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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==
==News==


[http://www.buffaloctrc.org//news/entries/working_group_seeks_to_extend_the_depth_and_functionality_of_biomedical_ont Working group seeks to extend the depth and functionality of biomedical ontologies], October 14, 2017
[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://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],  
[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://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
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[[UB Applied Informatics Portal]] unveiled.
[[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]
 
[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]


[[Problems in Ontology]], Department of Philosophy, University at Buffalo, NY, Mondays from 4-6pm, August 29 - December 5, 2012
==Why Machines Will Never Rule the World==


[http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2013 Ontological Engineering], Department of Industrial and Systems Engineering, University at Buffalo, NY, Fall 2013
'''Interviews and Podcasts'''


[[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], Aug. 12, 2022


[[Analytic Metaphysics | Analytical Metaphysics]], Department of Philosophy, University at Buffalo, NY, Tuesdays 1-3:50pm, Spring Semester, 2016
[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]


[http://ncorwiki.buffalo.edu/index.php/Biomedical_Ontology_2016 Biomedical Ontology] Departments of Philosophy and Biomedical Informatics, University at Buffalo, Fall Semester 2016
[https://www.youtube.com/watch?v=T4HJi7dQzvg Systems Conversation] (with Dr Oliver Gao, Director, Systems Engineering, Cornell University, Ithaca, NY, September 2, 2022)


[http://ncorwiki.buffalo.edu/index.php/Applied_Ontology Applied Ontology 2017], Spring Semester Online Course, Department of Philosophy, University at Buffalo
[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].


[[Advanced Biomedical Ontology]] 2017, Fall Semester, Departments of Philosophy and Biomedical Informatics, University at Buffalo
[https://www.youtube.com/watch?v=f7I6mtFkrOM Machines Will Never Rule Us!], LocoFoco, September 27, 2022


==Tutorials==
[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


[[How to Develop and Use OBO Foundry Ontologies]], Tutorial and Workshop at ICBO, Graz, Austria, July 21, 2012
[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]  


[[Basic Formal Ontology 2.0: Tutorial at ICBO/FOIS]], Graz, Austria, July 25, 2012
[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)


[[Introduction to Protégé]], Tutorial, Buffalo, NY, August 11-12, 2012
[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


[[Basic Formal Ontology 2.0]], Tutorial, Buffalo, NY, August 18-19, 2012
[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.


[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
[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)


Tutorial: [[Ontology of Military Planning and Operations Assessment]], [http://stids.c4i.gmu.edu STIDS Conference], November 18, 2014
[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.


Tutorial: [[Basic Formal Ontology 2015]], International Conference on Biomedical Ontology, Lisbon, 2015
[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


==Defining Ontology==
[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


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.
 
 
'''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==
==The Philosophome==


[http://philosophome.org Philosophome Website]
[http://ontology.buffalo.edu/philosophome/index_files/philosophome.html Philosophome Website]


[[Philosophome | Philosophome Wiki]]
[[Philosophome | Philosophome Wiki]]
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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
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)
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==
[http://ncorwiki.buffalo.edu/index.php/BFO-Based_Data_and_Information_Ontologies BFO-based data and information ontologies]


==Military and Intelligence Ontology==
==Military and Intelligence Ontology==
[[Common Core Ontologies]]


JFCOM: [[Semantic Web and Joint Training]] (2010)
JFCOM: [[Semantic Web and Joint Training]] (2010)
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[[Joint Doctrine Ontology]]
[[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 ==
== Ontology of Planning ==
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== Ontology of Engineering ==
== 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]]
[[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]]
[[Product Life Cycle Ontologies]]


[[Modeling and Simulation]]
[[Modeling and Simulation]]
[[Systems Engineering Bootcamp]]


== Materials Ontology ==
== 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://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]
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[[Clinical and Translational Science Ontology Group]]
[[Clinical and Translational Science Ontology Group]]
[[Infectious Disease Ontology]]


[http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies Immunology Ontologies]
[http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies Immunology Ontologies]
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== Microbiome Ontology ==
== Microbiome Ontology ==


[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989460/ The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation]
'''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://www.biorxiv.org/content/early/2017/08/16/176784 MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments]
Line 148: Line 299:
[https://hmpdacc.org Human Microbiome Project]
[https://hmpdacc.org Human Microbiome Project]


[http://www.earthmicrobiome.org/protocols-and-standards/emp-ontology-empo/ Earth micro biome Project Ontology:EMPO]  
[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]


[http://muse.jhu.edu/article/564608/pdf Parts and Wholes: The Human Microbiome, Ecological Ontology, and the Challenges of Community]  
[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]
[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]

Revision as of 13:30, 12 July 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

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 2.0

Basic Formal Ontology 2020

BFO 2020

Buffalo Toronto Ontology Alliance (BoaT)

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 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

Suggested Reading

Ontology: An Introduction

Coordinated Evolution of Biomedical Ontologies

Avoiding Perspective-Relative Silos

Universal Core Semantic Layer

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

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