Applied Ontology - Revision history

Phismith at 16:01, 18 February 2018

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	[[Applied Ontology Spring 2017]]		[[Applied Ontology Spring 2017]]
			[[Ontology for Data Science \| Introduction to Ontology for Data Science and Information Fusion]]
	'''Title:''' PHI 549 Applied Ontology, Spring 2017		'''Title:''' PHI 549 Applied Ontology, Spring 2017

Phismith at 17:44, 26 May 2017

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			[[Applied Ontology Spring 2017]]

	'''Title:''' PHI 549 Applied Ontology, Spring 2017		'''Title:''' PHI 549 Applied Ontology, Spring 2017

Phismith at 20:01, 15 May 2017

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	'''Faculty: Barry Smith'''		'''Faculty: Barry Smith'''
	~~[[Tutorial on Basic Formal Ontology]]~~
	'''Registration:''' [http://www.buffalo.edu/cas/philosophy/grad-study/grad_courses/springcourses_grad.html#title_0 Class# 24197]. Registration details for off-campus students are provided under Part Time/Graduate [http://studentaccounts.buffalo.edu/tuition/spring.php here].		'''Registration:''' [http://www.buffalo.edu/cas/philosophy/grad-study/grad_courses/springcourses_grad.html#title_0 Class# 24197]. Registration details for off-campus students are provided under Part Time/Graduate [http://studentaccounts.buffalo.edu/tuition/spring.php here].

Phismith: /* Apr 23: The Ontology of Social Reality (continued) */

2017-04-25T12:12:45Z

Apr 23: The Ontology of Social Reality (continued)

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	:[https://www.youtube.com/watch?v=WIJJlnLLWGU Deontology Ontology]		:[https://www.youtube.com/watch?v=WIJJlnLLWGU Deontology Ontology]

	::Basic Formal Ontology provides no obvious category under which deontic entities such as claims, rights, obligations, permissions fall. The lecture provides a summary of how such entities may be treated in a way that is consistent with BFO, focusing on the case of obligations generated through acts of promising. a longer version of this material is presented [https://www.youtube.com/watch?v=W4Vefe5p6p4 here] and [https://www.youtube.com/~~edit~~?o=~~U&video_id=41N8biCJWHI~~ here].		::Basic Formal Ontology provides no obvious category under which deontic entities such as claims, rights, obligations, permissions fall. The lecture provides a summary of how such entities may be treated in a way that is consistent with BFO, focusing on the case of obligations generated through acts of promising. a longer version of this material is presented [https://www.youtube.com/watch?v=W4Vefe5p6p4 here] and [https://www.youtube.com/watch?v=Hk6Df2geYiQ here].

	:[https://www.youtube.com/watch?v=bp3B2GkgaB8 Ontology of the Organigram]		:[https://www.youtube.com/watch?v=bp3B2GkgaB8 Ontology of the Organigram]

Phismith: /* Apr 23: The Ontology of Social Reality (continued) */

2017-04-17T21:03:40Z

Apr 23: The Ontology of Social Reality (continued)

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	:[https://www.youtube.com/watch?v=WIJJlnLLWGU Deontology Ontology]		:[https://www.youtube.com/watch?v=WIJJlnLLWGU Deontology Ontology]

	::Basic Formal Ontology provides no obvious category under which deontic entities such as claims, rights, obligations, permissions fall. The lecture provides a summary of how such entities may be treated in a way that is consistent with BFO, focusing on the case of obligations generated through acts of promising. a longer version of this material is presented [https://www.youtube.com/watch?v=W4Vefe5p6p4 here] and here.		::Basic Formal Ontology provides no obvious category under which deontic entities such as claims, rights, obligations, permissions fall. The lecture provides a summary of how such entities may be treated in a way that is consistent with BFO, focusing on the case of obligations generated through acts of promising. a longer version of this material is presented [https://www.youtube.com/watch?v=W4Vefe5p6p4 here] and [https://www.youtube.com/edit?o=U&video_id=41N8biCJWHI here].

	:[https://www.youtube.com/watch?v=bp3B2GkgaB8 Ontology of the Organigram]		:[https://www.youtube.com/watch?v=bp3B2GkgaB8 Ontology of the Organigram]

Phismith: /* Apr 30: Ontology of Medicine */

2017-04-17T21:02:28Z

Apr 30: Ontology of Medicine

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	:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records]		:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records]

	::Starting from around 2005, national programs for the introduction of Electronic Health Records (EHRs) were launched with great enthusiasm in the US and UK. EHRs were seen as a means of increasing quality, safety and continuity of clinical care while at the same time reducing healthcare costs. I will survey the results of these, pointing out both achievements and failures. Specific topics to be addressed include: problems of data interoperability; ‘meaningful use’; the role of SNOMED CT, openEHR, and FHIR; and the prospects for secondary use of EHR data in information-driven clinical and translational research.		::Starting from around 2005, national programs for the introduction of Electronic Health Records (EHRs) were launched with great enthusiasm in the US and UK. EHRs were seen as a means of increasing quality, safety and continuity of clinical care while at the same time reducing healthcare costs. I will survey the results of these, pointing out both achievements and failures. Specific topics to be addressed include: problems of data interoperability; ‘meaningful use’; the role of SNOMED CT, openEHR, and FHIR; and the prospects for secondary use of EHR data in information-driven clinical and translational research.While bioinformatics has witnessed enormous technological advances since the turn of the millennium, progress in the EHR field has been stymied by outdated approaches entrenched through ill-conceived government mandates. In the US, especially, the dominant EHR systems are expensive, difficult to use, fail to ensure even a minimal level of interoperability, and detract from patient care. I will conclude by sketching an evolutionary path towards the sort of EHR landscape that will be needed in the future, in which consistency with biomedical ontologies will play a central role.

	~~::~~While bioinformatics has witnessed enormous technological advances since the turn of the millennium, progress in the EHR field has been stymied by outdated approaches entrenched through ill-conceived government mandates. In the US, especially, the dominant EHR systems are expensive, difficult to use, fail to ensure even a minimal level of interoperability, and detract from patient care. I will conclude by sketching an evolutionary path towards the sort of EHR landscape that will be needed in the future, in which consistency with biomedical ontologies will play a central role.

	:[https://www.youtube.com/watch?v=PhW-ix-FoOQ Ethics, Informatics and Obamacare]		:[https://www.youtube.com/watch?v=PhW-ix-FoOQ Ethics, Informatics and Obamacare]

Phismith: /* Apr 30: Ontology of Medicine */

2017-04-17T21:02:07Z

Apr 30: Ontology of Medicine

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	::Starting from around 2005, national programs for the introduction of Electronic Health Records (EHRs) were launched with great enthusiasm in the US and UK. EHRs were seen as a means of increasing quality, safety and continuity of clinical care while at the same time reducing healthcare costs. I will survey the results of these, pointing out both achievements and failures. Specific topics to be addressed include: problems of data interoperability; ‘meaningful use’; the role of SNOMED CT, openEHR, and FHIR; and the prospects for secondary use of EHR data in information-driven clinical and translational research.		::Starting from around 2005, national programs for the introduction of Electronic Health Records (EHRs) were launched with great enthusiasm in the US and UK. EHRs were seen as a means of increasing quality, safety and continuity of clinical care while at the same time reducing healthcare costs. I will survey the results of these, pointing out both achievements and failures. Specific topics to be addressed include: problems of data interoperability; ‘meaningful use’; the role of SNOMED CT, openEHR, and FHIR; and the prospects for secondary use of EHR data in information-driven clinical and translational research.

	::While bioinformatics has witnessed enormous technological advances since the turn of the millennium, progress in the EHR field has been stymied by outdated approaches entrenched through ill-conceived government mandates. In the US, especially, the dominant EHR systems are expensive, difficult to use, fail to ensure even a minimal level of interoperability, and detract from patient care. I will conclude by sketching an evolutionary path towards the sort of EHR landscape that will be needed in the future, in which consistency with biomedical ontologies will play a central role.		::While bioinformatics has witnessed enormous technological advances since the turn of the millennium, progress in the EHR field has been stymied by outdated approaches entrenched through ill-conceived government mandates. In the US, especially, the dominant EHR systems are expensive, difficult to use, fail to ensure even a minimal level of interoperability, and detract from patient care. I will conclude by sketching an evolutionary path towards the sort of EHR landscape that will be needed in the future, in which consistency with biomedical ontologies will play a central role.

Phismith: /* Apr 30: Ontology of Medicine */

2017-04-17T21:01:38Z

Apr 30: Ontology of Medicine

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	:[https://www.youtube.com/watch?v=b4kULamlFaM The Ontology of Disease]		:[https://www.youtube.com/watch?v=b4kULamlFaM The Ontology of Disease]

	::A recent paper in the journal Healthcare Informatics Research identifies a paradigm shift - 'from concept representations to ontologies' - in the ways medical terminologies and vocabularies are used to describe medical data [1]. We will describe what this paradigm shift involves, what it means to talk about 'ontologies' in the medical context, and how such talk relates to the traditional concerns of philosophical ontologists. We shall conclude with an ontological definition of disease, and illustrations of how this definition can be applied to a range of clinical examples.		::A recent paper in the journal Healthcare Informatics Research identifies a paradigm shift - 'from concept representations to ontologies' - in the ways medical terminologies and vocabularies are used to describe medical data [1]. We will describe what this paradigm shift involves, what it means to talk about 'ontologies' in the medical context, and how such talk relates to the traditional concerns of philosophical ontologists. We shall conclude with an ontological definition of disease, and illustrations of how this definition can be applied to a range of clinical examples. [1] See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920035/
	[1] See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920035/

	:[https://www.youtube.com/watch?v=3U55vU8SfEo How to Build an Imaging Ontology]		:[https://www.youtube.com/watch?v=3U55vU8SfEo How to Build an Imaging Ontology]

	We will provide an introduction to the field of biomedical ontology with special reference to the field of pathology informatics. We will look at examples of existing ontologies especially the Ontology for Biomedical Investigations (OBI), the Ontology for Biological and Clinical Statistics (OBCS), and the Ontology for General Medical Science (OGMS). We will then draw lessons from these examples for an ontology of pathology imaging.		::We will provide an introduction to the field of biomedical ontology with special reference to the field of pathology informatics. We will look at examples of existing ontologies especially the Ontology for Biomedical Investigations (OBI), the Ontology for Biological and Clinical Statistics (OBCS), and the Ontology for General Medical Science (OGMS). We will then draw lessons from these examples for an ontology of pathology imaging.

	:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records]		:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records]

Phismith: /* Apr 30: Ontology of Medicine */

2017-04-17T21:01:20Z

Apr 30: Ontology of Medicine

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	==Apr 30: Ontology of Medicine ==		==Apr 30: Ontology of Medicine ==

	:The Ontology of Disease		:[https://www.youtube.com/watch?v=b4kULamlFaM The Ontology of Disease]

	:~~How~~ to ~~Build~~ an ~~Imaging Ontology~~		::A recent paper in the journal Healthcare Informatics Research identifies a paradigm shift - 'from concept representations to ontologies' - in the ways medical terminologies and vocabularies are used to describe medical data [1]. We will describe what this paradigm shift involves, what it means to talk about 'ontologies' in the medical context, and how such talk relates to the traditional concerns of philosophical ontologists. We shall conclude with an ontological definition of disease, and illustrations of how this definition can be applied to a range of clinical examples.
			[1] See http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920035/

	:~~The Glory and Misery of Electronic Health Records~~		:[https://www.youtube.com/watch?v=3U55vU8SfEo How to Build an Imaging Ontology]

	:Ethics, Informatics and Obamacare		We will provide an introduction to the field of biomedical ontology with special reference to the field of pathology informatics. We will look at examples of existing ontologies especially the Ontology for Biomedical Investigations (OBI), the Ontology for Biological and Clinical Statistics (OBCS), and the Ontology for General Medical Science (OGMS). We will then draw lessons from these examples for an ontology of pathology imaging.

			:[https://www.youtube.com/watch?v=gc5a0LaXaBo The Glory and Misery of Electronic Health Records]

			::Starting from around 2005, national programs for the introduction of Electronic Health Records (EHRs) were launched with great enthusiasm in the US and UK. EHRs were seen as a means of increasing quality, safety and continuity of clinical care while at the same time reducing healthcare costs. I will survey the results of these, pointing out both achievements and failures. Specific topics to be addressed include: problems of data interoperability; ‘meaningful use’; the role of SNOMED CT, openEHR, and FHIR; and the prospects for secondary use of EHR data in information-driven clinical and translational research.
			::While bioinformatics has witnessed enormous technological advances since the turn of the millennium, progress in the EHR field has been stymied by outdated approaches entrenched through ill-conceived government mandates. In the US, especially, the dominant EHR systems are expensive, difficult to use, fail to ensure even a minimal level of interoperability, and detract from patient care. I will conclude by sketching an evolutionary path towards the sort of EHR landscape that will be needed in the future, in which consistency with biomedical ontologies will play a central role.

			:[https://www.youtube.com/watch?v=PhW-ix-FoOQ Ethics, Informatics and Obamacare]

			::Surveys a series of ethical, economic, clinical and also safety issues relating to the application of informatics to healthcare, focusing especially on the role of informatics in the Patient Protection and Affordable Care Act. Talk presented in the University at Buffalo Clinical/Research Ethics Seminar - Ethics, Informatics and Obamacare, November 20, 2012. Slides are available here: http://ontology.buffalo.edu/13/ethics-informatics-obamacare.pptx

	==May 7 Student video presentations==		==May 7 Student video presentations==

Phismith: /* Apr 23: The Ontology of Social Reality (continued) */

2017-04-17T20:48:13Z

Apr 23: The Ontology of Social Reality (continued)

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	:[https://www.youtube.com/watch?v=bp3B2GkgaB8 Ontology of the Organigram]		:[https://www.youtube.com/watch?v=bp3B2GkgaB8 Ontology of the Organigram]

			::An organigram is a graph-theoretic structure consisting of nodes and edges. The nodes standardly represent three sorts of entities: divisions within the organization, offices of the persons who head these divisions, and the current holders of such offices. The edges represent relations of sub- and superordination between the entities represented by the nodes. Where such a relation obtains the subordinate has obligations based upon his consent to perform certain duties as directed and controlled by the superordinate. We will evaluate the hypothesis that an organization is itself a graph-theoretic structure that is (or is capable of being) represented by an organigram.

	==Apr 30: Ontology of Medicine ==		==Apr 30: Ontology of Medicine ==