NCBO Wiki - User contributions [en]

Meetings and Events

2006-04-06T12:46:46Z

Ma11: /* Past meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''Gene Ontology Workshop'''
**March 31-April 3, 2006, St. Croix
** Attending: Barry, Michael, Suzi, Chris M.

*'''Fish Evolutionary Biology Working Group Meeting'''
**April 9-11, National Evolutionary Synthesis Center (NESCent), Durham, NC
**Attending: Monte, Paula, Mark G., Chris M.

*'''Phenotype Annotation Meeting'''
**May 19, location on East Coast TBD
**Attending: Monte, Michael, Suzi, BIRN people, Plant Ontology people, etc.

*'''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
**Barry

*'''NSF/RCN workshop on ontology and phylogeny'''
**May 21-24, St. Louis
**Attending: Michael, Suzi, Monte

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''NCBC All Hands Meeting'''
**July 17-19, 2006, Washington, DC
**Attending: Mark, Daniel, Monte, Michael, Chris M., Peggy or Chris Ca., ?

*'''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, Suzi

*'''ISMB, 2006'''
**August 6-19, 2006. Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending: Michael, Suzi (Keynote speaker in Bio-ontologies)

*'''IEEE Computational Systems Bioinformatics, 2006'''
*August, 2006. Stanford University
**[http://conferences.computer.org/bioinformatics/ http://conferences.computer.org/bioinformatics/]
** Attending: Mark Musen (Keynote speaker), rest of Stanford group (tutorial in bioontologies/semantic web)

*'''Anatomy Ontology Workshop'''
**September 8-9, 2006, Seattle
**[[Anatomy Ontology Workshop | information on the Anatomy Ontology Workshop]]
**Attending: Michael, Suzi, Monte, Barry, Fabian

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

*'''Disease Ontology Workshop'''
**In association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University, Baltimore
**[[Workshop on Ontology of Diseases | information on the Disease Ontology Workshop]]
**Attending: Barry, Suzi, Chris, Rex, Monte, Fabian

----
'''2007'''

*'''Ontology Interoperability in Biomedicine'''
**March 27-30, 2007, Dagstuhl, Germany
**Invitation only

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

*'''Ontology Summer School'''
**Aug. ??? 2007, Buffalo

*'''NECTAR Clinical Research Ontology Workshop'''
**???, 2007, Bethesda ???

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

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

== Past meetings ==

* '''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.

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies
** Attending: Barry, Suzi, Stanford Group

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

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

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

*'''[[Minutes & presentations, March 2-4, 2006 Project meeting|cBio Project Meeting]]'''
**March 2-4, 2006, Stanford University
** [[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
** Attending: Carol, Chris C., Suzi, Barry, Stanford group

*'''NLM vocabulary collection and distribution meeting'''
**February 27-28, 2006, NLM, Washington, DC
** Attending: Chris M., Chris C., Harold, Deepak, James, Tom, John?, Archana?

*'''[[cBIO Project Meeting|cbio_proj_meeting_0306]]'''
**March 2-4, 2006

*'''NIAID meeting'''
**February, 2006, DC
**Attending: Mark M.

*'''cBio Phenotype Annotation tool specification'''
**February 21-23, 2006, LBNL
** Attending: Melissa & Sierra (ZFIN), Suzi, Chris M., Mark G., John, Shu (Berkeley)

*'''Mini-Syposium on Semantic Enrichment of Scientific Literature'''
**February 20, 2006 at the European Bioinformatics Institute, Hinxton
**Attending: Michael Ashburner [talk]

*'''cBio OBD specification'''
**February 17, 2006, LBNL
** Attending: Ida & Ben (UCSF), Daniel (Stanford), Suzi, Chris M., Mark G., Sima, Shu (Berkeley)

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

*'''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

*'''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: Suzi, Barry

*'''PharmGKB and cBiO meeting'''
** January 31, 2006, Stanford
** Attending: Daniel (Stanford), Suzi & Sima (Berkeley), Teri Klein, Tina Boussard, Mark Woon, Russ Altman (PharmGKB)

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

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi, Monte
**Introducting new NCBCs to each other and NIH staff

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

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will gave presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-04-06T12:46:02Z

Ma11: /* Past meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''Gene Ontology Workshop'''
**March 31-April 3, 2006, St. Croix
** Attending: Barry, Michael, Suzi, Chris M.

*'''Fish Evolutionary Biology Working Group Meeting'''
**April 9-11, National Evolutionary Synthesis Center (NESCent), Durham, NC
**Attending: Monte, Paula, Mark G., Chris M.

*'''Phenotype Annotation Meeting'''
**May 19, location on East Coast TBD
**Attending: Monte, Michael, Suzi, BIRN people, Plant Ontology people, etc.

*'''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
**Barry

*'''NSF/RCN workshop on ontology and phylogeny'''
**May 21-24, St. Louis
**Attending: Michael, Suzi, Monte

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''NCBC All Hands Meeting'''
**July 17-19, 2006, Washington, DC
**Attending: Mark, Daniel, Monte, Michael, Chris M., Peggy or Chris Ca., ?

*'''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, Suzi

*'''ISMB, 2006'''
**August 6-19, 2006. Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending: Michael, Suzi (Keynote speaker in Bio-ontologies)

*'''IEEE Computational Systems Bioinformatics, 2006'''
*August, 2006. Stanford University
**[http://conferences.computer.org/bioinformatics/ http://conferences.computer.org/bioinformatics/]
** Attending: Mark Musen (Keynote speaker), rest of Stanford group (tutorial in bioontologies/semantic web)

*'''Anatomy Ontology Workshop'''
**September 8-9, 2006, Seattle
**[[Anatomy Ontology Workshop | information on the Anatomy Ontology Workshop]]
**Attending: Michael, Suzi, Monte, Barry, Fabian

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

*'''Disease Ontology Workshop'''
**In association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University, Baltimore
**[[Workshop on Ontology of Diseases | information on the Disease Ontology Workshop]]
**Attending: Barry, Suzi, Chris, Rex, Monte, Fabian

----
'''2007'''

*'''Ontology Interoperability in Biomedicine'''
**March 27-30, 2007, Dagstuhl, Germany
**Invitation only

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

*'''Ontology Summer School'''
**Aug. ??? 2007, Buffalo

*'''NECTAR Clinical Research Ontology Workshop'''
**???, 2007, Bethesda ???

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

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

== Past meetings ==

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

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies
** Attending: Barry, Suzi, Stanford Group

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

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

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

*'''[[Minutes & presentations, March 2-4, 2006 Project meeting|cBio Project Meeting]]'''
**March 2-4, 2006, Stanford University
** [[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
** Attending: Carol, Chris C., Suzi, Barry, Stanford group

*'''NLM vocabulary collection and distribution meeting'''
**February 27-28, 2006, NLM, Washington, DC
** Attending: Chris M., Chris C., Harold, Deepak, James, Tom, John?, Archana?

*'''[[cBIO Project Meeting|cbio_proj_meeting_0306]]'''
**March 2-4, 2006

*'''NIAID meeting'''
**February, 2006, DC
**Attending: Mark M.

*'''cBio Phenotype Annotation tool specification'''
**February 21-23, 2006, LBNL
** Attending: Melissa & Sierra (ZFIN), Suzi, Chris M., Mark G., John, Shu (Berkeley)

*'''Mini-Syposium on Semantic Enrichment of Scientific Literature'''
**February 20, 2006 at the European Bioinformatics Institute, Hinxton
**Attending: Michael Ashburner [talk]

*'''cBio OBD specification'''
**February 17, 2006, LBNL
** Attending: Ida & Ben (UCSF), Daniel (Stanford), Suzi, Chris M., Mark G., Sima, Shu (Berkeley)

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

*'''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

*'''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: Suzi, Barry

*'''PharmGKB and cBiO meeting'''
** January 31, 2006, Stanford
** Attending: Daniel (Stanford), Suzi & Sima (Berkeley), Teri Klein, Tina Boussard, Mark Woon, Russ Altman (PharmGKB)

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

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi, Monte
**Introducting new NCBCs to each other and NIH staff

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

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will gave presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-02-22T16:47:40Z

Ma11: /* Past meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

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

*'''NIAID meeting'''
**February, 2006, DC
**Attending: Mark M.

*'''cBio OBD specification'''
**February 17, 2006, LBNL
** Attending: Ida, Ben, Suzi, Chris M., Mark G., Sima, Shu

*'''cBio Phenotype Annotation tool specification'''
**February 21-23, 2006, LBNL
** Attending: Melissa, Suzi, Chris M., Mark G., John, Shu

*'''NLM vocabulary collection and distribution meeting'''
**February 27-28, 2006, NLM, Washington, DC
** Attending: Chris M., Chris C., Harold, Deepak, James, Tom, John?, Archana?

*'''BIRN ontology workshop'''
**February 28-March 1, 2006, Stanford
** Attending: Carol, Chris C., Stanford group

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford University
** [[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

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

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

*'''NIAID Ontology Workshop: Focus on Immunity'''
**March 21-22, 2006, Bethesda, MD
** Attending: Mark (Session chair), Suzi (speaker)

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

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

*'''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
**Barry

*'''NSF/RCN workshop on ontology and phylogeny'''
**May 21-24, St. Louis
**Attending: Michael, Suzi

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''NCBC All Hands Meeting'''
**July 17-19, 2006, Washington, DC
**Attending: Mark, Daniel, Sima, Chris M., ?

*'''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

*'''ISMB, 2006'''
**August 6-19, 2006. Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending: Michael, Suzi (Keynote speaker in Bio-ontologies), Nipam & Fabian (Tutorial)

*'''IEEE Computational Systems Bioinformatics, 2006'''
*August, 2006. Stanford University
**[http://conferences.computer.org/bioinformatics/ http://conferences.computer.org/bioinformatics/]
** Attending: Mark Musen (Keynote speaker), rest of Stanford group (tutorial in bioontologies/semantic web)

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

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

== Past meetings ==

*'''Mini-Syposium on Semantic Enrichment of Scientific Literature'''
**February 20, 2006 at the European Bioinformatics Institute, Hinxton
**Attending: Michael Ashburner [talk]

*'''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

*'''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: Suzi, Barry

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

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi, Monte
**Introducting new NCBCs to each other and NIH staff

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

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will gave presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-02-22T16:47:13Z

Ma11: /* Upcoming meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

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

*'''NIAID meeting'''
**February, 2006, DC
**Attending: Mark M.

*'''cBio OBD specification'''
**February 17, 2006, LBNL
** Attending: Ida, Ben, Suzi, Chris M., Mark G., Sima, Shu

*'''cBio Phenotype Annotation tool specification'''
**February 21-23, 2006, LBNL
** Attending: Melissa, Suzi, Chris M., Mark G., John, Shu

*'''NLM vocabulary collection and distribution meeting'''
**February 27-28, 2006, NLM, Washington, DC
** Attending: Chris M., Chris C., Harold, Deepak, James, Tom, John?, Archana?

*'''BIRN ontology workshop'''
**February 28-March 1, 2006, Stanford
** Attending: Carol, Chris C., Stanford group

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford University
** [[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

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

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

*'''NIAID Ontology Workshop: Focus on Immunity'''
**March 21-22, 2006, Bethesda, MD
** Attending: Mark (Session chair), Suzi (speaker)

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

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

*'''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
**Barry

*'''NSF/RCN workshop on ontology and phylogeny'''
**May 21-24, St. Louis
**Attending: Michael, Suzi

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''NCBC All Hands Meeting'''
**July 17-19, 2006, Washington, DC
**Attending: Mark, Daniel, Sima, Chris M., ?

*'''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

*'''ISMB, 2006'''
**August 6-19, 2006. Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending: Michael, Suzi (Keynote speaker in Bio-ontologies), Nipam & Fabian (Tutorial)

*'''IEEE Computational Systems Bioinformatics, 2006'''
*August, 2006. Stanford University
**[http://conferences.computer.org/bioinformatics/ http://conferences.computer.org/bioinformatics/]
** Attending: Mark Musen (Keynote speaker), rest of Stanford group (tutorial in bioontologies/semantic web)

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

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

== Past meetings ==

*'''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

*'''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: Suzi, Barry

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

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi, Monte
**Introducting new NCBCs to each other and NIH staff

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

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will gave presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-02-09T09:25:24Z

Ma11: /* Upcoming meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''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

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

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

*'''cBio OBD specification'''
**February 17, 2006, LBNL
** Attending: Ida, Ben, Suzi, Chris M., Mark, Sima, Shu

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

*'''cBio Phenotype Annotation tool specification'''
**February 21-23, 2006, LBNL
** Attending: Melissa, Suzi, Chris M., Mark, John, Shu

*'''NLM vocabulary collection and distribution meeting'''
**February 27-28, 2006, NLM, Washington, DC
** Attending: Chris M., Chris C., Harold, Deepak, James, Tom, John?, Archana?

*'''BIRN ontology workshop'''
**February 28-March 1, 2006, Stanford
** Attending: Carol, Chris C., Stanford group

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford University
** [[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

*'''NIAID Ontology Workshop: Focus on Immunity'''
**March 21-22, 2006, Bethesda, MD
** Attending: Mark (Session chair), Suzi (speaker)

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

*'''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
**Barry

*'''NSF/RCN workshop on ontology and phylogeny'''
**May 21-24, St. Louis
**Attending: Michael, Suzi

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''NCBC All Hands Meeting'''
**July 17-19, 2006, Washington, DC

*'''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

*'''ISMB, 2006'''
**August 6-19, 2006. Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending: Michael, Suzi (Keynote speaker in Bio-ontologies), Nipam & Fabian (Tutorial)

*'''IEEE Computational Systems Bioinformatics, 2006'''
*August, 2006. Stanford University
**[http://conferences.computer.org/bioinformatics/ http://conferences.computer.org/bioinformatics/]
** Attending: Mark Musen (Keynote speaker), rest of Stanford group (tutorial in bioontologies/semantic web)

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

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

== Past meetings ==

*'''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: Suzi, Barry

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

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi, Monte
**Introducting new NCBCs to each other and NIH staff

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

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will gave presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-02-09T09:24:10Z

Ma11: /* Upcoming meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''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

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

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

*'''cBio OBD specification'''
**February 17, 2006, LBNL
** Attending: Ida, Ben, Suzi, Chris M., Mark, Sima, Shu

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

*'''cBio Phenotype Annotation tool specification'''
**February 21-23, 2006, LBNL
** Attending: Melissa, Suzi, Chris M., Mark, John, Shu

*'''NLM vocabulary collection and distribution meeting'''
**February 27-28, 2006, NLM, Washington, DC
** Attending: Chris M., Chris C., Harold, Deepak, James, Tom, John?, Archana?

*'''BIRN ontology workshop'''
**February 28-March 1, 2006, Stanford
** Attending: Carol, Chris C., Stanford group

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford University
** [[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

*'''NIAID Ontology Workshop: Focus on Immunity'''
**March 21-22, 2006, Bethesda, MD
** Attending: Mark (Session chair), Suzi (speaker)

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

*'''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
**Barry

*'''NSF/RCN workshop on ontology and phylogeny'''
**Late May
**Attending: Michael, Suzi

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''NCBC All Hands Meeting'''
**July 17-19, 2006, Washington, DC

*'''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

*'''ISMB, 2006'''
**August 6-19, 2006. Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending: Michael, Suzi (Keynote speaker in Bio-ontologies), Nipam & Fabian (Tutorial)

*'''IEEE Computational Systems Bioinformatics, 2006'''
*August, 2006. Stanford University
**[http://conferences.computer.org/bioinformatics/ http://conferences.computer.org/bioinformatics/]
** Attending: Mark Musen (Keynote speaker), rest of Stanford group (tutorial in bioontologies/semantic web)

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

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

== Past meetings ==

*'''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: Suzi, Barry

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

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi, Monte
**Introducting new NCBCs to each other and NIH staff

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

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will gave presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

File:OBO-criteria-v7.doc

2006-01-14T18:41:25Z

Ma11:

File:OBO-criteria-v6.1.doc

2006-01-11T21:38:44Z

Ma11: Minor edit made. Michael

Minor edit made. Michael

Meetings and Events

2006-01-11T21:31:40Z

Ma11: /* Past meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''ISMB, 2006'''
**August 6-19, 2006. Fortaleza, Brazil.
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]
** Attending
*** From cBio: Michael Ashburner, Suzanna Lewis

*'''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
*** From cBio: Michael Ashburner

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford Unversity
**Entire project & Scientific Advisory board
**Project meeting & internal workshop led by Barry.

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

*'''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
**Barry

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

== Past meetings ==

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Phenotype Annotation Meeting'''
**December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]
** Attending
*** From ZFIN: Monte Westerfield, Erik Segerdell, Melissa Haendel, Paula Mabee
*** From FlyBase: Gillian Millburn (hopefully George Gkoutos as well)
*** From Berkeley: Suzi Lewis, John Day-Richter, Chris Mungall, Mark Gibson
*** From Victoria: Peggy Storey, Chris Callendar, Sean Falconer
** Define requirements of phenotype annotation tools

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi
**Introducting new NCBCs to each other and NIH staff

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will gave presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-01-11T21:31:01Z

Ma11: /* Upcoming meetings */

Meetings and Events

2006-01-11T21:13:26Z

Ma11: /* Past meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Phenotype Annotation Meeting'''
**December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]
** Attending
*** From ZFIN: Monte Westerfield, Erik Segerdell, Melissa Haendel, Paula Mabee
*** From FlyBase: Gillian Millburn (hopefully George Gkoutos as well)
*** From Berkeley: Suzi Lewis, John Day-Richter, Chris Mungall, Mark Gibson
*** From Victoria: Peggy Storey, Chris Callendar, Sean Falconer
** Define requirements of phenotype annotation tools

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi
**Introducting new NCBCs to each other and NIH staff

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford Unversity
**Entire project & Scientific Advisory board
**Project meeting & internal workshop led by Barry.

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

*'''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
**Barry

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

== Past meetings ==

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will give presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-01-11T21:13:05Z

Ma11: /* Past meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Phenotype Annotation Meeting'''
**December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]
** Attending
*** From ZFIN: Monte Westerfield, Erik Segerdell, Melissa Haendel, Paula Mabee
*** From FlyBase: Gillian Millburn (hopefully George Gkoutos as well)
*** From Berkeley: Suzi Lewis, John Day-Richter, Chris Mungall, Mark Gibson
*** From Victoria: Peggy Storey, Chris Callendar, Sean Falconer
** Define requirements of phenotype annotation tools

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi
**Introducting new NCBCs to each other and NIH staff

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford Unversity
**Entire project & Scientific Advisory board
**Project meeting & internal workshop led by Barry.

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

*'''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
**Barry

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

== Past meetings ==

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will give presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil'''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-01-11T21:12:28Z

Ma11: /* Past meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Phenotype Annotation Meeting'''
**December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]
** Attending
*** From ZFIN: Monte Westerfield, Erik Segerdell, Melissa Haendel, Paula Mabee
*** From FlyBase: Gillian Millburn (hopefully George Gkoutos as well)
*** From Berkeley: Suzi Lewis, John Day-Richter, Chris Mungall, Mark Gibson
*** From Victoria: Peggy Storey, Chris Callendar, Sean Falconer
** Define requirements of phenotype annotation tools

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi
**Introducting new NCBCs to each other and NIH staff

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford Unversity
**Entire project & Scientific Advisory board
**Project meeting & internal workshop led by Barry.

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

*'''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
**Barry

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

== Past meetings ==

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will give presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil''''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Meetings and Events

2006-01-11T21:11:49Z

Ma11: /* Past meetings */

On the [http://datebook.stanford.edu:88/cBiO_Calendar internal calendar].

== Upcoming meetings ==

*'''Phenotype Ontology Content Workshop'''
**Nov. 19-20, 2005, CSHL
** Attending
*** From cBio: Mark, Nigam, Suzi, Chris, John, Michael, George, Monte, Erik (not Barry)
*** Jonathan Bard, XSPAN
*** Thomas Bittner, Lou Goldberg, Fabian Neuhaus, NCOR
*** Judy Blake, MGD
*** Mike Cherry, Jane Lomax, GO
*** Rex Chisolm, Pascale Gaudet, NuGene project
*** Rachel Drysdale, FlyBase
*** Akhilesh Pandey, OMIM
*** Anne Kwitek, RGD
*** Yves Lussier, SNOMED
** [[Media:PhenoAgenda.doc]]

*'''Stanford/Mayo/Berkeley Meetings'''
**Nov. 21, 10am-3pm, Stanford; Nov. 22, 10am-3pm, Berkeley
** Attending
*** From Stanford: Mark, Daniel, Archana, Lynn, Nigam
*** From Berkeley: Suzi, Chris, Sima, Shu, Nomi
*** From Mayo: Deepak, Harold, Jim
** [[Draft Agenda, Mayo/Berkeley Visit, Monday, Nov 21, 2005]]

*'''Phenotype Annotation Meeting'''
**December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]
** Attending
*** From ZFIN: Monte Westerfield, Erik Segerdell, Melissa Haendel, Paula Mabee
*** From FlyBase: Gillian Millburn (hopefully George Gkoutos as well)
*** From Berkeley: Suzi Lewis, John Day-Richter, Chris Mungall, Mark Gibson
*** From Victoria: Peggy Storey, Chris Callendar, Sean Falconer
** Define requirements of phenotype annotation tools

*'''NCBC Meeting'''
**Dec. 15-16, NIH
**Attending: Mark, Suzi
**Introducting new NCBCs to each other and NIH staff

*'''cBio Project Meeting'''
**March 2-4, 2006, Stanford Unversity
**Entire project & Scientific Advisory board
**Project meeting & internal workshop led by Barry.

*'''Biomedical Image Ontology Workshop'''
**March 24-25, 2006, Stanford University
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies

*'''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
**Barry

*'''Biomedical Ontology Workshop in association with FOIS 2006 (Formal Ontology and Information Systems)
**November 6-8, 2006, John Hopkins University
**Barry

*'''NCBC Biomedical Ontology Workshop'''
**Later in 2006
**Other NCBC's

*'''American Society of Human Genetics'''
**October 10-14, 2006, New Orleans, LA
**Presentation to find collaborators, also ontology workshop

== Past meetings ==

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

*'''National Bioinformatics Network, South Africa'''
**December 2, 2005, University of Cape Town.
**Michael Ashburner, Keynote talk at Official Opening.

*'''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: Suzi, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill
**Training session on making ontologies better

*'''Forbes Dewey Meeting'''
**Late October, MIT
**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, CSHL
**Suzi will give presentation on cBio.
**Birds of a feather sessions, one on ontology.

*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology, Caxambu, Brazil''''
**October, 2006
**Michael Ashburner, Keynote.

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

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

Phenotype Reading List

2005-12-14T16:40:30Z

Ma11: /* Papers by George */

=Phenotype readling list=

I have some of these in my endnote library, but endnote is terrible
for collecting non-bio references. I'm guessing the CS and logiv
people use Latex? If so, if they post their bibtexes here I can
compile both an endnote and a bibtex library.

==Intro to phenotypes for non-biologists==

This list is very fly-centric. If someone can contribute zebrafish and
human clinical genetics pointers that would be great.

===Genetics of Development===

Only looked briefly at this, but seems like it might be a useful non-biologists intro. Nice images.

http://www.learner.org/channel/courses/biology/units/gendev/

===EBI Introduction to cell biology===

This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist

http://www.ebi.ac.uk/microarray/biology_intro.html

===Drysdale R: Phenotypic data in FlyBase===
Brief Bioinform 2001,2(1):68-80.

This is an ideal intro for folks familiar with biological databases
looking to make the first step into genetics and phenotypes.

===Essential Developmental Biology===
by J. M. W. Slack

http://books.google.com/books?ie=UTF-8&hl=en&id=BXfdbKLTiZQC&dq=essential+developmental+biology&prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&lpg=PP5&pg=PP5&printsec=4&sig=FIivE3wd7u_AC9ojAEdW-BpD90A

I found this to be a really useful and accessible introduction to
developmental biology. Remember, most of the phenotypes we're dealing
with will be developmental. It may be challenging for those with
virtually no biology, but I'd still highly recommend it. Covers fly,
zebrafish and other major model organisms.

===Other books===

Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994

Lewin B: Genes VII, New York, Oxford University Press, 2000

===THE ART AND DESIGN OF GENETIC SCREENS===

This is actually a whole collection of reviews in Nature Reviews
Genetics coverisg zebrafish, mouse, etc. Go to their website and
search on the above:

http://search.nature.com/search/?sp_a=sp1001702d&sp_sfvl_field=subject%7Cujournal&sp_t=results&sp_q_1=Nature+Reviews+Genetics&sp_x_1=ujournal&sp_p_1=phrase&go.x=0&go.y=0&sp-q=the+art+and+design+of+genetic+screens

Here's the one on zebrafish
http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4

These are highly recommended for the tools developers

===The Making of a Fly: The Genetics of Animal Design [BOOK]===

http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&n=283155

May be hard going for those without any knowledge of genetics

===Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]===
aka the grey book
http://www.cshlpress.com/default.tpl?action=full&cart=1133810703113928&--eqskudatarq=467&newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition

Everything you ever wanted to know about Drosophila genetics but were
afraid to ask Michael. This may be a little overwhelming for the CS
folks

==Formal ontology and logic==

References on formal ontology and logic and qualities that are tied to
qualities

===A formal theory of substances, qualities, and universals.===

Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.:
Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS
Press (2004) 49–59

Available from: http://ontology.buffalo.edu/bfo/SQU.pdf

This paper may be heavy-going for those without a background in logic,
but I would still highly recommend the first couple of pages to
everyone involved in this project.

===Stanford Encyclopedia of Philosophy===

Entry on properties: http://plato.stanford.edu/entries/properties/

I think properties here are used in the sense that Fabian Neuhaus and
I would use "quality", rather than in the looser sense that a CS or
OWL person may use the term.

Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/

I was hesitant about adding this one. Inquiring minds may want to
check this out. Determinate vs determinable roughly corresponds to
value vs attribute

==Data modeling==

===J. Diederich. Basic properties for biological databases: character development and support===
in Math. Comput. Modelling 25 (1997), 109-127.

Required reading for everyone in the project. 1997, but it anticipated
many of the problems we are facing. This has more of a systematics
focus, but really the design of ontologies for phenotypic characters
should be independent of whether we are applying this to genetic
screens or to phylogenetic classisification.

==See also an application of the work from this paper in:
Diederich, J., R. Fortuner and J. Milton. 1997. Construction and integration
of large character sets for nematode morpho-anatomical data. ''Fundam. appl. Nematol.'' 20: 409-424

===Papers by George===

George gets his own section here. The GB is paper is a good
introduction to the EAV model as it was originally formulated in 2003.

Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building
mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.
http://helix-web.stanford.edu/psb04/gkoutos.pdf

Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using
ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.
http://dx.doi.org/10.1186/gb-2004-6-1-r8

G. V. Gkoutos, E. C. J. Green, A.-M. Mallon, A. Blake, S. Greenaway 1, J. M. Hancock, D. Davidson
Ontologies for the description of mouse phenotypes
MRC Mammalian Genetics Unit, Harwell, UK
http://doi.wiley.com/10.1002/cfg.430

Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM:
CRAVE: a database, middleware and visualization system for phenotype
ontologies. Bioinformatics 2005, 21(7):1257-1262.
http://www.bioinformatics.oupjournals.org/cgi/doi/10.1093/bioinformatics/bti147

[[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)

Phenotype Reading List

2005-12-14T16:39:29Z

Ma11: /* Basic properties for biological databases: character development and support */

=Phenotype readling list=

I have some of these in my endnote library, but endnote is terrible
for collecting non-bio references. I'm guessing the CS and logiv
people use Latex? If so, if they post their bibtexes here I can
compile both an endnote and a bibtex library.

==Intro to phenotypes for non-biologists==

This list is very fly-centric. If someone can contribute zebrafish and
human clinical genetics pointers that would be great.

===Genetics of Development===

Only looked briefly at this, but seems like it might be a useful non-biologists intro. Nice images.

http://www.learner.org/channel/courses/biology/units/gendev/

===EBI Introduction to cell biology===

This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist

http://www.ebi.ac.uk/microarray/biology_intro.html

===Drysdale R: Phenotypic data in FlyBase===
Brief Bioinform 2001,2(1):68-80.

This is an ideal intro for folks familiar with biological databases
looking to make the first step into genetics and phenotypes.

===Essential Developmental Biology===
by J. M. W. Slack

http://books.google.com/books?ie=UTF-8&hl=en&id=BXfdbKLTiZQC&dq=essential+developmental+biology&prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&lpg=PP5&pg=PP5&printsec=4&sig=FIivE3wd7u_AC9ojAEdW-BpD90A

I found this to be a really useful and accessible introduction to
developmental biology. Remember, most of the phenotypes we're dealing
with will be developmental. It may be challenging for those with
virtually no biology, but I'd still highly recommend it. Covers fly,
zebrafish and other major model organisms.

===Other books===

Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994

Lewin B: Genes VII, New York, Oxford University Press, 2000

===THE ART AND DESIGN OF GENETIC SCREENS===

This is actually a whole collection of reviews in Nature Reviews
Genetics coverisg zebrafish, mouse, etc. Go to their website and
search on the above:

http://search.nature.com/search/?sp_a=sp1001702d&sp_sfvl_field=subject%7Cujournal&sp_t=results&sp_q_1=Nature+Reviews+Genetics&sp_x_1=ujournal&sp_p_1=phrase&go.x=0&go.y=0&sp-q=the+art+and+design+of+genetic+screens

Here's the one on zebrafish
http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4

These are highly recommended for the tools developers

===The Making of a Fly: The Genetics of Animal Design [BOOK]===

http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&n=283155

May be hard going for those without any knowledge of genetics

===Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]===
aka the grey book
http://www.cshlpress.com/default.tpl?action=full&cart=1133810703113928&--eqskudatarq=467&newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition

Everything you ever wanted to know about Drosophila genetics but were
afraid to ask Michael. This may be a little overwhelming for the CS
folks

==Formal ontology and logic==

References on formal ontology and logic and qualities that are tied to
qualities

===A formal theory of substances, qualities, and universals.===

Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.:
Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS
Press (2004) 49–59

Available from: http://ontology.buffalo.edu/bfo/SQU.pdf

This paper may be heavy-going for those without a background in logic,
but I would still highly recommend the first couple of pages to
everyone involved in this project.

===Stanford Encyclopedia of Philosophy===

Entry on properties: http://plato.stanford.edu/entries/properties/

I think properties here are used in the sense that Fabian Neuhaus and
I would use "quality", rather than in the looser sense that a CS or
OWL person may use the term.

Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/

I was hesitant about adding this one. Inquiring minds may want to
check this out. Determinate vs determinable roughly corresponds to
value vs attribute

==Data modeling==

===J. Diederich. Basic properties for biological databases: character development and support===
in Math. Comput. Modelling 25 (1997), 109-127.

Required reading for everyone in the project. 1997, but it anticipated
many of the problems we are facing. This has more of a systematics
focus, but really the design of ontologies for phenotypic characters
should be independent of whether we are applying this to genetic
screens or to phylogenetic classisification.

==See also an application of the work from this paper in:
Diederich, J., R. Fortuner and J. Milton. 1997. Construction and integration
of large character sets for nematode morpho-anatomical data. ''Fundam. appl. Nematol.'' 20: 409-424

===Papers by George===

George gets his own section here. The GB is paper is a good
introduction to the EAV model as it was originally formulated in 2003.

Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building
mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.
http://helix-web.stanford.edu/psb04/gkoutos.pdf

Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using
ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.
http://dx.doi.org/10.1186/gb-2004-6-1-r8

G. V. Gkoutos 1 *, E. C. J. Green 1, A.-M. Mallon 1, A. Blake 1, S. Greenaway 1, J. M. Hancock 1, D. Davidson 2
Ontologies for the description of mouse phenotypes
MRC Mammalian Genetics Unit, Harwell, UK
http://doi.wiley.com/10.1002/cfg.430

Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM:
CRAVE: a database, middleware and visualization system for phenotype
ontologies. Bioinformatics 2005, 21(7):1257-1262.
http://www.bioinformatics.oupjournals.org/cgi/doi/10.1093/bioinformatics/bti147

[[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)