NCBO Wiki - User contributions [en]

Ontologies for Biomedicine – How to make and use them

2011-12-16T03:21:47Z

JoanneLuciano:

When: July 21, 2007
Where: [http://www.iscb.org/ismbeccb2007/ ISMB 2007], Vienna, Austria
What: Tutorial on Ontologies for Biomedicine – How to make and use them
Faculty: [http://bmir.stanford.edu/people/view.php/nigam_h_shah Nigam Shah] (Stanford), [http://ontology.buffalo.edu/smith Barry Smith] (Buffalo)

'''Brief:''' The tutorial provides an overview of current uses of ontologies in bioinformatics, instruction on ontology development using OWL, and an outline of principles of good ontology design. It comprises an interactive session devoted to developing an ontology, and a session illustrating how good design practices effect the usefulness of ontologies in molecular biology.

'''Tutorial level:''' Introductory/Intermediate

'''Prior knowledge required:''' Participants should be at least aware of ontologies such as the Gene Ontology and BioPAX. Familiarity with basic biology terms such as genes, proteins, promoter, intron and exon is required.

'''Abstract:''' Ontologies are becoming essential with the rapid increase in the quantities and types of data we need to handle in the molecular biology domain. Simultaneously, the need to organise, co-ordinate and disseminate ontologies as well as coherent ontology development methods is now accepted and is evidenced by the funding of the National Center for Biomedical Ontology (NCBO). Though the need to use ontologies is widely appreciated, the right manner in which they should be developed and applied is not well understood. Researchers still resort to ad hoc methods in developing and using ontologies, with the result that many opportunities for integration and cross-disciplinary communication are lost, and many obstacles to cross-domain reasoning are created.
This tutorial will provide an overview of the various ways in which ontologies are used in bioinformatics and biomedicine, along with pointers to innovative applications of ontologies such as to validate pathway data and enable cross-database reasoning. It will educate the participants on what ontologies are and in how they are currently used in molecular biology. It will provide guidance on how to create ontologies using OWL and on best practices for ontology development and use.
This tutorial will be aimed at advanced graduate students and active researchers who need to understand the basic principles underlying ontology development in order to use ontologies more effectively for interpreting their own data (for example interpreting microarray data using the Gene Ontology or pathway information from Reactome). It will be of value, too, to researchers who need to participate in ontology development efforts in their scientific respective communities.

Download the [[Media:ISMB_2007_Handout.pdf|handout]]
See the [[Media:ISMB_2007_Final.ppt|slides]]
----

==Overview of current applications of ontologies in bioinformatics==
* As a controlled vocabulary to annotate genes and gene products (e.g The Gene Ontology)
* As a data exchange format and for data integration (e.g. MGED, SBML and BioPAX)
* To define a knowledgebase schema (e.g. BioCyc and Reactome)
* For driving natural language processing (e.g. Textpresso and Geneways)
* For semantically rich querying of federated databases (e.g. TAMBIS)
* Creating formal representations of biological processes for hypothesis evaluation (e.g. HyBrow)

==Ontologies – What they are and what they are not==
* We will discuss “ontology” as understood in philosophy, computer science and information science to explain how the computer/information science meanings are different - but related to - the philosophical meaning of ontology. In practice, ontologies provide standardized labels which are used to annotate different experimental data. We will discuss the implications of this annotation-based view of ontology to clarify the difference between terminologies, taxonomies, application ontologies and reference ontologies.

==Building ontologies using OWL==
* We will provide an overview of the various constructs available in OWL and of how they can be used to represent biomedical knowledge in an ontology
* We will demonstrate an example of how DL-reasoners can be used to verify ontologies created in OWL and how such reasoning will help in reducing errors in biomedical ontologies.
* We will provide indications of some of the problems facing ontology developers using OWL in the bioinformatics domain, and offer solutions to these problems.

==Interactive session: developing a small ontology==
This session will consist of an audience-driven discussion with the goal of developing an ontology to represent DNA sequences. We will focus on the task of representing relationships between introns, exons, start sites, promoters, genes and chromosomes. (We have used this topic before and have found that it is accessible to participants with a wide background and has enough complexity that a large fraction of the common mistakes do happen)

==The do’s and don’ts of ontology creation (highlight common mistakes and recommended design strategies)==
* We will describe the key principles of ontology design that address the most common sources of mistakes in biomedical ontologies.
* We will present rules of thumb for good ontology design, along with examples of how they will enhance the quality of the resulting ontologies. We will also outline the guiding principles of the OBO Foundry, and describe how they can enable cross-ontology reasoning.

==Wrap up question and answers with discussion==

Total time = 3.5 hours [2 sessions of 105 minutes each] + 30 min break

Networks

2008-03-28T18:20:53Z

JoanneLuciano: /* Confirmed Participants */

== Workshop on Ontologies of Cellular Networks ==

This NCBO workshop is organized by Yves Lussier (Chicago/MAGNet), Alan Ruttenberg (Neurocommons) and Barry Smith (Buffalo/NCBO). It is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics].

'''THIS EVENT IS NOW FULLY SUBSCRIBED.'''

== Goals ==
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on ontologies of cellular networks.

The goals of this workshop are:

*1. to provide an introduction to the basic tools and methods of ontology
*2. to foster networking of, and enhanced coordination between, those groups already working on ontologies of cellular networks
*3. to identify problems which must be solved if ontology methods are to be extended to represent biological mechanisms in greater detail
*4. to promote further ontology development in this area with the goal of accelerating our ability to understand basic biological phenomena and to leverage experimental data

Potential topics for discussion include:

*signalling pathways
*metabolic pathways
*regulatory networks
*interaction networks
*gene expression correlation networks
*physiological networks
*neurocurrent networks

== Agenda ==

'''Thursday, March 27, 2008'''

* 9:00am Registration and Continental Breakfast

* 9:30am Participant Self-Introductions

* 10:00am '''Session 1 - Biology of Pathways and Networks (Moderator: Yves Lussier)'''

::Chris Sander: Pathways and Networks: An Overview of the Science
::Nancy Gough: [http://ontology.buffalo.edu/08/networks/Gough.ppt Challenges to Representing Pathways]

* 11:00am Refreshment Break

* 11:15am (Session 1, continued)

::Richard Scheuermann: [http://ontology.buffalo.edu/08/networks/Scheuermann.ppt Biological Network Analysis and Representational Implications]
::Yves Lussier: [http://ontology.buffalo.edu/08/networks/Lussier.pdf Resources for Multiscale Analysis of Cellular Networks and ECM]

* 12:30pm Lunch Break

* 1:30pm '''Session 2 - Introduction to Ontology (Moderator: Barry Smith)'''

::Barry Smith: [http://ontology.buffalo.edu/08/networks/smith.ppt An Introduction to Biomedical Ontology]
::Lindsay Cowell: [http://ontology.buffalo.edu/08/networks/cowell.ppt Using Ontologies to Represent Immunological Networks]
::Jose L. V. Mejino, Jr.: [http://ontology.buffalo.edu/08/networks/mejino.ppt The Foundational Model of Anatomy (FMA) Ontology: Framework for Cellular and Subcellular Anatomy]

* 3:30pm Refreshment Break
* 3:45pm '''Session 3 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg)

::Nigam Shah: [http://ontology.buffalo.edu/08/networks/Shah.ppt Computations using pathways and networks]
::Andrea Splendini: [http://ontology.buffalo.edu/08/networks/Splendiani.pdf Using BioPAX Computationally]

* 5:00pm End of Day 1

'''Friday, March 28, 2008'''

* 8:30am Continental Breakfast

* 9:00am Session 4: '''Current Approaches to Pathway and Network Ontologies (Moderator: Richard Scheuermann)'''

::Markus Krummenacker: [http://ontology.buffalo.edu/08/networks/krummenacker.ppt The BioCyc Ontologies]
::Ken Fukuda: [http://ontology.buffalo.edu/08/networks/fukuda.pdf The INOH Pathway Database: Curation, Annotation, Integration]
::Erick Antezana: [http://ontology.buffalo.edu/08/networks/Antezana.ppt The Cell Cycle Ontology]

* 10:30am Refreshment Break
* 10:45am (Session 4, continued)

::Peter D'Eustachio and Gopal Gopinathrao: [http://ontology.buffalo.edu/08/networks/Gopinathrao.ppt Representing Biological Processes: The Reactome Database]
::Darren Natale: [http://ontology.buffalo.edu/08/networks/Natale.ppt Protein Ontology: Addressing the Need for Precision in Representing Protein Networks]

* 12.30pm Lunch Break

* 1:30pm '''Session 5 - Gaps in Pathway and Network Ontology (Moderator: Alan Ruttenberg)'''

::Andrey Rzhetsky: [Text-Mining & Ontologies]
::Oliver Ruebenacker: [Systems Biology Pathway Exchange]
::Gopal Gopinathrao: [Gaps in Reactome]
::Open discussion.

* 4:00pm End of Day 2

==Confirmed Participants==

Erick Antezana (VIB / Ghent University, Belgium)

Mikel Egana Aranguren (University of Manchester, UK)

Robert Arp (NCBO / University at Buffalo)

Gary Bader (BioPAX / University of Toronto, Canada)

Michael Blinov (Center of Cell Analysis & Modeling / University of Connecticut Health Center)

Kei Cheung (Yale University / Center for Medical Informatics)

Lindsay Cowell (Infectious Disease Ontology / Duke University Medical Center)

Emek Demir (BioPAX / Memorial Sloan-Kettering Cancer Center)

Peter D'Eustachio (Reactome / New York University School of Medicine)

Ken Fukuda (INOH Pathway Database / Computational Biology Research Center, Advanced Industrial Science & Technology, Japan)

Louis Goldberg (Ontology Research Group / University at Buffalo)

Gopal Gopinathrao (Stein Lab / Cold Spring Harbor Laboratory)

Nancy Gough (Science Signaling, AAAS)

Matt Holford (Yale University)

Markus Krummenacker (SRI International)

Yves Lussier (University of Chicago)

Joanne S. Luciano (MITRE, BioPAX, BioPathways Consortium)

Peter Lyster (NIGMS / National Institutes of Health)

Avi Ma'ayan (Mount Sinai School of Medicine)

Jose L. V. Mejino, Jr. (FMA Ontology / University of Washington, Seattle)

Richard Morse (CHDI Management Inc. / CHDI Foundation Inc.)

Josefina (Fina) Nash (Coriell Institute)

Darren Natale (Protein Ontology / PIR, Georgetown University Medical Center)

Elgar Pichler (BioPAX / AstraZeneca)

Othel Rolle (Pfizer, Inc.)

Oliver Ruebenacker (Center for Cell Analysis and Modeling / University of Connecticut Health Center)

Alan Ruttenberg (BioPAX / Science Commons)

Andrey Rzhetsky (University of Chicago)

Chris Sander (BioPAX / Memorial Sloan-Kettering Cancer Center)

Richard Scheuermann (UT Southwestern Medical Center at Dallas)

Nigam Shah (NCBO / Stanford University)

Barry Smith (NCBO / University at Buffalo)

Andrea Splendiani (BioPAX/Medical Informatics, University of Rennes, France)

Balaji S. Srinivasan (Stanford University, Statistics)

John Westbrook (Rutgers)

Ulrike Wittig (EML Research gGmbH, Germany)

Cathy Wu (Protein Ontology / PIR, Georgetown University Medical Center)

==Venue / Lodging / Transportation==

'''VENUE:'''
The NCBO Workshop on Ontologies of Cellular Networks will take place on March 27-28, 2008 at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] (''Junior Ballroom'').

'''LODGING:'''
Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make room reservations either by calling 1-800-HILTONS and asking for the '''"National Center for Biomedical Ontology"''' block, or by entering group/convention code '''"NCB"''' when making reservations online at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] website.

NOTE: To qualify for the special room block rate of $149 (+ tax) per night, reservations must be secured no later than '''Wednesday, March 5'''. After this date, reservations will be accepted based on availability and at prevailing rates.

'''TRANSPORTATION / DRIVING DIRECTIONS TO VENUE:'''

''FROM NEWARK AIRPORT:''

HOTEL SHUTTLE: The Hilton Newark Airport Hotel provides complimentary shuttle service from (and to) the airport. When you arrive at the Newark Airport, follow signs to the Baggage Claim Area. Take the Airtrain to Airstation '''P4'''. The shuttle pickup is every 20 minutes from this location.

TAXI: Typical minimum charge is USD 20.00

DRIVING DIRECTIONS: Follow signs to airport exit, US Rte 1&9 N. to Haynes Ave. Take US Rte 1&9 S. After McClellan St. overpass, bear right to Service Road. The Hilton Hotel entrance is the 2nd driveway.

''DRIVING DIRECTIONS FROM ELSEWHERE:''

TRAVELLING SOUTHBOUND ON ROUTES 1 & 9: Local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right.

TRAVELLING NORTHBOUND ON ROUTES 1 & 9: Exit at McClellan Street. At the base of the ramp, turn left, and the Hilton Hotel is on the right.

FROM THE N.J. TURNPIKE NORTHBOUND: Take exit 13A. Get on Routes 1 & 9 North to the McClellan Street exit. At base of ramp, turn left and the Hilton Hotel is on the right.

FROM THE N.J. TURNPIKE SOUTHBOUND: Take exit 14 to Routes 1 & 9 south, local lanes, go past the McClellan Street exit. Immediately as you go under the overpass, get onto the Service Road in the right lane. The Hilton Hotel is immediately on your right.

==Links ==

* [http://sig.biostr.washington.edu/projects/fm/ FMA: Foundational Model of Anatomy]

* [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]

* [http://obofoundry.org OBO Foundry]

==Literature==

*[http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]

*[http://xml.coverpages.org/OntologyExchange.html An evaluation of ontology exchange languages for bioinformatics]

*[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Coordinated Evolution of Ontologies to Support Biomedical Data Integration]

==Addendum: Do Mountains Exist?==

This paper:

::Barry Smith and David M. Mark, [http://ontology.buffalo.edu/smith/articles/Mountains.pdf “Do Mountains Exist? Towards an Ontology of Landforms”], Environment and Planning B (Planning and Design), 30(3) (2003), 411–427.

defends the thesis that mountains do indeed exist. But it argues that this assertion is non-trivial, in virtue of the fact that mountains have no determinate boundaries.

Similarly in the case of pathways and networks; pathways and networks do indeed exist -- but different groups of researchers place their boundaries in different places. To find ways to pool their data these different groups would need to acknowledge the differences in demarcation on which their pathway and network representations rest. See presentation [http://ontology.buffalo.edu/08/networks/smith2.ppt Pathways and Networks for Realists].

Meetings and Events

2008-03-03T21:07:32Z

JoanneLuciano: /* Upcoming meetings */

== Upcoming meetings ==

*'''[http://www.dagstuhl.de/de/programm/kalender/semhp/?semid=29453 Dagstuhl Seminar: Ontology Interoperability in Biomedicine]'''
**March 27-30, 2007, Dagstuhl, Germany
**Attending: Barry Smith, Michael Ashburner, Mark Musen, Nigam Shah, Fabian Neuhaus, Suzanna Lewis, Werner Ceusters
**Invitation only

*'''Workshop on Clinical Trial Ontology'''
**May 16-17 2007, venue TBD
**[[Workshop on Clinical Trial Ontology | information about Clinical Trial Ontology workshop]]

*'''Reasoning with Biomedical Ontologies'''
**June 20-23, 2007: Schloss Dagstuhl, Germany
**Attending: Deborah McGuinness, Fabian Neuhaus, Nigam Shah, Barry Smith.

*'''[http://cbms07.biomap.org/ Ontologies for Biomedical Systems II at 20th IEEE CBMS 2007]'''
**June 20-22, 2007, Maribor, Slovenia

*'''Dagstuhl Seminar: Ontologies and Text Mining for Life Sciences'''
**July 23-27, 2007: Schloss Dagstuhl, Germany
**Organizers: Ulf Leser, Dietrich Rebholz-Schuhmann & Michael Ashburner
** Attending: Michael Ashburner
**[http://www.dagstuhl.de/07301 http://www.dagstuhl.de/07301]

*'''All NCBCs Ontology workshop'''
**Fall 2007, with Andreas Califano, Columbia, NY

* '''Phenotype Ontology (Upper Level) workshop'''
**2007?

== Past meetings ==

*'''Phenotype Ontology (Workshop)'''
**December 1-2, 2006, Clark Center, Stanford, CA
**[[PATO_Meeting| PATO meeting agenda]]
**Attending: Suzanna Lewis, Chris Mungall, Mark Gibson, Nicole Washington, Nigam Shah, Fabian Neuhaus, Michael Ashburner, Monte Westerfield

*'''Panel on the Future of HL7'''
**AMIA Anual Symposium
**November 14, 3.30-5.00pm., Washington DC
**http://ontology.buffalo.edu/HL7/panel.htm
**Attending: Barry Smith

*'''Tutorial on Genomics Knowledge Representation for Clinical Trials'''
**AMIA Annual Symposium
**November 12, 2006, Washington DC
**http://ontology.buffalo.edu/06/AMIAWorkshop.htm

*'''Biomedical Ontology in Action'''
**KR-MED 2006
**November 8, 2006, Baltimore
**http://www.imbi.uni-freiburg.de/medinf/kr-med-2006/index.html
**Attending: Werner Ceusters, Barry Smith

*'''Workshop on Ontology of Diseases'''
**In association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-7, 2006, John Hopkins University, Baltimore
**[[Workshop on Ontology of Diseases | information on the Disease Ontology Workshop]]
**Attending: Werner Ceusters, Christopher Chute, Suzanna Lewis, Chris Mungall, Fabian Neuhaus, Nigam Shah, Barry Smith, Monte Westerfield

*'''Fall NCBO Project Meeting'''
**Oct. 23-25, 2006, Stanford
** All Hands meeting
** Advisory Comm. & NIH Program & Science officers invited

*'''Workshop on Philosophy of Biology'''
**October 14-15, 2006, Buffalo, NY
**http://ontology.buffalo.edu/06/pob
**Attending: Werner Ceusters, Barry Smith

*'''American Society of Human Genetics'''
**October 9-13, 2006, New Orleans, LA
**[http://genetics.faseb.org/genetics/ashg/menu-annmeet.shtml http://genetics.faseb.org/genetics/ashg/menu-annmeet.shtml]
**Presentation to find collaborators, also ontology workshop

*'''Genomics Standards Consortium Workshop
**National Institute for Environmental e-Science (NIEeS)
**September 11-13, 2006, Hinxton, UK.
** [http://www.niees.ac.uk/events/egenomics2006/index.shtml http://www.niees.ac.uk/events/egenomics2006/index.shtml]
**Attending: Suzanna Lewis, Michael Ashburner, George Gkoutos

*'''Anatomy Ontology Workshop'''
**September 8-9, 2006, Seattle
**[[Anatomy Ontology Workshop | information on the Anatomy Ontology Workshop]]
**Attending: Michael Ashburner, Melissa Haendel, Suzanna Lewis, Chris Mungall, Fabian Neuhaus, Nigam Shah, Barry Smith, David Sutherland, Monte Westerfield

*'''Tutorial on Standards and Ontologies
**Medical Informatics Europe
**August 27, 2006, Maastricht, Netherlands.
**http://ontology.buffalo.edu/06/MIE_Tutorial.htm
**Attending: Werner Ceusters, Barry Smith

*'''IEEE Computational Systems Bioinformatics, 2006'''
**August 14-18, 2006. Stanford University
**[http://www.lifesciencessociety.org/CSB2006/index.html http://www.lifesciencessociety.org/CSB2006/index.html]
** Attending: Mark Musen (Keynote), rest of Stanford group (tutorial in bioontologies/semantic web)

*'''ISMB, 2006'''
**August 6-10, 2006, Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending: Michael Ashburner, Suzanna Lewis (Keynote speaker for Bio-ontologies SIG)

*'''In Silico Analysis of Proteins. Celebrating the 20th Anniversary of Swiss-Prot'''
**Jul 30- August 4, 2006, Fortaleza, Brazil.
** [http://www.swissprot20.org/ http://www.swissprot20.org/]
** Attending: Michael Ashburner, Suzanna Lewis

*'''Functional Genomics investigation Ontology (FuGO) 2nd Workshop'''
**July 24-28, 2006, Hinxton, UK
**http://fugo.sourceforge.net/news/index.php
**Attending: Barry Smith

*'''9th International Protege Conference'''
**July 23-26, 2006, Stanford, CA
**[http://protege.stanford.edu/conference/2006/ http://protege.stanford.edu/conference/2006/]
** Attending: Chris Callendar, Christopher Chute, Tricia d'Entremont, Chris Mungall, Mark Musen, Natasha Noy, Daniel Rubin, Nigam Shah, Kaustubh Supekar

*'''NCBC All Hands Meeting'''
**July 17-19, 2006, NIH, Bethesda, MD
**Attending: Michael Ashburner, James Buntrock, Chris Callendar, Simona Carini, Louis Goldberg, Deborah McGuinness, Chris Mungall,Mark Musen, Fabian Neuhaus, Daniel Rubin, Nigam Shah, Barry Smith, Nicole Washington, Monte Westerfield
**[http://www.bisti.nih.gov/ahm2006/ http://www.bisti.nih.gov/ahm2006/]
**[http://www.bisti.nih.gov/ahm2006/ncbo_dissemination.htm Ontology: A Vision for the Future and Its Realization] Dissemination Event
***Organizers: Mark Musen, Barry Smith

* '''Core 1 & 2 Project Meeting'''
** June 27-28, 2006, Berkeley, CA
** Attending: Julie Moseley, Lynn Murphy, Mark Musen, Daniel Rubin, Nigam Shah, Archana Vembakam (Stanford); Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu, Nicole Washington (Berkeley); James Buntrock, Christopher Chute, Harold Solbrig (Mayo); Margaret-Anne Storey (UVic); Sherri De Coronado (NIH)
** Working plan for core 1 & 2 goals

* '''Core 1 & 2 Meeting'''
** June 9, 2006, Berkeley, CA
** Attending: Dilvan Moreira, Lynn Murphy, Daniel Rubin, Nigam Shah, Archana Vembakam (Stanford); Suzanna Lewis, Chris Mungall, ShengQiang Shu, Nicole Washington (Berkeley); James Buntrock, Harold Solbrig (Mayo by phone); Chris Callendar (UVic by phone)

*'''Training Course in Biomedical Ontologies'''
**[http://ontology.buffalo.edu/06/os2/index.html http://ontology.buffalo.edu/06/os2/index.html]
**May 21-24, 2006, Schloss Dagstuhl, Germany
**Attending: Werner Ceusters, Mark Musen, Barry Smith

*'''NSF/RCN workshop on ontology and phylogeny'''
**May 21-24, St. Louis, MO
**Attending: Michael Ashburner, Suzanna Lewis, Monte Westerfield

*'''Phenotype Annotation Meeting'''
**May 17-20, Hinxton, UK
**Attending: Michael Ashburner, Mark Gibson, George Gkoutos, Suzanna Lewis, Gillian Millburn, Chris Mungall, Fabian Neuhaus, Erik Segerdell, Nigam Shah, Monte Westerfield
**[[Agenda PaTO | PATO meeting agenda]]

*'''Fish Evolutionary Biology Working Group Meeting'''
**April 9-11, National Evolutionary Synthesis Center (NESCent), Durham, NC
**Attending: Mark Gibson,Paula Mabee, Chris Mungall, Monte Westerfield

*'''Gene Ontology Workshop'''
**March 31-April 3, 2006, St. Croix
** Attending: Michael Ashburner, Suzanna Lewis, Chris Mungall, Barry Smith

* '''Bio-IT LifeSciences Conference'''
**April 3-6, 2006, Boston, MA'''
**[http://www.lifesciencesexpo.com/live/26/ http://www.lifesciencesexpo.com/live/26/]
** Speaker: Michael Ashburner, Ben Franklin Award Lecture.

*'''Workshop on Ontology of Images'''
**March 24-25, 2006, Stanford, CA
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies
**[Workshop on Ontology of Images | info on Ontology of Images workshop]
** Attending: Suzanna Lewis, Chris Mungall, Mark Musen, Daniel Rubin, Nigam Shah, Barry Smith, Kaushtubh Supekar

*'''Immunology Ontology Workshop: NIAID'''
**March 21-22, 2006, Gaitherburg, MD
** Attending: Suzanna Lewis (speaker), Mark Musen (Session chair), Barry Smith

*'''Semantic Technology Conference'''
**March 6-9, 2006, San Jose, CA
** [http://www.semantic-conference.com/ http://www.semantic-conference.com/ ]
** Attending: Deborah McGuinness (Keynote, tutorial), Mark Musen (speaker), Daniel Rubin, Kaustubh Superkar (speaker)

*'''NIH NCRR Animal Models workshop'''
**March 6-7, 2006, Bethesda, MD
** Attending: Monte Westerfield

*'''[[Minutes & presentations, March 2-4, 2006 Project meeting|cBio Project Meeting]]'''
**March 2-4, 2006, Stanford, CA
** [[Agenda, Project Meeting, Thursday, March 2-Saturday, March 4, 2006|Agenda]]
**[http://www.smi.stanford.edu/research/cbio/cbio_meeting.html http://www.smi.stanford.edu/research/cbio/cbio_meeting.html]
**Entire project, NIH Program & Lead Science officers

*'''BIRN ontology workshop'''
**February 28-March 1, 2006, Stanford, CA
** Attending: Christopher Chute, Suzanna Lewis, Mark Musen, Daniel Rubin, Nigam Shah, Barry Smith

*'''NLM vocabulary collection and distribution meeting'''
**February 27-28, 2006, NLM, Washington, DC
** Attending: James Buntrock, Christopher Chute, Tom Johnson, Chris Mungall, Deepak Sharma, Harold Solbrig

*'''NIAID meeting'''
**February, 2006, Washington, DC
**Attending: Mark Musen

*'''cBio Phenotype Annotation tool specification'''
**February 21-23, 2006, Berkeley, CA
** Attending: Melissa Haendel, Sierra Taylor (ZFIN); John Day-Richter, Mark Gibson, Suzanna Lewis, Chris Mungall, ShengQiang Shu (Berkeley)

*'''Mini-Syposium on Semantic Enrichment of Scientific Literature'''
**February 20, 2006 at the European Bioinformatics Institute, Hinxton, UK
**Attending: Michael Ashburner (speaker)

*'''cBio OBD specification'''
**February 17, 2006, Berkeley, CA
** Attending: Ben Olasov, Ida Sim (UCSF); Mark Gibson, Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu (Berkeley); Daniel Rubin (Stanford by phone)

*'''FuGO meeting'''
** February 13-15, 2006, Philadelphia, PA
**[http://fugo.sourceforge.net/news/index.php http://fugo.sourceforge.net/news/index.php]
**Attending: Barry Smith

*'''Fourth Semantic Interoperability for E-Government Conference'''
** February 9-10, 2006, MITRE, McLean, VA
** [http://colab.cim3.net/cgi-bin/wiki.pl?FourthSemanticInteroperabilityforEGovernmentConference_2006_2_0910 http://colab.cim3.net/cgi-bin/wiki.pl?FourthSemanticInteroperabilityforEGovernmentConference_2006_2_0910]
**Attending: Barry Smith

*'''NIAID BRC3 and Inter Operability Working Group meeting'''
** February 6-7, 2006, Philadelphia, PA
** [http://www.niaid.nih.gov/dmid/genomes/brc/brc3.htm http://www.niaid.nih.gov/dmid/genomes/brc/brc3.htm]
** Attending: Suzanna Lewis, Barry Smith

*'''PharmGKB and cBiO meeting'''
** January 31, 2006, Stanford, CA
** Attending: Daniel Rubin (Stanford); Suzanna Lewis, Sima Misra (Berkeley); Russ Altman, Tina Boussard, Teri Klein, Mark Woon (PharmGKB)

*'''Pacific Symposium on Biocomputing, 2006'''
**January 2-6, 2006, Maui, HI
**Michael Ashburner (Keynote)
**[http://psb.stanford.edu/ http://psb.stanford.edu/]

*'''NCBC Meeting'''
**Dec. 15-16, NIH, Bethesda, MD
**Attending: Mark Musen, Suzanna Lewis, Monte Westerfield
**Introducting new NCBCs to each other and NIH staff

*'''Phenotype Annotation Meeting'''
**December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]
** Attending: Melissa Haendel, Paula Mabee, Erik Segerdell, Monte Westerfield (ZFIN); Gillian Millburn (FlyBase); Mark Gibson, Suzanna Lewis, Chris Mungall (Berkeley); Chris Callendar, Sean Falconer, Margaret-Anne Storey (UVic)
** Define requirements of phenotype annotation tools

*'''International Biocurator Meeting'''
**December 8-11, 2005, Asilomar, CA
**[http://biocurator.org/intnlbiocurator.html http://biocurator.org/intnlbiocurator.html]
**Attending: Sima Misra (organizer), Chris Mungall (speaker), Monte Westerfield (speaker)

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town, SA
**Michael Ashburner (Keynote)

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, Cold Spring Harbor, NY
** Attending: Michael Ashburner, John Day-Richter, George Gkoutos, Suzanna Lewis, Chris Mungall, Mark Musen, Erik Segerdell, Nigam Shah, Monte Westerfield
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford, CA; Nov. 22, 10am-3pm, Berkeley, CA
** Attending: Lynn Murphy, Mark Musen, Daniel Rubin, Nigam Shah, Archana Vembakam, (Stanford); Nomi Harris, Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu (Berkeley); James Buntrock, Deepak Sharma, Harold Solbrig (Mayo by phone)

*'''Forbes Dewey Meeting'''
**Late October, MIT, Cambridge, MA
**Michael Ashburner, chair
**Goal to see if anonymous foundation would pay for ontology content unification, standards, collaboration, etc.

*'''Genome Informatics Meeting'''
**Oct. 28-Nov. 1, 2005, Cold Spring Harbor, NY
**Suzanna Lewis (organizer, speaker)

*'''Workshop on Bio-Ontologies'''
**October 28, 2005, Buffalo, NY
**[http://ontology.buffalo.edu/05/bio-ontologies.pdf http://ontology.buffalo.edu/05/bio-ontologies.pdf]
**Presenting: Suzanna Lewis, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session: making ontologies better

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology'''
**October, 2005, Caxambu, Brazil
**Michael Ashburner (Keynote)

*'''Applied Biosystems Inc., Science Meeting'''
**September, 2005, Asilomar, CA
**Michael Ashburner (Keynote)

*'''MGED8, Bergen'''
**September, 2005
**Michael Ashburner (Keynote)

Meetings and Events

2008-03-03T21:07:07Z

JoanneLuciano: /* Upcoming meetings */

== Upcoming meetings ==

*'''[http://www.dagstuhl.de/de/programm/kalender/semhp/?semid=29453 Dagstuhl Seminar: Ontology Interoperability in Biomedicine]'''
**March 27-30, 2008, Dagstuhl, Germany
**Attending: Barry Smith, Michael Ashburner, Mark Musen, Nigam Shah, Fabian Neuhaus, Suzanna Lewis, Werner Ceusters
**Invitation only

*'''Workshop on Clinical Trial Ontology'''
**May 16-17 2007, venue TBD
**[[Workshop on Clinical Trial Ontology | information about Clinical Trial Ontology workshop]]

*'''Reasoning with Biomedical Ontologies'''
**June 20-23, 2007: Schloss Dagstuhl, Germany
**Attending: Deborah McGuinness, Fabian Neuhaus, Nigam Shah, Barry Smith.

*'''[http://cbms07.biomap.org/ Ontologies for Biomedical Systems II at 20th IEEE CBMS 2007]'''
**June 20-22, 2007, Maribor, Slovenia

*'''Dagstuhl Seminar: Ontologies and Text Mining for Life Sciences'''
**July 23-27, 2007: Schloss Dagstuhl, Germany
**Organizers: Ulf Leser, Dietrich Rebholz-Schuhmann & Michael Ashburner
** Attending: Michael Ashburner
**[http://www.dagstuhl.de/07301 http://www.dagstuhl.de/07301]

*'''All NCBCs Ontology workshop'''
**Fall 2007, with Andreas Califano, Columbia, NY

* '''Phenotype Ontology (Upper Level) workshop'''
**2007?

== Past meetings ==

*'''Phenotype Ontology (Workshop)'''
**December 1-2, 2006, Clark Center, Stanford, CA
**[[PATO_Meeting| PATO meeting agenda]]
**Attending: Suzanna Lewis, Chris Mungall, Mark Gibson, Nicole Washington, Nigam Shah, Fabian Neuhaus, Michael Ashburner, Monte Westerfield

*'''Panel on the Future of HL7'''
**AMIA Anual Symposium
**November 14, 3.30-5.00pm., Washington DC
**http://ontology.buffalo.edu/HL7/panel.htm
**Attending: Barry Smith

*'''Tutorial on Genomics Knowledge Representation for Clinical Trials'''
**AMIA Annual Symposium
**November 12, 2006, Washington DC
**http://ontology.buffalo.edu/06/AMIAWorkshop.htm

*'''Biomedical Ontology in Action'''
**KR-MED 2006
**November 8, 2006, Baltimore
**http://www.imbi.uni-freiburg.de/medinf/kr-med-2006/index.html
**Attending: Werner Ceusters, Barry Smith

*'''Workshop on Ontology of Diseases'''
**In association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-7, 2006, John Hopkins University, Baltimore
**[[Workshop on Ontology of Diseases | information on the Disease Ontology Workshop]]
**Attending: Werner Ceusters, Christopher Chute, Suzanna Lewis, Chris Mungall, Fabian Neuhaus, Nigam Shah, Barry Smith, Monte Westerfield

*'''Fall NCBO Project Meeting'''
**Oct. 23-25, 2006, Stanford
** All Hands meeting
** Advisory Comm. & NIH Program & Science officers invited

*'''Workshop on Philosophy of Biology'''
**October 14-15, 2006, Buffalo, NY
**http://ontology.buffalo.edu/06/pob
**Attending: Werner Ceusters, Barry Smith

*'''American Society of Human Genetics'''
**October 9-13, 2006, New Orleans, LA
**[http://genetics.faseb.org/genetics/ashg/menu-annmeet.shtml http://genetics.faseb.org/genetics/ashg/menu-annmeet.shtml]
**Presentation to find collaborators, also ontology workshop

*'''Genomics Standards Consortium Workshop
**National Institute for Environmental e-Science (NIEeS)
**September 11-13, 2006, Hinxton, UK.
** [http://www.niees.ac.uk/events/egenomics2006/index.shtml http://www.niees.ac.uk/events/egenomics2006/index.shtml]
**Attending: Suzanna Lewis, Michael Ashburner, George Gkoutos

*'''Anatomy Ontology Workshop'''
**September 8-9, 2006, Seattle
**[[Anatomy Ontology Workshop | information on the Anatomy Ontology Workshop]]
**Attending: Michael Ashburner, Melissa Haendel, Suzanna Lewis, Chris Mungall, Fabian Neuhaus, Nigam Shah, Barry Smith, David Sutherland, Monte Westerfield

*'''Tutorial on Standards and Ontologies
**Medical Informatics Europe
**August 27, 2006, Maastricht, Netherlands.
**http://ontology.buffalo.edu/06/MIE_Tutorial.htm
**Attending: Werner Ceusters, Barry Smith

*'''IEEE Computational Systems Bioinformatics, 2006'''
**August 14-18, 2006. Stanford University
**[http://www.lifesciencessociety.org/CSB2006/index.html http://www.lifesciencessociety.org/CSB2006/index.html]
** Attending: Mark Musen (Keynote), rest of Stanford group (tutorial in bioontologies/semantic web)

*'''ISMB, 2006'''
**August 6-10, 2006, Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending: Michael Ashburner, Suzanna Lewis (Keynote speaker for Bio-ontologies SIG)

*'''In Silico Analysis of Proteins. Celebrating the 20th Anniversary of Swiss-Prot'''
**Jul 30- August 4, 2006, Fortaleza, Brazil.
** [http://www.swissprot20.org/ http://www.swissprot20.org/]
** Attending: Michael Ashburner, Suzanna Lewis

*'''Functional Genomics investigation Ontology (FuGO) 2nd Workshop'''
**July 24-28, 2006, Hinxton, UK
**http://fugo.sourceforge.net/news/index.php
**Attending: Barry Smith

*'''9th International Protege Conference'''
**July 23-26, 2006, Stanford, CA
**[http://protege.stanford.edu/conference/2006/ http://protege.stanford.edu/conference/2006/]
** Attending: Chris Callendar, Christopher Chute, Tricia d'Entremont, Chris Mungall, Mark Musen, Natasha Noy, Daniel Rubin, Nigam Shah, Kaustubh Supekar

*'''NCBC All Hands Meeting'''
**July 17-19, 2006, NIH, Bethesda, MD
**Attending: Michael Ashburner, James Buntrock, Chris Callendar, Simona Carini, Louis Goldberg, Deborah McGuinness, Chris Mungall,Mark Musen, Fabian Neuhaus, Daniel Rubin, Nigam Shah, Barry Smith, Nicole Washington, Monte Westerfield
**[http://www.bisti.nih.gov/ahm2006/ http://www.bisti.nih.gov/ahm2006/]
**[http://www.bisti.nih.gov/ahm2006/ncbo_dissemination.htm Ontology: A Vision for the Future and Its Realization] Dissemination Event
***Organizers: Mark Musen, Barry Smith

* '''Core 1 & 2 Project Meeting'''
** June 27-28, 2006, Berkeley, CA
** Attending: Julie Moseley, Lynn Murphy, Mark Musen, Daniel Rubin, Nigam Shah, Archana Vembakam (Stanford); Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu, Nicole Washington (Berkeley); James Buntrock, Christopher Chute, Harold Solbrig (Mayo); Margaret-Anne Storey (UVic); Sherri De Coronado (NIH)
** Working plan for core 1 & 2 goals

* '''Core 1 & 2 Meeting'''
** June 9, 2006, Berkeley, CA
** Attending: Dilvan Moreira, Lynn Murphy, Daniel Rubin, Nigam Shah, Archana Vembakam (Stanford); Suzanna Lewis, Chris Mungall, ShengQiang Shu, Nicole Washington (Berkeley); James Buntrock, Harold Solbrig (Mayo by phone); Chris Callendar (UVic by phone)

*'''Training Course in Biomedical Ontologies'''
**[http://ontology.buffalo.edu/06/os2/index.html http://ontology.buffalo.edu/06/os2/index.html]
**May 21-24, 2006, Schloss Dagstuhl, Germany
**Attending: Werner Ceusters, Mark Musen, Barry Smith

*'''NSF/RCN workshop on ontology and phylogeny'''
**May 21-24, St. Louis, MO
**Attending: Michael Ashburner, Suzanna Lewis, Monte Westerfield

*'''Phenotype Annotation Meeting'''
**May 17-20, Hinxton, UK
**Attending: Michael Ashburner, Mark Gibson, George Gkoutos, Suzanna Lewis, Gillian Millburn, Chris Mungall, Fabian Neuhaus, Erik Segerdell, Nigam Shah, Monte Westerfield
**[[Agenda PaTO | PATO meeting agenda]]

*'''Fish Evolutionary Biology Working Group Meeting'''
**April 9-11, National Evolutionary Synthesis Center (NESCent), Durham, NC
**Attending: Mark Gibson,Paula Mabee, Chris Mungall, Monte Westerfield

*'''Gene Ontology Workshop'''
**March 31-April 3, 2006, St. Croix
** Attending: Michael Ashburner, Suzanna Lewis, Chris Mungall, Barry Smith

* '''Bio-IT LifeSciences Conference'''
**April 3-6, 2006, Boston, MA'''
**[http://www.lifesciencesexpo.com/live/26/ http://www.lifesciencesexpo.com/live/26/]
** Speaker: Michael Ashburner, Ben Franklin Award Lecture.

*'''Workshop on Ontology of Images'''
**March 24-25, 2006, Stanford, CA
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies
**[Workshop on Ontology of Images | info on Ontology of Images workshop]
** Attending: Suzanna Lewis, Chris Mungall, Mark Musen, Daniel Rubin, Nigam Shah, Barry Smith, Kaushtubh Supekar

*'''Immunology Ontology Workshop: NIAID'''
**March 21-22, 2006, Gaitherburg, MD
** Attending: Suzanna Lewis (speaker), Mark Musen (Session chair), Barry Smith

*'''Semantic Technology Conference'''
**March 6-9, 2006, San Jose, CA
** [http://www.semantic-conference.com/ http://www.semantic-conference.com/ ]
** Attending: Deborah McGuinness (Keynote, tutorial), Mark Musen (speaker), Daniel Rubin, Kaustubh Superkar (speaker)

*'''NIH NCRR Animal Models workshop'''
**March 6-7, 2006, Bethesda, MD
** Attending: Monte Westerfield

*'''[[Minutes & presentations, March 2-4, 2006 Project meeting|cBio Project Meeting]]'''
**March 2-4, 2006, Stanford, CA
** [[Agenda, Project Meeting, Thursday, March 2-Saturday, March 4, 2006|Agenda]]
**[http://www.smi.stanford.edu/research/cbio/cbio_meeting.html http://www.smi.stanford.edu/research/cbio/cbio_meeting.html]
**Entire project, NIH Program & Lead Science officers

*'''BIRN ontology workshop'''
**February 28-March 1, 2006, Stanford, CA
** Attending: Christopher Chute, Suzanna Lewis, Mark Musen, Daniel Rubin, Nigam Shah, Barry Smith

*'''NLM vocabulary collection and distribution meeting'''
**February 27-28, 2006, NLM, Washington, DC
** Attending: James Buntrock, Christopher Chute, Tom Johnson, Chris Mungall, Deepak Sharma, Harold Solbrig

*'''NIAID meeting'''
**February, 2006, Washington, DC
**Attending: Mark Musen

*'''cBio Phenotype Annotation tool specification'''
**February 21-23, 2006, Berkeley, CA
** Attending: Melissa Haendel, Sierra Taylor (ZFIN); John Day-Richter, Mark Gibson, Suzanna Lewis, Chris Mungall, ShengQiang Shu (Berkeley)

*'''Mini-Syposium on Semantic Enrichment of Scientific Literature'''
**February 20, 2006 at the European Bioinformatics Institute, Hinxton, UK
**Attending: Michael Ashburner (speaker)

*'''cBio OBD specification'''
**February 17, 2006, Berkeley, CA
** Attending: Ben Olasov, Ida Sim (UCSF); Mark Gibson, Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu (Berkeley); Daniel Rubin (Stanford by phone)

*'''FuGO meeting'''
** February 13-15, 2006, Philadelphia, PA
**[http://fugo.sourceforge.net/news/index.php http://fugo.sourceforge.net/news/index.php]
**Attending: Barry Smith

*'''Fourth Semantic Interoperability for E-Government Conference'''
** February 9-10, 2006, MITRE, McLean, VA
** [http://colab.cim3.net/cgi-bin/wiki.pl?FourthSemanticInteroperabilityforEGovernmentConference_2006_2_0910 http://colab.cim3.net/cgi-bin/wiki.pl?FourthSemanticInteroperabilityforEGovernmentConference_2006_2_0910]
**Attending: Barry Smith

*'''NIAID BRC3 and Inter Operability Working Group meeting'''
** February 6-7, 2006, Philadelphia, PA
** [http://www.niaid.nih.gov/dmid/genomes/brc/brc3.htm http://www.niaid.nih.gov/dmid/genomes/brc/brc3.htm]
** Attending: Suzanna Lewis, Barry Smith

*'''PharmGKB and cBiO meeting'''
** January 31, 2006, Stanford, CA
** Attending: Daniel Rubin (Stanford); Suzanna Lewis, Sima Misra (Berkeley); Russ Altman, Tina Boussard, Teri Klein, Mark Woon (PharmGKB)

*'''Pacific Symposium on Biocomputing, 2006'''
**January 2-6, 2006, Maui, HI
**Michael Ashburner (Keynote)
**[http://psb.stanford.edu/ http://psb.stanford.edu/]

*'''NCBC Meeting'''
**Dec. 15-16, NIH, Bethesda, MD
**Attending: Mark Musen, Suzanna Lewis, Monte Westerfield
**Introducting new NCBCs to each other and NIH staff

*'''Phenotype Annotation Meeting'''
**December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]
** Attending: Melissa Haendel, Paula Mabee, Erik Segerdell, Monte Westerfield (ZFIN); Gillian Millburn (FlyBase); Mark Gibson, Suzanna Lewis, Chris Mungall (Berkeley); Chris Callendar, Sean Falconer, Margaret-Anne Storey (UVic)
** Define requirements of phenotype annotation tools

*'''International Biocurator Meeting'''
**December 8-11, 2005, Asilomar, CA
**[http://biocurator.org/intnlbiocurator.html http://biocurator.org/intnlbiocurator.html]
**Attending: Sima Misra (organizer), Chris Mungall (speaker), Monte Westerfield (speaker)

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town, SA
**Michael Ashburner (Keynote)

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, Cold Spring Harbor, NY
** Attending: Michael Ashburner, John Day-Richter, George Gkoutos, Suzanna Lewis, Chris Mungall, Mark Musen, Erik Segerdell, Nigam Shah, Monte Westerfield
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford, CA; Nov. 22, 10am-3pm, Berkeley, CA
** Attending: Lynn Murphy, Mark Musen, Daniel Rubin, Nigam Shah, Archana Vembakam, (Stanford); Nomi Harris, Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu (Berkeley); James Buntrock, Deepak Sharma, Harold Solbrig (Mayo by phone)

*'''Forbes Dewey Meeting'''
**Late October, MIT, Cambridge, MA
**Michael Ashburner, chair
**Goal to see if anonymous foundation would pay for ontology content unification, standards, collaboration, etc.

*'''Genome Informatics Meeting'''
**Oct. 28-Nov. 1, 2005, Cold Spring Harbor, NY
**Suzanna Lewis (organizer, speaker)

*'''Workshop on Bio-Ontologies'''
**October 28, 2005, Buffalo, NY
**[http://ontology.buffalo.edu/05/bio-ontologies.pdf http://ontology.buffalo.edu/05/bio-ontologies.pdf]
**Presenting: Suzanna Lewis, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session: making ontologies better

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology'''
**October, 2005, Caxambu, Brazil
**Michael Ashburner (Keynote)

*'''Applied Biosystems Inc., Science Meeting'''
**September, 2005, Asilomar, CA
**Michael Ashburner (Keynote)

*'''MGED8, Bergen'''
**September, 2005
**Michael Ashburner (Keynote)

Networks

2008-02-05T16:11:46Z

JoanneLuciano: /* Participants */

== Workshop on Ontologies of Cellular Networks ==
To ensure highly interactive and productive sessions, the number of workshop participants will be limited. If you are interested in participating, please contact: [mailto:phismith@buffalo.edu Barry Smith]

This workshop is organized by Yves Lussier (Chicago/MAGNet), Alan Ruttenberg (Neurocommons) and Barry Smith (Buffalo/NCBO). It is funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics].

== Goals ==
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on ontologies of cellular networks.

The goals of this workshop are:

*1. to provide an introduction to the basic tools and methods of ontology
*2. to foster networking of, and enhanced coordination between, those groups already working on ontologies of cellular networks
*3. to identify problems which must be solved if ontology methods are to be extended to represent biological mechanisms in greater detail
*4. to promote further ontology development in this area with the goal of accelerating our ability to understand basic biological phenomena and to leverage experimental data

== Preliminary Agenda ==

'''Thursday, March 27, 2008'''

* 9:00am Registration and Continental Breakfast

* 9:30am Participant Self-Introductions

* 10:00am '''Session 1 - Biology of Pathways and Networks (Moderator: Yves Lussier)'''

:Presenters will include:
::Yves Lussier: The Extracellular Membrane

:Potential topics:
::signalling pathways, metabolic pathways, regulatory networks, interaction networks, gene expression correlation networks, physiological networks, neurocurrent networks

* 11:00am Refreshment Break

* 11:15am (Session 1, contd.)

* 12:30pm Lunch Break

* 1:30pm '''Session 2 - Computational Analysis of Pathway and Network Data (Moderator: Alan Ruttenberg)

:Presenters will include:
::Richard Scheuermann: Networks and Modularity

* 3:30pm Refreshment Break
* 3:45pm '''Session 3 - Introduction to Ontology (Moderator: Barry Smith)'''

:Presenters will include
::Lindsay Cowell
::Barry Smith

* 5:00pm End of Day 1

'''Friday, March 28, 2008'''

* 8:30am Continental Breakfast

* 9:00am Session 4: '''Current Approaches to Pathway and Network Ontologis (Moderator: Richard Scheuermann)'''

:Presenters will include:
::Peter d'Eustachio: Reactome
::Ken Fukuda: INOH Pathway Database
::Balaji S. Srinivasan

* 10:45am Refreshment Break
* 11:00am (Session 4, contd.)
* 12.30pm Lunch Break

* 1:30 '''Session 5 - Gaps in Network Ontology (Moderator: Alan Ruttenberg)'''

:Open discussion; presenters and topics to be decided
::(example:) Approaches to extending the OBO Foundry to include pathway and network ontologies

* 4:00pm End of Day 2

==Participants==

''Participants will include:''

Robert Arp (NCBO / University at Buffalo)

Gary Bader (BioPAX / University of Toronto)

Helen Berman (Protein Data Bank / Rutgers University)

William Bug (BIRN Ontology Task Force, UC San Diego)

Kei Cheung (Yale Center for Medical Informatics)

Lindsay Cowell (Infectious Disease Ontology / Duke University)

Emek Demir (BioPAX / Memorial Sloan-Kettering Cancer Center)

Peter D'Eustachio (Reactome / New York University)

Ken Ichiro Fukuda (INOH Pathway Database, Tokyo)

Louis Goldberg (Ontology Research Group / University at Buffalo)

Gopal Gopinathrao (Reactome / Cold Spring Harbor Laboratories)

Nancy Gough (''Science'')

Joanne Luciano (BioPAX / MITRE)

Peter Lyster (NIGMS / National Institutes of Health)

Avi Ma'ayan (Mount Sinai School of Medicine)

J. L. E. Mejino, Jr. (FMA Ontology / University of Washington, Seattle)

Darren Natale (Protein Ontology / PIR, Georgetown University)

Oliver Ruebenacker (Center for Cell Analysis and Modelling / University of Connecticut Health Center)

Alan Ruttenberg (BioPAX / Science Commons)

Andrey Rzhetsky (University of Chicago)

Chris Sander (BioPAX / Memorial Sloan-Kettering Cancer Center)

Richard Scheuermann (UTexas SW Medical Center at Dallas)

Stuart Sealfon (Mount Sinai School of Medicine)

Barry Smith (NCBO / University at Buffalo)

Andrea Splendiani (Medical Informatics, Rennes, France)

Balaji S. Srinivasan (Stanford University)

Cathy Wu (Protein Ontology / PIR, Georgetown University)

==Venue / Hotel Reservations ==

[http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel]

Participants of the NCBO Workshop on Ontologies of Cellular Networks wishing to stay at the Hilton Newark Airport Hotel can make reservations either by calling 800-HILTONS and asking for the '''"National Center for Biomedical Ontology"''' block, or by entering group/convention code '''"NCB"''' when making reservations online at the [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Newark Airport Hotel] website.

'''NOTE:''' To qualify for the special room block rate of $149 (+ tax) per night, reservations must be secured no later than '''Wednesday, March 5'''. After this date, reservations will be accepted based on availability and at prevailing rates.

==Links ==

* [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]

==Literature==

[http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]

[http://xml.coverpages.org/OntologyExchange.html An evaluation of ontology exchange languages for bioinformatics]