View source for ConferenceCall 2021 02 17

{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10"
|-
! scope="row" | Session
| [[session::Definitions]]
|-
! scope="row" | Duration
| [[duration::1.5 hour]]
|-
! scope="row" rowspan="3" | Date/Time
| [[has date::17 Feb 2021 17:00 GMT]]
|-
| 9:00am PST/12:00pm EST
|-
| 5:00pm GMT/6:00pm CET
|-
! scope="row" | Convener
| [[convener::GaryBergCross|Gary Berg-Cross]]
|-
| scope="row" | Track
| [[Track::B]]
|}

= [[OntologySummit2021|Ontology Summit 2021]] {{#show:{{PAGENAME}}|?Session}} =
{{:OntologySummit2021/Description}}

== Agenda ==
* 12:00 - 12:20 EST Intro to Harmonizing Definitions & Envo  Gary Berg-Cross 
* 12:20 - 12:40 EST Cryosphere vocabulary harmonizations with ENVO/SWEET ontologies and extensions to marine science UN Ocean Decade and other initiatives  [[PierButtigieg|Pier Buttigieg]]
* 12:40 -12:50 Example of Tools [[KaiBlumberg|Kai Blumberg]]
* [https://bit.ly/3pnkwdG Combined Slides]
* 12:50- 13:15 EST Discussion
* [https://bit.ly/3dvLsW8 Video Recording]

== Conference Call Information ==
* Date: '''Wednesday, 17 Feb 2021''' 
* 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=02&day=17&year=2021&hour=12&min=00&sec=0&p1=179 World Clock] 
* Expected Call Duration: 1.5 hours
{{:OntologySummit2021/ConferenceCallInformation}}

== Attendees ==
* [[AlexShkotin|Alex Shkotin]]
* [[AndreaWesterinen|Andrea Westerinen]]
* [[AndrewDougherty|Andrew Dougherty]]
* [[BobbinTeegarden|Bobbin Teegarden]]
* [[CassiopeiaMiles|Cassiopeia Miles]]
* [[DaliaVaranka|Dalia Varanka]]
* [[DaveWhitten|Dave Whitten]]
* [[DavidEddy|David Eddy]]
* [[DougHolmes|Doug Holmes]]
* [[DouglasRMiles|Douglas R Miles]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[IgorToujilov|Igor Toujilov]]
* [[JamesWilson|James Wilson]]
* [[JanetSinger|Janet Singer]]
* [[JanetteWong|Janette Wong]]
* [[KaiBlumberg|Kai Blumberg]]
* [[KenBaclawski|Ken Baclawski]]
* [[LeiaDickerson|Leia Dickerson]]
* [[MariyaEvtimova|Mariya Evtimova]]
* [[MarkUnderwood|Mark Underwood]]
* [[MichaelGruninger|Michael Gr&uuml;ninger]]
* [[MichaelSinger|Michael Singer]]
* [[MikeBennett|Mike Bennett]]
* [[NancyWiegand|Nancy Wiegand]]
* [[ParastooDelgoshaei|Parastoo Delgoshaei]]
* [[PeteRivett|Pete Rivett]]
* [[PierButtigieg|Pier Luigi Buttigieg]]
* [[RamSriram|Ram D. Sriram]]
* [[RaviSharma|Ravi Sharma]]
* [[SeanGordon|Sean Gordon]]
* [[SeljaSeppala|Selja Sepp&auml;l&auml;]]
* [[SteveRay|Steve Ray]]
* [[TerryLongstreth|Terry Longstreth]]
* [[ToddSchneider|Todd Schneider]]
* [[TomTinsley|Tom Tinsley]]

== Discussion ==
An attempt was made to split up the various threads during the discussion.  No doubt some mistakes were made.  Let me know if your comments were misclassified.  [[KenBaclawski|Ken Baclawski]]
=== Alignment ===
[12:35] Mariya Evtimova:
Can I use ROBOT for alignment of OBO file with another ontology

[12:50] Mariya Evtimova:
could you recommend me a tool for manual alignment?

[12:59] Kai Blumberg:
@[12:50] Mariya Evtimova: could you recommend me a tool for manual alignment?
Manual alignment of what?
@[12:35] Mariya Evtimova: Can I use ROBOT for alignment of OBO file with another ontology?
You could use a robot template to semi automate the process but it would need another tool or manual strategy to find the mappings. Usually these are done semi-manually

[13:03] Mariya Evtimova:
yes I am asking about OBO format ontology
OK thank you
if you have more information about a useful tool I am interested

[13:12] Alex Shkotin:
Mariya, join our group here https://groups.google.com/g/ontolog-forum

[13:15] Alex Shkotin:
Mariya, and ask your questions in the group

[13:18] Mariya Evtimova:
OK I will ask also in the group
thanks
=== Foundation ===
[12:49] Pier Luigi Buttigieg: https://github.com/EnvironmentOntology/envo/releases/tag/v2020-06-10

[12:50] MichaelGruninger: that sounds like the Foundationless Ontology approach

[12:51] MichaelGruninger: i.e. the ability to use domain ontologies with different upper ontologies

[12:51] MichaelGruninger: that was @Todd

[12:53] Pier Luigi Buttigieg: This where we'll store templates as dead simple design patterns: https://github.com/EnvironmentOntology/envo/tree/v2020-06-10/src/envo/patterns

[12:53] Gary Berg-Cross: You can see more about the Robot template at https://github.com/EnvironmentOntology/envo/wiki/ENVO-Robot-template-and-merge-workflow

[12:55] Pier Luigi Buttigieg: @Michael: We have a foundation in BFO, the fact that we're reasonably confident about being able to port to other upper levels doesn't imply otherwise

[12:56] Pier Luigi Buttigieg: Most upper-level ontologies don't diverge that much from the implementation side

[12:56] MichaelGruninger: @Pier Luigi Buttigieg: the ability to port to other upper ontologies is precisely the idea of the foundationless approach.

[12:57] Pier Luigi Buttigieg: https://github.com/mapping-commons/SSSOM

[12:58] MichaelGruninger: There are proponents of particular top-level ontologies that implicitly require the complete adoption of a their top level ontology as a prerequisite for interoperability

[12:58] Pier Luigi Buttigieg: Hmm, I'd say that's more like about portability than lacking a foundation - more like a multi-foundational approach

[12:59] MikeBennett: As a minimum I would think it is important to understand whether the TLO someone chooses to use is Realist of Conceptualist. Less significant for e.g. snow and rocks, but critical for business, finance etc.
=== OBO ===
[12:35] Leia Dickerson: @Kai-- is the template only for OBO or could it be adapted for RDF/OWL?

[12:37] Pier Luigi Buttigieg:
https://robot.obolibrary.org/
OBO, as a format, is essentially deprecated I think
@Kai - is that supported

[12:38] Kai Blumberg:
Link to ENVO documentation: https://github.com/EnvironmentOntology/envo/wiki/ENVO-Robot-template-and-merge-workflow
=== General ===
[12:09] RaviSharma: Welcome everyone including our speakers.

[12:08] David Eddy:
STARTING with controlled vocabularies! Surely you jest.

[12:09] Terry Longstreth: I concur with David E

[12:10] David Eddy: History we tossed a good vocabulary enforcement tool into the trash in 1993 when told, with the approach of magical search engines, any sort of discipline around terms & meanings simply wouldn't be necessary.

[12:12] Mike Bennett:
That diagram always causes confusion - to me it shows the expressiveness (the ability to convey some semantics), not actual semantics. Also some more expressive formats (e.g. XML) are less used to express semantics than less expressive formats (OWL).

[12:12] Alex Shkotin: yes

[12:13] David Eddy:
@Gary.. classic is a 700+ page Pentagon dictionary, with 140+ pages of acronyms most with a single meaning.In whose reality does an acronym/abbreviation/initialism have single meaning?

[12:13] Mike Bennett:
(cough)

[12:21] David Eddy: "semantically undisciplined".... that's a keeper

[12:17] Pier Luigi Buttigieg:
Note that some of these views are showing the inferred hierarchies, rather than the asserted ones

[12:32] Leia Dickerson: Glad to hear about Pier's challenges to balance rigor with the users' thoughts on definitions.  It's something we are trying to anticipate on the project I am working on.

[12:36] RaviSharma: Notes, Comments and Questions from Ravi Sharma
Feb 17, 2021 Ontology Harmonization Presentations

Case established for Vocabularies (Terms) Harmonization from different domains and existing different domain ontologies.
However, we need example of a harmonized multi domain ontology starting with harmonized vocabulary.
Can we assume that un-ambiguous telescoping ontologies that are meaningfully integrated such as you have shown are harmonized and for example could connect marine-ecosystems, marine biology, phytoplankton, and physical oceanography?
Look at NIEM which has approved identities (word combinations) and built-in relations that operate among domains. Is it an example of harmonized vocabularies only or is also a harmonized Ontology?
As far as SWEET and ENVO and similar earth science themes integration, it is lot easier compared to non-terrestrial planetary freezing and sublimation processes dealing with freezing processes in different than water species.
Specific case of event relating to Ice-glacier-lake-landslide and ablation is the Nanda-Devi Chamoli Himalayan glacier tragedy where 150+ lives are lost last week. Cryosphere modeling challenge is to explain what happened as there are post incidence data available! Options include soil-landslide, glacier  ice ablation, Lake formation and then tsunami like river-flow breaking dams.
Another case is recent snow-ice throughout the US but particular ice-forms in Texas causing havoc to life and utilities.

[12:39] MikeBennett: It amuses me that many Texans are throwing out food because they have no power to fridges and freezers. Are they not aware of the fundamental properties of snow? Perhaps this ontology would help

[13:00] Pier Luigi Buttigieg: @Ravi: we can use mass wasting semantics with process relations to link them to downstream mechanical waves : http://purl.obolibrary.org/obo/ENVO_01000690,

[13:03] David Eddy: a huge issue here is that given a lot of initial term capture starts with spreadsheets... where is the change control / Git for spreadsheets?

[13:10] RaviSharma: Kai, Gary other speaker - we thank you for the interaction and making us aware of status of progress in merging and or harmonizing vocabularies etc.?

[13:11] RaviSharma: this is a challenge

[13:12] David Eddy: @ToddS... "requirements" ... like specifications?   We're Agile now... we don't need no stinking specs

[13:15] Gary Berg-Cross: https://github.com/mapping-commons/SSSOM

[13:19] RaviSharma: what are the top 3-4 impediments in harmonizing ontologies

[13:19] Gary Berg-Cross: Next week 12:00 - 12:30 EST Artur Garcez, City University of London, Topic: Introduction to NeuroSymbolic Computing
12:30 - 13:00 EST Pascal Hitzler, Kansas State University, Topic: Neural-Symbolic Integration and Ontologies

[13:22] RaviSharma: Ken excellent comment about neuro semantic providing help to the harmonizing efforts such as ENVO

[13:25] ToddSchneider: Meeting ends @13:24 EST

== Resources ==
The planned topics to be covered at this session include the following:
* Introduction to harmonizing “definitions”
* Example of Global Cryosphere Watch vocabulary harmonization efforts
* The Environmental ontology (EnvO) – scope, topics, methods, status, philosophy….
* More on the Cryosphere/EnvO+ harmonization efforts
* Issues and next steps
* Planned and unplanned discussion

Here are some references to some of the relevant work involved:
* Ontology Tools and Resources
** http://www.obofoundry.org/resources
** Matentzoglu, N., Malone, J., Mungall, C. et al. MIRO: guidelines for minimum information for the reporting of an ontology. J Biomed Semant 9, 6 (2018). https://doi.org/10.1186/s13326-017-0172-7
** Seppälä, Selja, Alan Ruttenberg, and Barry Smith. "Guidelines for writing definitions in ontologies." Ciência da informação 46.1 (2017).
* DEFINITIONS IN ONTOLOGIES
** Selja Seppälä, Alan Ruttenberg, Yonatan Schreiber, Barry Smith, Michie, Susan, Robert West, and Janna Hastings. "Creating ontological definitions for use in science." Qeios (2019). https://pdfs.semanticscholar.org/139c/3e8cd4d82b4520300404da5f6001e71d6006.pdf
** All things EnvO see https://github.com/EnvironmentOntology/envo Buttigieg, P. L., Pafilis, E., Lewis, S. E., Schildhauer, M. P., Walls, R. L., & Mungall, C. J. (2016). The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. Journal of biomedical semantics, 7(1), 1-12.
** Advances in Semantic Harmonization: from the Cryosphere, to the Earth System (ESIP 2021) https://docs.google.com/presentation/d/1bmP8mC_VKpfIUXkejEBtNTqOqrf73NJ5gljeWTFtic0/edit#slide=id.gb44943ed1f_0_9

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