Main Page: Difference between revisions

Latest revision as of 13:40, 10 October 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

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

Interviews and Podcasts

AI is cool, but will never reach human capability, Aug. 12, 2022

Blog of the American Philosophical Association: Interview with Charlie Taben, August 30, 2022. Youtube version

Systems Conversation (with Dr Oliver Gao, Director, Systems Engineering, Cornell University, Ithaca, NY, September 2, 2022)

AI is here, but will it rule us?, Wirkman Comments, podcast with David Ramsey Steele (September 27, 2022). See also here.

Machines Will Never Rule Us!, LocoFoco, September 27, 2022

Will Machines Rule the World? NAS Podcast with Scott Turner, October 4, 2022

Why AI will never rule the world, Interview by Luke Dormehl on Digital Trends Philpapers

Walid Saba on Why Machines Will Never Rule the World, Machine Learning Street Talk, December 15, 2022 (review starts half way through)

Why Machines Will Never Rule the World – On AI and Faith, Conversation between Jobst Landgrebe, Barry Smith and Rev. Jamie Franklin, Irreverend, November 30, 2022

Why the Singularity Might Never Come. Interview with Richard Hanania, Center for the Study of Partisanship and Ideology, January 30, 2023.

Where there’s no will there’s no way, Interview with Alex Thomson, UKCommons (April 2023)

Conversation with Jobst Landgrebe and Barry Smith: Why AI won’t rule the world, The Pangburn Hangout, May 5, 2023.

AI and ChatGPT: Should we be worried? Stever Peterson, Jobst Landgrebe and Barry Smith, National Association of Scholars, May 19, 2023

Why Machines Will Never Rule the World, Jobst Landgrebe and Barry Smith, Interview with Kyle Polich, Data Sceptic, May 29, 2023

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 13:40, 10 October 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 ==
-'''MatOnto Ontology Meetings'''
+See '''[http://ncorwiki.buffalo.edu/index.php/Newsevents here]'''
-:Date: April 3-5, 2017
+For '''past events''' see [http://ncorwiki.buffalo.edu/index.php/Past_Events here]
-:Venue: All meetings are on the UB North Campus in Amherst, NY
-''Guest Participants''
+For Buffalo Toronto Ontology Alliance (BoaT) see [https://urbandatacentre.ca/boat]
-:[https://www.linkedin.com/in/clarepaulohio/ Clare Paul], Materials and Ontology Engineer, Air Force Research Lab, Wright-Patterson AFB, Dayton, Ohio
+==News==
-:[http://www.enit.fr/fr/_plugins/mypage/mypage/content/mkarray.html Hedi Karray], Production Engineering Laboratory, ENIT, Toulouse, France
+[https://apablog.substack.com/p/commercializing-ontology-lucrative APA Blog interview with Barry Smith and John Beverley], October 4, 2024.
-'''Schedule'''
+[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.
-''Monday, April 3''
+[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.
-:9am-noon: Park 141
+[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:
-:Throughout: Review the BFO Principles of Best Practice (BS)
+: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 ...
-Part 1 (Clare):
+:For full text see [https://buffalo.box.com/v/KI-und-Philosophie here].
-:Review of the OPEN (= not legally encumbered) portions of the [https://github.com/cpauloh/semmd Materials, Manufacturing, and Design (MMD)] vocabulary
-:Structure of MMD vocabulary
-:Use of MMD definitions in creating Airistotelian definitions.
-:1pm-4pm: Park 142
+[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
-''Review of categories'' (against the background of the BFO distinction between universals and defined classes)
-:Portion of Solid Material
+[[Interviews and podcasts on ''Why Machines Will Never Rule the World'']]
-:Property
-::compare with QUDT quantity kind
-::color
-::hardness
-:Composition
+[https://www.routledge.com/9781032309934 New book on limits of AI published], August 12, 2022.
-::Elemental
-::Mass Fraction, Volume Fraction
-::Parts
-:Form
+[https://www.dpaonthenet.net/article/192369/Machines-ruling-the-world--Impossible--say-researchers.aspx Machines ruling the world? Impossible, say researchers]
-::Plate
-::Forging
-::Laminated
-:Internal Structure
+[https://www.amazon.com/gp/customer-reviews/R35NHUZZQN8226?ref=pf_vv_at_pdctrvw_srp This will totally blow your mind]
-::Quality?
-:State
+[https://www.buffalo.edu/news/releases/2022/04/0290.html UB professor’s ontology work recognized in an international standard], April 29, 2022.
-::Stress State
-::Damage State
-::Thermal State
-:Environment
+[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.
-::Chemical
-::Mechanical Load
-::Thermal
-''Tuesday, April 4''
+[https://www.youtube.com/watch?v=0giPMMoKR9s Video recording of talk by Barry Smith on "Defining Intelligence"], February 17, 2021
-''Legacy ontologies''
-:Relevant source ontologies in the public domain that are applicable to the development of a BFO-aligned materials ontology.
-::QUDT (version 2.0) (to Information Artifact Ontology)
-::Additive Manufacturing (NIST)
-::Laminated Composites (eDesign, UMass)
-::Functionally Graded Materials (Buffalo)
-::MatOnto (Hedi Karray)
-::Materials Property (Clare Paul)
-::Ontorule Steel (Diaz, Polo)
-::MASON (LGIPM, RPK)
-::CEN SERES and ELSSI-EMD Workshop Output
-::CheEBI (already aligned with BFO)
-::Dumontier Chemistry
-::Dumontier Physics
-::Dumontier Periodic Elements
-::PROV-O (W3C)
-:::others?
--- Open BFO in an ontology editor on one computer and project that onto a screen.
+[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
--- Open one of the domain ontologies in another and project that onto a 2nd screen beside the BFO projection.
--- If possible, project information about the domain ontology onto a 3rd screen; have network connectivity
--- 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?)
--- Clare leaves no later than 3:00pm on Wed
-At the conclusion of activity on Wed afternoon, we should have
+[https://ncor-brasil.org/about/ NCOR-Brasil] established, December 1, 2020
--- 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
+[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
+[http://www.buffalo.edu/news/releases/2020/06/016.html Leveraging a powerful weapon in the fight against COVID-19 — ontology], June 10, 2020
-:10am-noon Park 142
-:noon-5pm: Jeannete Martin Room, 5th Floor, Capen Hall
+[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
-''Wednesday, April 5''
+[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
-:9am-noon Park 141
+[http://www.buffalo.edu/cas/philosophy/news/latestnews/2016-win-ontology.html Barry Smith wins 2016 IAOA Ontology Competition], August 18, 2016
-''Resources''
+[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
-[http://wiki.knoesis.org/index.php/MaterialWays MaterialWays]
+[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://www.ontobee.org/ontology/CHEBI Chemical Entities of Biological Interest (ChEBI)]
+[http://ontology.buffalo.edu/IMMPORT/UB-Press-Release-2013.pdf UB Ontologists Win Bioinformatics Integration Award to Support National Institutes of Health]
-''Background''
+[[Announcing Clinical and Translational Science Ontology Affinity Group]]
-[http://www.wpafb.af.mil/News/Article-Display/Article/1000017/metals-affordability-initiative-hub-enhances-data-exchange-for-researchers-teams Metals Affordability Initiative Hub]
+[http://www.sciencedaily.com/releases/2012/08/120820161058.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+(ScienceDaily%3A+Latest+Science+News) Information Overload in the Era of Big Data]
-[http://www.oagi.org/dnn2/Home/ASpecialMessagefromourMemberandPartner,NIS.aspx Industry Ontologies Foundry (IOF)]
+[http://www.kurzweilai.net/botanists-building-ontologies-to-cope-with-information-overload Botanists building ontologies to cope with information overload]
-[http://www.buffalo.edu/cas/philosophy/news-events/latest_news/smith-champ.html DMDII CHAMP initiative]
+[[UB Applied Informatics Portal]] unveiled.
-==Past Events==
-'''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]
-:2) Jonathan Blaisure: Improving Secondary Use of Electronic healthcare record data [http://ncor.buffalo.edu/2017/blaisure.pptx Slides]
-:3) CHAMP: Coordinated Holistic Alignment of Manufacturing Processes
-:4) MatOnto: The Materials Ontology
-:5) IOF: Industry Ontology Foundry
-: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]
-:7) Controlled Natural Language (CNL) interfaces to OWL and ontology editors
-: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]
-:00pm Close
-----
-'''Past'''
+==[https://ncorwiki.buffalo.edu/index.php/Education Education]==
+[[Ontology 101]]
-'''[[Top_Level_Ontology_10-21-2016 | Ontology Group Meeting]], October 21, 2016'''
+==Online Courses==
-'''[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
+[http://ncorwiki.buffalo.edu/index.php/Education Barry Smith]
-'''Ontology Group Meeting, Monday, April 25, 2016'''
+[http://www.referent-tracking.com/RTU/ceusters_vita.html#teaching Werner Ceusters]
-Venue: Jeannette Martin Room, 567 Capen Hall, Buffalo
+==Defining 'Ontology'==
-*José M. Parente de Oliveira (ITA Brazil): "[[A Visual Formalism for BFO-Based Ontologies]]" [http://ncor.buffalo.edu/2016/Parente.pdf Slides]
+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.
-*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]
+== Basic Formal Ontology 2.0 ==
-*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://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology 2.0]
-Organized jointly with the UB Center for Multisource Information Fusion
+== Basic Formal Ontology 2020 ==
-----
-June 10, 2016
+[http://ncorwiki.buffalo.edu/index.php/BFO_2020 BFO 2020]
-: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
+==Buffalo Toronto Ontology Alliance (BoaT)==
-'''[http://ncgia.buffalo.edu/OntologyConference/ Ontological Approaches to Sensor Data Analysis]''', Amherst, NY
-March 21, 2016, 141 Park Hall, Buffalo
+*[https://urbandatacentre.ca/boat BoaT Home Page]
-:Fabian Neuhaus talk on '''DOL: The Distributed Ontology Language'''
-February 17-19, 2016 Gainesville, FL
+*[https://ncorwiki.buffalo.edu/index.php/Ontology_Day_(with_visitors_from_Toronto),_October_24,_2022 Inaugural meeting, October 24, 2022]
-:[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
+*[https://ncorwiki.buffalo.edu/index.php/List_of_Toronto_ontology_contributions_(as_of_November_1,_2022 University of Toronto ontologies]
-: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
+*[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]
-'''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
+==Why Machines Will Never Rule the World==
-[[Information Meeting on Joint Doctrine Ontology]], Herndon, VA 20171, September 16-17, 2015
+'''Interviews and Podcasts'''
-[[The Role of Ontology in Big Cancer Data]], National Cancer Institute, Bethesda, MD, May 12-13, 2015
+[https://www.futurity.org/artificial-intelligence-ai-2789642-2/ AI is cool, but will never reach human capability], Aug. 12, 2022
-[[CTS Ontology Workshop 2015]], Ontology in Practice.
+[https://blog.apaonline.org/2022/09/23/why-machines-will-never-rule-the-world-artificial-intelligence-without-fear/ Blog of the American Philosophical Association: Interview with Charlie Taben], August 30, 2022. [https://www.youtube.com/watch?v=Zle7pJIIfFc Youtube version]
-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
+[https://www.youtube.com/watch?v=T4HJi7dQzvg Systems Conversation] (with Dr Oliver Gao, Director, Systems Engineering, Cornell University, Ithaca, NY, September 2, 2022)
-See also [http://ncorwiki.buffalo.edu/index.php/Past_Events here] and [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki here]
+[https://wirkman.com/2022/09/27/ai-is-here/ AI is here, but will it rule us?], Wirkman Comments, podcast with David Ramsey Steele (September 27, 2022). See also [https://soundcloud.com/locofoco-net/machines-will-never-rule-us here].
-==Studying Ontology in Buffalo==
+[https://www.youtube.com/watch?v=f7I6mtFkrOM Machines Will Never Rule Us!], LocoFoco, September 27, 2022
-[http://www.philosophy.buffalo.edu/graduate/areas_of_study/phd/ Areas of Study]
+[https://www.nas.org/blogs/media/video-will-machines-rule-the-world? Will Machines Rule the World?] NAS Podcast with Scott Turner, October 4, 2022
-[http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2011_02_11/caredit.a1100012 Careers in ontology]
+[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 [https://philpapers.org/archive/DORWAW-2.pdf Philpapers]
-==News==
+[https://www.youtube.com/watch?v=IMnWAuoucjo Walid Saba on Why Machines Will Never Rule the World], Machine Learning Street Talk, December 15, 2022 (review starts half way through)
-[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]
+[https://www.cspicenter.com/p/why-the-singularity-might-never-come Why Machines Will Never Rule the World – On AI and Faith], Conversation between Jobst Landgrebe, Barry Smith and Rev. Jamie Franklin, Irreverend, November 30, 2022
-[http://ontology.buffalo.edu/IMMPORT/UB-Press-Release-2013.pdf UB Ontologists Win Bioinformatics Integration Award to Support National Institutes of Health]
+[https://www.cspicenter.com/p/why-the-singularity-might-never-come Why the Singularity Might Never Come]. Interview with Richard Hanania, Center for the Study of Partisanship and Ideology, January 30, 2023.
-[[Announcing Clinical and Translational Science Ontology Affinity Group]]
+[https://www.youtube.com/watch?v=Y-yovYmd1_c Where there’s no will there’s no way], Interview with Alex Thomson, UKCommons (April 2023)
-[http://www.sciencedaily.com/releases/2012/08/120820161058.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+(ScienceDaily%3A+Latest+Science+News) Information Overload in the Era of Big Data]
+[https://www.callin.com/episode/a-conversation-with-barry-smith-and-jobst-MVBPLOVvOI Conversation with Jobst Landgrebe and Barry Smith: Why AI won’t rule the world], The Pangburn Hangout, May 5, 2023.
-[http://www.kurzweilai.net/botanists-building-ontologies-to-cope-with-information-overload Botanists building ontologies to cope with information overload]
+[https://www.youtube.com/watch?v=3Ni3NiA29Pw AI and ChatGPT: Should we be worried?] Stever Peterson, Jobst Landgrebe and Barry Smith, National Association of Scholars, May 19, 2023
-[[UB Applied Informatics Portal]] unveiled.
+[https://dataskeptic.com/blog/episodes/2023/why-machines-will-never-rule-the-world Why Machines Will Never Rule the World], Jobst Landgrebe and Barry Smith, Interview with Kyle Polich, Data Sceptic, May 29, 2023
-==Courses==
-[[Problems in Ontology]], Department of Philosophy, University at Buffalo, NY, Mondays from 4-6pm, August 29 - December 5, 2012
-[http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2013 Ontological Engineering], Department of Industrial and Systems Engineering, University at Buffalo, NY, Fall 2013
+'''Press Items and Notices'''
-[[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
+[https://www.futurity.org/artificial-intelligence-ai-2789642-2/ '''AI is cool, but will never reach human capability'''], Bert Gambini, August 25, 2022
-[[Analytic Metaphysics | Analytical Metaphysics]], Department of Philosophy, University at Buffalo, NY, Tuesdays 1-3:50pm, Spring Semester, 2016
+[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)]
-==Tutorials==
+[https://calendar.buffalo.edu/event/iad-distinguished-speaker-series--why-machines-will-never-rule-the-world/ UB Lecture], September 20, 2022
-[[How to Develop and Use OBO Foundry Ontologies]], Tutorial and Workshop at ICBO, Graz, Austria, July 21, 2012
+[https://philpapers.org/rec/SOLLAN L’intelligenza artificiale non dominerà il mondo], interview with Barry Smith, ''Il sole de 24 ore'', April 27, 2024.:
-[[Basic Formal Ontology 2.0: Tutorial at ICBO/FOIS]], Graz, Austria, July 25, 2012
-[[Introduction to Protégé]], Tutorial, Buffalo, NY, August 11-12, 2012
-[[Basic Formal Ontology 2.0]], Tutorial, Buffalo, NY, August 18-19, 2012
-[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
-Tutorial: [[Ontology of Military Planning and Operations Assessment]], [http://stids.c4i.gmu.edu STIDS Conference], November 18, 2014
-Tutorial: [[Basic Formal Ontology 2015]], International Conference on Biomedical Ontology, Lisbon, 2015
-==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.”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.
 ==The Philosophome==
-[http://philosophome.org Philosophome Website]
+[http://ontology.buffalo.edu/philosophome/index_files/philosophome.html Philosophome Website]
 [[Philosophome | Philosophome Wiki]]
@@ Line 296: / Line 180: @@
 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 308: / Line 230: @@
 [[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 315: / Line 239: @@
 == 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 327: / Line 259: @@
 '''[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 340: / Line 270: @@
 [[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 362: / Line 341: @@
 [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]