Difference between revisions of "Main Page"

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−	<big>'''Welcome to the National Center for Ontological Research (NCOR) Collaboration Plaform'''</big>	+	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.
−	Ontology is both a branch of philosophy and a fast-growing component of computer science concerned with the development of formal representations of the entities and relations existing in a variety of application domains. Ontology has been shown to have considerable potential on the level of both pure research and applications. It provides foundations for diverse technologies in areas such as information integration, natural language processing, data annotation, and the construction of intelligent computer systems.	+	== Events ==
−	The University at Buffalo and Stanford University have established the National Center for Ontological Research (NCOR) (http://ncor.buffalo.edu), with Buffalo and Stanford as the two principal sites, together with a number of partner institutions drawn from academia, government, and industry (http://ncor.buffalo.edu/about2.htm#researchpartners).	+	See '''[http://ncorwiki.buffalo.edu/index.php/Newsevents here]'''
		+	==News==
−	<big>'''Goal'''</big>	+	[https://www.youtube.com/watch?v=0giPMMoKR9s Video recording of talk by Barry Smith on "Defining Intelligence"], February 17, 2021
−	NCOR has the goal of advancing ontological investigation within the United States. It will serve as a vehicle to coordinate, to enhance, to publicize, and to seek funding for ontological research activities in its two principal sites and in its partner institutions. A special focus will be on the establishment of tools and measures for quality assurance of ontologies.	+	[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
−	NCOR will provide coordination, infrastructure, and other forms of support for investigators working in the United States on theoretical ontology and on applications in fields such as ontology of the sciences, spatial and cognitive ontology, terminological systems, enterprise ontology and in a variety of defense- and homeland security-related projects.	+	[https://ncor-brasil.org/about/ NCOR-Brasil] established, December 1, 2020
−	It will also provide US researchers working in ontology-related areas with specialized support in seeking external funding and in assembling collaborative, interdisciplinary teams both nationally and internationally. It will aid the coordination of ontological projects being pursued by its partner institutions and also develop resources for the implementation and evaluation of ontologies. The Center will also engage in outreach endeavors that are designed to broaden the range of institutions and individuals accepting the goals of high quality ontology in both theory and practice.	+	[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
−	<big>'''Methodology'''</big>	+	[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
−	Previous efforts at ontology building have been conceived primarily in pragmatic terms, as outgrowths of knowledge engineering or artificial intelligence research, or more generally as projects motivated by the need to solve problems internal to the development of computer systems. NCOR, in contrast, looks beyond the realm of software artifacts, starting out from the idea that the development of ontologies can profit from the application of theoretical rigor based in logic and philosophical ontology.	+	[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
−	Too many ontologies used in information systems have been constructed largely by taking as their starting point existing database systems or the conceptualizations used by the practitioners within given domains, without sufficiently checking whether these conceptualizations correspond with identifiable entities and relationships in the world beyond. NCOR advocates a view according to which, in advance of implementation, careful attention should be paid to what the world is like. Our approach does not dictate any particular philosophical or metaphysical stance with respect to the world being modeled. Indeed, we recognize that the same reality may be sliced in different ways when addressed from different perspectives. Our approach requires, however, that, whatever philosophical stance is taken, it is used consistently and rigorously and on the basis of clearly stated principles. At the same time we are devoting our energies to the development of tools designed to help in the selection between ontological frameworks on the basis of criteria such as usability, usefulness and accuracy of reasoning support.	+	[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
−	<big>'''Contact'''</big>	+	[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
−	For more information - or to submit content - please contact ontology@buffalo.edu.	+	[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]
		+
		+	[http://www.kurzweilai.net/botanists-building-ontologies-to-cope-with-information-overload Botanists building ontologies to cope with information overload]
		+
		+	[[UB Applied Informatics Portal]] unveiled.
		+
		+	==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.”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://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
		+
		+	== 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)
		+
		+	I2WD: Semantic Enhancement for DSGS-A: [[Distributed Development of a Shared Semantic Resource]] (2012-13)
		+
		+	I2WD: [http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=2298761 PED Fusion via Enterprise Ontology]
		+
		+	[http://ncor.buffalo.edu/ontologies/AIRS_Ontologies.pdf Common Core Ontologies (preliminary statement)]
		+
		+	[[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]]
		+
		+	== 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 ==
		+
		+	[http://ontology.buffalo.edu/smith/articles/ontologies.htm Ontology: An Introduction]
		+
		+	[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Coordinated Evolution of Biomedical Ontologies]
		+
		+	[[Avoiding Perspective-Relative Silos]]
		+
		+	[http://ceur-ws.org/Vol-555/paper5.pdf Universal Core Semantic Layer]
		+
		+	== Training Videos  ==
		+
		+	[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]
		+
		+	[http://www.youtube.com/v/Z5o1SpPqNrA Avoiding Semantic Stovepipes: Five Ontological Principles for Interoperability]
		+
		+	[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]

---

Latest revision as of 13:38, 19 February 2021

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

News

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.

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.”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

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

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