Microbiology for the CTSA: Ontological Approaches - Revision history

Phismith: /* Schedule Day 2: October 26 */

2019-01-26T20:20:57Z

Schedule Day 2: October 26

← Older revision		Revision as of 20:20, 26 January 2019
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	1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas		1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

	2:00pm: ''Working session: Building the Microbiome Ontology '' [https://buffalo.box.com/s/7822qqz5ly6o70f21t8p76zia97o8v3g Slides] ~~- Introduced by Barry Smith~~		2:00pm: ''Working session: Building the Microbiome Ontology '' Barry Smith <sup>[https://buffalo.box.com/s/7822qqz5ly6o70f21t8p76zia97o8v3g Slides]</sup>

	4:00pm: ''Close''		4:00pm: ''Close''

Phismith: /* Schedule Day 2: October 26 */

2019-01-26T20:19:54Z

Schedule Day 2: October 26

← Older revision		Revision as of 20:19, 26 January 2019
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	1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas		1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

	2:00pm: ''Working session: Building the Microbiome Ontology '' - Introduced by Barry Smith		2:00pm: ''Working session: Building the Microbiome Ontology '' [https://buffalo.box.com/s/7822qqz5ly6o70f21t8p76zia97o8v3g Slides] - Introduced by Barry Smith

	4:00pm: ''Close''		4:00pm: ''Close''

Phismith at 20:03, 19 October 2018

2018-10-19T20:03:19Z

← Older revision		Revision as of 20:03, 19 October 2018
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	== '''Announcement''' ==		== '''Announcement''' ==

	~~[[Ontology for Precision Medicine: From Genomes to Public Health]]~~

	'''The Clinical and Translational Science Ontology Group (CTSOG)''' invites you to join us this October 25-26, 2017 in Ann Arbor, Michigan to discuss the state of the art in ontologies and terminologies towards standardized data and metadata and data integration in various areas of clinical and translational microbiology. Example areas of discussion include microbiomes, host-microbiome interactions, microbial pathogens (e.g., bacteria, viruses, and parasites), infectious diseases, host immunity, vaccines and drugs treating infectious diseases, and vaccine and drug adverse events and safety. We will focus on how ontologies can be developed and used to support clinical and translational microbiology data recording, standardization, and analysis.		'''The Clinical and Translational Science Ontology Group (CTSOG)''' invites you to join us this October 25-26, 2017 in Ann Arbor, Michigan to discuss the state of the art in ontologies and terminologies towards standardized data and metadata and data integration in various areas of clinical and translational microbiology. Example areas of discussion include microbiomes, host-microbiome interactions, microbial pathogens (e.g., bacteria, viruses, and parasites), infectious diseases, host immunity, vaccines and drugs treating infectious diseases, and vaccine and drug adverse events and safety. We will focus on how ontologies can be developed and used to support clinical and translational microbiology data recording, standardization, and analysis.

Phismith at 20:02, 19 October 2018

2018-10-19T20:02:17Z

← Older revision		Revision as of 20:02, 19 October 2018
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	== '''Announcement''' ==		== '''Announcement''' ==

			[[Ontology for Precision Medicine: From Genomes to Public Health]]

	'''The Clinical and Translational Science Ontology Group (CTSOG)''' invites you to join us this October 25-26, 2017 in Ann Arbor, Michigan to discuss the state of the art in ontologies and terminologies towards standardized data and metadata and data integration in various areas of clinical and translational microbiology. Example areas of discussion include microbiomes, host-microbiome interactions, microbial pathogens (e.g., bacteria, viruses, and parasites), infectious diseases, host immunity, vaccines and drugs treating infectious diseases, and vaccine and drug adverse events and safety. We will focus on how ontologies can be developed and used to support clinical and translational microbiology data recording, standardization, and analysis.		'''The Clinical and Translational Science Ontology Group (CTSOG)''' invites you to join us this October 25-26, 2017 in Ann Arbor, Michigan to discuss the state of the art in ontologies and terminologies towards standardized data and metadata and data integration in various areas of clinical and translational microbiology. Example areas of discussion include microbiomes, host-microbiome interactions, microbial pathogens (e.g., bacteria, viruses, and parasites), infectious diseases, host immunity, vaccines and drugs treating infectious diseases, and vaccine and drug adverse events and safety. We will focus on how ontologies can be developed and used to support clinical and translational microbiology data recording, standardization, and analysis.

Yongqunh: /* Schedule Day 1: October 25 */

2017-10-31T23:47:15Z

Schedule Day 1: October 25

← Older revision		Revision as of 23:47, 31 October 2017
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	10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He <sup>[http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]</sup>		10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He <sup>[http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]</sup>

	11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng <sup>[http://ncorwiki.buffalo.edu/images/f/f8/MicrobiomeDB_OHMI_Jie_Zheng.pdf ~~Slide~~]</sup>		11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng <sup>[http://ncorwiki.buffalo.edu/images/f/f8/MicrobiomeDB_OHMI_Jie_Zheng.pdf Slides]</sup>

	11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko <sup> [http://ncorwiki.buffalo.edu/index.php/File:MUSC_%C2%B5Biome.pptx Slides]</sup>		11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko <sup> [http://ncorwiki.buffalo.edu/index.php/File:MUSC_%C2%B5Biome.pptx Slides]</sup>

	11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci		11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci<sup>[http://ncorwiki.buffalo.edu/images/f/fd/Masci_Ann_Arbor_2017.pdf Slides]</sup>

	11:45-12:15: Discussion on the morning session topics		11:45-12:15: Discussion on the morning session topics

Yongqunh: /* Schedule Day 1: October 25 */

2017-10-31T23:39:52Z

Schedule Day 1: October 25

← Older revision		Revision as of 23:39, 31 October 2017
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	10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He <sup>[http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]</sup>		10:30-11:00 am: ''Brief OHMI introduction and OHMI representation of rheumatism-associated host-microbiome interactions'' - Oliver He <sup>[http://ncorwiki.buffalo.edu/images/a/ac/OHMI-He.pdf Slides]</sup>

	11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / ~~Daniel Beiting~~		11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng <sup>[http://ncorwiki.buffalo.edu/images/f/f8/MicrobiomeDB_OHMI_Jie_Zheng.pdf Slide]</sup>

	11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko <sup> [http://ncorwiki.buffalo.edu/index.php/File:MUSC_%C2%B5Biome.pptx Slides]</sup>		11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko <sup> [http://ncorwiki.buffalo.edu/index.php/File:MUSC_%C2%B5Biome.pptx Slides]</sup>

Yongqunh: /* Schedule Day 2: October 26 */

2017-10-30T17:32:07Z

Schedule Day 2: October 26

← Older revision		Revision as of 17:32, 30 October 2017
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	Session coordinators: Lindsay Cowell, Barry Smith		Session coordinators: Lindsay Cowell, Barry Smith

	9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell, Barry Smith		9:45am: ''The Present State of the Infectious Disease Ontology'' - Lindsay Cowell<sup>[http://ncorwiki.buffalo.edu/images/b/b8/IDO_CTSOG_Meeting_2017.10.24.pdf Slides]</sup>, Barry Smith

	10:30am: Break		10:30am: Break

Aehicks: /* Schedule Day 1: October 25 */

2017-10-30T16:52:00Z

Schedule Day 1: October 25

← Older revision		Revision as of 16:52, 30 October 2017
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	9:00am: OMP: The ontology for microbial phenotypes - Deborah A. Siegele / Jim Hu <sup>[http://ncorwiki.buffalo.edu/images/8/8b/OMP-Debby.pdf Slides]</sup>		9:00am: OMP: The ontology for microbial phenotypes - Deborah A. Siegele / Jim Hu <sup>[http://ncorwiki.buffalo.edu/images/8/8b/OMP-Debby.pdf Slides]</sup>

	9:20am: ''The MicrO ontology; enabling the acquisition of higher-order knowledge of phenotypes from prokaryotic taxonomic descriptions and the construction of very large character matrices'' - Carrine E. Blank		9:20am: ''The MicrO ontology; enabling the acquisition of higher-order knowledge of phenotypes from prokaryotic taxonomic descriptions and the construction of very large character matrices'' - Carrine E. Blank <sup> [http://ncorwiki.buffalo.edu/index.php/File:MicroOntology_CTSO.Oct2017.pptx Slides]</sup>

	9:40am: ''MEOWL: Microbial Environments described using OWL'' - Ramona L. Walls		9:40am: ''MEOWL: Microbial Environments described using OWL'' - Ramona L. Walls <sup>[http://ncorwiki.buffalo.edu/index.php/File:Walls_CTSOG_meowl.pdf Slides]</sup>

	10:00-10:30am: Break		10:00-10:30am: Break
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	1:00pm: ''Ontological Representation of Software to Make it FAIR'' - Bill Hogan		1:00pm: ''Ontological Representation of Software to Make it FAIR'' - Bill Hogan

	1:30pm: ''FAIR principles and the Immune Epitope Database (IEDB)'' - James Overton		1:30pm: ''FAIR principles and the Immune Epitope Database (IEDB)'' - James Overton <sup>[http://ncorwiki.buffalo.edu/index.php/File:Overton-FAIR-20171025.pdf Slides]</sup>

	2:00pm: ''Using cyberinfrastructure to make life sciences data FAIR: lessons learned'' - Ramona Walls		2:00pm: ''Using cyberinfrastructure to make life sciences data FAIR: lessons learned'' - Ramona Walls <sup>[http://ncorwiki.buffalo.edu/index.php/File:Walls-CyVerse_FAIR_CTSOG.pdf Slides]</sup>

	2:30pm: ''Measuring Interannotator Agreement in the Florida Annotated Corpus for Translational Science - The difficult ontological task'' - Amanda Hicks <sup>[http://ncorwiki.buffalo.edu/index.php/File:FACTS-CTSOG_2017.pptx Slides]</sup>		2:30pm: ''Measuring Interannotator Agreement in the Florida Annotated Corpus for Translational Science - The difficult ontological task'' - Amanda Hicks <sup>[http://ncorwiki.buffalo.edu/index.php/File:FACTS-CTSOG_2017.pptx Slides]</sup>

Aehicks: /* Schedule Day 2: October 26 */

2017-10-30T16:43:07Z

Schedule Day 2: October 26

← Older revision		Revision as of 16:43, 30 October 2017
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	8:20am: Remarks from Dr. Bob Dysko (University of Michigan)		8:20am: Remarks from Dr. Bob Dysko (University of Michigan)

	8:30am: '''Keynote address 2: Ontology support of clinical, epidemiological, and microbiome data exploration ''' - Dr. Chris Stoeckert (UPenn)		8:30am: '''Keynote address 2: Ontology support of clinical, epidemiological, and microbiome data exploration ''' - Dr. Chris Stoeckert (UPenn) <sup>[http://ncorwiki.buffalo.edu/index.php/File:StoeckertOntologyClinicalEpidemiologyMIcrobiome.pptx Slides]</sup>

	[[File:Stoeckert-photo.jpg\|thumb\|150px\|left\|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403\|Chris Stoeckert]] '''Abstract''': The challenge of working with Big Data is not only scale but in many situations, also the complexity of what the data is about. This is especially true of clinical and epidemiological data where data is obtained for critical variables but often in an ad hoc and inconsistent manner. Critical understanding of how these variables impact health and host microbiome interactions requires analyses across different studies and data sources. Ontologies are key to meeting this challenge through providing semantic harmonization of common and specialized types of data; the realist process approach followed by ontologies in Open Biomedical Ontologies (OBO) Foundry (http://obofoundry.org/) provides a common understanding of what the data is about. We are using application ontologies based on OBO Foundry ontologies to encode our understanding of data dictionaries in multiple projects. The projects range from the epidemiology and transmission patterns of malaria to enteric pathogen influence on morbidity and mortality in young children. An additional challenge is to transform ontologic representations into user-friendly web interface terminologies for data exploration. MicrobiomeDB (http://microbiomedb.org/mbio/) provides a web-based data-mining platform for interrogating microbiome experiments and makes use of our ontology and web interface terminology approach. The real power of ontologies will come from instantiation of data in these ontologies and the ability to do inferencing and searches of such data. A goal of the TURBO (Transforming and Unifying Research with Biomedical Ontologies) project at Penn is to instantiate an OBO Foundry-based application ontology with clinical data to support research starting with finding patient cohorts and biobank specimens.		[[File:Stoeckert-photo.jpg\|thumb\|150px\|left\|link=http://www.med.upenn.edu/apps/faculty/index.php/g306/c404/p6403\|Chris Stoeckert]] '''Abstract''': The challenge of working with Big Data is not only scale but in many situations, also the complexity of what the data is about. This is especially true of clinical and epidemiological data where data is obtained for critical variables but often in an ad hoc and inconsistent manner. Critical understanding of how these variables impact health and host microbiome interactions requires analyses across different studies and data sources. Ontologies are key to meeting this challenge through providing semantic harmonization of common and specialized types of data; the realist process approach followed by ontologies in Open Biomedical Ontologies (OBO) Foundry (http://obofoundry.org/) provides a common understanding of what the data is about. We are using application ontologies based on OBO Foundry ontologies to encode our understanding of data dictionaries in multiple projects. The projects range from the epidemiology and transmission patterns of malaria to enteric pathogen influence on morbidity and mortality in young children. An additional challenge is to transform ontologic representations into user-friendly web interface terminologies for data exploration. MicrobiomeDB (http://microbiomedb.org/mbio/) provides a web-based data-mining platform for interrogating microbiome experiments and makes use of our ontology and web interface terminology approach. The real power of ontologies will come from instantiation of data in these ontologies and the ability to do inferencing and searches of such data. A goal of the TURBO (Transforming and Unifying Research with Biomedical Ontologies) project at Penn is to instantiate an OBO Foundry-based application ontology with clinical data to support research starting with finding patient cohorts and biobank specimens.
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	10:30am: Break		10:30am: Break

	10:45am: ''Infectious Disease Ontology Round Table'' - Lindsay Cowell, Barry Smith, Oliver He<sup>[http://ncorwiki.buffalo.edu/images/b/b1/IDOBRU-VO-He.pdf Slides]</sup>, Chris Stoeckert, Richard Scheuermann		10:45am: ''Infectious Disease Ontology Round Table'' - Lindsay Cowell, Barry Smith, Oliver He<sup>[http://ncorwiki.buffalo.edu/images/b/b1/IDOBRU-VO-He.pdf Slides]</sup>, Chris Stoeckert<sup> [http://ncorwiki.buffalo.edu/index.php/File:EuPath_ontology_for_IDO_session_2017.pptx Slides] </sup>, Richard Scheuermann

	11:45am: ''The Antibody Ontology'' - Alex Diehl		11:45am: ''The Antibody Ontology'' - Alex Diehl
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	Session coordinator: Bill Hogan		Session coordinator: Bill Hogan

	1:00pm: ''Microbiology Data in the Real World -- Examples and Thoughts from One Site'' - Gigi Lipori		1:00pm: ''Microbiology Data in the Real World -- Examples and Thoughts from One Site'' - Gigi Lipori <sup>[http://ncorwiki.buffalo.edu/index.php/File:Micro-Ontology-Presentation.pptx Slides]</sup>

	1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas		1:30pm: ''Tissue Collection and Data Management in the Microbiome Clinical Studies'' - Dominick Lemas

Aehicks: /* Schedule Day 1: October 25 */

2017-10-30T16:26:56Z

Schedule Day 1: October 25

← Older revision		Revision as of 16:26, 30 October 2017
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	11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / Daniel Beiting		11:00-11:15 am: ''Ontology of Host-Microbiome Interactions use case at UPenn'' - Jie Zheng / Daniel Beiting

	11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko		11:15-11:30 am: ''Ontology of Host-Microbiome Interactions use case at MUSC'' - Jihad Obeid / Alexander Alekseyenko <sup> [http://ncorwiki.buffalo.edu/index.php/File:MUSC_%C2%B5Biome.pptx Slides]</sup>

	11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci		11:30-11:45 noon: ''Ontology of Host-Microbiome Interactions use case at Duke'' - Anna Maria Masci