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Ontolog Forum

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== Agenda ==
== Agenda ==
* '''Kenneth Baclawski''' ''Overview of the Pandemics Track'' [https://bit.ly/3HuLFV9 Slides]
* Synthesis
* '''Asiyah Lin''' ''Post-workshop Report of WCO-2020: Workshop on COVID-19 Ontologies'' [https://bit.ly/3MqscZu Slides]
** [https://bit.ly/3IlgTzh Video Recording]
** 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/ .
* [https://bit.ly/3HLc1SL Video Recording]


== Conference Call Information ==
== Conference Call Information ==
* Date: '''Wednesday, 02 Mar 2022'''  
* Date: '''Wednesday, 23 Feb 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=02&year=2022&hour=12&min=00&sec=0&p1=179 World Clock]  
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=02&day=23&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}}
Line 39: Line 37:
== Attendees ==
== Attendees ==
* [[AndrewDougherty|Andrew Dougherty]]
* [[AndrewDougherty|Andrew Dougherty]]
* [[AsiyahLin|Asiyah Lin]]
* [[BevCorwin|Bev Corwin]]
* [[BiswanatDutta|Biswanath Dutta]]
* [[CassiopeiaMiles|Cassiopeia Miles]]
* [[CassiopeiaMiles|Cassiopeia Miles]]
* [[ChrisAhern|Chris Ahern]]
* [[DougHolmes|Doug Holmes]]
* [[DouglasRMiles|Douglas R Miles]]
* [[DouglasRMiles|Douglas R Miles]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[JanetSinger|Janet Singer]]
* [[JanetSinger|Janet Singer]]
* [[KenBaclawski|Ken Baclawski]]
* [[KenBaclawski|Ken Baclawski]]
* [[LeiaDickerson|Leia Dickerson]]
* [[MadelineIseminger|Madeline Iseminger]]
* [[NancyWiegand|Nancy Wiegand]]
* [[RamSriram|Ram D. Sriram]]
* [[RamSriram|Ram D. Sriram]]
* [[RaviSharma|Ravi Sharma]]
* [[RaviSharma|Ravi Sharma]]
* [[RhiannonCameron|Rhiannon Cameron]]
* [[RobertRovetto|Robert Rovetto]]
* [[ToddSchneider|Todd Schneider]]
* [[ToddSchneider|Todd Schneider]]


== Discussion ==
== Discussion ==
[11:55] RaviSharma: Hello and welcome
[12:06] Gary Berg-Cross: I would add that the Launch had some ideas, such as the Semantic spectrum as a frame.
Another is the challenge of diverse definitions  The chat asked Is there common 'agreement' on the definition of 'disaster'?
The UN DRR is a start:


[12:09] RaviSharma: Asiyah Lin is reporting on a 2-day workshop
A serious disruption of the functioning of a community or society involving widespread human, material, economic or environmental losses and impacts, which exceeds the ability of the affected community or society to cope with using its own resources.


[12:11] RaviSharma: Speakers included Yamagata, Asiyah and members of the Jackson Lab
[12:12] Gary Berg-Cross: I think that we can leverage much from Mark Fox's talk on Public  Health  Events (within a city framework).  He covered ontology design patterns/modules and light ontology work.


[12:12] RaviSharma: Ontologies included Covoc, Codo and Cido
[12:14] RaviSharma: Todd and Gary suggestions on Ken's Q on disaster meaning.


[12:13] RaviSharma: Harmonization and standardization were the main issues
[12:15] RaviSharma: Risk - is not context dependent


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


[12:17] RaviSharma: Data was in semantically connected property graphs and Knowledge graphs
[12:16] RaviSharma: Gary look at Mark Fox talk for cities.


[12:17] RaviSharma: Asiyah is reviewing the workshop
[12:16] RaviSharma: pandemic health risk


[12:19] Leia Dickerson: What language are semantic labeled property graphs written and which graph platform is used?  (is it Cypher or something else)
[12:17] RaviSharma: Janet - parametric view


[12:19] RaviSharma: Health Canada, N3C and others participated in the workshop.
[12:18] RaviSharma: ontological view of disasters Janet and Todd


[12:20] RaviSharma: Workshop activities included
[12:19] RaviSharma: Gary said about OGC
* 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.
[12:22] Andrew Dougherty: OpenCYC has #$DisasterEvent


[12:29] RaviSharma: There will be a Mini Hackathon on March 15, 2022.
[12:28] Gary Berg-Cross: Parameters to understand pandemics include incubation period, transmissibility, the average stay in hospital, proportion of reported cases, proportion of deaths amount critial cases....from "Ten Epidemiological Parameters of COVID-19: Use of Rapid Literature Review to Inform Predictive Models During the Pandemic"


[12:30] RaviSharma: Testing
[12:29] Gary Berg-Cross: KG speakers Chris and Justin


[12:30] RaviSharma: FDA EUA
[12:33] RaviSharma: Ram outlined overview, start with definitions, patterns and speakers


[12:33] RaviSharma: FDA NIH Health Canada and Univ collaborations (Miami) focussing on tools
[12:33] RaviSharma: Janet reiterated that and a few diagrams in communique


[12:33] RaviSharma: FDA Data standards work
[12:34] Gary Berg-Cross: Mark made the point, that we can include in our communique that investigators  of disasters seek a deep  understanding  of  the extent  to  which  legacy  systems  have  created  disaster data  silos  across  the departments/divisions/areas dealing with disasters.
A  first  step  to  breaking  down  the  silos  is  the  creation  of  data  standards.  Stating that Data Standards  for  X  is  the  most  important  is  not  helpful


[12:36] RaviSharma: Data are being used by communities, FAIR ontologies, data challenges,
[12:36] Gary Berg-Cross: Alternate definition of Disaster - any accidental, natural or malicious event which threatens or
disrupts normal operations, or services, for sufficient time to affect significantly,or to cause failure of, the enterprise. from Glossary of Disaster
Management Terms


[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.
[12:37] ToddSchneider: From https://www.iso.org/obp/ui/#iso:std:iso:22300:ed-3:v1:en:term:3.1.73.: Disaster - 3.1.73
disaster
situation where widespread human, material, economic or environmental losses have occurred that exceeded the ability of the affected organization (3.1.165), community (3.1.39) or society to respond and recover using its own resources (3.1.207)


[12:44] RaviSharma: Gary - roles, ENVO, ES, hierarchies were to be consistent
[12:38] Andrew Dougherty: A specialization of #$Emergency.  Each instance of #$DisasterEvent is a #$PhysicalDestructionEvent in which at least some of the objects destroyed or harmed are considered to be of significant value.  (We use 'value' in its most general sense, to include monetary value, social value, moral value, etc.)  Obviously, this is a very subjective and norm-laden concept; however, there are many things which <i>clearly</i> qualify as #$DisasterEvents, e.g. #$TitanicSinking, #$BombingOfHiroshima, and #$TerroristAttack-September-11-2001-NYC-PENN-WDC.  Two important specializations are #$NaturalDisaster and #$ManMadeDisaster.


[12:46] RaviSharma: OBO foundry needs to better align, BFO is old 20 years?
[12:41] RaviSharma: Janet - Cyc definition, other dimensions, speakers comments, etc


[12:46] RaviSharma: Not yet productive level, a lot of work TBD on OBO foundries.
[12:42] RaviSharma: Todd - what were discussed, organize and highlight, use some of it in communique


[12:47] RaviSharma: Asiyah's portfolio work is to improve ontologies
[12:43] RaviSharma: Gary - talks, semantics, used by speakers, semantic approach to disasters, also KG


[12:51] RaviSharma: Asiyah's email addresses are available on request.
[12:45] RaviSharma: Ram- we are in the front end of laying foundations for theme of summit and connect the stories


[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.
[12:45] RaviSharma: Disasters - fundamental, Doug, mark, and others. from Ram


[12:58] RaviSharma: Asiyah agreed and showed interest in data sharing models
[12:46] Gary Berg-Cross: Smart cities shows and model levels approach


[13:01] RaviSharma: Gary contact gbergcross@gmail.com
Service Level (5087-n) spans concepts commonly associated
with a particular service but still shared with other services,
such as Vehicles and Transportation network. Can be read by
multiple services, but updated only by one service.


[13:01] RaviSharma: Asiyah made request for Workshop proposal
City Level (5087-2) spans concepts that are general to cities
and span all services such as Households, Services, Residents.
Can be read and updated by multiple services.


[13:02] RaviSharma: End of Sept is new data after ICBO meeting
Foundation  Level  (5087-1)  spans  very  general  concepts  such as  Time,  Location,  and  Activity,  upon  which  other  levels  are based.


[13:03] RaviSharma: Ram - on validation of BFO What is possible
[12:47] ToddSchneider: 0Since this is the 'Ontology Summit' how can the use of an ontological approach or the use of ontologies aid in 'disaster' planning, mitigation, or responses?


[13:03] RaviSharma: OBO foundry is somewhat using BFO
[12:49] Gary Berg-Cross: We talk about risks in a disaster such as on human, material, economic and environmental losses and impacts.


[13:06] Gary Berg-Cross: Trojahn, Cassia, et al. "Foundational ontologies meet ontology matching: A survey." Semantic Web Preprint (2021): 1-20.
[12:55] RaviSharma: Andrew and Doug volunteered to create a summary of Doug's talk on Cyc


[13:07] Robert Rovetto: There are and have been other top level ontologies, such as DOLCE, GFO, UFO, SUMO, Cyc, YAMATO
[12:56] RaviSharma: Ravi reminded that Doug Cyc needs feedback from his talk, Qs and comments, etc.


[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
[12:59] RaviSharma: Three other talks, volunteers needed, Josh OGC Pilot, (Andrew Volunteered)


[13:09] Gary Berg-Cross: see also "BFO and DOLCE: So Far, So Close... NICOLA GUARINO"
[13:01] RaviSharma: We have to schedule Andrew on April 13 or April 20
 
[13:02] RaviSharma: Doug Lenat talk has been viewed 1000 times (reviewed)
 
[13:02] RaviSharma: Other sessions views are in hundreds stats from Ken
 
[13:03] RaviSharma: Cas will try to Summarize the first talk
 
[13:03] Janet singer: Factors from the definitions of disaster, each evoking interesting parameters 1) a physical event 2) with risks 3) of harmful/disruptive/destructive impacts 4) on objects, services, systems 5) valued at various scales 6) according to economic, social, moral criteria
 
[13:04] RaviSharma: we still need two more for other speakers
 
[13:06] Janet singer: adding 7) evaluation from the perspective of some stakeholder (may be positive for some stakeholders while negative for others)
 
[13:08] Cas Miles: loosely associated thought: It seems several relief foundations define disasters with an element of 'capacity' of a community as well, "Disasters are serious disruptions to the functioning of a community that exceed its capacity to cope using its own resources." (but I'm not sure how that would work with existing ontologies or who and how capacity is defined yet.)
 
[13:11] RaviSharma: to Ken - request - we need to consolidate all comments relating to Cyc from Doug Miles and Andrew to send to Cyc Doug Lenat
 
[15:06] Douglas R. Miles: BTW..  at first I offered to do a summary of Lenat's talk but everyone realized it have very little to do with disasters and decided no one would need to summarize his talk..  So instead what we want is a description of what Cyc has along the lines of representing Risks and Disasters.
 
[15:06] Douglas R. Miles: Is that correct @Ken ?
 
[20:24] Ken Baclawski: @Douglas R. Miles: Yes that is correct.


== Resources ==
== Resources ==
* [https://bit.ly/3HLc1SL Video Recording]
* [https://bit.ly/3IlgTzh Video Recording]
* [https://icbo-conference.github.io/icbo2022/ ICBO 2022 meeting website]
* [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_03_02]]
{{#ask: [[Category:OntologySummit2022]] [[Category:Icom_conf_Conference]] [[<<ConferenceCall_2022_02_23]]
         |?|?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_02]]
{{#ask: [[Category:OntologySummit2022]] [[Category:Icom_conf_Conference]] [[>>ConferenceCall_2022_02_23]]
         |?|?Session|mainlabel=-|order=asc|limit=3}}
         |?|?Session|mainlabel=-|order=asc|limit=3}}



Latest revision as of 18:29, 16 December 2022

Session Synthesis
Duration 1 hour
Date/Time 23 Feb 2022 17:00 GMT
9:00am PST/12:00pm EST
5:00pm GMT/6:00pm CET
Convener Ravi Sharma
Track Disaster Landscape

Ontology Summit 2022 Synthesis

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

Conference Call Information

  • Date: Wednesday, 23 Feb 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

[12:06] Gary Berg-Cross: I would add that the Launch had some ideas, such as the Semantic spectrum as a frame. Another is the challenge of diverse definitions The chat asked Is there common 'agreement' on the definition of 'disaster'? The UN DRR is a start:

A serious disruption of the functioning of a community or society involving widespread human, material, economic or environmental losses and impacts, which exceeds the ability of the affected community or society to cope with using its own resources.

[12:12] Gary Berg-Cross: I think that we can leverage much from Mark Fox's talk on Public Health Events (within a city framework). He covered ontology design patterns/modules and light ontology work.

[12:14] RaviSharma: Todd and Gary suggestions on Ken's Q on disaster meaning.

[12:15] RaviSharma: Risk - is not context dependent

[12:15] RaviSharma: Gary said look at ontologies

[12:16] RaviSharma: Gary look at Mark Fox talk for cities.

[12:16] RaviSharma: pandemic health risk

[12:17] RaviSharma: Janet - parametric view

[12:18] RaviSharma: ontological view of disasters Janet and Todd

[12:19] RaviSharma: Gary said about OGC

[12:22] Andrew Dougherty: OpenCYC has #$DisasterEvent

[12:28] Gary Berg-Cross: Parameters to understand pandemics include incubation period, transmissibility, the average stay in hospital, proportion of reported cases, proportion of deaths amount critial cases....from "Ten Epidemiological Parameters of COVID-19: Use of Rapid Literature Review to Inform Predictive Models During the Pandemic"

[12:29] Gary Berg-Cross: KG speakers Chris and Justin

[12:33] RaviSharma: Ram outlined overview, start with definitions, patterns and speakers

[12:33] RaviSharma: Janet reiterated that and a few diagrams in communique

[12:34] Gary Berg-Cross: Mark made the point, that we can include in our communique that investigators of disasters seek a deep understanding of the extent to which legacy systems have created disaster data silos across the departments/divisions/areas dealing with disasters. A first step to breaking down the silos is the creation of data standards. Stating that Data Standards for X is the most important is not helpful

[12:36] Gary Berg-Cross: Alternate definition of Disaster - any accidental, natural or malicious event which threatens or disrupts normal operations, or services, for sufficient time to affect significantly,or to cause failure of, the enterprise. from Glossary of Disaster Management Terms

[12:37] ToddSchneider: From https://www.iso.org/obp/ui/#iso:std:iso:22300:ed-3:v1:en:term:3.1.73.: Disaster - 3.1.73 disaster situation where widespread human, material, economic or environmental losses have occurred that exceeded the ability of the affected organization (3.1.165), community (3.1.39) or society to respond and recover using its own resources (3.1.207)

[12:38] Andrew Dougherty: A specialization of #$Emergency. Each instance of #$DisasterEvent is a #$PhysicalDestructionEvent in which at least some of the objects destroyed or harmed are considered to be of significant value. (We use 'value' in its most general sense, to include monetary value, social value, moral value, etc.) Obviously, this is a very subjective and norm-laden concept; however, there are many things which clearly qualify as #$DisasterEvents, e.g. #$TitanicSinking, #$BombingOfHiroshima, and #$TerroristAttack-September-11-2001-NYC-PENN-WDC. Two important specializations are #$NaturalDisaster and #$ManMadeDisaster.

[12:41] RaviSharma: Janet - Cyc definition, other dimensions, speakers comments, etc

[12:42] RaviSharma: Todd - what were discussed, organize and highlight, use some of it in communique

[12:43] RaviSharma: Gary - talks, semantics, used by speakers, semantic approach to disasters, also KG

[12:45] RaviSharma: Ram- we are in the front end of laying foundations for theme of summit and connect the stories

[12:45] RaviSharma: Disasters - fundamental, Doug, mark, and others. from Ram

[12:46] Gary Berg-Cross: Smart cities shows and model levels approach

Service Level (5087-n) spans concepts commonly associated with a particular service but still shared with other services, such as Vehicles and Transportation network. Can be read by multiple services, but updated only by one service.

City Level (5087-2) spans concepts that are general to cities and span all services such as Households, Services, Residents. Can be read and updated by multiple services.

Foundation Level (5087-1) spans very general concepts such as Time, Location, and Activity, upon which other levels are based.

[12:47] ToddSchneider: 0Since this is the 'Ontology Summit' how can the use of an ontological approach or the use of ontologies aid in 'disaster' planning, mitigation, or responses?

[12:49] Gary Berg-Cross: We talk about risks in a disaster such as on human, material, economic and environmental losses and impacts.

[12:55] RaviSharma: Andrew and Doug volunteered to create a summary of Doug's talk on Cyc

[12:56] RaviSharma: Ravi reminded that Doug Cyc needs feedback from his talk, Qs and comments, etc.

[12:59] RaviSharma: Three other talks, volunteers needed, Josh OGC Pilot, (Andrew Volunteered)

[13:01] RaviSharma: We have to schedule Andrew on April 13 or April 20

[13:02] RaviSharma: Doug Lenat talk has been viewed 1000 times (reviewed)

[13:02] RaviSharma: Other sessions views are in hundreds stats from Ken

[13:03] RaviSharma: Cas will try to Summarize the first talk

[13:03] Janet singer: Factors from the definitions of disaster, each evoking interesting parameters 1) a physical event 2) with risks 3) of harmful/disruptive/destructive impacts 4) on objects, services, systems 5) valued at various scales 6) according to economic, social, moral criteria

[13:04] RaviSharma: we still need two more for other speakers

[13:06] Janet singer: adding 7) evaluation from the perspective of some stakeholder (may be positive for some stakeholders while negative for others)

[13:08] Cas Miles: loosely associated thought: It seems several relief foundations define disasters with an element of 'capacity' of a community as well, "Disasters are serious disruptions to the functioning of a community that exceed its capacity to cope using its own resources." (but I'm not sure how that would work with existing ontologies or who and how capacity is defined yet.)

[13:11] RaviSharma: to Ken - request - we need to consolidate all comments relating to Cyc from Doug Miles and Andrew to send to Cyc Doug Lenat

[15:06] Douglas R. Miles: BTW.. at first I offered to do a summary of Lenat's talk but everyone realized it have very little to do with disasters and decided no one would need to summarize his talk.. So instead what we want is a description of what Cyc has along the lines of representing Risks and Disasters.

[15:06] Douglas R. Miles: Is that correct @Ken ?

[20:24] Ken Baclawski: @Douglas R. Miles: Yes that is correct.

Resources

Previous Meetings

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

Next Meetings

 Session
ConferenceCall 2022 03 02Workshop Report
ConferenceCall 2022 03 09Knowledge Graph Approach to Combat COVID-19
ConferenceCall 2022 03 16Semantic Agents
... further results