Main Page: Difference between revisions

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 ==
+See '''[http://ncorwiki.buffalo.edu/index.php/Newsevents here]'''
+For '''past events''' see [http://ncorwiki.buffalo.edu/index.php/Past_Events here]
+For Buffalo Toronto Ontology Alliance (BoaT) see [https://urbandatacentre.ca/boat]
 ==News==
+[http://www.techguide.org/barry-smith Techguide Podcast], Careers in Tech for non-STEM students, October 30, 2024
+[https://apablog.substack.com/p/commercializing-ontology-lucrative APA Blog interview with Barry Smith and John Beverley], October 4, 2024.
+[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.
+[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.
+[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:
+: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 [https://buffalo.box.com/v/KI-und-Philosophie here].
+[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
+[[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.
+[https://www.dpaonthenet.net/article/192369/Machines-ruling-the-world--Impossible--say-researchers.aspx Machines ruling the world? Impossible, say researchers]
+[https://www.amazon.com/gp/customer-reviews/R35NHUZZQN8226?ref=pf_vv_at_pdctrvw_srp This will totally blow your mind]
+[https://www.buffalo.edu/news/releases/2022/04/0290.html UB professor’s ontology work recognized in an international standard], April 29, 2022.
+[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.
+[https://www.youtube.com/watch?v=0giPMMoKR9s Video recording of talk by Barry Smith on "Defining Intelligence"], February 17, 2021
+[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
+[https://ncor-brasil.org/about/ NCOR-Brasil] established, December 1, 2020
+[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
+[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
+[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
+[http://www.buffalo.edu/cas/philosophy/news/latestnews/2016-win-ontology.html Barry Smith wins 2016 IAOA Ontology Competition], August 18, 2016
+[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://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://ontology.buffalo.edu/IMMPORT/UB-Press-Release-2013.pdf UB Ontologists Win Bioinformatics Integration Award to Support National Institutes of Health]
+[[Announcing Clinical and Translational Science Ontology Affinity Group]]
 [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]
@@ Line 9: / Line 69: @@
 [[UB Applied Informatics Portal]] unveiled.
-==Tutorials and Courses==
+==[https://ncorwiki.buffalo.edu/index.php/Education Education]==
+[[Ontology 101]]
+==Online Courses==
+[http://ncorwiki.buffalo.edu/index.php/Education Barry Smith]
+[http://www.referent-tracking.com/RTU/ceusters_vita.html#teaching 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 ==
+[http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Basic Formal Ontology 2.0]
+== Basic Formal Ontology 2020 ==
+[http://ncorwiki.buffalo.edu/index.php/BFO_2020 BFO 2020]
+==Buffalo Toronto Ontology Alliance (BoaT)==
+*[https://urbandatacentre.ca/boat BoaT Home Page]
+*[https://ncorwiki.buffalo.edu/index.php/Ontology_Day_(with_visitors_from_Toronto),_October_24,_2022 Inaugural meeting, October 24, 2022]
+*[https://ncorwiki.buffalo.edu/index.php/List_of_Toronto_ontology_contributions_(as_of_November_1,_2022 University of Toronto ontologies]
+*[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]
+==Why Machines Will Never Rule the World==
+See [https://ncorwiki.buffalo.edu/index.php/Why_Machines here]
+'''Press Items and Notices'''
+[https://www.futurity.org/artificial-intelligence-ai-2789642-2/ '''AI is cool, but will never reach human capability'''], Bert Gambini, August 25, 2022
+[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://ontology.buffalo.edu/philosophome/index_files/philosophome.html Philosophome Website]
+[[Philosophome | Philosophome Wiki]]
+==Semantics of Biodiversity==
+Paper: [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089606 Semantics in Support of Biodiversity Knowledge Discovery (PLoS ONE, 2013)]
+Video Presentations from: [http://biocodecommons.org/workshops/sob.html Semantics of Biodiversity Workshop (2012)]
+::[http://www.youtube.com/watch?v=ZrHYi7mgF9g Ontologies as a method of viewing data]
+::[http://www.youtube.com/watch?v=Fot1dOPLv_c Basic Formal Ontology (BFO)]
+::[http://www.youtube.com/watch?v=rWy3C0WmpZM How to build an ontology with BFO]
+::[http://www.youtube.com/watch?v=kaG92j0WqmI Tracking referents with Instance Unique Identifiers (IUIs)]
+::[http://www.youtube.com/watch?v=fHP0Dlk5wuo Tracking Changes in Our Understanding of Reality: Reality vs. Beliefs]
+::[http://www.youtube.com/watch?v=Of6bj28MQhY 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==
+[http://www.slideshare.net/BarrySmith3/an-application-of-bfo-to-services 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, [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)
-[[How to Develop and Use OBO Foundry Ontologies]], Tutorial and Workshop at ICBO, Graz, Austria, July 21, 2012
+  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)
-[[Basic Formal Ontology 2.0: Tutorial at ICBO/FOIS]], Graz, Austria, July 25, 2012
+== Information Ontology==
-[[Introduction to Protégé]], Tutorial, Buffalo, NY, August 11-12, 2012
+[http://ncorwiki.buffalo.edu/index.php/BFO-Based_Data_and_Information_Ontologies BFO-based data and information ontologies]
-[[Basic Formal Ontology 2.0]], Tutorial, Buffalo, NY, August 18-19, 2012
+==Military and Intelligence Ontology==
-[[Problems in Ontology]], Class, Buffalo, NY, Mondays from 4-6pm, August 29 - December 5, 2012
+[[Common Core Ontologies]]
-==Events==
+JFCOM: [[Semantic Web and Joint Training]] (2010)
-'''[[Past Events]]'''
+I2WD: Semantic Enhancement for DSGS-A: [[Distributed Development of a Shared Semantic Resource]] (2012-13)
-[[Contact]]
+I2WD: [http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=2298761 PED Fusion via Enterprise Ontology]
-==Defining Ontology==
+[http://ncor.buffalo.edu/ontologies/AIRS_Ontologies.pdf Common Core Ontologies (preliminary statement)]
-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.
+[[Joint Doctrine Ontology]]
-[[Semantic Enhancement]]
+[http://ncorwiki.buffalo.edu/index.php/Ontology_and_the_Navy_SYSCOMs_Systems_Engineering_Transformation_Process Ontology for Navy Systems Engineering]
+== Ontology of Planning ==
+[[Ontology of Planning]]
+== Ontology of Engineering ==
+[[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 ==
+'''[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://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]
+----
+[[Buffalo Engineering Ontology]]
+== Ontology for Clinical and Translational Science ==
+[[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 43: / Line 304: @@
 [http://ceur-ws.org/Vol-555/paper5.pdf Universal Core Semantic Layer]
-[[Papers on Semantic Enhancement and Intelligence Analysis]]
+== Training Videos  ==
-== Ontology Videos by William Mandrick ==
+[http://ncorwiki.buffalo.edu/index.php/Ontology_for_Intelligence,_Defense_and_Security Ontology for Intelligence, Defense and Security]
 [http://www.youtube.com/watch?v=fB6BjF4lAQ4&feature=related A Repeatable Process for Ontology Development]
@@ Line 53: / Line 314: @@
 [http://www.youtube.com/watch?v=JkQG1_gsXtc War-Fighter Ontology]
-[http://ncorwiki.buffalo.edu/index.php/Mandrick_Vita William Mandrick]
+==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]