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Latest revision as of 17:43, 2 November 2024

The goal of the National Center for Ontological Research is to advance ontological investigation within the United States. NCOR serves as a vehicle to coordinate, to enhance, to publicize, and to seek funding for ontological research activities. It lays a special focus on ontology training and on the establishment of tools and measures for quality assurance of ontologies. NCOR provides ontology services to multiple organizations, including the US Department of Defense.

Events

See here

For past events see here

For Buffalo Toronto Ontology Alliance (BoaT) see [1]

News

Techguide Podcast, Careers in Tech for non-STEM students, October 30, 2024

APA Blog interview with Barry Smith and John Beverley, October 4, 2024.

DOD, Intelligence Community adopt resource developed by UB ontologists, Bert Gambini, UBNow, February 29, 2024.

U.S. Defense and Intelligence to Adopt BFO and CCO Standards for Enhanced Data Management,Shivani Chauhan, 28 Feb 2024.

Article on BFO in the Frankfurter Allgemeine Zeitung, September 28, 2022, p. N3. Translation of opening paragraph:

Industry standards are not usually associated with philosophy or the humanities. That is why the new ISO/IEC 21838 standard conceals a minor scientific-historical sensation. Because for the first time, a philosophical theory has now been declared an industry standard, namely: the "Basic Formal Ontology", BFO for short. When you try to pronounce this acronym, it sounds a lot like "Buffalo," and that's no coincidence. Because Barry Smith, the main brain behind this norm, is the Julian Park Professor of Philosophy at the University of Buffalo in northern New York State, not far from Niagara Falls ...

For full text see here.

Interview with Barry Smith on Careers in Ontology, September 15, 2022

Interviews and podcasts on ''Why Machines Will Never Rule the World''

New book on limits of AI published, August 12, 2022.

Machines ruling the world? Impossible, say researchers

This will totally blow your mind

UB professor’s ontology work recognized in an international standard, April 29, 2022.

Press release on launch of Industrial Ontologies Foundry, February 19, 2021.

Video recording of talk by Barry Smith on "Defining Intelligence", February 17, 2021

Press-release launching the new Industrial Ontologies Foundry, February 19, 2021

NCOR-Brasil established, December 1, 2020

Using Ontology as Powerful Weapon in COVID-19 Fight, July 14, 2020

Leveraging a powerful weapon in the fight against COVID-19 — ontology, June 10, 2020

UB workshop to address human and machine capabilities, April 20, 2018

Working group seeks to extend the depth and functionality of biomedical ontologies, October 14, 2017

Barry Smith wins 2016 IAOA Ontology Competition, August 18, 2016

Doctoral Candidate Invited to Work on United Nations Project, January 4, 2016

Advantages of the Financial Report Ontology in Accounting Research, February 23, 2013

UB Ontologists Win Bioinformatics Integration Award to Support National Institutes of Health

Announcing Clinical and Translational Science Ontology Affinity Group

Information Overload in the Era of Big Data

Botanists building ontologies to cope with information overload

UB Applied Informatics Portal unveiled.

Education

Ontology 101

Online Courses

Barry Smith

Werner Ceusters

Defining 'Ontology'

An ontology is a representation of some part of reality, (e.g. medicine, social reality, physics, etc.). Smith states that: “Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality…Ontology seeks to provide a definitive and exhaustive classification of entities in all spheres of being.” To be an accurate representation of reality an ontology includes the types of entities and events in a given domain (along with their definitions) arranged in a hierarchical structure, along with relations (such as part-of, depends-on, caused-by, etc. where necessary). Ontologies enable the formulation of robust and shareable descriptions of a given domain by providing a common controlled vocabulary for doctrine writers, IT Developers, and war-fighters alike, thereby allowing these disparate communities to communicate with each other. An ontology should be a shared resource between communities, and its continued collaborative development should support the integration of information and facilitate knowledge discovery. These two goals are realized by ensuring wide dissemination of the ontology, so that it will be used by many stakeholders, and its terms will be correspondingly familiar and readily used for search.

Basic Formal Ontology 2.0

Basic Formal Ontology 2020

BFO 2020

Buffalo Toronto Ontology Alliance (BoaT)

BoaT Home Page

Inaugural meeting, October 24, 2022

University of Toronto ontologies

BFO Summit Meeting, May 23-25, 2023 Includes UB-Toronto-DHS session on government ontologies]

Why Machines Will Never Rule the World

See here

Press Items and Notices

AI is cool, but will never reach human capability, Bert Gambini, August 25, 2022

Why AI will never rule the world Interview by Luke Dormehl on Digital Trends, September 25, 2022 (Recording)

UB Lecture, September 20, 2022

L’intelligenza artificiale non dominerà il mondo, interview with Barry Smith, Il sole de 24 ore, April 27, 2024.

The Philosophome

Philosophome Website

Philosophome Wiki

Semantics of Biodiversity

Paper: Semantics in Support of Biodiversity Knowledge Discovery (PLoS ONE, 2013)

Video Presentations from: Semantics of Biodiversity Workshop (2012)

Ontologies as a method of viewing data

Basic Formal Ontology (BFO)

How to build an ontology with BFO

Tracking referents with Instance Unique Identifiers (IUIs)

Tracking Changes in Our Understanding of Reality: Reality vs. Beliefs

Darwin Core (DwC) and Basic Formal Ontology: Putting it All Together

Building Darwin Core top-down in BFO

Organisms, photographs, media

How to re-use ontologies

Principles of singular nouns, secondary use, understandability

Writing good definitions (DwC Examples)

Management strategies

Ontologies for reuse (BFO, EnvO, IDO, OBI, Plant Ontology , Uberon, IAO)

Educational resources (OBI, Protege, BFO)

Finance and Economics

An Application of Basic Formal Ontology to the Ontology of Services and Commodities, Institute for Business Informatics, University of Koblenz, Germany July 23, 2013

Barry Smith, Reference Data Integration: A Strategy for the Future, Financial Reference Data Management Conference (FIMA), New York, March 2012

The Wernicke Ontology Principle

Wernicke is an ontology-dependent AI system used to automate recurring business processes. Wernicke is based on formal logic developed by Jobst Landgrebe and co-workers at Cognotekt. Its ontologies do not have an Aristotelian taxonomic structure, but are fully axiomatised and logically describe the syntactic structure of recurring language patterns in the Prolog-subset of first order logic. The use of terms in two or more axiomatic definitions of ontological entities creates an implicit network structure within the ontology.

Examples (in German)

1. Implication relations for verbs and verb phrases. (There are hundreds of examples of such formulae in each Wernicke ontology.)

 ((zahlung(Y) AND nachkommen(Z) AND verb(Z,X,Y)) IMPL zahlen(Z))
 ((geld(Y) AND schicken(Z) AND (verb(Z,X) OR verb(Z,X,Y1))) IMPL zahlen(Z))
 ((kosten(Y) AND tragen(Z) AND verb(Z,X,Y)) IMPL zahlen(Z))
 ((überweisungsträger(Y) AND einwerfen(Z) AND verb(Z,X,Y)) IMPL zahlen(Z))
 ((bringen(Z) AND ausgleich(A) AND zum(B) AND mod(B,A,Z) AND verb(Z,X,Y)) IMPL zahlen(Z))
 ((möglich(A) AND mod(A,Z) AND sein(Z) AND (verb(Z,X) OR verb(Z,X,Y))) IMPL möglichsein(Z))  
 ((bitten(Z) AND mod(B,A,Z) AND möglichkeit(A) AND verb(Z,X,Y)) IMPL möglichsein(Z))

2. Temporal structures

 ((übermorgen(W) AND (Y=2)) IMPL zeitabstand(W,in,Y,tagen))
 ((morgen(W) AND (Y=1)) IMPL zeitabstand(W,in,Y,tagen))
 ((heute(W) AND (Y=0)) IMPL zeitabstand(W,in,Y,tagen))
 ((gestern(W) AND (Y=1)) IMPL zeitabstand(W,vor,Y,tagen))
 ((vorgestern(W) AND (Y=2)) IMPL zeitabstand(W,vor,Y,tagen))

3. Domain pattern formulae (ontologic entities)

 past payment a: ((zahlung(X) OR geld(X)) AND rausgehen(Z) AND (I=vergangen) AND verb(Z,X) AND vergangentemp(Z))
 past payment b: ((zahlung(Y) AND tätigen(Z) AND verb(Z,X,Y) AND (I=vergangen) AND vergangentemp(Z))
 past payment c: ((sein(Z) AND (betrag(X) OR forderung(X)) AND zahlen(A) AND mod(A,Z) AND (I=vergangen)
 AND verb(Z,X) AND NOT temp_mod(Z, praet, konj2)

Information Ontology

BFO-based data and information ontologies

Military and Intelligence Ontology

Common Core Ontologies

JFCOM: Semantic Web and Joint Training (2010)

I2WD: Semantic Enhancement for DSGS-A: Distributed Development of a Shared Semantic Resource (2012-13)

I2WD: PED Fusion via Enterprise Ontology

Common Core Ontologies (preliminary statement)

Joint Doctrine Ontology

Ontology for Navy Systems Engineering

Ontology of Planning

Ontology of Engineering

BFO-Based Engineering Ontologies

Bob Young: Towards a Reference Ontology for Manufacturing (2016)

Interoperable Manufacturing Knowledge Systems (2017)

Ontology of Engineering

Ontology for Navy Systems Engineering

Product Life Cycle Ontologies

Modeling and Simulation

Systems Engineering Bootcamp

Materials Ontology

Toshihiro Ashino and Mitsutane Fujita: Definition of a Web Ontology for Design-Oriented Material Selection (2006)

Steel Industry Ontology / .owl file

A Systematic Approach to Developing Ontologies for Manufacturing Service Modeling

Buffalo Engineering Ontology

Ontology for Clinical and Translational Science

Clinical and Translational Science Ontology Group

Infectious Disease Ontology

Immunology Ontologies

Microbiome Ontology

Ontology

Improved Gene Ontology Annotation for Biofilm Formation, Filamentous Growth, and Phenotypic Switching in Candida albicans

What Biofilms Can Teach Us about Individuality

MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies

Designing an Ontology Tool for the Unification of Biofilms Data

Eearth Microbiome Project Ontlogy EMPO

The Human Microbiome

Functional and phylogenetic assembly of microbial communities in the human microbiome

The human microbiome, including as appendix: A microbiome glossary

Defining the Human Microbiome

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

Human Microbiome Project

Parts and Wholes: The Human Microbiome, Ecological Ontology, and the Challenges of Community

Microbiomes and the external environment

The Earth Microbiome

Earth Microbiome Project Ontology:EMPO

A communal catalogue reveals Earth’s multiscale microbial diversity

MetaSUB: Metagenomics and Metadesign of Subways & Urban Biome

Tracking human sewage microbiome in a municipal wastewater treatment plant

http://metasub.org/

Varia

Collective bio-molecular processes: The hidden ontology of systems biology

A review of methods and databases for metagenomic classification and assembly

Training Videos

Ontology for Intelligence, Defense and Security

A Repeatable Process for Ontology Development

Avoiding Semantic Stovepipes: Five Ontological Principles for Interoperability

War-Fighter Ontology

Studying Ontology in Buffalo

Areas of Study

Careers in ontology

Main Page: Difference between revisions

Latest revision as of 17:43, 2 November 2024

Contents

Events

News

Education

Online Courses

Defining 'Ontology'

Basic Formal Ontology 2.0

Basic Formal Ontology 2020

Buffalo Toronto Ontology Alliance (BoaT)

Why Machines Will Never Rule the World

The Philosophome

Semantics of Biodiversity

Finance and Economics

Information Ontology

Military and Intelligence Ontology

Ontology of Planning

Ontology of Engineering

Materials Ontology

Ontology for Clinical and Translational Science

Microbiome Ontology

Suggested Reading

Training Videos

Studying Ontology in Buffalo

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@@ Line 1: / Line 1: @@
-The goal of the National Center for Ontological Research is to advance ontological investigation within the United States. NCOR serves as a vehicle to coordinate, to enhance, to publicize, and to seek funding for ontological research activities. It lays a special focus on ontology training and on the establishment of tools and measures for quality assurance of ontologies. NCOR provides ontology services to multiple organizations, including the US Department of Defense.
+The goal of the [https://ubwp.buffalo.edu/ncor/ National Center for Ontological Research] is to advance ontological investigation within the United States. NCOR serves as a vehicle to coordinate, to enhance, to publicize, and to seek funding for ontological research activities. It lays a special focus on ontology training and on the establishment of tools and measures for quality assurance of ontologies. NCOR provides ontology services to multiple organizations, including the US Department of Defense.
-==Events==
+== Events ==
-CTS Ontology Workshop 2017, [http://ncorwiki.buffalo.edu/index.php/Microbiology_for_the_CTSA:_Ontological_Approaches, Microbiology for the CTSA: Ontological Approaches], Ann Arbor, October 25-26, 2017
+See '''[http://ncorwiki.buffalo.edu/index.php/Newsevents here]'''
-==Past Events==
+For '''past events''' see [http://ncorwiki.buffalo.edu/index.php/Past_Events here]
-'''MatOnto Ontology Meetings'''
+For Buffalo Toronto Ontology Alliance (BoaT) see [https://urbandatacentre.ca/boat]
-:Date: April 3-5, 2017
+==News==
-:Venue: All meetings are on the UB North Campus in Amherst, NY
-''Guest Participants''
-:[https://www.linkedin.com/in/clarepaulohio/ Clare Paul], Materials and Ontology Engineer, Air Force Research Lab, Wright-Patterson AFB, Dayton, Ohio
-:[http://www.enit.fr/fr/_plugins/mypage/mypage/content/mkarray.html Hedi Karray], Production Engineering Laboratory, ENIT, Toulouse, France
-:[https://www.linkedin.com/in/stephen-kahmann-220a2211/ Stephen Kahmann], [http://www.inovexcorp.com/ Inovex Information Systems]
-:[https://www.linkedin.com/in/jordan-lewis-490764105/ Jordan Lewis], [http://www.inovexcorp.com/ Inovex Information Systems]
-''Note on 'MatOnto''': The current [http://matonto.org MatOnto] site hosts the Inovex semantic web software, which is in process of being rebranded as 'Mobi'.
-'''Schedule'''
-'''Monday 9am-noon: Park 141'''
-:Review of the open (= not legally encumbered) portions of the [https://github.com/cpauloh/semmd Materials, Manufacturing, and Design (MMD)] vocabulary
-:Structure of the MMD vocabulary
-:Use of MMD in creating Aristotelian definitions.
-'''Monday 1pm-4pm: Park 142'''
-:Review of [[Categories]] (against the background of the BFO distinction between universals and defined classes)
-By close of Monday session: determination of the scope of MatOnto.
-'''Tuesday 10am-noon: Park 141'''
-:Review of legacy ontologies in the public domain that might serve as inputs to MatOnto
-:Tom Hagedorn (Center for eDesign, UMass Amherst):
-::[[Center for eDesign General Overview]]
-::[http://computingengineering.asmedigitalcollection.asme.org/article.aspx?articleid=2599266 Additive Manufacturing] [http://edesign.ecs.umass.edu/ontologies/Framework2.0/ Ontologies]
-::[http://dl.acm.org/citation.cfm?id=2580238 A Semantic Knowledge Management System for Laminated Composites] [http://edesign.ecs.umass.edu/ontologies/Framework2.0/SLACKSed.owl Ontology]
-:Clare Paul (AFRL)
-::[https://github.com/cpauloh/semmd/tree/master/onto Materials Property Ontology] (moving towards alignment with BFO)
-::[http://www.qudt.org/release2/qudt-catalog.html QUDT] (version 2.0) (under Information Artifact Ontology)
-::[https://github.com/cpauloh/semmd Semantic Materials, Manufacturing, and Design] (includes modified QUDT)
-:Hedi Karray (Toulouse, ENIT)
-::[http://www.dfki.uni-kl.de/~imcod/htdocs/Bernd/Paper/paper/paper.html Ontology of Materials]
-::[http://musigny.rds.toyo.ac.jp:8080/oml.html Information Commons for Material Science]
-::[https://www.jstage.jst.go.jp/article/dsj/9/0/9_008-041/_pdf Material Ontology]
-::[http://ontorule-project.eu/resources/steel Ontorule Steel] (Diaz, Polo)
-:Ruoyu Yang (UB Department of Mechanical and Aerospace Engineering)
-::Functionally Graded Materials (Buffalo) [http://philpapers.org/rec/FURDOA Paper on original version] [http://ncor.buffalo.edu/2017/FGM_Ontology-Paper.pdf Paper on enhanced ontology] [http://ncor.buffalo.edu/2017/FGM-Ontology.owl Enhanced ontology in OWL]
-:TBD (and subject to time available)
-::[http://ieeexplore.ieee.org/document/1633441/?reload=true MASON] (LGIPM, RPK)
-::[http://wiki.knoesis.org/index.php/MaterialWays MaterialWays]
-::[http://www.ontobee.org/ontology/CHEBI Chemical Entities of Biological Interest (ChEBI)]
-::CEN SERES and ELSSI-EMD Workshop Output
-::CheEBI (already aligned with BFO)
-::Dumontier Chemistry
-::Dumontier Physics
-::Dumontier Periodic Elements
-:::others?
-'''Tuesday noon-5pm: Jeannette Martin Room, 5th Floor, Capen Hall''' (please bring lunch)
-This session will be a heavy-duty working session involving multiple screens.
-:Screen 1: BFO open in an ontology editor
-:Screen 2: candidate domain ontology MatOnto input in another and project that onto a 2nd screen beside the BFO projection. We will feature in particular the [http://dl.acm.org/citation.cfm?id=2580238 SLACKS] Semantic Knowledge Management System for Laminated Composites, which will be presented by Ian Grosse (UMass Amherst)
-:Screen 3: project information about the domain ontology onto a 3rd screen;
--- Annotate the classes and properties of the domain ontology to identify where the domain ontology entities would seem to align with BFO (first iteration).
--- Annotate the classes and properties of the domain ontology with the initial set of "portion of material" categories
--- Assess the domain ontology hierarchy from a mono-hierarchy perspective
--- Remain in-session until Wed at 11:00 am, have lunch, organize and consolidate all material, discuss next steps (rather than Tue?)
-'''Wednesday 9am-noon Park 141: Conclusion'''
-At the conclusion of activity on Wed afternoon, we should have
--- at least one location known to all where open MMD definitions for can be sourced
--- an organized set of public domain information about each of the domain ontologies (location, description, articles, general initial assessment)
--- a starting point for aligning the domain ontologies with the BFO (via class and property annotation of domain ontologies)
--- some level of understanding about the correctness of any hierarchies; and as a result, a starting point for reengineering the hierarchy
--- Clare leaves no later than 3:00pm on Wed
-'''Background'''
-[http://www.oagi.org/dnn2/Home/ASpecialMessagefromourMemberandPartner,NIS.aspx Industry Ontologies Foundry (IOF)]
-[http://www.buffalo.edu/cas/philosophy/news-events/latest_news/smith-champ.html DMDII CHAMP initiative]
-'''Buffalo Ontology Group Meeting'''
-Date: March 13, 4:00pm
-Venue: Jeanette Martin Room, 5th Floor of Capen Hall, University at Buffalo (North Campus)
-Dial-in details are provided below
-''Schedule''
-:00pm Brief surveys of current ontology projects at UB:
-:1) [http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403 Chris Stoeckert]: Implementation of a referent tracking system with UPenn TURBO [http://ncor.buffalo.edu/2017/TURBO.pptx Slides]
+[http://www.techguide.org/barry-smith Techguide Podcast], Careers in Tech for non-STEM students, October 30, 2024
-:2) Jonathan Blaisure: Improving Secondary Use of Electronic healthcare record data [http://ncor.buffalo.edu/2017/blaisure.pptx Slides]
+[https://apablog.substack.com/p/commercializing-ontology-lucrative APA Blog interview with Barry Smith and John Beverley], October 4, 2024.
-:3) CHAMP: Coordinated Holistic Alignment of Manufacturing Processes
+[https://www.buffalo.edu/news/releases/2024/02/department-of-defense-ontology.html DOD, Intelligence Community adopt resource developed by UB ontologists], Bert Gambini, UBNow, February 29, 2024.
-:4) MatOnto: The Materials Ontology
+[https://bnnbreaking.com/world/us/us-defense-and-intelligence-to-adopt-bfo-and-cco-standards-for-enhanced-data-management U.S. Defense and Intelligence to Adopt BFO and CCO Standards for Enhanced Data Management],Shivani Chauhan, 28 Feb 2024.
-:5) IOF: Industry Ontology Foundry
+[https://buffalo.app.box.com/v/KI-und-Philosophie Article on BFO in the ''Frankfurter Allgemeine Zeitung'', September 28, 2022, p. N3]. Translation of opening paragraph:
-:6) Mark Jensen: Ontology for the Research Domain Criteria framework of the National Institute of Mental Health [http://ncor.buffalo.edu/2017/Jensen.pptx Slides]
+:Industry standards are not usually associated with philosophy or the humanities. That is why the new ISO/IEC 21838 standard conceals a minor scientific-historical sensation. Because for the first time, a philosophical theory has now been declared an industry standard, namely: the "Basic Formal Ontology", BFO for short. When you try to pronounce this acronym, it sounds a lot like "Buffalo," and that's no coincidence. Because Barry Smith, the main brain behind this norm, is the Julian Park Professor of Philosophy at the University of Buffalo in northern New York State, not far from Niagara Falls ...
-:7) Controlled Natural Language (CNL) interfaces to OWL and ontology editors
+:For full text see [https://buffalo.box.com/v/KI-und-Philosophie here].
-:45pm  [http://stl.mie.utoronto.ca/gruninger.html Michael Grüninger](University of Toronto): The Quest for Semantic Integration in the Context of Manufacturing [http://ncor.buffalo.edu/2017/gruninger.pdf Slides]
+[https://blog.apaonline.org/2022/09/15/careers-in-ontology-an-interview-with-professor-barry-smith/ Interview with Barry Smith on '''Careers in Ontology'''], September 15, 2022
-:00pm Close
+[[Interviews and podcasts on ''Why Machines Will Never Rule the World'']]
-----
+[https://www.routledge.com/9781032309934 New book on limits of AI published], August 12, 2022.
-'''Past'''
+[https://www.dpaonthenet.net/article/192369/Machines-ruling-the-world--Impossible--say-researchers.aspx Machines ruling the world? Impossible, say researchers]
-'''[[Top_Level_Ontology_10-21-2016 | Ontology Group Meeting]], October 21, 2016'''
+[https://www.amazon.com/gp/customer-reviews/R35NHUZZQN8226?ref=pf_vv_at_pdctrvw_srp This will totally blow your mind]
-'''[http://ncorwiki.buffalo.edu/index.php/Clinical_Terminology_Shock_and_Awe CTS Ontology Workshop 2016], Clinical Terminology Shock and Awe, Buffalo, NY, September 7-8, 2016
+[https://www.buffalo.edu/news/releases/2022/04/0290.html UB professor’s ontology work recognized in an international standard], April 29, 2022.
-'''Ontology Group Meeting, Monday, April 25, 2016'''
+[https://www.prnewswire.com/news-releases/oagi-and-iof-agree-to-produce-industrial-ontologies-301231565.html Press release on launch of Industrial Ontologies Foundry], February 19, 2021.
-Venue: Jeannette Martin Room, 567 Capen Hall, Buffalo
+[https://www.youtube.com/watch?v=0giPMMoKR9s Video recording of talk by Barry Smith on "Defining Intelligence"], February 17, 2021
-*José M. Parente de Oliveira (ITA Brazil): "[[A Visual Formalism for BFO-Based Ontologies]]" [http://ncor.buffalo.edu/2016/Parente.pdf Slides]
+[https://www.prnewswire.com/news-releases/oagi-and-iof-agree-to-produce-industrial-ontologies-301231565.html Press-release launching the new Industrial Ontologies Foundry], February 19, 2021
-*Hedi Karray (ENIT, [https://en.wikipedia.org/wiki/Tarbes Tarbes], France): "[[Applications of Ontologies in Astrophysics and Manufacturing Domains]]" [http://ncor.buffalo.edu/2016/Karray.pdf Slides]
+[https://ncor-brasil.org/about/ NCOR-Brasil] established, December 1, 2020
-*Mark Jensen (United Nations Environment Programme): "[http://www.dataversity.net/ontology-has-big-part-to-play-in-united-nations-sustainable-development-goals-project The UNEP Sustainable Development Goals Interface Ontology (SDGIO)]" [http://ncor.buffalo.edu/2016/Jensen.pdf Slides]
+[http://medicine.buffalo.edu/news_and_events/news/2020/07/smith-ontology-covid-11561.html Using Ontology as Powerful Weapon in COVID-19 Fight], July 14, 2020
-Organized jointly with the UB Center for Multisource Information Fusion
+[http://www.buffalo.edu/news/releases/2020/06/016.html Leveraging a powerful weapon in the fight against COVID-19 — ontology], June 10, 2020
-----
+[http://www.buffalo.edu/ubnow/campus.host.html/content/shared/university/news/ub-reporter-articles/stories/2018/04/smith-capabilities-workshop.detail.html UB workshop to address human and machine capabilities], April 20, 2018
-June 10, 2016
+[https://www.buffalo.edu/ctsi/ctsi-news.host.html/content/shared/www/ctsi/articles/academic_articles/working-group-seeks-to-extend-the-depth-and-functionality-of-bio.detail.html Working group seeks to extend the depth and functionality of biomedical ontologies], October 14, 2017
-:2pm Discussion on establishing an Industry Ontology Foundry, with talks by Barry Smith and Hedi Karay
-:3pm Presentation by Boran Brodaric on '''Water Feature Ontology and Timeless Wholes'''
-May 19-20, 2016
+[http://www.buffalo.edu/cas/philosophy/news/latestnews/2016-win-ontology.html Barry Smith wins 2016 IAOA Ontology Competition], August 18, 2016
-'''[http://ncgia.buffalo.edu/OntologyConference/ Ontological Approaches to Sensor Data Analysis]''', Amherst, NY
-March 21, 2016, 141 Park Hall, Buffalo
+[https://medicine.buffalo.edu/news_and_events/news.host.html/content/shared/smbs/news/2016/01/jensen-doctoral-un-5573.detail.html Doctoral Candidate Invited to Work on United Nations Project], January 4, 2016
-:Fabian Neuhaus talk on '''DOL: The Distributed Ontology Language'''
-February 17-19, 2016 Gainesville, FL
+[http://xbrl.squarespace.com/journal/2013/2/23/advantages-of-financial-report-ontology-in-accounting-resear.html Advantages of the Financial Report Ontology in Accounting Research], February 23, 2013
-:[http://ncorwiki.buffalo.edu/index.php/Workshop_on_BFO_and_the_Ontology_of_Social_Entities_2016 Workshop on BFO and the Ontology of Social Entities]'''
-Feb 2 and all Tuesdays until April 19 1-3:50pm, 141 Park Hall, Buffalo
-:A series of seminars on various ontology-related topics, listed [http://ncorwiki.buffalo.edu/index.php/Analytic_Metaphysics here].
-Feb. 1, 2016,  567 Capen Hall, Buffalo
-'''Meeting on various ontology topics''', including:
-:Non-Coding RNA Ontology (Alan Ruttenberg)
-:Ontology for Manufacturing (Francesco Furini)
-:*We propose an ontology focused on the representation of composite materials in general and what are called 'Functionally Graded Materials' (FGM) in particular. The scope of the ontology is to provide information about the components of such materials, the manufacturing processes involved in creating such materials, and different sorts of applications in dentistry and other fields. The ontology is developed using Basic Formal Ontology (BFO) and parts of of Ontology for Biomedical Investigation (OBI).
-:Plant Life Cycle Ontology (Barry Smith)
-[[Meeting on Current UB Ontology Projects]], IHI, 3pm, December 14, 2015
-[[Information Meeting on Joint Doctrine Ontology]], Herndon, VA 20171, September 16-17, 2015
-[[The Role of Ontology in Big Cancer Data]], National Cancer Institute, Bethesda, MD, May 12-13, 2015
-[[CTS Ontology Workshop 2015]], Ontology in Practice.
-The Fourth Clinical and Translational Science Ontology Workshop.
-Charleston, SC, September 23-25, 2015
-[[Symposium on Military Codes of Ethics]], Buffalo, NY 14260, November 2, 2015
-See also [http://ncorwiki.buffalo.edu/index.php/Past_Events here] and [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki here]
-==Studying Ontology in Buffalo==
-[http://www.philosophy.buffalo.edu/graduate/areas_of_study/phd/ Areas of Study]
-[http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2011_02_11/caredit.a1100012 Careers in ontology]
-==News==
-[http://xbrl.squarespace.com/journal/2013/2/23/advantages-of-financial-report-ontology-in-accounting-resear.html Advantages of the Financial Report Ontology in Accounting Research]
 [http://ontology.buffalo.edu/IMMPORT/UB-Press-Release-2013.pdf UB Ontologists Win Bioinformatics Integration Award to Support National Institutes of Health]
@@ Line 201: / Line 69: @@
 [[UB Applied Informatics Portal]] unveiled.
-==Courses==
+==[https://ncorwiki.buffalo.edu/index.php/Education Education]==
+[[Ontology 101]]
+==Online Courses==
+[http://ncorwiki.buffalo.edu/index.php/Education Barry Smith]
-[[Problems in Ontology]], Department of Philosophy, University at Buffalo, NY, Mondays from 4-6pm, August 29 - December 5, 2012
+[http://www.referent-tracking.com/RTU/ceusters_vita.html#teaching Werner Ceusters]
-[http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2013 Ontological Engineering], Department of Industrial and Systems Engineering, University at Buffalo, NY, Fall 2013
+==Defining 'Ontology'==
-[[Ontological Engineering 2014 | Ontological Engineering]], Department of Industrial and Systems Engineering, Department of Computer Science and Department of Philosophy University at Buffalo, NY, Mondays from 4-7pm, August 25 - December 1, 2014
+An ontology is a representation of some part of reality, (e.g. medicine, social reality, physics, etc.).  Smith states that: “Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality…Ontology seeks to provide a definitive and exhaustive classification of entities in all spheres of being.”  To be an accurate representation of reality an ontology includes the types of entities and events in a given domain (along with their definitions) arranged in a hierarchical structure, along with relations (such as part-of, depends-on, caused-by, etc. where necessary).  Ontologies enable the formulation of robust and shareable descriptions of a given domain by providing a common controlled vocabulary for doctrine writers, IT Developers, and war-fighters alike, thereby allowing these disparate communities to communicate with each other.  An ontology should be a shared resource between communities, and its continued collaborative development should support the integration of information and facilitate knowledge discovery.  These two goals are realized by ensuring wide dissemination of the ontology, so that it will be used by many stakeholders, and its terms will be correspondingly familiar and readily used for search.
-[[Analytic Metaphysics | Analytical Metaphysics]], Department of Philosophy, University at Buffalo, NY, Tuesdays 1-3:50pm, Spring Semester, 2016
+== Basic Formal Ontology 2.0 ==
-[http://ncorwiki.buffalo.edu/index.php/Biomedical_Ontology_2016 Biomedical Ontology] Departments of Philosophy and Biomedical Informatics, University at Buffalo, Fall Semester 2016
+[http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology 2.0]
-Applied Ontology 2017, Spring Semester Online Course, Department of Philosophy, University at Buffalo
+== Basic Formal Ontology 2020 ==
-Advanced Biomedical Ontology 2017, Fall Semester, Departments of Philosophy and Biomedical Informatics, University at Buffalo
+[http://ncorwiki.buffalo.edu/index.php/BFO_2020 BFO 2020]
-==Tutorials==
+==Buffalo Toronto Ontology Alliance (BoaT)==
-[[How to Develop and Use OBO Foundry Ontologies]], Tutorial and Workshop at ICBO, Graz, Austria, July 21, 2012
+*[https://urbandatacentre.ca/boat BoaT Home Page]
-[[Basic Formal Ontology 2.0: Tutorial at ICBO/FOIS]], Graz, Austria, July 25, 2012
+*[https://ncorwiki.buffalo.edu/index.php/Ontology_Day_(with_visitors_from_Toronto),_October_24,_2022 Inaugural meeting, October 24, 2022]
-[[Introduction to Protégé]], Tutorial, Buffalo, NY, August 11-12, 2012
+*[https://ncorwiki.buffalo.edu/index.php/List_of_Toronto_ontology_contributions_(as_of_November_1,_2022 University of Toronto ontologies]
-[[Basic Formal Ontology 2.0]], Tutorial, Buffalo, NY, August 18-19, 2012
+*[https://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_Summit_Meeting BFO Summit Meeting, May 23-25, 2023] Includes UB-Toronto-DHS session on government ontologies]
-[http://ncorwiki.buffalo.edu/index.php/STIDS_2013 Tutorial: Information Ontologies for the Intelligence Community, [http://stids.c4i.gmu.edu STIDS Conference], November 11, 2013
+==Why Machines Will Never Rule the World==
-Tutorial: [[Ontology of Military Planning and Operations Assessment]], [http://stids.c4i.gmu.edu STIDS Conference], November 18, 2014
+See [https://ncorwiki.buffalo.edu/index.php/Why_Machines here]
-Tutorial: [[Basic Formal Ontology 2015]], International Conference on Biomedical Ontology, Lisbon, 2015
+'''Press Items and Notices'''
-==Defining Ontology==
+[https://www.futurity.org/artificial-intelligence-ai-2789642-2/ '''AI is cool, but will never reach human capability'''], Bert Gambini, August 25, 2022
-An ontology is a representation of some part of reality, (e.g. medicine, social reality, physics, etc.).  Smith states that: “Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality…Ontology seeks to provide a definitive and exhaustive classification of entities in all spheres of being.”1  To be an accurate representation of reality an ontology includes the types of entities and events in a given domain (along with their definitions) arranged in a hierarchical structure, along with relations (such as part-of, depends-on, caused-by, etc. where necessary).  Ontologies enable the formulation of robust and shareable descriptions of a given domain by providing a common controlled vocabulary for doctrine writers, IT Developers, and war-fighters alike, thereby allowing these disparate communities to communicate with each other.  An ontology should be a shared resource between communities, and its continued collaborative development should support the integration of information and facilitate knowledge discovery.2  These two goals are realized by ensuring wide dissemination of the ontology, so that it will be used by many stakeholders, and its terms will be correspondingly familiar and readily used for search.
+[https://www.digitaltrends.com/computing/why-ai-will-never-rule-the-world/ Why AI will never rule the world] '''Interview by Luke Dormehl on Digital Trends''', September 25, 2022 [https://buffalo.box.com/v/Digital-trends-revised (Recording)]
+[https://calendar.buffalo.edu/event/iad-distinguished-speaker-series--why-machines-will-never-rule-the-world/ UB Lecture], September 20, 2022
+[https://philpapers.org/rec/SOLLAN L’intelligenza artificiale non dominerà il mondo], interview with Barry Smith, ''Il sole de 24 ore'', April 27, 2024.
 ==The Philosophome==
-[http://philosophome.org Philosophome Website]
+[http://ontology.buffalo.edu/philosophome/index_files/philosophome.html Philosophome Website]
 [[Philosophome | Philosophome Wiki]]
@@ Line 275: / Line 152: @@
 Barry Smith, [http://www.slideshare.net/BarrySmith3/2012-fima-talk Reference Data Integration: A Strategy for the Future], Financial Reference Data Management Conference (FIMA), New York, March 2012
+''The Wernicke Ontology Principle''
+Wernicke is an ontology-dependent AI system used to automate recurring business processes. Wernicke is based on formal logic developed by Jobst Landgrebe and co-workers at Cognotekt. Its ontologies do not have an Aristotelian taxonomic structure, but are fully axiomatised and logically describe the syntactic structure of recurring language patterns in the Prolog-subset of first order logic. The use of terms in two or more axiomatic definitions of ontological entities creates an implicit network structure within the ontology.
+Examples (in German)
+. Implication relations for verbs and verb phrases. (There are hundreds of examples of such formulae in each Wernicke ontology.)
+  ((zahlung(Y) AND nachkommen(Z) AND verb(Z,X,Y)) IMPL zahlen(Z))
+  ((geld(Y) AND schicken(Z) AND (verb(Z,X) OR verb(Z,X,Y1))) IMPL zahlen(Z))
+  ((kosten(Y) AND tragen(Z) AND verb(Z,X,Y)) IMPL zahlen(Z))
+  ((überweisungsträger(Y) AND einwerfen(Z) AND verb(Z,X,Y)) IMPL zahlen(Z))
+  ((bringen(Z) AND ausgleich(A) AND zum(B) AND mod(B,A,Z) AND verb(Z,X,Y)) IMPL zahlen(Z))
+  ((möglich(A) AND mod(A,Z) AND sein(Z) AND (verb(Z,X) OR verb(Z,X,Y))) IMPL möglichsein(Z))
+  ((bitten(Z) AND mod(B,A,Z) AND möglichkeit(A) AND verb(Z,X,Y)) IMPL möglichsein(Z))
+. Temporal structures
+  ((übermorgen(W) AND (Y=2)) IMPL zeitabstand(W,in,Y,tagen))
+  ((morgen(W) AND (Y=1)) IMPL zeitabstand(W,in,Y,tagen))
+  ((heute(W) AND (Y=0)) IMPL zeitabstand(W,in,Y,tagen))
+  ((gestern(W) AND (Y=1)) IMPL zeitabstand(W,vor,Y,tagen))
+  ((vorgestern(W) AND (Y=2)) IMPL zeitabstand(W,vor,Y,tagen))
+. Domain pattern formulae (ontologic entities)
+  past payment a: ((zahlung(X) OR geld(X)) AND rausgehen(Z) AND (I=vergangen) AND verb(Z,X) AND vergangentemp(Z))
+  past payment b: ((zahlung(Y) AND tätigen(Z) AND verb(Z,X,Y) AND (I=vergangen) AND vergangentemp(Z))
+  past payment c: ((sein(Z) AND (betrag(X) OR forderung(X)) AND zahlen(A) AND mod(A,Z) AND (I=vergangen)
+  AND verb(Z,X) AND NOT temp_mod(Z, praet, konj2)
+== Information Ontology==
+[http://ncorwiki.buffalo.edu/index.php/BFO-Based_Data_and_Information_Ontologies BFO-based data and information ontologies]
 ==Military and Intelligence Ontology==
+[[Common Core Ontologies]]
 JFCOM: [[Semantic Web and Joint Training]] (2010)
@@ Line 287: / Line 202: @@
 [[Joint Doctrine Ontology]]
+[http://ncorwiki.buffalo.edu/index.php/Ontology_and_the_Navy_SYSCOMs_Systems_Engineering_Transformation_Process Ontology for Navy Systems Engineering]
 == Ontology of Planning ==
@@ Line 294: / Line 211: @@
 == Ontology of Engineering ==
-'''[https://s3.amazonaws.com/ontologforum/OntologySummit2016/2016-03-17_Engineering/Reference-Ontology-for-Manufacturing--BobYoung_20160317.pdf Bob Young: Towards a Reference Ontology for Manufacturing] (2016)'''
+[[BFO-Based Engineering Ontologies]]
+[https://s3.amazonaws.com/ontologforum/OntologySummit2016/2016-03-17_Engineering/Reference-Ontology-for-Manufacturing--BobYoung_20160317.pdf Bob Young: Towards a Reference Ontology for Manufacturing] (2016)
+[http://www.tandfonline.com/eprint/sUe6G9RNtb7tgjQtgtkC/full Interoperable Manufacturing Knowledge Systems] (2017)
 [[Ontology of Engineering]]
+[http://ncorwiki.buffalo.edu/index.php/Ontology_and_the_Navy_SYSCOMs_Systems_Engineering_Transformation_Process Ontology for Navy Systems Engineering]
 [[Product Life Cycle Ontologies]]
 [[Modeling and Simulation]]
+[[Systems Engineering Bootcamp]]
 == Materials Ontology ==
@@ Line 306: / Line 231: @@
 '''[http://datascience.codata.org/articles/abstract/10.2481/dsj.5.52/ Toshihiro Ashino and Mitsutane Fujita: Definition of a Web Ontology for Design-Oriented Material Selection] (2006)'''
-:[http://www.codata.jp:8080 file archive]
+:[http://ontorule-project.eu/resources/steel.html Steel Industry Ontology] / [http://ontorule-project.eu/resources/steel.owl .owl file]
-:[http://ontorule-project.eu/resources/steel.html Steel Industry Ontology] "[http://ontorule-project.eu/resources/steel.owl .owl file]"
 :[http://ceur-ws.org/Vol-886/paper_1.pdf A Systematic Approach to Developing Ontologies for Manufacturing Service Modeling]
@@ Line 319: / Line 242: @@
 [[Clinical and Translational Science Ontology Group]]
+[[Infectious Disease Ontology]]
 [http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies Immunology Ontologies]
+== Microbiome Ontology ==
+'''Ontology'''
+[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535841/ Improved Gene Ontology Annotation for Biofilm Formation, Filamentous Growth, and Phenotypic Switching in Candida albicans]
+[http://www.oxfordscholarship.com/view/10.1093/acprof:oso/9780199382514.001.0001/acprof-9780199382514-chapter-7 What Biofilms Can Teach Us about Individuality]
+[https://ac.els-cdn.com/S1532046415000507/1-s2.0-S1532046415000507-main.pdf?_tid=ca8ad71a-c168-11e7-b687-00000aacb35f&acdnat=1509804327_c9962782780a7f2935bfc9140684d5c0 MorphoCol: An ontology-based knowledgebase for the characterisation of clinically significant bacterial colony morphologies]
+[http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.1024.59&rep=rep1&type=pdf Designing an Ontology Tool for the Unification of Biofilms Data]
+[http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/empo/ Eearth Microbiome Project Ontlogy EMPO]
+'''The Human Microbiome'''
+[http://www.cell.com/trends/microbiology/fulltext/S0966-842X(14)00023-7 Functional and phylogenetic assembly of microbial communities in the human microbiome]
+[http://www.cmaj.ca/content/187/11/825.short#sec-2 The human microbiome], including as appendix: [http://www.cmaj.ca/content/suppl/2015/05/19/cmaj.141072.DC1/14-1072-1-at.pdf A microbiome glossary]
+[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426293/ Defining the Human Microbiome]
+[https://www.biorxiv.org/content/early/2017/08/16/176784 MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments]
+[https://hmpdacc.org Human Microbiome Project]
+[http://muse.jhu.edu/article/564608/pdf Parts and Wholes: The Human Microbiome, Ecological Ontology, and the Challenges of Community]
+'''Microbiomes and the external environment'''
+[http://www.earthmicrobiome.org/ The Earth Microbiome]
+:[http://www.earthmicrobiome.org/protocols-and-standards/empo/ Earth Microbiome Project Ontology:EMPO]
+[https://www.nature.com/nature/journal/vaop/ncurrent/full/nature24621.html A communal catalogue reveals Earth’s multiscale microbial diversity]
+[http://metasub.org/ MetaSUB: Metagenomics and Metadesign of Subways & Urban Biome]
+[https://www.ncbi.nlm.nih.gov/pubmed/24305737/ Tracking human sewage microbiome in a municipal wastewater treatment plant]
+http://metasub.org/
+'''Varia'''
+[http://www.frontiersinai.com/turingfiles/July/12.pdf#page=9 Collective bio-molecular processes: The hidden ontology of systems biology]
+[https://academic.oup.com/bib/article/doi/10.1093/bib/bbx120/4210288/A-review-of-methods-and-databases-for-metagenomic A review of methods and databases for metagenomic classification and assembly]
 == Suggested Reading ==
@@ Line 341: / Line 313: @@
 [http://www.youtube.com/watch?v=JkQG1_gsXtc War-Fighter Ontology]
+==Studying Ontology in Buffalo==
+[http://www.philosophy.buffalo.edu/graduate/areas_of_study/phd/ Areas of Study]
+[http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2011_02_11/caredit.a1100012 Careers in ontology]