https://www.bioontology.org//mediawiki/index.php?action=history&feed=atom&title=Ontology_of_Networks_and_Pathways 2026-06-05T11:21:30Z Revision history for this page on the wiki MediaWiki 1.35.9 https://www.bioontology.org//mediawiki/index.php?title=Ontology_of_Networks_and_Pathways&diff=6262&oldid=prev 2007-11-01T17:41:44Z

<p><span dir="auto"><span class="autocomment">Goals</span></span></p> <table class="diff diff-contentalign-left diff-editfont-monospace" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 17:41, 1 November 2007</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l9" >Line 9:</td> <td colspan="2" class="diff-lineno">Line 9:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*1. to provide an introduction to the basic tools and methods of ontology  </div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*1. to provide an introduction to the basic tools and methods of ontology  </div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*2. to overview existing work on the ontology of networks and pathways with a view to enhanced coordination</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*2. to overview existing work on the ontology of networks and pathways with a view to enhanced coordination</div></td></tr> <tr><td class='diff-marker'>−</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*3. to foster networking <del class="diffchange diffchange-inline">between </del>ontology developer groups in the field of networks and pathways</div></td><td class='diff-marker'>+</td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*3. to foster networking <ins class="diffchange diffchange-inline">among </ins>ontology developer <ins class="diffchange diffchange-inline">and user </ins>groups in the field of networks and pathways</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Rough Draft Agenda ==</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Rough Draft Agenda ==</div></td></tr> <!-- diff cache key ncbowiki:diff::1.12:old-6261:rev-6262 --> </table>

Phismith https://www.bioontology.org//mediawiki/index.php?title=Ontology_of_Networks_and_Pathways&diff=6261&oldid=prev 2007-11-01T17:37:48Z

<p>New page: == General Information == The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of networks and pathways. The meeting will be ...</p> <p><b>New page</b></p><div>== General Information == <br /> <br /> The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of networks and pathways. The meeting will be held in Newark NJ in March 2008.<br /> <br /> == Goals ==<br /> <br /> The goals of this workshop are:<br /> <br /> *1. to provide an introduction to the basic tools and methods of ontology <br /> *2. to overview existing work on the ontology of networks and pathways with a view to enhanced coordination<br /> *3. to foster networking between ontology developer groups in the field of networks and pathways<br /> <br /> == Rough Draft Agenda ==<br /> <br /> '''Day 1'''<br /> <br /> ''Morning''<br /> <br /> * 8.30am Registration and Continental Breakfast<br /> <br /> '''Ontology of Networks and Pathways: Some Basic Ingredients'''<br /> * Moderator: Peter Lyster (NIH/NIGMS)<br /> <br /> * 9am Participant Self-Introductions<br /> * 9.15am Barry Smith (NCBO, Buffalo): What is a Network?<br /> * 9.45am Lindsay Cowell (Duke): The Cell Ontology<br /> * 10.15am Coffee<br /> * 10.45am Chris Mungall (NCBO, Berkeley): Representing Relations: The Methodology of Cross-Products<br /> * 11.15am BioPAX/Reactome/TBD<br /> <br /> * 12.45pm Lunch Break<br /> <br /> ''Afternoon'' <br /> <br /> '''Constructing an Ontology of Networks and Pathways'''<br /> * Moderator: Alan Ruttenberg (Science Commons / Semantic Web HCLSIG)<br /> <br /> This will be an interactive hands-on session, in which data annotation needs will be presented, on the basis of which the attempt will be made to construct the beginnings of a cellular network ontology.<br /> <br /> '''Wednesday '''<br /> <br /> ''Morning''<br /> <br /> *8.30am Continental Breakfast<br /> <br /> '''Alternative Approaches'''<br /> * Moderator: TBD<br /> <br /> * 9.00am Aris Floratos (MAGNET, Columbia University): BISON - The Bioinformatics Interface Structured Ontology<br /> * 9.30pm Balaji S. Srinivasan (Stanford): Automatic Population of a Network Ontology<br /> * 10.00am TBD<br /> * 10.30am Coffee<br /> * 11.00am Yves Lussier (Chicago): Integrating the Cell Ontology with other Ontologies and with Text - Bridging the Modeling Gap<br /> * 11.30am Discussion on Statistical/NLP vs. Manual Approaches to Ontology Construction<br /> <br /> *12.45pm Lunch Break<br /> <br /> ''Afternoon''<br /> <br /> '''The Next Steps'''<br /> * Moderator: Suzanna Lewis (NCBO, Berkeley)<br /> <br /> Session starts at 2pm<br /> <br /> == Potential Participants ==<br /> <br /> Robert Arp - NCBO, Buffalo, NY<br /> <br /> Michael Ashburner - NCBO, Cambridge University Department of Genetics<br /> <br /> Ed Barbour - Rockefeller University<br /> <br /> Werner Ceusters - University at Buffalo<br /> <br /> Kei Cheung - Yale, CT<br /> <br /> Lindsay Cowell - Duke University<br /> <br /> Peter D'Eustachio - Reactome<br /> <br /> Marc Halfon - Buffalo<br /> <br /> Nick Khazanov - Rockefeller University<br /> <br /> Natasha Lenkova - Rockefeller University<br /> <br /> Suzanna Lewis - NCBO, Berkeley, CA<br /> <br /> Peter Lyster - NIH/NIGMS<br /> <br /> Yves Lussier - MagNet, University of Chicago, IL<br /> <br /> Avi Ma'ayan - Department of Pharmacology &amp; Systems Therapeutics, Mount Sinai School of Medicine<br /> <br /> Chris Mungall -- NCBO, Berkeley, CA<br /> <br /> Alan Ruttenberg - Science Commons, Boston, MA<br /> <br /> Nigam Shah - NCBO, Stanford, CA<br /> <br /> Karen Skinner - NIH/NIDA<br /> <br /> Barry Smith - NCBO, Buffalo, NY<br /> <br /> Balaji S. Srinivasan - PharmGKB, Stanford, CA<br /> <br /> David States - NCIBI, University of Michigan<br /> <br /> Ross Whitaker - NA-MIC, Utah<br /> <br /> ==Venue ==<br /> <br /> [http://www1.hilton.com/en_US/hi/hotel/EWRAHHH-Hilton-Newark-Airport-New-Jersey/index.do Hilton Hotel Newark Airport] A block of rooms has been set aside for early registrants.<br /> <br /> ==Links ==<br /> <br /> * [http://www.ncbcs.org/summary.html#ncbo National Center for Biomedical Ontology]<br /> <br /> ==Literature==<br /> <br /> [http://jinome.stanford.edu/pdfs/bbm038v1.pdf Current progress in network research]</div>

Phismith