The Role of Ontology in Big Cancer Data - Revision history

Phismith: /* Venue */

2015-05-24T15:37:28Z

Venue

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	== Venue ==		== Venue ==

	*Day 1 ~~(10am-4:30pm) will be in~~ [http://www.hhs.gov/ash/bloodsafety/advisorycommittee/nih-fisherslane-conferencecenter-directions.pdf FISHERS LANE CONFERENCE CENTER], 5635 Fishers Lane, Rockville, MD 20852 [[Directions to Fishers Lane Conference Center]]		*Day 1 [http://www.hhs.gov/ash/bloodsafety/advisorycommittee/nih-fisherslane-conferencecenter-directions.pdf FISHERS LANE CONFERENCE CENTER], 5635 Fishers Lane, Rockville, MD 20852 [[Directions to Fishers Lane Conference Center]]

	*Day 2 ~~(9am-3:30pm) will be a public session in~~ [http://www.nih.gov/icd/od/ocpl/VIC/index.htm Balcony A, Natcher Conference Center, NIH Building 45, Bethesda, MD 20892]		*Day 2 [http://www.nih.gov/icd/od/ocpl/VIC/index.htm Balcony A, Natcher Conference Center, NIH Building 45, Bethesda, MD 20892]

	~~'''<u> SECURITY </u>'''~~

	All attendees should bring a government-issued ID such as a driver’s license, and arrive at least 30 minutes early to pass through security collect coffee/drinks before settling in. Attendees can expect to have purses, computers, and luggage scanned and potentially searched.

	==Session 1: Addressing cancer big data challenges through imaging ontologies==		==Session 1: Addressing cancer big data challenges through imaging ontologies==

Phismith at 15:37, 24 May 2015

2015-05-24T15:37:05Z

← Older revision		Revision as of 15:37, 24 May 2015
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	10:45 '''Susan Mockus (The Jackson Laboratory, Genomic Medicine):''' Using the Disease Ontology to Translate Pathology Reports to NGS Clinical Reports [http://ncor.buffalo.edu/2015/NCI/Mockus.pptx Slides]		10:45 '''Susan Mockus (The Jackson Laboratory, Genomic Medicine):''' Using the Disease Ontology to Translate Pathology Reports to NGS Clinical Reports [http://ncor.buffalo.edu/2015/NCI/Mockus.pptx Slides]

	11:00 '''Peter Elkin (University at Buffalo):''' Ontology-based cancer biomarker discovery		11:00 '''Peter Elkin (University at Buffalo):''' Ontology-based cancer biomarker discovery [http://ncor.buffalo.edu/2015/NCI/Elkin.pptx Slides]

	<u>'''11:15 Discussion and Session Wrap Up'''</u>		<u>'''11:15 Discussion and Session Wrap Up'''</u>

Phismith at 00:24, 14 May 2015

2015-05-14T00:24:39Z

← Older revision		Revision as of 00:24, 14 May 2015
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	All attendees should bring a government-issued ID such as a driver’s license, and arrive at least 30 minutes early to pass through security collect coffee/drinks before settling in. Attendees can expect to have purses, computers, and luggage scanned and potentially searched.		All attendees should bring a government-issued ID such as a driver’s license, and arrive at least 30 minutes early to pass through security collect coffee/drinks before settling in. Attendees can expect to have purses, computers, and luggage scanned and potentially searched.

	~~== Participation ==~~

	~~'''Space is now at capacity on both days of this meeting.''' Access via webex is as follows:~~

	~~Day 1: https://cbiit.webex.com/cbiit/onstage/g.php?d=732232676&t=a~~
	~~: Event number: 732 232 676~~
	~~: Event password: 1234Abcd!~~
	~~: Enter your phone number for a call back option, or dial 1-855-244-8681, access code 732 232 676.~~

	~~Day 2: https://cbiit.webex.com/cbiit/onstage/g.php?d=734433118&t=a~~
	~~: Event number: 734 433 118~~
	~~: Event password: 1234Abcd!~~
	~~: Enter your phone number for a call back option, or dial 1-855-244-8681, access code 734 433 118.~~

	~~Information for instance regarding service interruptions will always be posted here.~~

	~~[[Hotels]]~~

	==Session 1: Addressing cancer big data challenges through imaging ontologies==		==Session 1: Addressing cancer big data challenges through imaging ontologies==

Phismith: /* Session 3: Cancer big data and the Ontology of Disease: Addressing Cancer Big Data Challenges */

2015-05-14T00:23:22Z

Session 3: Cancer big data and the Ontology of Disease: Addressing Cancer Big Data Challenges

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	<u>'''Roles of Ontologies in Cancer Big Data'''</u>		<u>'''Roles of Ontologies in Cancer Big Data'''</u>

	9:00 '''Larry Wright (NCI Enterprise Vocabulary Services):''' NCI Thesaurus and Enterprise Vocabulary Services: Resources for Cancer Research		9:00 '''Larry Wright (NCI Enterprise Vocabulary Services):''' NCI Thesaurus and Enterprise Vocabulary Services: Resources for Cancer Research [http://ncor.buffalo.edu/2015/NCI/Wright.pptx Slides]

	9:15 '''Lynn Schriml (University of Maryland Baltimore):''' The Human Disease Ontology: DO_cancer_slim - a unified representation of cancer disease terms [http://ncor.buffalo.edu/2015/NCI/Schriml.pptx Slides]		9:15 '''Lynn Schriml (University of Maryland Baltimore):''' The Human Disease Ontology: DO_cancer_slim - a unified representation of cancer disease terms [http://ncor.buffalo.edu/2015/NCI/Schriml.pptx Slides]

Phismith: /* Session 3: Cancer big data and the Ontology of Disease: Addressing Cancer Big Data Challenges */

2015-05-14T00:11:50Z

Session 3: Cancer big data and the Ontology of Disease: Addressing Cancer Big Data Challenges

← Older revision		Revision as of 00:11, 14 May 2015
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	<u>'''Roles of Ontologies in Cancer Big Data'''</u>		<u>'''Roles of Ontologies in Cancer Big Data'''</u>

	9:00 '''Larry Wright (NCI Enterprise Vocabulary Services):''' NCI Thesaurus and Enterprise Vocabulary Services: Resources for Cancer Research		9:00 '''Larry Wright (NCI Enterprise Vocabulary Services):''' NCI Thesaurus and Enterprise Vocabulary Services: Resources for Cancer Research

	9:15 '''Lynn Schriml (University of Maryland Baltimore):''' The Human Disease Ontology: DO_cancer_slim - a unified representation of cancer disease terms		9:15 '''Lynn Schriml (University of Maryland Baltimore):''' The Human Disease Ontology: DO_cancer_slim - a unified representation of cancer disease terms [http://ncor.buffalo.edu/2015/NCI/Schriml.pptx Slides]

	9:30 '''Ada Hamosh (Hopkins):''' OMIM		9:30 '''Ada Hamosh (Hopkins):''' OMIM [http://ncor.buffalo.edu/2015/NCI/Hamosh.pptx Slides]

	9:45 '''Olivier Bodenreider (NLM):''' Oncology in SNOMED CT [http://ncor.buffalo.edu/2015/NCI/Bodenreider.pptx Slides]		9:45 '''Olivier Bodenreider (NLM):''' Oncology in SNOMED CT [http://ncor.buffalo.edu/2015/NCI/Bodenreider.pptx Slides]
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	10:30 '''Raja Mazumder (George Washington University):''' The need for cancer disease ontology for pan-cancer data integration and analysis. [http://ncor.buffalo.edu/2015/NCI/Maxumder.pptx Slides]		10:30 '''Raja Mazumder (George Washington University):''' The need for cancer disease ontology for pan-cancer data integration and analysis. [http://ncor.buffalo.edu/2015/NCI/Maxumder.pptx Slides]

	10:45 '''Susan Mockus (The Jackson Laboratory, Genomic Medicine):''' Using the Disease Ontology to Translate Pathology Reports to NGS Clinical Reports		10:45 '''Susan Mockus (The Jackson Laboratory, Genomic Medicine):''' Using the Disease Ontology to Translate Pathology Reports to NGS Clinical Reports [http://ncor.buffalo.edu/2015/NCI/Mockus.pptx Slides]

	11:00 '''Peter Elkin (University at Buffalo):''' Ontology-based cancer biomarker discovery		11:00 '''Peter Elkin (University at Buffalo):''' Ontology-based cancer biomarker discovery

Phismith: /* Session 3: Cancer big data and the Ontology of Disease: Addressing Cancer Big Data Challenges */

2015-05-13T23:52:53Z

Session 3: Cancer big data and the Ontology of Disease: Addressing Cancer Big Data Challenges

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	9:30 '''Ada Hamosh (Hopkins):''' OMIM		9:30 '''Ada Hamosh (Hopkins):''' OMIM

	9:45 '''Olivier Bodenreider (NLM):''' Oncology in SNOMED CT		9:45 '''Olivier Bodenreider (NLM):''' Oncology in SNOMED CT [http://ncor.buffalo.edu/2015/NCI/Bodenreider.pptx Slides]

	10:00 Break		10:00 Break
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	'''<u>The Role of Ontology in Cancer Big Data Use Cases</u>'''		'''<u>The Role of Ontology in Cancer Big Data Use Cases</u>'''

	10:15 '''Lindsay Cowell (UT Southwestern):''' HPV and cervical cancer data in Electronic Health Records -- A Big Data challenge		10:15 '''Lindsay Cowell (UT Southwestern):''' HPV and cervical cancer data in Electronic Health Records -- A Big Data challenge [http://ncor.buffalo.edu/2015/NCI/Cowell.pptx Slides]
	:what types of data do we need to represent? HPV and cervical cancer and the Infectious Disease Ontology; challenges involved in keeping and using large collections of samples and of sample data		:what types of data do we need to represent? HPV and cervical cancer and the Infectious Disease Ontology; challenges involved in keeping and using large collections of samples and of sample data

	10:30 '''Raja Mazumder (George Washington University):''' The need for cancer disease ontology for pan-cancer data integration and analysis.		10:30 '''Raja Mazumder (George Washington University):''' The need for cancer disease ontology for pan-cancer data integration and analysis. [http://ncor.buffalo.edu/2015/NCI/Maxumder.pptx Slides]

	10:45 '''Susan Mockus (The Jackson Laboratory, Genomic Medicine):''' Using the Disease Ontology to Translate Pathology Reports to NGS Clinical Reports.		10:45 '''Susan Mockus (The Jackson Laboratory, Genomic Medicine):''' Using the Disease Ontology to Translate Pathology Reports to NGS Clinical Reports

	11:00 '''Peter Elkin (University at Buffalo):''' Ontology-based cancer biomarker discovery		11:00 '''Peter Elkin (University at Buffalo):''' Ontology-based cancer biomarker discovery

Phismith: /* Public Session: Cancer Big Data to Knowledge */

2015-05-13T23:39:03Z

Public Session: Cancer Big Data to Knowledge

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	13:00 '''Mark Musen (Stanford / NCBO)''': [http://metadatacenter.org CEDAR]: Making it Easier to Use Ontologies to Author Clinical Metadata [http://ncor.buffalo.edu/2015/NCI/Musen.pdf Slides]		13:00 '''Mark Musen (Stanford / NCBO)''': [http://metadatacenter.org CEDAR]: Making it Easier to Use Ontologies to Author Clinical Metadata [http://ncor.buffalo.edu/2015/NCI/Musen.pdf Slides]

	13:40 '''Judith Blake (GO / Jackson Lab)''': The Impact of Ontologies on Comparative Genomics for Cancer: The Human-Mouse Connection		13:40 '''Judith Blake (GO / Jackson Lab)''': The Impact of Ontologies on Comparative Genomics for Cancer: The Human-Mouse Connection [http://ncor.buffalo.edu/2015/NCI/Blake.pptx Slides]

	14:20 '''Cathy Wu (University of Delaware / PRO)''': Ontology and the [http://www.nejm.org/doi/full/10.1056/NEJMp1500523#t=article Precision Medicine Initiative]: The Role of the Protein Ontology in Cancer Knowledge Network Discovery		14:20 '''Cathy Wu (University of Delaware / PRO)''': Ontology and the [http://www.nejm.org/doi/full/10.1056/NEJMp1500523#t=article Precision Medicine Initiative]: The Role of the Protein Ontology in Cancer Knowledge Network Discovery [http://ncor.buffalo.edu/2015/NCI/Wu.pptx Slides]

	14:50 '''Sherri de Coronado (NIH / NCI)''': The importance of Semantics in NCI Efforts to Achieve Precision Oncology		14:50 '''Sherri de Coronado (NIH / NCI)''': The importance of Semantics in NCI Efforts to Achieve Precision Oncology [http://ncor.buffalo.edu/2015/NCI/de-Coronado.ppt Slides]

	== Sponsors ==		== Sponsors ==

Phismith: /* Participants */

2015-05-13T18:59:38Z

Participants

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	*Jonathan Bona (PRO / Buffalo)		*Jonathan Bona (PRO / Buffalo)
	*William Bone (NIH/NHGRI)		*William Bone (NIH/NHGRI)
	*Philip E. Bourne (NIH / ADDS)
	*Gully Burns (Information Sciences Institute, University of Southern California)		*Gully Burns (Information Sciences Institute, University of Southern California)
	*Kisha Coa (NIH/NCI)		*Kisha Coa (NIH/NCI)
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	*Hong Yu (University of Massachusetts, Worcester)		*Hong Yu (University of Massachusetts, Worcester)
	*Shadia Zaman (FDA)		*Shadia Zaman (FDA)
	*Wenjin J. Zheng (Center for Computational Biomedicine, University of Texas at Houston)

Phismith: /* Public Session: Cancer Big Data to Knowledge */

2015-05-13T18:59:05Z

Public Session: Cancer Big Data to Knowledge

← Older revision		Revision as of 18:59, 13 May 2015
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	13:00 '''Mark Musen (Stanford / NCBO)''': [http://metadatacenter.org CEDAR]: Making it Easier to Use Ontologies to Author Clinical Metadata [http://ncor.buffalo.edu/2015/NCI/Musen.pdf Slides]		13:00 '''Mark Musen (Stanford / NCBO)''': [http://metadatacenter.org CEDAR]: Making it Easier to Use Ontologies to Author Clinical Metadata [http://ncor.buffalo.edu/2015/NCI/Musen.pdf Slides]

	14:00 '''Judith Blake (GO / Jackson Lab)''': The Impact of Ontologies on Comparative Genomics for Cancer: The Human-Mouse Connection		13:40 '''Judith Blake (GO / Jackson Lab)''': The Impact of Ontologies on Comparative Genomics for Cancer: The Human-Mouse Connection

	14:30 '''Cathy Wu (University of Delaware / PRO)''': Ontology and the [http://www.nejm.org/doi/full/10.1056/NEJMp1500523#t=article Precision Medicine Initiative]: The Role of the Protein Ontology in Cancer Knowledge Network Discovery		14:20 '''Cathy Wu (University of Delaware / PRO)''': Ontology and the [http://www.nejm.org/doi/full/10.1056/NEJMp1500523#t=article Precision Medicine Initiative]: The Role of the Protein Ontology in Cancer Knowledge Network Discovery

	15:00 '''Sherri de Coronado (NIH / NCI)''': The importance of Semantics in NCI Efforts to Achieve Precision Oncology		14:50 '''Sherri de Coronado (NIH / NCI)''': The importance of Semantics in NCI Efforts to Achieve Precision Oncology

	== Sponsors ==		== Sponsors ==

Phismith: /* Public Session: Cancer Big Data to Knowledge */

2015-05-13T18:28:47Z

Public Session: Cancer Big Data to Knowledge

← Older revision		Revision as of 18:28, 13 May 2015
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	==Public Session: Cancer Big Data to Knowledge==		==Public Session: Cancer Big Data to Knowledge==

	13:00 ~~'''Philip E. Bourne (NIH / ADDS)''': The NIH Big Data Strategy~~		13:00 '''Mark Musen (Stanford / NCBO)''': [http://metadatacenter.org CEDAR]: Making it Easier to Use Ontologies to Author Clinical Metadata [http://ncor.buffalo.edu/2015/NCI/Musen.pdf Slides]

	~~13:30~~ '''Mark Musen (Stanford / NCBO)''': [http://metadatacenter.org CEDAR]: Making it Easier to Use Ontologies to Author Clinical Metadata

	14:00 '''Judith Blake (GO / Jackson Lab)''': The Impact of Ontologies on Comparative Genomics for Cancer: The Human-Mouse Connection		14:00 '''Judith Blake (GO / Jackson Lab)''': The Impact of Ontologies on Comparative Genomics for Cancer: The Human-Mouse Connection