds a Bachelors's degree in Physics (1999) and a Bachelors's degree in Library and Information Science (LIS) (2000). He holds a master's degree in LIS from ISI Bangalore (2003) and has obtained a Ph.D. degree in LIS from the University of Pune (India), 2010 for his research conducted in ISI Bangalore. His area of study was online learning systems and semantic technologies. He was a Post-Doctoral Fellow at the Department of Information Engineering and Computer Science (DISI) of University of Trento, Italy (2009-2012). He has worked as a research assistant at the Department of Computer Science, Dalhousie University, Halifax, Canada. He has visited Interactive Media Lab, University of Toronto, Canada, and Max Plank Institut Informatic (MPII), Germany. He has actively worked on a European Commission funded research project ‘LivingKnowledge: LivingKnowledge - Facts, Opinions, and Bias in Time’ [http://livingknowledge-project.eu/]. He has worked in ITPAR II and III. Currently, he is handling (as a PI) a research project on COVID-19 and knowledge graph funded by Indian Statistical Institute, Kolkata [https://www.isibang.ac.in/~bisu/covid19project.html].  He provides consultancy services to the industries. He currently serves as a secretary of the International Society for Knowledge Organization (ISKO) - India Chapter.  He has published more than 50 scientific papers in national and international journals and conferences.  He has four books to his credit. His current research interests lie in the areas of ontology, metadata, knowledge graph, data science, and semantic technologies (for more, visit [https://sites.google.com/view/bdutta]/).
* [https://bit.ly/3HLc1SL Video Recording]
* [https://bit.ly/3w3icQ8 Video Recording]


== Conference Call Information ==
== Conference Call Information ==
* Date: '''Wednesday, 09 Mar 2022'''  
* Date: '''Wednesday, 02 Mar 2022'''  
* Start Time: 9:00am PST / 12:00pm EST / 6:00pm CET / 5:00pm GMT / 1700 UTC  
* Start Time: 9:00am PST / 12:00pm EST / 6:00pm CET / 5:00pm GMT / 1700 UTC  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=03&day=09&year=2022&hour=12&min=00&sec=0&p1=179 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=03&day=02&year=2022&hour=12&min=00&sec=0&p1=179 World Clock]  
* Expected Call Duration: 1 hour
* Expected Call Duration: 1 hour
{{:OntologySummit2022/ConferenceCallInformation}}
{{:OntologySummit2022/ConferenceCallInformation}}
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* [[CassiopeiaMiles|Cassiopeia Miles]]
* [[CassiopeiaMiles|Cassiopeia Miles]]
* [[ChrisAhern|Chris Ahern]]
* [[ChrisAhern|Chris Ahern]]
* [[DamionDooley|Damion Dooley]]
* [[DougHolmes|Doug Holmes]]
* [[DougHolmes|Doug Holmes]]
* [[DouglasRMiles|Douglas R Miles]]
* [[DouglasRMiles|Douglas R Miles]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[GeorgeHurlburt|George Hurlburt]]
* [[JanetSinger|Janet Singer]]
* [[JanetSinger|Janet Singer]]
* [[KenBaclawski|Ken Baclawski]]
* [[KenBaclawski|Ken Baclawski]]
* [[MarciaZeng|Marcia Zeng]]
* [[LeiaDickerson|Leia Dickerson]]
* [[MadelineIseminger|Madeline Iseminger]]
* [[NancyWiegand|Nancy Wiegand]]
* [[NancyWiegand|Nancy Wiegand]]
* [[RamSriram|Ram D. Sriram]]
* [[RamSriram|Ram D. Sriram]]
* [[RaviSharma|Ravi Sharma]]
* [[RaviSharma|Ravi Sharma]]
* [[RhiannonCameron|Rhiannon Cameron]]
* [[RobertRovetto|Robert Rovetto]]
* [[RobertRovetto|Robert Rovetto]]
* [[MichaelDeBellis|Michael DeBellis]]
* [[ToddSchneider|Todd Schneider]]


== Discussion ==
== Discussion ==
[12:14] RaviSharma: hello and welcome
[11:55] RaviSharma: Hello and welcome


[12:15] RaviSharma: Michael - What about Ramsidivir and others repurposed, did you keep track of these. Can you also follow groups where combinations of drugs are used, such as steroids interaction?
[12:09] RaviSharma: Asiyah Lin is reporting on a 2-day workshop


[12:17] RaviSharma: Michael - How do you use semantics in a query?
[12:11] RaviSharma: Speakers included Yamagata, Asiyah and members of the Jackson Lab


[12:22] Asiyah Lin: I'd like to say CIDO is an ontology rather than a vocabulary, maybe controlled vocabulary is more precise. And the whole OBO ontologies the same, should be more ontologies rather than vocabularies.
[12:12] RaviSharma: Ontologies included Covoc, Codo and Cido


[12:23] RaviSharma: Are KGs a part of Property Graph?
[12:13] RaviSharma: Harmonization and standardization were the main issues


[12:25] Asiyah Lin: Michael, your observation is correct. OWL has a higher request, it is more for a knowledge system, rather a data system.
[12:15] RaviSharma: One purpose of harmonization was to find protein targets and drug candidates for treating COVID-19.


[12:35] RaviSharma: For Dr Dutta - Are all types / combos of queries like the one you showed possible, for example multiple drugs used or by comorbidities and in another level which and which genes are affected?
[12:17] RaviSharma: Data was in semantically connected property graphs and Knowledge graphs


[12:36] RaviSharma: For Both: How does virus genome interact with human genome? Are there any overlaps and overlays between them?
[12:17] RaviSharma: Asiyah is reviewing the workshop


[12:42] RaviSharma: What distributions and other aspects of multivariate analysis are important in CODO?
[12:19] Leia Dickerson: What language are semantic labeled property graphs written and which graph platform is used? (is it Cypher or something else)


[12:44] Gary Berg-Cross: CIDO reuses some OBO foundry work.  Did CODO reuse the same work for vaccines, Dx, treatments etc.?  How harmonized is CODO with CIDO?
[12:19] RaviSharma: Health Canada, N3C and others participated in the workshop.


[12:46] Gary Berg-Cross: What was the pattern used for weather situation?
[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


[12:47] RaviSharma: How many individuals and institutes are collaborating now - active, informational and contributors and in analysis as well?
[12:24] RaviSharma: DeBellis and Dutta will be discussing CODO from India next week.


[12:49] Gary Berg-Cross: I now think of KG design methods as a hybrid that brings together data management methods  with graph development methods that leverage ontology engineering methods.  Worth a paper if anyone interested.....
[12:29] RaviSharma: There will be a Mini Hackathon on March 15, 2022.


[12:51] Gary Berg-Cross: The materials consulted slide is a rich one that would take time to understand.
[12:30] RaviSharma: Testing


[12:51] RaviSharma: Dr Dutta - Are you able to see gaps among different sources for example private, state and federal sources for same item in vocabulary or graph?
[12:30] RaviSharma: FDA EUA


[12:55] Gary Berg-Cross: Understanding the relations you used in the work is critical.  So for disease transmission/contact tracing you have "has close relationship with" between people.
[12:33] RaviSharma: FDA NIH Health Canada and Univ collaborations (Miami) focussing on tools


[13:00] RaviSharma: Q for both - How can KG SQL developed by Ken Baclawski be used?
[12:33] RaviSharma: FDA Data standards work


[13:13] Ram D. Sriram: Do you have a COVID disease ontology in your system. If so, what are its characteristics
[12:36] RaviSharma: Data are being used by communities, FAIR ontologies, data challenges,


[13:31] Gary Berg-Cross and Asiyah Lin: For real world data and evidence, please check out this group:
[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.
OHDSI (https://www.ohdsi.org/) Observational Health Data Sciences and Informatics
 
[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"


== Resources ==
== Resources ==
* Michael DeBellis [https://bit.ly/3w5ZQ0X Semantic Technology and the COVID-19 Pandemic]
* [https://bit.ly/3HLc1SL Video Recording]
* Biswanath Dutta [https://bit.ly/3tCltTD CODO: an ontology for collection and analysis of multiparadigm COVID-19 data]
* [https://icbo-conference.github.io/icbo2022/ ICBO 2022 meeting website]
* [https://bit.ly/3w3icQ8 Video Recording]
* [https://bit.ly/3HuLFV9 Slides for Overview of the Pandemics Track]  
* [https://bit.ly/3MqscZu Slides for Post-workshop Report of WCO-2020: Workshop on COVID-19 Ontologies]


== Previous Meetings ==
== Previous Meetings ==
{{#ask: [[Category:OntologySummit2022]] [[Category:Icom_conf_Conference]] [[<<ConferenceCall_2022_]]
{{#ask: [[Category:OntologySummit2022]] [[Category:Icom_conf_Conference]] [[<<ConferenceCall_2022_03_02]]
         |?|?Session|mainlabel=-|order=desc|limit=3}}
         |?|?Session|mainlabel=-|order=desc|limit=3}}
== Next Meetings ==
== Next Meetings ==
{{#ask: [[Category:OntologySummit2022]] [[Category:Icom_conf_Conference]] [[>>ConferenceCall_2022_03_09]]
{{#ask: [[Category:OntologySummit2022]] [[Category:Icom_conf_Conference]] [[>>ConferenceCall_2022_03_02]]
         |?|?Session|mainlabel=-|order=asc|limit=3}}
         |?|?Session|mainlabel=-|order=asc|limit=3}}



Latest revision as of 18:29, 16 December 2022

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"

Resources

Previous Meetings

 Session
ConferenceCall 2022 02 23Synthesis
ConferenceCall 2022 02 16Mark Fox
ConferenceCall 2022 02 09COVID-19 KGs
... further results

Next Meetings

 Session
ConferenceCall 2022 03 09Knowledge Graph Approach to Combat COVID-19
ConferenceCall 2022 03 16Semantic Agents
ConferenceCall 2022 03 23Risk
... further results