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This page has a TinyURL: http://tinyurl.com/Trait-Ontology =Meeting Sponsors and Organizers= Co-organized by: [http://www.plantontology.org/ The Plant Ontology], the [http://www.bbsrc.ac.uk/home/home.aspx BBSRC] and the [http://www.generationcp.org/ Generation Challenge Programme]. Travel Funds provided by: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0822201 NSF Award #0822201] (Plant Ontology) and BB/H531519/1 (BBSRC), as well as by most participants. Additional support has been provided for the workshop by: [http://www.generationcp.org/ Generation Challenge Programme] and [http://www.syngenta.com Syngenta] =Background- What is an Ontology?= An ontology is a structured vocabulary that provides a consensus set of terms (or classes) to describe the types of entities within a given domain of reality and the relationships among these types. In the age of genomics and big data, ontologies have become indispensable tools for data annotation by suing the same standardized reference vocabulary (ontology). Once the entities are annotated in a consistent manner it is possible to compare the annotations and perform analysis. The analysis of large data sets from molecular, genetic, and genomic diversity studies has the potential to improve our current understanding of phenotype traits of economic relevance, how plants of different and similar species develop respond to various biotic and abiotic stresses. =Goals of the Workshop= To establish a semantic framework for meaningful cross-species queries across gene expression and phenotype data sets from plant genomics, genetics experiments and annotation of the crop germplasm. Vision statement on the Common Reference Trait Ontology for all plants will be presented at the [http://www.keod.ic3k.org/ Knowledge Engineering and Ontology Development] which is part of the International Conference on Knowledge Discovery and Information Retrieval ([http://www.ic3k.org/ IC3K2012]) to be held in Barcelona, Spain, October 4-7th, 2012. Vision Paper [[Media:Ref_TO_KEOD_2012.pdf]] Primary targets are: # Poaceae family crops (e.g. wheat, barley, rice, maize, sorghum, Miscanthus) # Solanaceae (e.g. potato and tomato) # Leguminosae (e.g. soybean and Medicago) # Grapes The strategy would be to develop Ontology terms and definitions to describe and annotate # Morphological and anatomical features of the major crops # Developmental stages of crop plants # Crop plant traits and phenotypes, as an extension of the Plant Ontology and other ontologies, such as the Trait Ontology (TO) and Phenotypic Quality Ontology (PATO) Additional discussions and efforts will be on developing applications to help: # Annotate data in a consistent manner by developing community standards # Integrate ontologies and annotations in various plant genomics and genetics resources # Develop analysis tools =Ontologies for Plant Biology= Here are some links to more information ==Plant Ontology== * [http://www.plantontology.org/ Plant Ontology] home page * [[Relations_in_the_Plant_Ontology]] * [[How_to_use_the_SourceForge_tracker]] * See this recent publication for more information about the PO and ontologies for plant sciences: [http://www.amjbot.org/content/99/8/1263.abstract?etoc Walls et al (2012)] Ontologies as integrative tools for plant science. American Journal of Botany ==Trait Ontology== An ontology of phenotype traits * Link to: [http://www.gramene.org/plant_ontology/ontology_browse.html browser at Gramene] * Link to development browser at OSU: [http://palea.cgrb.oregonstate.edu/trait_ontology/cgi-bin/trait_amigo/go.cgi Plant Trait Ontology] * [https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHYzU1JsT3hmeDEwR0hQWXJobHJldWc Workshop Trait List] ==cROP: Common Reference Ontologies for Plants== The vision is to develop a reference set of ontologies for all plants. Some of these ontologies will be developed within the Planteome framework. First proposed set of cROP ontologies are listed here: [[The cROP (Common Reference Ontologies for Plants) Initiative]] =Software Tools for Ontology Development and Annotations= * [http://oboedit.org/ OBO-Edit] * [http://protege.stanford.edu/ Protégé] * Semantic Image Annotator (SIA) *: - pre-release; the public release will be announced on the PO mailing list and available for download at the [http://jaiswallab.cgrb.oregonstate.edu Jaiswal Lab web site] soon =Meeting Agenda [[Crop Plant Trait Ontology Workshop Agenda]]= Note all times listed are LOCAL- US Pacific Daylight Time *All sessions will be held in the Willamette Room; [http://oregonstate.edu/conferences/ch2m-hill-alumni-center CH2M Hill Alumni Center] (725 SW 26th Street, Oregon State University, Corvallis, OR) *Rooms for break-out sessions: Trysting Tree and Elle/Burlingham Conference Room Detailed agenda by day: # [[Crop_Plant_Trait_Ontology_Workshop_Agenda#Thursday_September_13]] # [[Crop_Plant_Trait_Ontology_Workshop_Agenda#Friday_September_14]] # [[Crop_Plant_Trait_Ontology_Workshop_Agenda#Saturday_September_15]] Links to: [http://oregonstate.edu/ Oregon State University] Home Page and [http://oregonstate.edu/campusmap/ Campus Map] =Attendees= ==Organizing Committee:== * Laurel Cooper- [http://www.plantontology.org/ Plant Ontology] and [http://www.gramene.org/plant_ontology/ontology_browse.html#to/ Trait Ontology] Projects, Oregon State University, Corvallis, Oregon (cooperl@science.oregonstate.edu) * Pankaj Jaiswal, [http://www.plantontology.org/ Plant Ontology], [http://www.gramene.org/plant_ontology/ontology_browse.html#to/ Trait Ontology] and [http://www.gramene.org/ Gramene] Projects, Oregon State University, Corvallis, Oregon (jaiswalp@science.oregonstate.edu) * Ruth Bastow, [http://www.garnetcommunity.org.uk/ GARNet Coordinator], University of Warwick (ruth@garnetcommunity.org.uk) * Elizabeth Arnaud, Crop Ontology, [http://www.generationcp.org/ Generation Challenge Program], Bioversity International, Rome, Italy (e.arnaud@cgiar.org) * Naama Menda, [http://solgenomics.net/ Sol Genomics Network], Boyce Thompson institute for Plant Research, Ithaca NY (nm249@cornell.edu) * Rex Nelson, [http://soybase.org/ SoyBase], USDA-ARS, Ames, IA (nelsonrt@iastate.edu) * Paul Kersey, [http://www.ebi.ac.uk/ European Bioinformatics Institute], Hinxton, UK (pkersey@ebi.ac.uk) (not attending) ==From the Plant Ontology Consortium:== * Laurel Cooper- Plant Ontology and Trait Ontology Projects, Oregon State University, Corvallis, Oregon (cooperl@science.oregonstate.edu) * Pankaj Jaiswal, Plant Ontology, Trait Ontology and Gramene Projects, Oregon State University, Corvallis, Oregon (jaiswalp@science.oregonstate.edu) * Justin Preece, Bioinformatics and Software Development, PO/OSU * Justin Elser, Bioinformatics and Software Development, PO/OSU * Laura Moore, Undergrad researcher- Plant and Trait Ontology Projects * Barry Smith, University at Buffalo [http://ontology.buffalo.edu/smith/ Ontology site], [http://philosophy.buffalo.edu/people/faculty/smith/ Department of Philosophy site]- ''will attend remotely'' ==Invited Expert Guests:== * Pawel Krajewski; Leading the standards WP in [http://transplantdb.eu/node/17 transPLANT] * Cyril Pommier INRA France; [http://urgi.versailles.inra.fr/Projects/URGI-softwares/Ephesis Ephesis] * Jacques Legouis; curator of the Wheat trait lists for INRA, France [http://www4.clermont.inra.fr/umr1095_eng/Staff/Business-cards/LE-GOUIS-Jacques] * C Tom Hash- Sorghum GCP challenge initiative; Representative for ICRISAT’s sorghum (and pearl millet) breeding teams (and the genebanks), Niger * Reinhard Simon; Integrated IT and Computational Research [http://cipotato.org/ potato trait ontology CIP][http://www.cropontology.org/ontology/CO_330] * Sonia Dias; Medicago [http://agrobiodiversityplatform.org/database/?expert=sonia-dias Trait Information Portal] [http://www.pgrsecure.bham.ac.uk/home PGRSecure] * Dan Bosler; EBI, Ensembl Plants Project Leader, potato genomics; [http://plants.ensembl.org/index.html] * John Doonan; UK phenomics centre, all crops, EU phenomics network; [http://www.aber.ac.uk/en/ibers/staff/staff-list/doonan,-prof.-john/ IBERS, Aberystwyth University, Wales] * Mary Schaeffer; USDA, Missouri [http://www.maizegdb.org/ MaizeGDB] * Victoria Blake; USDA, ARS, CA [http://wheat.pw.usda.gov/GG2/index.shtml GrainGenes] Bioinformatics and Triticeae Genomics * Ken McNally; [http://irri.org/ IRRI] * Melissa Haendel; Ontology Development Group, [http://www.ohsu.edu/library/ OHSU Library] * Sunita Kumari, [http://genomicscience.energy.gov/compbio/ KBase] * Luke Ramsay; Barley [http://www.hutton.ac.uk/staff/luke-ramsay Hutton Institute] * Sharon Lewis Syngenta; Information governance * Bob Bensen- Trait Genetics Lead, Quantitative Genetics * Michael Dingkuhn; [http://irri.org/ IRRI] * Alice Clara Augustine, Biotech Ontology Lead, Monsanto * Aloke Gupta, Hewlett Packard ==Invited Experts OSU:== Botany and Plant Pathology Dept: * Lynda Ciuffetti Horticulture Dept: * Laurent Deluc * Sushma Naithani ==Workshop Group Photo== [[Media:Workshop_Group_photo_9-14-12.JPG]] =Meeting Logistics:= ==Transportation== The two nearest airports for coming to Corvallis, OR are: # Portland (PDX) about 96 miles N of Corvallis. ~1.5 hours away, but more convenient in terms of connections, prices and shuttle # Eugene (EUG) about 35 miles S of Corvallis. Note: Prepaid shuttles and rental car options are available at both the airports ===Arriving from Portland, OR=== * '''HUT Shuttle from Portland Airport (PDX) to Corvallis '''- Arrive at the shuttle stop '''Hilton Garden Inn''' ** Shuttle contact Phone# (541) 926-2525 ** Link to shuttle arrival/departure schedules: [http://www.hutshuttle.com/ HUT Shuttle] Runs every 2 hours ** '''At PDX''': HUT shuttle picks up in front of the 'Scheduled Buses and Vans' sign in Ground Transportation. Directly across from baggage claim carousel #8. ===Arriving from Eugene, OR=== There is smaller regional airport in Eugene, OR, which is about 45 minutes away and is serviced by [http://www.omnishuttle.com/offer.htm Omnishuttle] Phone: 541 461-7959 Fax: 541 461-7981 Omnishuttle will drop you right at Finley Hall ==Directions== ===Walk: If you arrive by HUT shuttle from Portland=== * '''ATTENTION: HUT shuttle will not be stopping at the OSU Bookstore from Monday September 10th through Monday September 17th''' due to the roadway closure on Jefferson Way. Reservations for those times will need to be made for our stop at the Corvallis Hilton Garden Inn. '''Walking directions to Finley Hall from Hilton Garden Inn''' * It is a ~7 minute walk to Finley Hall, about 0.4 mile (~ 1 km) [[File:Hilton to Finley map.png]] Finley Hall, 2100 Southwest May Way, Corvallis, OR 97333 1. Head northeast on SW Western Blvd toward SW 2. Turn left onto SW 26th St 0.2 mi 3. Turn right onto SW Stadium Ave 0.2 mi 4. Turn left 112 ft 5. Slight left Finley Hall will be on the left Finley Hall 2100 Southwest May Way, Corvallis, OR ===Driving Directions from Portland airport (PDX)=== Link to Google map: [http://goo.gl/maps/8FfwY map] # Head southwest on NE Airport Way 0.4 mi # Keep right at the fork 0.1 mi # Slight right to stay on NE Airport Way 1.7 mi # Take the Interstate 205 S ramp to Interstate 84/Portland/salem 0.5 mi # Merge onto I-205 S 23.4 mi # Keep left at the fork and merge onto I-5 S 60.7 mi # Take exit 228 for Oregon 34 toward Lebanon/Corvallis 0.2 mi # Turn right onto OR-34 W/Corvallis-Lebanon Hwy Continue to follow OR-34 W 9.6 mi # Turn left onto OR-34 Bypass W/Corvallis-Newport Hwy/Newport-Corvallis Hwy Continue to follow OR-34 Bypass W 1.1 mi # Continue onto OR-34 W 0.6 mi # Turn right onto SW 26th St 0.5 mi # Turn right onto SW Washington Way 0.2 mi # Turn right onto SW 17th St 207 ft # Turn right Finley Hall, will be on the left 348 ft == Parking on OSU Campus== * You can park in any Student/Visitor lots, during the workshop- no permit required. * OSU [http://oregonstate.edu/campusmap/Map with parking] * There is a parking structure just west of Finley and two small parking lots to the north. * [http://oregonstate.edu/uhds/finley Finley Hall], Location: 2100 SW May Way. * See [http://oregonstate.edu/campusmap/ campus map] ==Accommodation== ===Accommodation on OSU campus- Finley Hall=== [http://oregonstate.edu/uhds/finley Finley Hall], Location: 2100 SW May Way. * Guests will be accommodated at on-campus dorm-style housing at OSU; Reasonably priced, close and convenient * Floors 3 to 7 are reserved to host visiting scholars, researchers, INTO OSU monthly after hours arrivals, and conference groups similar to what many institutions throughout the region provide. (we are all on floor 7) * Single or double rooms (not shared unless requested) with shared bathroom facilities in the wing * Internet access- See [http://oregonstate.edu/campusmap/ campus map] *Check-in instructions: ** When guests arrive they will call the conferences phone at +1-(541) 230-4071 to receive their keys. There are yellow call boxes outside of the entrance in case anyone doesn’t have a cell phone. ** In their room they will have linens provided and Monday-Friday from 7:30a-5:30p the front desk will be open should anyone want to switch out their bath towel for a new towel. *Check-out instructions: **As people are ready to checkout on they can leave their room keys with the conferences staff at the Finley front desk, or drop key and fob in the Mail slot if the office is closed. * Check-out time: We request that people '''check out by 11.00am on their scheduled check out date'''. * On-site contact for the conference: Chris Anderson (anderch2@onid.orst.edu) *For after hours access: Finley Hall Conference duty phone# +1-541 230-4071. There are yellow call boxes outside of the entrance in case anyone doesn’t have a cell phone. ===Other accommodations (non-OSU)=== Also: If attendees prefer not to stay on campus they can '''stay at their own cost''' at: [http://hiltongardeninn3.hilton.com/en/hotels/oregon/hilton-garden-inn-corvallis-CVOCHGI/index.html Hilton Garden Inn] '''* As of Aug 24th, the Hilton was fully booked for Weds Sept 13th, but other nights may be available''' [http://book.bestwestern.com/bestwestern/US/OR/Corvallis-hotels/BEST-WESTERN-Grand-Manor-Inn---Suites/Hotel-Overview.do?propertyCode=38111 Best Western Grand Manor Inn & Suites] =Campus Visitor Information- Oregon state University and Corvallis, OR= [http://oregonstate.edu/ Oregon State University] Link to: [http://oregonstate.edu/campusmap/ Campus Map] [http://oregonstate.edu/conferences/ch2m-hill-alumni-center CH2M Hill Alumni Center] Corvallis, OR [http://visitcorvallis.com/?action=events_info&rowid=1882 Corvallis Visitor Center] [http://www.weather.com/weather/tenday/Corvallis+OR+97333:4:US Weather in Corvallis] ==OSU is a Smoke-Free Campus== A reminder that '''smoking is no longer permitted anywhere on the Oregon State University Corvallis campus''' and select OSU property within Benton County signed as nonsmoking. Smoking is permissible on sidewalks that border OSU's boundaries. Smoking receptacles are being installed in strategic, high-traffic areas around the periphery of the Corvallis campus for disposal of smoking-related litter. Their locations will be updated soon on the policy’s website at http://oregonstate.edu/smokefree. The smoke-free policy is in effect year-round, including game days, so visitors to campus who are participating in tailgating activities will also be prohibited from smoking. Enforcement will focus on educating students, staff and visitors about the policy, but those who refuse to abide by the campus’ smoke-free policy may be cited by OSU Department of Public Safety. Students will be held accountable under the student conduct code and employees under OSU employment policies. Contractors, vendors, event attendees, those who rent or lease university property and other visitors to OSU could be subject to exclusion from campus for violation of the new policy. Smoking also is not permitted inside personal vehicles on campus. Among the prohibited smoking devices are cigars, cigarettes, pipes, electronic cigarettes or other devices intended to simulate smoking. ==Optional activities taking place Saturday Sept. 15th in and around Corvallis== These are from your personal expenses and are not covered by the meeting sponsors. Please contact Laurel Cooper for making arrangements. * [http://visitcorvallis.com/ai1ec_event/rhapsody-in-the-vineyard-a-downtown-wine-walk/?instance_id=31939 Downtown Wine Walk] * [http://www.corvallisenvironmentalcenter.org/enjoy-supper-at-sage-this-september/ Supper at Sage] * Possible excursion destination: [http://www.oregonstateparks.org/park_211.php Silver Falls State Park] or [http://discovernewport.com/ Newport, Oregon Coast]

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