Immunology Ontology - Revision history

Phismith: /* Morning Lecture */

2013-06-13T16:19:07Z

Morning Lecture

← Older revision		Revision as of 16:19, 13 June 2013
Line 15:		Line 15:


	8:30am Introduction to biomedical ontology building (Barry Smith [http://ncor.buffalo.edu/2013/Immunology/BS.ppt Slides])		8:30am Introduction to biomedical ontology building (Barry Smith, [http://ncor.buffalo.edu/2013/Immunology/BS.ppt Slides])

	:Identification of participant areas of interest in preparation for the afternoon practical session		:Identification of participant areas of interest in preparation for the afternoon practical session

Phismith: /* Morning Lecture */

2013-06-13T16:18:52Z

Morning Lecture

← Older revision		Revision as of 16:18, 13 June 2013
Line 15:		Line 15:


	8:30am Introduction to biomedical ontology building [http://ncor.buffalo.edu/2013/Immunology/BS.ppt Slides]		8:30am Introduction to biomedical ontology building (Barry Smith [http://ncor.buffalo.edu/2013/Immunology/BS.ppt Slides])

	:Identification of participant areas of interest in preparation for the afternoon practical session		:Identification of participant areas of interest in preparation for the afternoon practical session
Line 31:		Line 31:
	::The Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI])		::The Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI])

	9:15am Overview of ontologies with content relevant to immunology		9:15am Overview of ontologies with content relevant to immunology (Lindsay Cowell, [http://ncor.buffalo.edu/2013/Immunology/LC.pdf Slides])

	:Use of ontology portals and search engines		:Use of ontology portals and search engines

Phismith: /* Afternoon Practical Session: Building Small Ontologies in the Immunological Domain */

2013-06-12T20:04:36Z

Afternoon Practical Session: Building Small Ontologies in the Immunological Domain

← Older revision		Revision as of 20:04, 12 June 2013
Line 61:		Line 61:
	1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise.		1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise.

	Adaptive immunity		:Adaptive immunity
	Immune tolerance		:Immune tolerance
	Inflammation		:Inflammation
	Adaptive immunity		:Adaptive immunity
	Innate immunity		:Innate immunity
	Mucosal immunity		:Mucosal immunity
	Transplantation immunology /MHC		:Transplantation immunology /MHC
	Tumor microenvironment / Cancer		:Tumor microenvironment / Cancer
	Virology		:Virology

	(These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].)		(These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].)

Phismith: /* Afternoon Practical Session: Building Small Ontologies in the Immunological Domain */

2013-06-12T17:38:01Z

Afternoon Practical Session: Building Small Ontologies in the Immunological Domain

← Older revision		Revision as of 17:38, 12 June 2013
Line 61:		Line 61:
	1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise.		1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise.

	~~:innate~~ immunity		Adaptive immunity
	~~:autoimmune disease~~		Immune tolerance
	~~:asthma~~		Inflammation
	~~:immune~~ tolerance		Adaptive immunity
	~~:transplantation~~		Innate immunity
	~~:medical countermeasures against radiological and nuclear threats~~		Mucosal immunity
	~~:tissue engineering~~		Transplantation immunology /MHC
	~~:wounds and injuries~~		Tumor microenvironment / Cancer
	~~:diseases of inflammation~~		Virology
	~~:tumor microenvironments~~
	~~:acquired~~/~~adaptive immunity~~
	~~:mucosal immunity~~
	~~:primary immunodeficiency~~

	(These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].)		(These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].)

	1:~~10pm Participants will vote to select ca.~~ 10 ~~topics, for each of which we have~~		1:10 Participants will be divided into corresponding breakout groups. The task of each group will be to create a workplan for building an ontology (or ontologies) for their selected area. The workplan will consist minimally of
	~~six or so people who have some relevant domain knowledge~~

	~~1:20~~ Participants will be divided into corresponding breakout groups. The task of each group will be to create a workplan for building an ontology (or ontologies) for their selected area. The workplan will consist minimally of

	: i. a list of main terms in their selected area -- to create this list participants can use the terminological resources they use in their own work or any other source		: i. a list of main terms in their selected area -- to create this list participants can use the terminological resources they use in their own work or any other source

Phismith: /* Afternoon Practical Session: Building Small Ontologies in the Immunological Domain */

2013-06-12T17:36:57Z

Afternoon Practical Session: Building Small Ontologies in the Immunological Domain

← Older revision		Revision as of 17:36, 12 June 2013
Line 99:		Line 99:
	:Slide 3: List of the principal ontologies selected to be used as sources / starting points for development of the needed ontology		:Slide 3: List of the principal ontologies selected to be used as sources / starting points for development of the needed ontology
	:Slide 4: List of the main terms in the ontology (if possible with some rudimentary BFO organization)		:Slide 4: List of the main terms in the ontology (if possible with some rudimentary BFO organization)

			[http://ncor.buffalo.edu/2013/Immunology/Slides Slides]

	2.50 Summation		2.50 Summation

Phismith: /* Afternoon Practical Session: Building Small Ontologies in the Immunological Domain */

2013-06-10T22:43:10Z

Afternoon Practical Session: Building Small Ontologies in the Immunological Domain

← Older revision		Revision as of 22:43, 10 June 2013
Line 98:		Line 98:
	:Slide 2: Quick comparison of the experience of using the 4 ontology browsers listed above; optional report on experience using MeSH		:Slide 2: Quick comparison of the experience of using the 4 ontology browsers listed above; optional report on experience using MeSH
	:Slide 3: List of the principal ontologies selected to be used as sources / starting points for development of the needed ontology		:Slide 3: List of the principal ontologies selected to be used as sources / starting points for development of the needed ontology
	:Slide 4: List of the main terms in the ontology		:Slide 4: List of the main terms in the ontology (if possible with some rudimentary BFO organization)

	2.50 Summation		2.50 Summation

Phismith: /* Afternoon Practical Session: Building Small Ontologies in the Immunological Domain */

2013-06-10T22:32:09Z

Afternoon Practical Session: Building Small Ontologies in the Immunological Domain

← Older revision		Revision as of 22:32, 10 June 2013
Line 60:		Line 60:

	1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise.		1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise.


	:innate immunity		:innate immunity
	~~:[http://ncor.buffalo.edu/2013/Immunology/allergy-example.docx allergy and allergic disease]~~
	:autoimmune disease		:autoimmune disease
	:asthma		:asthma
Line 71:		Line 69:
	:tissue engineering		:tissue engineering
	:wounds and injuries		:wounds and injuries
	~~:[http://ncor.buffalo.edu/2013/Immunology/HIPC-Example/ HIPC]~~
	:diseases of inflammation		:diseases of inflammation
	:tumor microenvironments		:tumor microenvironments
	:acquired/adaptive immunity		:acquired/adaptive immunity
	:mucosal immunity		:mucosal immunity
			:primary immunodeficiency

	(These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].)		(These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].)
Line 85:		Line 83:

	: i. a list of main terms in their selected area -- to create this list participants can use the terminological resources they use in their own work or any other source		: i. a list of main terms in their selected area -- to create this list participants can use the terminological resources they use in their own work or any other source

			Two samples:
			:[http://ncor.buffalo.edu/2013/Immunology/allergy-example.docx allergy and allergic disease]
			:[http://ncor.buffalo.edu/2013/Immunology/HIPC-Example/ soluble proteins (including cytokines and chemokines) relevant to the work of HIPC]]

	: ii. a list of the main ontologies they would harvest as starting points; in identifying these ontologies participants should experiment with two or more of the ontology portals listed below		: ii. a list of the main ontologies they would harvest as starting points; in identifying these ontologies participants should experiment with two or more of the ontology portals listed below

Phismith: /* Morning Lecture */

2013-06-10T21:59:27Z

Morning Lecture

← Older revision		Revision as of 21:59, 10 June 2013
Line 27:		Line 27:
	:::Reinventing the wheel		:::Reinventing the wheel
	:::Confusing words with things		:::Confusing words with things
	:~~Example~~		:Examples
	::The [http://www.obofoundry.org/ OBO (Open Biological and Biomedical Ontologies) Foundry]		::The [http://www.obofoundry.org/ OBO (Open Biological and Biomedical Ontologies) Foundry]
	::The Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI])		::The Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI])

Phismith: /* Morning Lecture */

2013-06-10T21:58:36Z

Morning Lecture

← Older revision		Revision as of 21:58, 10 June 2013
Line 15:		Line 15:


	8:30am Introduction to biomedical ontology building		8:30am Introduction to biomedical ontology building [http://ncor.buffalo.edu/2013/Immunology/BS.ppt Slides]

	:Identification of participant areas of interest in preparation for the afternoon practical session		:Identification of participant areas of interest in preparation for the afternoon practical session
Line 56:		Line 56:
	::[http://ontofox.hegroup.org/ Ontofox] [http://ncor.buffalo.edu/2013/Immunology/Ontofox.pptx Slides]		::[http://ontofox.hegroup.org/ Ontofox] [http://ncor.buffalo.edu/2013/Immunology/Ontofox.pptx Slides]
	::SPARQL		::SPARQL


	== '''Afternoon Practical Session: Building Small Ontologies in the Immunological Domain''' ==		== '''Afternoon Practical Session: Building Small Ontologies in the Immunological Domain''' ==

Phismith: /* Afternoon Practical Session: Building Small Ontologies in the Immunological Domain */

2013-06-10T12:26:51Z

Afternoon Practical Session: Building Small Ontologies in the Immunological Domain

← Older revision		Revision as of 12:26, 10 June 2013
Line 60:		Line 60:
	== '''Afternoon Practical Session: Building Small Ontologies in the Immunological Domain''' ==		== '''Afternoon Practical Session: Building Small Ontologies in the Immunological Domain''' ==

	1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above)		1:00pm Establish target areas of interest (drawing on the work initiated in the 8:30am session above). Participants will suggest possible target areas, expanding this list in light of their own areas of interest and expertise.

	~~First draft list of possible target areas (they should be areas for which a suitable single ontology does not already exist)~~

	:innate immunity		:innate immunity
Line 74:		Line 73:
	:wounds and injuries		:wounds and injuries
	:[http://ncor.buffalo.edu/2013/Immunology/HIPC-Example/ HIPC]		:[http://ncor.buffalo.edu/2013/Immunology/HIPC-Example/ HIPC]
			:diseases of inflammation
			:tumor microenvironments
			:acquired/adaptive immunity
			:mucosal immunity

	(Some of ~~these~~ items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].)		(These are all areas for which a suitable single ontology does not already exist. Some of the items are taken from the DAIT list [http://www.niaid.nih.gov/about/organization/dait/Pages/default.aspx here].)

	1:10pm Participants will vote~~, in order~~ to select ca. 10 topics, for each of which we have		1:10pm Participants will vote to select ca. 10 topics, for each of which we have
	six or so people who have some relevant domain knowledge		six or so people who have some relevant domain knowledge

	1:20 Participants will be divided into corresponding groups. The task of each group will be to		1:20 Participants will be divided into corresponding breakout groups. The task of each group will be to create a workplan for building an ontology (or ontologies) for their selected area. The workplan will consist minimally of
	create a workplan for ~~creating~~ an ontology (or ontologies) for their selected area. The workplan will consist minimally of

	: i. a list of main terms in their selected area -- to create this list participants can use the terminological resources they use in their own work or on any other source		: i. a list of main terms in their selected area -- to create this list participants can use the terminological resources they use in their own work or any other source
	: ii. a list of the main ontologies they would harvest as starting points; in identifying these ontologies participants should experiment with two or more of the ontology portals listed below		: ii. a list of the main ontologies they would harvest as starting points; in identifying these ontologies participants should experiment with two or more of the ontology portals listed below

Line 89:		Line 91:

	2:20 Presentation of results: Each group is required to produce at least 4 slides		2:20 Presentation of results: Each group is required to produce at least 4 slides
	summarizing the results of their work ~~in 3 minutes~~.		summarizing the results of their work.

	:Slide 1: Title and author list		:Slide 1: Title and author list