ImmPort: Difference between revisions

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'''[[ImmPort]]: A Guide for Submitters'''
'''Training and Strategy Workshop for [[ImmPort]] Data Submitters'''


'''Date:''' October 9-10, 2013
'''Date:''' October 9-10, 2013
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'''Venue:''' Alpha-Beta Room, [http://www.rhoworld.com/rho/federal-research Rho Federal Systems Division] (6330 Quadrangle Dr. Suite 500, Chapel Hill, NC 27517)
'''Venue:''' Alpha-Beta Room, [http://www.rhoworld.com/rho/federal-research Rho Federal Systems Division] (6330 Quadrangle Dr. Suite 500, Chapel Hill, NC 27517)


'''Parking and Security:''' Non-Rho attendees can park anywhere, although there are visitor parking spaces near the front door. You need to check into the front desk where they will receive a name tag and be escorted to the room where we will be meeting.  People who are traveling and have luggage with them have the option of leaving items in a locked closet during the meeting.
'''Parking and Security:''' Non-Rho attendees can park anywhere, although there are visitor parking spaces near the front door. You need to check into the front desk where you will receive a name tag and be escorted to the room where we will be meeting.  People who are traveling and have luggage with them have the option of leaving items in a locked closet during the meeting.


'''Goals of this meeting:'''  
'''Goals of this meeting:'''  
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----
----
'''Draft Schedule'''  
'''Schedule'''  
*All participants should feel free to propose additional topics for discussion by writing to [mailto:phismith@buffalo.edu Barry Smith]


<u>'''Day 1: Wednesday, October 9'''</u>
<u>'''Day 1: Wednesday, October 9'''</u>
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9:00 David Ikle (Rho Federal): '''Database Creation and Data Analysis Processes at Rho Federal'''
9:00 David Ikle (Rho Federal): '''Database Creation and Data Analysis Processes at Rho Federal'''


9:30 Barry Smith : '''A Practical Introduction to ImmPort and to NIH Mandates for Data Sharing and Reuse'''
9:30 Barry Smith : '''A Practical Introduction to ImmPort and to NIH Mandates for Data Sharing and Reuse''' [http://ncor.buffalo.edu/2013/Rho/Smith-Rho.pptx Slides]
:-- overview of the goals of ImmPort  
:-- overview of the goals of ImmPort  
:-- role of standards and ontologies (1) for data submission (2) for data reuse
:-- role of standards and ontologies (1) for data submission (2) for data reuse
:-- successes and failures we can learn from
:-- successes and failures we can learn from


10:00 Anna Maria Masci (Duke University): The ImmPort Submission Process. A View From Biology  
10:00 Anna Maria Masci (Duke University): '''The ImmPort Submission Process. A View From Biology''' [http://ncor.buffalo.edu/2013/Rho/MASCIAM.pptx Slides]
 
Masci: '''Which Standards Do We Need For Data Analysis''' [http://ncor.buffalo.edu/2013/Rho/Masci-standards.pptx Slides]


10:30 Break
10:30 Break


10:45 Discussion leader: Barry Smith
10:45 Herman Mitchell and Jeremy Wildire: '''NIAID Asthma Consortium Facilitated Data Explorer'''
 
11:00 Discussion leader: Barry Smith
:Brainstorming on  
:Brainstorming on  
:-- existing data management strategies and software tools to enhance data submission
:-- existing data management strategies and software tools to enhance data submission
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12:00 Lunch
12:00 Lunch


13:00 Jeff Wiser (ImmPort / Northrop Grumman): Training session on submitting data to immPort
13:00 Jeff Wiser (ImmPort / Northrop Grumman): '''Training session on submitting data to immPort
:-- the need to grow ImmPort's clinical submission area
:-- the need to grow ImmPort's clinical submission area


14:30 Break
14:30 Break


15:00 John Lim and Karen Kesler: The ImmPort Submission Process: Two Views from Rho
15:00 John Lim and Karen Kesler (Rho): '''The ImmPort Submission Process: Two Views from Rho'''
 
15:30 Jeff Abolafia (Rho): '''CDISC, C-DASH, SDTM, ADM'''


16:00 Discussion leader: Jeff Wiser  
16:00 Discussion leader: Jeff Wiser  
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8:00 Breakfast
8:00 Breakfast


8:30 Barry Smith: Initiating a consensus process for creating useful and usable standards and software approaches which will enhance the ImmPort submission process and guarantee discoverability
8:30 Lindsay Cowell: '''Immunology Ontologies''' [http://ncor.buffalo.edu/2013/Rho/Cowell-Rho.ppt Slides]


8:45 Tasking of break-out groups
9:45 Barry Smith: '''Introduction to Allergy Ontology''' [http://ncor.buffalo.edu/2013/Rho/Smith-Allergy.ppt Slides]
:the standards should be easy to use by ImmPort submitters,
:should be recommendable for incorporation into data
management resources (for instance CTMSs);
:be compatible with or derived from existing standards


9:00 Break-Out Groups (possible areas -- final division to be determined on the basis of user requests):
10:45 Break
:disease areas (allergy / asthma / transplantation / auto-immune diseases / ...)
:datatypes (clinical observations / mechanistic assays / ...)
:technical strategies (CTMS / ...)
:FDA and other standards (CDISC / ... )
:discoverability: what kind of data would you like to find in ImmPort and how would you search for it?


Each break-out group will
11:00 '''Who will be the users of ImmPort? / Next steps'''
:-- review existing standards and software in these areas
:-- identify future needs and strategies


11:45 Report back and discuss next steps
12:00 Close


12:30 Lunch / Close
[http://ncor.buffalo.edu/2013/Rho/Smith-Summary.pptx Slides summarizing results]


----
External participants


----
Break-Out Group Leaders and Presenters:
:[http://profiles.utsouthwestern.edu/profile/120432/lindsay-cowell.html Lindsay Cowell] is a computational immunologist at UT Southwestern
:[http://profiles.utsouthwestern.edu/profile/120432/lindsay-cowell.html Lindsay Cowell] is a computational immunologist at UT Southwestern
:[http://www.linkedin.com/profile/view?id=41459681&trk=nav_responsive_tab_profile Anna Maria Masci] is in charge of submission of data to ImmPort for the Multiscale System Immunology project
:[http://www.linkedin.com/profile/view?id=41459681&trk=nav_responsive_tab_profile Anna Maria Masci] is in charge of submission of data to ImmPort for the Multiscale System Immunology project
:[http://ontology.buffalo.edu/smith/ Barry Smith] is ImmPort ontology lead.
:[http://ontology.buffalo.edu/smith/ Barry Smith] is ImmPort ontology lead.
:[http://www.linkedin.com/pub/ravi-shankar/4/b17/b52 Ravi Shankar] is a researcher in the Atul Butte Lab at Stanford working on clinical trial ontology
:[http://www.linkedin.com/profile/view?id=6635310&authType=NAME_SEARCH&authToken=vXQ9&locale=en_US&srchid=27153661377103222322&srchindex=1&srchtotal=10&trk=vsrp_people_res_name&trkInfo=VSRPsearchId%3A27153661377103222322%2CVSRPtargetId%3A6635310%2CVSRPcmpt%3Aprimary Jeff Wiser] manages the ImmPort project at Northrop Grumman.
:[http://www.linkedin.com/profile/view?id=6635310&authType=NAME_SEARCH&authToken=vXQ9&locale=en_US&srchid=27153661377103222322&srchindex=1&srchtotal=10&trk=vsrp_people_res_name&trkInfo=VSRPsearchId%3A27153661377103222322%2CVSRPtargetId%3A6635310%2CVSRPcmpt%3Aprimary Jeff Wiser] manages the ImmPort project at Northrop Grumman.
:[http://www.zoominfo.com/p/Ashley-Xia/1208415813 Ashley Xia] is the NIH Program Officer overseeing the creation of the ImmPort portal and Immune Epitope Database (IEDB).

Latest revision as of 18:19, 17 October 2013

Training and Strategy Workshop for ImmPort Data Submitters

Date: October 9-10, 2013

Venue: Alpha-Beta Room, Rho Federal Systems Division (6330 Quadrangle Dr. Suite 500, Chapel Hill, NC 27517)

Parking and Security: Non-Rho attendees can park anywhere, although there are visitor parking spaces near the front door. You need to check into the front desk where you will receive a name tag and be escorted to the room where we will be meeting. People who are traveling and have luggage with them have the option of leaving items in a locked closet during the meeting.

Goals of this meeting:

  • to provide assistance to actual and potential submitters of data to ImmPort: how to make submission more intuitive and more efficient?
  • to enable interaction between submitters and those charged with managing and improving ImmPort in order to identify problems and opportunities for improvement
  • to improve extraction of data from ImmPort: how can we make ImmPort data more easily discoverable and more useful to researchers?

Schedule

Day 1: Wednesday, October 9

8:00 Breakfast

8:45 Barry Smith (ImmPort / University at Buffalo): Opening Remarks

8:50 Participant Self-Introductions

9:00 David Ikle (Rho Federal): Database Creation and Data Analysis Processes at Rho Federal

9:30 Barry Smith : A Practical Introduction to ImmPort and to NIH Mandates for Data Sharing and Reuse Slides

-- overview of the goals of ImmPort
-- role of standards and ontologies (1) for data submission (2) for data reuse
-- successes and failures we can learn from

10:00 Anna Maria Masci (Duke University): The ImmPort Submission Process. A View From Biology Slides

Masci: Which Standards Do We Need For Data Analysis Slides

10:30 Break

10:45 Herman Mitchell and Jeremy Wildire: NIAID Asthma Consortium Facilitated Data Explorer

11:00 Discussion leader: Barry Smith

Brainstorming on
-- existing data management strategies and software tools to enhance data submission
-- how to make your data discoverable and useable by external researchers

12:00 Lunch

13:00 Jeff Wiser (ImmPort / Northrop Grumman): Training session on submitting data to immPort

-- the need to grow ImmPort's clinical submission area

14:30 Break

15:00 John Lim and Karen Kesler (Rho): The ImmPort Submission Process: Two Views from Rho

15:30 Jeff Abolafia (Rho): CDISC, C-DASH, SDTM, ADM

16:00 Discussion leader: Jeff Wiser

Brainstorming on identifying pain points in submission and on strategies for improvement

Evening: Dinner


Day 2: Thursday, October 9

8:00 Breakfast

8:30 Lindsay Cowell: Immunology Ontologies Slides

9:45 Barry Smith: Introduction to Allergy Ontology Slides

10:45 Break

11:00 Who will be the users of ImmPort? / Next steps

12:00 Close

Slides summarizing results

External participants

Lindsay Cowell is a computational immunologist at UT Southwestern
Anna Maria Masci is in charge of submission of data to ImmPort for the Multiscale System Immunology project
Barry Smith is ImmPort ontology lead.
Ravi Shankar is a researcher in the Atul Butte Lab at Stanford working on clinical trial ontology
Jeff Wiser manages the ImmPort project at Northrop Grumman.
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