NCBO Wiki - User contributions [en]

Dissemination Wiki

2007-08-15T21:19:55Z

TedHopper: restoring correct page name link pointing to http://www.bioontology.org/wiki/index.php/Ontology_and_Cellular_Networks

==NCBO Dissemination ==

What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to events relevant to the NCBO's mission.

==Workshops 2006==

'''[[Workshops 2006]]'''

== Workshops 2007 ==

'''Mar 27-30, 2007'''

[http://www.dagstuhl.de/de/programm/kalender/semhp/?semid=29453 Towards Interoperability of Biomedical Ontologies], Schloss Dagstuhl, Germany.

'''May 16-17, 2007'''

[[Workshop on Clinical Trial Ontology]], Bethesda, MD

'''June 20-23, 2007'''

[http://www.ifomis.uni-saarland.de/Events/OntospringIII.html Training Course on Logical and Computational Tools for Biomedical Ontology Development, Schloss Dagstuhl, Germany.]

'''July 21, 2007'''

[[Ontologies for Biomedicine – How to make and use them]], Tutorial by Barry Smith and Nigam Shah at ISMB 2007

'''October 30-31, 2007'''

[[Ontology_and_Cellular_Networks]], Newark, NJ

== Related Events ==

'''[[Related Events 2007]]'''

'''January 29, 2007'''

[[Media:OverviewJan07LaJollaCJM.ppt|Overview Presentation]] of GO, NCBO, Phenotypes, and OBO Foundry by Suzi Lewis at the Ontologies for Biomedical Investigation Workshop, San Diego, CA

'''July 15, 2007'''

Tutorial, Building and Applying Biomedical Ontologies, Budapest, [http://protege.stanford.edu/conference/2007/ Protégé Conference] (BS)

'''July 22, 2007'''

Tutorial, [http://www.bioontology.org/wiki/index.php/Ontologies_for_Biomedicine_%E2%80%93_How_to_make_and_use_them Ontologies for Biomedicine], ISMB Conference, Vienna (BS and Nigam Shah)

'''December 2-4, 2007'''

Protein Ontology Kick-Off Meeting ([[PRO]]), Georgetown University, Washington DC.

Main Page

2007-06-12T05:04:11Z

TedHopper: Undo revision 5708 by Wwwzhudan (Talk) to remove spam content

Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br>
dissemination events conducted by the NCBO and publically shared materials from the NCBO.

=== NCBO Links ===
*[http://www.bioontology.org/ NCBO Home page]
*[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]
*[[Meetings and Events]]

=== Shared Materials===

*[[Public Requirements Redirect|Public Requirements]]

*[[Shared Materials]]

*[[Evaluation Activities]]

=== NCBC Links ===

*[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]

*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]

=== Ontology Development Area ===

Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki

*[[PATO:Main_Page]] - An ontology of phenotypic qualities

*[[RO:Main_Page]] - OBO Relations ontology

*[[CARO:Main_Page]] - Reference anatomical ontology

*[[CL:Main_Page]] - OBO Cell ontology

*[[SO:Main_Page]] - Sequence Ontology

*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders

*[[CTO:Main_Page]] - Clinical Trial Ontology

Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.

=== Software Development Area ===
*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
*[[Bioportal:Main_Page]]

BIRN Ontology workshop

2007-01-08T22:30:00Z

TedHopper: /* Useful Links */ fixed link to Image Ontology Workshop page, which was still pointing to the legacy cbio wiki

The [http://ncbo.us National Center for Biomedical Ontology] will be hosting a BIRN Ontology Workshop in Stanford on February 28 and March 1, 2006.

[[Workshop_Agenda]]

[http://www.smi.stanford.edu/research/cbio/cbio_birn_workshop.html Logistics]

[[Birn_Slides | Birn Slides]]

== Useful Links ==

[http://sigpubs.biostr.washington.edu/archive/00000160/ Problems and Solutions with Integrating Terminologies into Evolving Knowledge Bases]

[http://braininfo.rprc.washington.edu/menumain.html NeuroNames]

[http://nbirn.net/Resources/Users/Ontologies/index.htm BIRN Ontologies]

[http://www.comp.leeds.ac.uk/qsr/publications.html Qualitative Spatial Reasoning]

[http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]

[http://users.sdsc.edu/~ludaesch/Paper/diseasemap-final.pdf Towards a formalization of disease-specific ontologies for neuroinformatics]

[http://www.sdsc.edu/~ludaesch/Paper/BIRN-ontologies-AHM03.ppt BIRN Ontologies Session 2003]

See also the website for the [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images Image Ontology Workshop]

Dissemination Wiki

2007-01-08T22:21:53Z

TedHopper: /* Workshops */ fixing link to BIRN Ontology Workshop, which was still pointing to the legacy wiki

==NCBO Dissemination Core==

What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to events relevant to the NCBO's mission.

==Workshops==

'''Feb 28-March 1, 2006'''

[http://www.bioontology.org/wiki/index.php/BIRN_Ontology_workshop BIRN Ontology Workshop], Stanford University

'''March 24-25, 2006'''

[[Workshop on Ontology of Images]], Stanford University

'''May 21-24, 2006'''

[http://ontology.buffalo.edu/06/os2/index.html Training Course in Biomedical Ontology], Schloss Dagstuhl, Germany

'''September 8-9, 2006'''

[[Anatomy Ontology Workshop]], Seattle

'''November 6-7, 2006'''

[[Workshop on Ontology of Diseases]], Baltimore

'''November 30-December 2, 2006'''

[[PATO Meeting]] Stanford University Clark Center

'''May 16-17, 2007'''

[[Workshop on Clinical Trial Ontology]], venue tbd

'''June 20-23, 2007'''

[http://www.ifomis.uni-saarland.de/Events/OntospringIII.html Training Course on Logical and Computational Tools for Biomedical Ontology Development, Schloss Dagstuhl, Germany.]

== Related Events ==

'''July 19, 2006'''

[http://www.bisti.nih.gov/ahm2006/ncbo_dissemination.htm Ontology: A Vision for the Future and Its Realization], National Institutes of Health NCBC All-Hands Meeting, Bethesda MD.
*[[Media:Musen AHM Dissemination Event.pdf|Musen Slides]]

*[http://obofoundry.org/Smith_OBOFoundry_071906.ppt Smith Slides]

'''August 6, 2006'''

[http://ismb2006.cbi.cnptia.embrapa.br/ Keynote Address by Suzanna Lewis], ISMB 2006.
*[[Media:Lewis ISMB 2006 Keynote CSB.pdf|Lewis Slides]]

'''August 15, 2006'''

[http://www.lifesciencessociety.org/CSB2006/Abstracts/musenAbstract.pdf Keynote Address by Mark Musen], CSB 2006, Stanford 1:30-2:30pm.
*[[Media:Musen Keynote CSB.pdf|Musen Slides]]

'''August 27, 2006'''

[http://ontology.buffalo.edu/06/MIE_Tutorial.htm Tutorial on Standards and Ontologies], Medical Informatics Europe, Maastricht, Netherlands.

'''October 14-15, 2006'''

[http://ontology.buffalo.edu/06/pob Workshop on Philosophy of Biology], Buffalo.

'''October 25, 2006'''

How to Build an Ontology. Tutorial by Barry Smith at NCBO project meeting
*[[Media:BarrySmithTutorialNCBO.ppt | Smith Slides]]

*Windows Media Player: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV

*RealOne Player Streaming Video: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm

'''November 8, 2006'''

[http://www.imbi.uni-freiburg.de/medinf/kr-med-2006/index.html Biomedical Ontology in Action], KR-MED 2006, Baltimore.

'''November 11, 2006'''

[http://ontology.buffalo.edu/06/Biomedical_Imaging_Ontologies.pdf Biomedical Imaging Ontologies], AMIA, Washington DC

'''November 12, 2006'''

[http://ontology.buffalo.edu/06/AMIAWorkshop.htm Genomics Knowledge Representation for Clinical Trials], AMIA, Washington DC

ISWC Workshop, Pathway Knowledge Base, Presentation by Nigam Shah
*[[Media:Nigam-PKB.ppt|Shah Slides]]

'''November 14, 2006'''

[http://ontology.buffalo.edu/HL7/panel.htm Panel on the Future of HL7], AMIA, Washington, 3.30-5.00pm.
*[http://www.org.buffalo.edu/RTU/papers/HL7-AMIA2006.ppt Ceusters Slides]
*[http://ontology.buffalo.edu/HL7/AMIA_06_Audio/Ceusters.WMA Ceusters Audio]
*[http://ontology.buffalo.edu/hl7/AMIA_06.ppt Smith Slides]
*[http://ontology.buffalo.edu/HL7/AMIA_06_Audio/Smith.WMA Smith Audio]

AMIA Workshop, Formal Structuring of Genomics Knowledge, Presentations by Nigam Shah and Barry Smith
*[[Media:Nigam1.ppt|Shah Slides]]
*[http://ontology.buffalo.edu/ontology/medo/ClinicalTrialOntology/AMIA_Genome_Nov06.ppt Smith Slides]

Ontology-Driven Annotation of TMA Data, AMIA Presentation by Nigam Shah
*[[Media:Nigam2.ppt|Shah Slides]]

AMIA Tutorial on Ontologies by Mark Musen
*[[Media:Musen-AMIA2006.ppt|Musen Slides]]

'''November 20-21, 2006'''

BioPAX Tutorial. [http://biopaxwiki.org/cgi-bin/moin.cgi/SmithWorkshopInformation exploratory workshop and tutorial] on '''Connecting BioPAX to Other Biomedical Ontologies''' at MIT.

'''December 21, 2006'''

Ontolog Forum Talk by Barry Smith on [http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRW3 Ontology Evaluation in Biomedicine]: The OBO Foundry -- A Gold Standard Approach to Ontology Evaluation.
*[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRWB Smith Slides]
*[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRWQ Smith Audio]

Meetings and Events

2007-01-03T18:33:48Z

TedHopper: /* Past meetings */ inserting meetings from 2nd half of 2006 and cleaning up formatting

== 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.

*'''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

2007-01-03T18:04:58Z

TedHopper: /* Upcoming meetings */ moving past events down to proper section and removed 2007 subheader

== 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.

*'''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

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

*'''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)

PATO Meeting

2007-01-03T17:58:48Z

TedHopper: /* Minutes */

== General Information and Registration ==
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day meeting focused on the [http://obo.sourceforge.net/cgi-bin/detail.cgi?attribute_and_value Phenotype and Trait Ontology (PATO)] December 1-2, 2006 at Stanford University in Palo Alto, CA.

[http://www.fruitfly.org/pato/pato-form.html Register here.]

==Agenda==
[[Media:Pheno_workshop_Dec2006.pdf]]

==Minutes==

[http://www.bioontology.org/wiki/images/c/c6/Updated_Meeting_Notes.pdf Media: Updated Meeting Minutes]

==Presentations==

'''Day 1 presentations'''

Gully Burns: Ontology engineering approaches based on semi-automated curation of the primary literature [[Media:GullyBurns.ppt]]

Alexander Garcia: The use of concept maps and automatic terminology extraction during development of a domain ontology: Lessons learnt [[Media:AlexanderGarcia.ppt]]

Adrien Coulet: Suggested ontology for pharmacogenomics (SO-Pharm): modular construction and preliminary testing [[Media:Adrien Coulet.pdf]]

Tina Hernandez-Broussard: Challenges for representing phenotype in pharmacogenomics [[Media:TinaHernandez.ppt]]

James Reecy: A project for the Creation of a Unified Trait Vocabulary for Farm Animals [[Media:JamesReecy.ppt]]

Victoria Petri: Rat genome database disease portals: a platform for genetic and genomic research [[Media:VictoriaPetri.ppt]]

Carol A. Bastiani: WormBase phenotype ontology development, curation, and data integration [[Media:CarolBastiani.ppt]]

Janan Eppig: Ontologies and vocabularies supporting data integration: emphasis on mouse phenotypes and disease [[Media:JananEppig.ppt]]

Rex Chisholm: Phenotype curation tool and ontologies at dictyBase [[Media:RexChisholm.ppt]]

Minna Lehvaslaiho: HIV [[Media:MinnaLehvaslaiho.ppt]]

Eurie Hong: Yeast [[Media:EurieHong.ppt]]

Tanya Berardini: Arabidopsis [[Media:TanyaBerardini.ppt]]

Christopher Smith: Insect behavior [[Media:ChristopherSmith.ppt]]

Michael Ashburner: Drosophila (live demo, no slides)

Maryann Martone: BIRN

Jim Balhoff: NESCENT [[Media:JimBalhoff.pdf]]

'''Day 2 presentations'''
Chris Mungall [[Media:ChrisMungall.ppt]]

Monte Westerfield [[Media:MonteWesterfield.ppt]]

==Venue ==
[http://www.stanford.edu/home/welcome/campus/clark.html Stanford University Clark Center, room S360]

[http://med.stanford.edu/maps/ Directions to Stanford Medical Center]

[http://med.stanford.edu/maps/sumc.html Map of Stanford Medical Center]--see "C", Clark Center

[http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Directions on taking Free Marguerite Shuttle Bus]--take Line A to Medical Center

==Accommodations==

We aren't reserving a block of rooms anywhere, but these local hotels are close by and have Stanford shuttle service.

*[http://www.hotelcalifornia.com/ Hotel California]
*[http://www.cardinalhotel.com/ Cardinal Hotel]
*[http://woodsidehotels.com/stanford/index.html Stanford Park Hotel]
*[http://www.starwoodhotels.com/sheraton/property/overview/index.html?propertyID=214 Sheraton]
*[http://www.stanford.edu/dept/hds/SLAC/ SLAC Guest House]

PATO Meeting

2007-01-03T17:56:35Z

TedHopper: /* Minutes */

== General Information and Registration ==
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day meeting focused on the [http://obo.sourceforge.net/cgi-bin/detail.cgi?attribute_and_value Phenotype and Trait Ontology (PATO)] December 1-2, 2006 at Stanford University in Palo Alto, CA.

[http://www.fruitfly.org/pato/pato-form.html Register here.]

==Agenda==
[[Media:Pheno_workshop_Dec2006.pdf]]

==Minutes==

[[http://www.bioontology.org/wiki/images/c/c6/Updated_Meeting_Notes.pdf Media: Updated Meeting Minutes]]

==Presentations==

'''Day 1 presentations'''

Gully Burns: Ontology engineering approaches based on semi-automated curation of the primary literature [[Media:GullyBurns.ppt]]

Alexander Garcia: The use of concept maps and automatic terminology extraction during development of a domain ontology: Lessons learnt [[Media:AlexanderGarcia.ppt]]

Adrien Coulet: Suggested ontology for pharmacogenomics (SO-Pharm): modular construction and preliminary testing [[Media:Adrien Coulet.pdf]]

Tina Hernandez-Broussard: Challenges for representing phenotype in pharmacogenomics [[Media:TinaHernandez.ppt]]

James Reecy: A project for the Creation of a Unified Trait Vocabulary for Farm Animals [[Media:JamesReecy.ppt]]

Victoria Petri: Rat genome database disease portals: a platform for genetic and genomic research [[Media:VictoriaPetri.ppt]]

Carol A. Bastiani: WormBase phenotype ontology development, curation, and data integration [[Media:CarolBastiani.ppt]]

Janan Eppig: Ontologies and vocabularies supporting data integration: emphasis on mouse phenotypes and disease [[Media:JananEppig.ppt]]

Rex Chisholm: Phenotype curation tool and ontologies at dictyBase [[Media:RexChisholm.ppt]]

Minna Lehvaslaiho: HIV [[Media:MinnaLehvaslaiho.ppt]]

Eurie Hong: Yeast [[Media:EurieHong.ppt]]

Tanya Berardini: Arabidopsis [[Media:TanyaBerardini.ppt]]

Christopher Smith: Insect behavior [[Media:ChristopherSmith.ppt]]

Michael Ashburner: Drosophila (live demo, no slides)

Maryann Martone: BIRN

Jim Balhoff: NESCENT [[Media:JimBalhoff.pdf]]

'''Day 2 presentations'''
Chris Mungall [[Media:ChrisMungall.ppt]]

Monte Westerfield [[Media:MonteWesterfield.ppt]]

==Venue ==
[http://www.stanford.edu/home/welcome/campus/clark.html Stanford University Clark Center, room S360]

[http://med.stanford.edu/maps/ Directions to Stanford Medical Center]

[http://med.stanford.edu/maps/sumc.html Map of Stanford Medical Center]--see "C", Clark Center

[http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Directions on taking Free Marguerite Shuttle Bus]--take Line A to Medical Center

==Accommodations==

We aren't reserving a block of rooms anywhere, but these local hotels are close by and have Stanford shuttle service.

*[http://www.hotelcalifornia.com/ Hotel California]
*[http://www.cardinalhotel.com/ Cardinal Hotel]
*[http://woodsidehotels.com/stanford/index.html Stanford Park Hotel]
*[http://www.starwoodhotels.com/sheraton/property/overview/index.html?propertyID=214 Sheraton]
*[http://www.stanford.edu/dept/hds/SLAC/ SLAC Guest House]

PATO Meeting

2007-01-03T17:56:09Z

TedHopper: /* Minutes */ uploading updated minutes from S. Lewis

== General Information and Registration ==
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day meeting focused on the [http://obo.sourceforge.net/cgi-bin/detail.cgi?attribute_and_value Phenotype and Trait Ontology (PATO)] December 1-2, 2006 at Stanford University in Palo Alto, CA.

[http://www.fruitfly.org/pato/pato-form.html Register here.]

==Agenda==
[[Media:Pheno_workshop_Dec2006.pdf]]

==Minutes==

Minutes [[http://www.bioontology.org/wiki/images/c/c6/Updated_Meeting_Notes.pdf Media: Updated Meeting Minutes]]

==Presentations==

'''Day 1 presentations'''

Gully Burns: Ontology engineering approaches based on semi-automated curation of the primary literature [[Media:GullyBurns.ppt]]

Alexander Garcia: The use of concept maps and automatic terminology extraction during development of a domain ontology: Lessons learnt [[Media:AlexanderGarcia.ppt]]

Adrien Coulet: Suggested ontology for pharmacogenomics (SO-Pharm): modular construction and preliminary testing [[Media:Adrien Coulet.pdf]]

Tina Hernandez-Broussard: Challenges for representing phenotype in pharmacogenomics [[Media:TinaHernandez.ppt]]

James Reecy: A project for the Creation of a Unified Trait Vocabulary for Farm Animals [[Media:JamesReecy.ppt]]

Victoria Petri: Rat genome database disease portals: a platform for genetic and genomic research [[Media:VictoriaPetri.ppt]]

Carol A. Bastiani: WormBase phenotype ontology development, curation, and data integration [[Media:CarolBastiani.ppt]]

Janan Eppig: Ontologies and vocabularies supporting data integration: emphasis on mouse phenotypes and disease [[Media:JananEppig.ppt]]

Rex Chisholm: Phenotype curation tool and ontologies at dictyBase [[Media:RexChisholm.ppt]]

Minna Lehvaslaiho: HIV [[Media:MinnaLehvaslaiho.ppt]]

Eurie Hong: Yeast [[Media:EurieHong.ppt]]

Tanya Berardini: Arabidopsis [[Media:TanyaBerardini.ppt]]

Christopher Smith: Insect behavior [[Media:ChristopherSmith.ppt]]

Michael Ashburner: Drosophila (live demo, no slides)

Maryann Martone: BIRN

Jim Balhoff: NESCENT [[Media:JimBalhoff.pdf]]

'''Day 2 presentations'''
Chris Mungall [[Media:ChrisMungall.ppt]]

Monte Westerfield [[Media:MonteWesterfield.ppt]]

==Venue ==
[http://www.stanford.edu/home/welcome/campus/clark.html Stanford University Clark Center, room S360]

[http://med.stanford.edu/maps/ Directions to Stanford Medical Center]

[http://med.stanford.edu/maps/sumc.html Map of Stanford Medical Center]--see "C", Clark Center

[http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Directions on taking Free Marguerite Shuttle Bus]--take Line A to Medical Center

==Accommodations==

We aren't reserving a block of rooms anywhere, but these local hotels are close by and have Stanford shuttle service.

*[http://www.hotelcalifornia.com/ Hotel California]
*[http://www.cardinalhotel.com/ Cardinal Hotel]
*[http://woodsidehotels.com/stanford/index.html Stanford Park Hotel]
*[http://www.starwoodhotels.com/sheraton/property/overview/index.html?propertyID=214 Sheraton]
*[http://www.stanford.edu/dept/hds/SLAC/ SLAC Guest House]

File:Updated Meeting Notes.pdf

2007-01-03T17:45:34Z

TedHopper:

File:BSmithTalkLinks.xls

2006-11-07T21:11:59Z

TedHopper: contains hypertext links to RM and WMV versions of the streaming video of his talk

contains hypertext links to RM and WMV versions of the streaming video of his talk

Workshop on Ontology of Images

2006-03-29T03:26:00Z

TedHopper: /* Webcast */

[[Agenda]]

[[Hotel]]

[[Venue]]

[[#Participants|Participants]]

[[Presentations|ImagingWorkshopSlides]]

[[#Some Relevant Links|Some Relevant Links]]

== Webcast ==

Remote participants may follow a live webcast of this Workshop at: http://irt-video-02.stanford.edu/ramgen/broadcast/view.rm
using [Real Player http://www.real.com/]. Please contact Barry Smith <phismith@buffalo.edu> if you have questions.

== Background ==

The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford.

The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.

The following topics will be addressed:

- coordination and integration of ontologies in the imaging domain

- ontologies for classification of images, image features, interpretations,

- the role of a reference ontology such as the [http://sig.biostr.washington.edu/projects/fm/AboutFM.html FMA]

- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]), including relations among images, features, interpretations, and the underlying reality

- use of ontologies in reasoning

- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group Software and Data Integration Working Group] of the NIH Roadmap National Centers for Biomedical Computing).

The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies.

This workshop was funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. Additional support has been provided by GlaxoSmithKline (GSK), Language & Computing (L&C) and Agfa.

== Participants ==

Yasser alSafadi (Philips Research)

Carol Bean (NCRR)

Bruce Bray (Utah)

William Bug (BIRN)

James A Butler (GlaxoSmithKline)

David Channin (NMH)

Helen Chen (Agfa)

Beverly Collins (Radlex)

Sherri de Coronado (NCI)

C. Forbes Dewey (MIT)

Ivo Dinov (UCLA)

Keith Dreyer (Harvard)

Matthew Fielding (IFOMIS)

Daniel Gardner (Cornell)

Christine Golbreich (Rennes)

Louis Goldberg (Buffalo)

Jeff Grethe (BIRN)

Ammar Halawa (FujiFilm Medical Systems)

Donald Harrington (NIBIB)

David Hellman (L&C)

Peter Hunter (Aukland)

David Kennedy (Harvard)

Richard I. Kitney (Imperial College, London)

Anand Kumar (IFOMIS)

Curtis Langlotz (University of Pennsylvania)

Suzanna Lewis (Berkeley)

William Lorensen (General Electric)

Peter F. Lyster (NIH/NIGMS)

Maryann Martone (BIRN)

Dirk Marwede (IFOMIS / Department of Radiology, University of Leipzig)

Jose L. Mejino, Jr. (Foundational Model of Anatomy)

John Michon (Duke)

Chris Mungall (Berkeley)

Robert Murphy (CMU)

Mark Musen (Stanford)

Dianne Reeves (NCI)

Jens Rittscher (GE)

Daniel Rubin (Stanford)

Mariana Casella Dos Santos (L&C, Belgium)

Nigam Shah (Stanford)

Ken Shastri (FujiMed)

Barry Smith (Buffalo)

Kaushtubh Supekar (Stanford)

== Some Relevant Links ==

[http://genomebiology.com/2005/6/5/R47 The Open Microscopy Environment (OME) Data Model]

[http://obo.sourceforge.net/cgi-bin/detail.cgi?image OBO Biological Imaging Methods]

[http://www.rsna.org/Radlex/index.cfm RadLex: A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources]

[http://medical.nema.org/ DICOM]

[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]

[http://www.dclunie.com/ David Clunie's Medical Image Format Site]

[http://www.library.uthscsa.edu/internet/ImageDatabases.cfm Medical Image Databases]

[http://www.pathbase.net/Pathbase/ Mutant Mouse Images]

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

[http://www.structuredreporting.com/ Structured Reporting]

[http://murphylab.web.cmu.edu/services/ Murphy Lab Image Services]

[https://cabig.nci.nih.gov/workspaces/Imaging In Vivo Imaging]

[http://www.cl.cam.ac.uk/%7Eafb21/publications/TwD98.html A Taxonomy of Diagram Taxonomies]

[http://www.bioimage.org/ Bioimage Database]

[http://www.brainmap.org/ BrainMap:A Functional Neuroimaging Database]

== Tool Registries ==

[http://www.cma.mgh.harvard.edu/iatr/ Registry of Image Analysis Tools]

[http://www.brc-central.org/tdb/prok_manatee/brc-central/software.shtml BRC Central Bioinformatics Resource Center]

Workshop on Ontology of Images

2006-01-26T19:18:28Z

TedHopper: /* Participants */ - correcting spelling of Dave Hellman's last name

[[Agenda]]

[[Hotel]]

[[#Participants|Participants]]

[[#Some Relevant Links|Some Relevant Links]]

== Background ==

The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Stanford.

The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.

The following topics will be addressed:

- coordination and integration of ontologies in the imaging domain

- ontologies for classification of images, image features, interpretations,

- the role of a reference ontology such as the [http://sig.biostr.washington.edu/projects/fm/AboutFM.html FMA]

- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]), including relations among images, features, interpretations, and the underlying reality

- use of ontologies in reasoning

- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group Software and Data Integration Working Group] of the NIH Roadmap National Centers for Biomedical Computing).

The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies.

The workshop is funded by the National Institutes of Health through the [http://nihroadmap.nih.gov/bioinformatics NIH Roadmap for Medical Research], Grant 1 U 54 HG004028. It has been made possible by financial support from GlaxoSmithKline (GSK) and Language & Computing (L&C).

An [[agenda]] is provided here. [[Hotel]] and related information is provided here.

== Participants ==

Yasser alSafadi (Philips Research)

Carol Bean (NCRR)

Bruce Bray (Utah)

William Bug (BIRN)

James A Butler (GlaxoSmithKline)

John Carrino (Partners)

Werner Ceusters (Buffalo)

David Clunie (RadPharm, Princeton)

Beverly Collins (Radlex)

C. Forbes Dewey (MIT)

Ivo Dinov (UCLA)

Keith Dreyer (Harvard)

Christine Golbreich (Rennes)

Jeff Grethe (BIRN)

Donald Harrington (NIBIB)

Frank Hartel (NCI)

Dave Hellman (L&C)

Peter Hunter (Aukland)

David Kennedy (Harvard)

Richard I. Kitney (Imperial College, London)

Anand Kumar (IFOMIS)

Curtis Langlotz (University of Pennsylvania)

Suzanna Lewis (Berkeley)

William Lorensen (General Electric)

Peter F. Lyster (NIH/NIGMS)

Maryann Martone (BIRN)

Dirk Marwede (IFOMIS / Department of Radiology, University of Leipzig)

Robin A. McEntire (GlaxoSmithKline)

Chris Mungall (Berkeley)

Robert Murphy (CMU)

Mark Musen (Stanford)

Dianne Reeves (NCI)

Daniel Rubin (Stanford)

Mariana Casella Dos Santos (L&C, Belgium)

Nigam Shah (Stanford)

Kaushtubh Supekar (Stanford)

Barry Smith (Buffalo)

== Some Relevant Links ==

[http://genomebiology.com/2005/6/5/R47 The Open Microscopy Environment (OME) Data Model]

[http://obo.sourceforge.net/cgi-bin/detail.cgi?image OBO Biological Imaging Methods]

[http://www.rsna.org/Radlex/index.cfm RadLex: A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources]

[http://medical.nema.org/ DICOM]

[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]

[http://www.dclunie.com/ David Clunie's Medical Image Format Site]

[http://www.library.uthscsa.edu/internet/ImageDatabases.cfm Medical Image Databases]

[http://www.pathbase.net/Pathbase/ Mutant Mouse Images]

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

[http://www.structuredreporting.com/ Structured Reporting]

[http://www.cma.mgh.harvard.edu/iatr/ Registry of Image Analysis Tools]

[http://murphylab.web.cmu.edu/services/ Murphy Lab Image Services]

[https://cabig.nci.nih.gov/workspaces/Imaging In Vivo Imaging]

[http://www.cl.cam.ac.uk/%7Eafb21/publications/TwD98.html A Taxonomy of Diagram Taxonomies]