Crop Plant Trait Ontology Workshop OSU 2012

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Meeting Sponsors and Organizers

Co-organized by: The Plant Ontology, the BBSRC and the Generation Challenge Programme.

Travel Funds provided by: 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: Generation Challenge Programme and 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 Knowledge Engineering and Ontology Development which is part of the International Conference on Knowledge Discovery and Information Retrieval (IC3K2012) to be held in Barcelona, Spain, October 4-7th, 2012. 

Vision Paper Media:Ref_TO_KEOD_2012.pdf

Primary targets are:

  1. Poaceae family crops (e.g. wheat, barley, rice, maize, sorghum, Miscanthus)
  2. Solanaceae (e.g. potato and tomato)
  3. Leguminosae (e.g. soybean and Medicago)
  4. Grapes

The strategy would be to develop Ontology terms and definitions to describe and annotate

  1. Morphological and anatomical features of the major crops
  2. Developmental stages of crop plants
  3. 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:

  1. Annotate data in a consistent manner by developing community standards
  2. Integrate ontologies and annotations in various plant genomics and genetics resources
  3. Develop analysis tools

Ontologies for Plant Biology

Here are some links to more information

Plant Ontology

Trait Ontology

An ontology of phenotype traits

Planteome: Common Reference Ontologies for Plants

(formerly was named 'CROP'):

suggestion: PROBE- Plant Reference Ontologies for Breeding and Experimentation

The broader vision is to develop a reference set of ontologies for all plants.

The biological ontologies useful for Plant Biology are:

  1. PO*: Plant Ontology
  2. GO: Gene Ontology
  3. PRO: Protein Ontology
  4. TO*: Plant Trait Ontology TO browser
  5. EO*: Environment Ontology (plant treatments) browse at Gramene
  6. ENVO: Ontology of environmental features and habitats
  7. PATO: Phenotype Quality Ontology
  8. Taxonomy- USDA-GRIN / NCBI / New?
  9. GAZ: Gazetteer (geographical locations)
  10. Plant IDO*: Plant Infectious Disease Ontology A White Paper in PDF format
  11. Plant Diseases*: List of plant diseases
  12. CHEBI: dictionary of molecular entities
  13. PCO: population and community ontology
[* 'Planteome' group may adopt their development]

Software Tools for Ontology Development and Annotations

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; 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:

  1. Crop_Plant_Trait_Ontology_Workshop_Agenda#Thursday_September_13
  2. Crop_Plant_Trait_Ontology_Workshop_Agenda#Friday_September_14
  3. Crop_Plant_Trait_Ontology_Workshop_Agenda#Saturday_September_15


Links to: Oregon State University Home Page and Campus Map

Attendees

Organizing Committee:

  • Naama Menda, Sol Genomics Network, Boyce Thompson institute for Plant Research, Ithaca NY (nm249@cornell.edu)
  • Rex Nelson, SoyBase, USDA-ARS, Ames, IA (nelsonrt@iastate.edu)

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

Invited Expert Guests:

  • Pawel Krajewski; Leading the standards WP in transPLANT
  • Jacques Legouis; curator of the Wheat trait lists for INRA, France [1]
  • C Tom Hash- Sorghum GCP challenge initiative; Representative for ICRISAT’s sorghum (and pearl millet) breeding teams (and the genebanks), Niger
  • Dan Bosler; EBI, Ensembl Plants Project Leader, potato genomics; [3]
  • Victoria Blake; USDA, ARS, CA GrainGenes Bioinformatics and Triticeae Genomics
  • Sharon Lewis Syngenta; Information governance
  • Bob Bensen- Trait Genetics Lead, Quantitative Genetics
  • Michael Dingkuhn; 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

Meeting Logistics:

Transportation

The two nearest airports for coming to Corvallis, OR are:

  1. Portland (PDX) about 96 miles N of Corvallis. ~1.5 hours away, but more convenient in terms of connections, prices and shuttle
  2. 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: 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 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)

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: map

  1. Head southwest on NE Airport Way 0.4 mi
  2. Keep right at the fork 0.1 mi
  3. Slight right to stay on NE Airport Way 1.7 mi
  4. Take the Interstate 205 S ramp to Interstate 84/Portland/salem 0.5 mi
  5. Merge onto I-205 S 23.4 mi
  6. Keep left at the fork and merge onto I-5 S 60.7 mi
  7. Take exit 228 for Oregon 34 toward Lebanon/Corvallis 0.2 mi
  8. Turn right onto OR-34 W/Corvallis-Lebanon Hwy Continue to follow OR-34 W 9.6 mi
  9. Turn left onto OR-34 Bypass W/Corvallis-Newport Hwy/Newport-Corvallis Hwy Continue to follow OR-34 Bypass W 1.1 mi
  10. Continue onto OR-34 W 0.6 mi
  11. Turn right onto SW 26th St 0.5 mi
  12. Turn right onto SW Washington Way 0.2 mi
  13. Turn right onto SW 17th St 207 ft
  14. 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 with parking
  • There is a parking structure just west of Finley and two small parking lots to the north.
  • Finley Hall, Location: 2100 SW May Way.
  • See campus map

Accommodation

Accommodation on OSU campus

Accommodation at Finley Hall

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 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: Hilton Garden Inn

* As of Aug 24th, the Hilton was fully booked for Weds Sept 13th, but other nights may be available

Best Western Grand Manor Inn & Suites

Campus Visitor Information- Oregon state University and Corvallis, OR

Oregon State University Link to: Campus Map

CH2M Hill Alumni Center

Corvallis, OR

Corvallis Visitor Center


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.

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