Difference between revisions of "Ontology and Cellular Networks"
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*1. to provide an introduction to the basic tools and methods of ontology | *1. to provide an introduction to the basic tools and methods of ontology | ||
*2. to take the first steps towards developing an ontology of cellular networks. | *2. to take the first steps towards developing an ontology of cellular networks. | ||
| − | *3. to address alternative approaches to ontology construction, with an emphasis on statistical vs. manual approaches | + | *3. to address alternative approaches to ontology construction, with an emphasis on statistical/NLP vs. manual approaches |
*4. to foster networking between ontology developer groups in the field of biomedical informatics | *4. to foster networking between ontology developer groups in the field of biomedical informatics | ||
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* 8.30am Registration and Continental Breakfast | * 8.30am Registration and Continental Breakfast | ||
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| + | '''Ontology of Cellular Networks: Some Basic Ingredients''' | ||
* Moderator: Peter Lyster (NIH/NIGMS) | * Moderator: Peter Lyster (NIH/NIGMS) | ||
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| − | + | * 9am Participant Self-Introductions | |
| + | * 9.15am Barry Smith (NCBO, Buffal): What is a Network? | ||
| + | * 9.45am Lindsay Cowell (Duke): The Cell Ontology | ||
| + | * 10.15am Coffee | ||
| + | * 10.45am Chris Mungall (NCBO, Berkeley): Representing Relations: The Methodology of Cross-Products | ||
| + | * 11.15am BioPAX/Reactome/TBD | ||
* 12.45pm Lunch Break | * 12.45pm Lunch Break | ||
| − | '' | + | ''Afternoon'' |
| − | * Moderator: | + | '''Constructing an Ontology of Cellular Networks''' |
| − | + | * Moderator: Alan Ruttenberg (Science Commons / Semantic Web HCLSIG) | |
| − | + | ||
| − | + | This will be an interactive hands-on session, in which data annotation needs will be presented on the basis of which the attempt will be made to construct the beginnings of a cellular network ontology. | |
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'''Wednesday October 31''' | '''Wednesday October 31''' | ||
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*8.30am Continental Breakfast | *8.30am Continental Breakfast | ||
| − | ''' | + | '''Ontology of Cellular Networks: Alternative Approaches''' |
| − | * Moderator: | + | * Moderator: Michael Ashburner (Cambridge) |
| − | * | + | * 9.00am Aris Floratos (MAGNET, Columbia University): BISON - The Bioinformatics Interface Structured Ontology |
| − | *10.30am Coffee | + | * 9.30pm Balaji S. Srinivasan (Stanford): Automatic Population of a Network Ontology |
| − | *11.00am | + | * 10.00am |
| + | * 10.30am Coffee | ||
| + | * 11.00am Yves Lussier (Chicago): Integrating the Cell Ontology with other Ontologies and with Text - Bridging the Modeling Gap | ||
| + | * 11.30am Discussion on Statistical/NLP vs. Manual Approaches to Ontology Construction | ||
| − | + | ||
*12.45pm Lunch Break | *12.45pm Lunch Break | ||
| − | ''' | + | ''Afternoon'' |
| − | * | + | '''Ontology of Cellular Networks: The Next Steps''' |
| − | + | * Moderator: Suzanna Lewis (NCBO, Berkeley) | |
| − | + | ||
| + | Session starts at 2pm | ||
| + | |||
== Participants (Provisional List) == | == Participants (Provisional List) == | ||
Revision as of 06:45, 12 September 2007
General Information
The National Center for Biomedical Ontology will host a two-day workshop focused on ontology and cellular networks on October 30-31, 2007 in Newark, NJ.
Goals
The goals of this workshop are:
- 1. to provide an introduction to the basic tools and methods of ontology
- 2. to take the first steps towards developing an ontology of cellular networks.
- 3. to address alternative approaches to ontology construction, with an emphasis on statistical/NLP vs. manual approaches
- 4. to foster networking between ontology developer groups in the field of biomedical informatics
Agenda
Tuesday October 30
Morning
- 8.30am Registration and Continental Breakfast
Ontology of Cellular Networks: Some Basic Ingredients
- Moderator: Peter Lyster (NIH/NIGMS)
- 9am Participant Self-Introductions
- 9.15am Barry Smith (NCBO, Buffal): What is a Network?
- 9.45am Lindsay Cowell (Duke): The Cell Ontology
- 10.15am Coffee
- 10.45am Chris Mungall (NCBO, Berkeley): Representing Relations: The Methodology of Cross-Products
- 11.15am BioPAX/Reactome/TBD
- 12.45pm Lunch Break
Afternoon
Constructing an Ontology of Cellular Networks
- Moderator: Alan Ruttenberg (Science Commons / Semantic Web HCLSIG)
This will be an interactive hands-on session, in which data annotation needs will be presented on the basis of which the attempt will be made to construct the beginnings of a cellular network ontology.
Wednesday October 31
Morning
- 8.30am Continental Breakfast
Ontology of Cellular Networks: Alternative Approaches
- Moderator: Michael Ashburner (Cambridge)
- 9.00am Aris Floratos (MAGNET, Columbia University): BISON - The Bioinformatics Interface Structured Ontology
- 9.30pm Balaji S. Srinivasan (Stanford): Automatic Population of a Network Ontology
- 10.00am
- 10.30am Coffee
- 11.00am Yves Lussier (Chicago): Integrating the Cell Ontology with other Ontologies and with Text - Bridging the Modeling Gap
- 11.30am Discussion on Statistical/NLP vs. Manual Approaches to Ontology Construction
- 12.45pm Lunch Break
Afternoon Ontology of Cellular Networks: The Next Steps
- Moderator: Suzanna Lewis (NCBO, Berkeley)
Session starts at 2pm
Participants (Provisional List)
Robert Arp - NCBO, Buffalo, NY
Michael Ashburner - NCBO, Cambridge University Department of Genetics
Ed Barbour - Rockefeller University
Kei Cheung - Yale, CT
Lindsay Cowell - Duke University
Nick Khazanov - Rockefeller University
Natasha Lenkova - Rockefeller University
Suzanna Lewis - NCBO, Berkeley, CA
Peter Lyster - NIH/NIGMS
Yves Lussier - MagNet, University of Chicago, IL
Avi Ma'ayan - Department of Pharmacology & Systems Therapeutics, Mount Sinai School of Medicine
Chris Mungall -- NCBO, Berkeley, CA
Alan Ruttenberg - Science Commons, Boston, MA
Nigam Shah - NCBO, Stanford, CA
Karen Skinner - NIH/NIDA
Barry Smith - NCBO, Buffalo, NY
Balaji S. Srinivasan - PharmGKB, Stanford, CA
David States - NCIBI, University of Michigan
Ross Whitaker - NA-MIC, Utah
Venue
Hilton Hotel Newark Airport A block of rooms has been set aside for early registrants.
Links
National Centers for Biomedical Computing