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'''Dates:''' 5-7 February, 2012 (Sunday through Tuesday) '''Location:''' Lewis B. and Dorothy Cullman Conference Room, Pfizer Laboratory, New York Botanical Garden This page has a Tiny Url: http://tinyurl.com/woodontologymeeting =Attendees= ===From the Plant Ontology Consortium:=== * Dennis Stevenson, Vice President for Laboratory Research, New York Botanical Garden * Ramona Walls, Post-doctoral researcher and Plant Ontology curator, New York Botanical Garden * Maria Alejandra Gandolfo, Cornell University * Barry Smith, University at Buffalo [http://ontology.buffalo.edu/smith/ Ontology site], [http://philosophy.buffalo.edu/people/faculty/smith/ Department of Philosophy site] * Laurel Cooper, PO Project Coordinator and Curator, Oregon State University ===Invited attendees:=== * Andrew Groover: Plant Biology, Geneticist, [http://biosci3.ucdavis.edu/FacultyAndResearch/FacultyProfile.aspx?FacultyID=332 USDA Forest Service, Institute of Forest Genetics] * Jill Wegrzyn of the [http://dendrome.ucdavis.edu/treegenes/ TreeGenes Database] at UCDavis, Bioinformatics * Frederic Lens [http://www.nhn.leidenuniv.nl/index.php/nhn/institute/nlcb/ Netherlands Centre for Biodiversity Naturalis], wood anatomy * Barb Lachenbruch [http://woodscience.oregonstate.edu/people/faculty/lachenbruch-barb College of Forestry, Oregon State University], wood science and anatomy * Elisabeth Wheeler [http://cnr.ncsu.edu/fb/about/faculty/wheeler.php North Carolina State University], paleobotany and wood anatomy; curator of the [http://insidewood.lib.ncsu.edu/welcome Inside Wood database] ''-unable to attend due to a personal emergency'' * Rachel Spicer [http://www.conncoll.edu/academics/web_profiles/spicer.html Connecticut College], wood anatomy, development, and physiology * Meg (Margeret) Staton [http://www.fagaceae.org/ Fagaceae Genomics Web], curator; bioinformatics =Lodging and Transportation= Guests will be staying at the [http://hilton544-px.trvlclick.com/ Hamptom Inn and Suites], in Yonkers, NY, approximately 15 minutes from the NYBG. Transportation to and from the hotel will be provided by van service or private cars. The PO will arrange a car service from the airport to the hotel using [http://pondfieldtripservice.com/ PondField Car Service]. We do not recommend using taxis. ===Weather=== It will be cool, with highs is the low 40's. Please bring a sweater or jacket, as the conference room can be quite cold. =Meeting Goals= 1. Develop ontology terms and definitions for wood structure, as part of the Plant Anatomical Entity branch of the Plant Ontology. 2. Develop ontology terms and definitions the time course of development of wood, as part of the Plant Structure Development Stage branch of the Plant Ontology. 3. Develop ontology terms and definitions, as well as ontology structure, for wood qualities and phenotypes, as an extension of the Plant Ontology and other ontologies, such as the Trait Ontology (TO) and Phenotypic Quality Ontology (PATO, formerly the Phenotype and Trait Ontology). By the end of the meeting, we will have list of terms for these three areas (anatomy, development stages, qualities), plus proposed definitions, and a good idea of how the terms will fit into the PO. =Agenda, Sunday, Feb. 5, 2011= ==9:00AM-12:00PM Introduction to Bio-ontologies - Public Session== This session will be open to people outside the meeting participants, and will be advertised to the wider scientific community. If you are interested in attending this session, please contact [mailto:rwalls@nybg.org Ramona Walls] by February 1, 2012. Link to the [http://www.bioontology.org/wiki/index.php/Introduction_to_Bio-Ontologies meeting announcment]. ===9AM-9:15AM Welcome and Introductions (Dennis Stevenson)=== ===9:15AM-11:00AM Introduction to Bio-ontologies (Barry Smith)=== '''Barry Smith''', an ontology expert and consultant to the PO, will provide an introduction to ontologies for the life sciences. Link to Barry's presentation: [[Media:Smith_BioOntology_Intro_Feb2012.pdf]] See link to [http://www.bioontology.org/wiki/index.php/Introduction_to_Bio-Ontologies NCBO page] ====1. What is an ontology and what is it for?==== ====2. Ontology success stories in the life sciences==== ====3. The bio-ontologies landscape==== * Open Biomedical Ontologies (OBO) Foundry * National Center for Biomedical Ontology (NCBO) and its Bioportal * Ontologies and the Semantic Web ====4. How to build your first ontology==== -with illustrations from the Plant Ontology * definitions and cross-products * relations * types and instances * use of OBO-Edit and Protege ===11:00AM-11:15AM Coffee break=== ===11:15AM-12:00PM Introduction to the Plant Ontology (Ramona Walls)=== Link to Ramona's presentation: [[Media:PO_Walls_wood_meeting_short.pdf]] ====1. What is the Plant Ontology and what is it for?==== ====2. How the Plant Ontology is structured: anatomy and development stages ==== *The two main branches of the PO are '''plant anatomical entity''' and '''plant structure development stage''' ====3. Plant Ontology relations and definitions==== Relations: *Types and subtypes: is_a, the fundamental relation in the PO *Parts: part_of and has_part; what they means for anatomical entities (things) versus development stages (processes); when to use has_part instead of part_of *Development and derivation: the develops_from and derives_by_manipulation_from relations *Specifying spatial relations: adjacent_to, part_of, and other relations *Links between anatomical entities and development stages: the participates_in and has_participant relations Definitions: *Definitions for humans and computers *Genus-differentia definitions - importance of reading up the tree for properties of a term *Logical definitions and relations ====4. Neighboring ontologies of the PO: Traits (TO) and Phenotypes (PATO)==== *Domains of Trait Ontology (TO), and Phenotypic Quality Ontology (PATO), versus the PO *How do they differ? How are they similar? How do they interact? *The difference between an entity and a phenotype *What is a trait? What is a quality? ====5. Different types of plant data made available through the Plant Ontology==== *Linking genomic and phenomic data to PO terms *Example: mapping maize tissue samples to PO terms *How annotation files are created and maintained; responsibilities of the PO versus contributing databases. (''Will be covered by Laurel Cooper's presentation on Monday evening.'') ==12:00PM-1:00PM Lunch== Lunch at the Garden Cafe ==1:00PM-2:00PM Overview of the goals for the meeting== ===Review of goals=== The following goals were established prior to this meeting: 1. Develop ontology terms and definitions for wood structure, as part of the Plant Anatomical Entity branch of the Plant Ontology. 2. Develop ontology terms and definitions the time course of development of wood, as part of the Plant Structure Development Stage branch of the Plant Ontology. 3. Develop ontology terms and definitions, as well as ontology structure, for wood qualities and phenotypes, as an extension of the Plant Ontology and other ontologies, such as the Trait Ontology (TO) and Phenotypic Quality Ontology (PATO, formerly the Phenotype and Trait Ontology). '''What are users' needs?''' -In addition to working on the terms used to describe wood, we can review the needs for other anatomy terms for woody plants that may not be in the PO (e.g., reproductive structures in gymnosperms). ===Achieving our goals=== At the meeting, we will develop lists of new terms as well as revisions to existing terms that are needed for the PO, and begin work on definitions and relations for these terms. At the end of the meeting, we will assess our progress, and create a list of tasks to be completed, plus a timeline. All participants will set up an account to access our [https://sourceforge.net/tracker/?group_id=76834&atid=835555 SourceForge tracker]. This will allow us to continue to work on new terms and definitions after the workshop. ====Feedback after this meeting==== Interactive demo on how to: *give feedback on PO web page. *request new terms or revisions on PO's [https://sourceforge.net/tracker/?group_id=76834&atid=835555 SourceForge tracker]. ==2:00PM-2:45PM Flash talks by participants== 5 minutes per person. A computer and projector will be available if anyone wants to use them. Talks should be no more than 8 slides, but slides are not required. '''Links to presentations:''' * Maria Alejandra Gandolfo, Cornell University: [[Media:MAG_PO_Workshop.pdf]] * Andrew Groover: Plant Biology, Geneticist, [http://biosci3.ucdavis.edu/FacultyAndResearch/FacultyProfile.aspx?FacultyID=332 USDA Forest Service, Institute of Forest Genetics]: [[Media:Groover_NYBG.pdf]] * Frederic Lens [http://www.nhn.leidenuniv.nl/index.php/nhn/institute/nlcb/ Netherlands Centre for Biodiversity Naturalis]: [[Media:LENS_Wood_Mtg_Flash.pdf]] * Barb Lachenbruch [http://woodscience.oregonstate.edu/people/faculty/lachenbruch-barb College of Forestry, Oregon State University]: [[Media:LachenbruchFlashNYBG_2_12.pdf‎]] * Rachel Spicer [http://www.conncoll.edu/academics/web_profiles/spicer.html Connecticut College]:[[Media:SPICER_PlantOntology2012.pdf]] * Meg (Margeret) Staton [http://www.fagaceae.org/ Fagaceae Genomics Web]: [[Media:staton_plant_ontology.pdf ]] * Jill Wegrzyn at UCDavis [http://dendrome.ucdavis.edu/treegenes/ TreeGenes Database]: [[Media:Wegrzyn_PO_NYBG-2012.pdf]] ==2:45PM-3:00PM Coffee Break== ==3:00PM-6:30PM Work on goal 1 - Anatomical Entities== '''Goal 1. Develop ontology terms and definitions for wood structure, as part of the Plant Anatomical Entity branch of the Plant Ontology.''' *review existing anatomy/morphology terms and definitions *develop list of anatomy/morphology terms that are missing *work on definitions of new terms See separate page, [[Goal 1. Anatomical Entities]], for more details and minutes from the meeting. ==7:00PM-9:00PM Dinner at Wild Ginger== [http://www.wildgingerbronxville.com/#! Wild Ginger] is an Asian fusion restaurant in the village of Bronxville, about 15 minutes north of the NYBG. Address: 10 Park Place, Bronxville, NY 10708, (914)337-2198 Transportation to the restaurant and back to the hotel will be provided. =Agenda, Monday, Feb. 6, 2011= ==9:00AM-12:00PM Work on goal 2 - Development stages== '''Goal 2. Develop ontology terms and definitions for the time course of development of wood, as part of the Plant Structure Development Stage branch of the Plant Ontology''' *review existing development stage terms and definitions *develop list of development stage terms that are missing *work on definitions of new terms See separate page, [[Goal 2. Plant Structure Development Stages]], for more details and minutes from the meeting. -If necessary, we can also make suggestions for developmental processes in the Gene Ontology. There will be time for a coffee break in the middle of the morning. ==12:00PM-1:00PM Lunch== NYBG is closed on Mondays. We will order in lunch from a [http://www.arthuravenue.com/index.php/lunch-menu Mike's Deli]. ==1:00PM-2:00PM Continue work on goal 2== ==3:00PM-6:00PM Work on goal 3 - Qualities and Phenotypes== '''Goal 3. Develop ontology terms and definitions, as well as ontology structure, for wood qualities and phenotypes.''' *Wood qualitites and phenotypes will for an extension of the Plant Ontology and other ontologies, such as the Trait Ontology (TO) and Phenotypic Quality Ontology (PATO, formerly the Phenotype and Trait Ontology). *Background on PO, TO, PATO *How to describe qualities using ontologies *Resources for terms See separate page, [[Goal 3. Wood qualities and phenotypes]], for more details and minutes from the meeting. There will be time for a coffee break in the middle of the afternoon. ==6:00-8:30 Working dinner and evening session at NYBG== We will order in dinner from an Italian restaurant located in the Bronx's Little Italy, the Arthur Avenue neighborhood. ===6:45pm-7:30pm [[Developing and incorporating new annotations for woody plants]]=== * Laurel Cooper, PO Project Coordinator and Curator, Oregon State University: [[Media:Cooper_PO.pdf]] =Agenda, Tuesday, Feb. 7, 2011= ==8:30AM-9:30AM Review ontology structure from days 1 and 2== *Review of any unfinished items from goals 1-3. *Set priorities for remaining tasks. ==9:30AM-10:40AM Break-out groups== '''1.''' Compile list of wood traits for which genomic data are currently being collected (Laurel, Meg, Jill, Andrew). '''2.''' Complete definitions for secondary xylem development stages. Work on terms for sub-cellular anatomical entities needed to describe wood. (Ramona, Frederic, Barb, Dennis, Rachel) ==10:40AM-11:20PM Wrap up== Action items: *What still needs to be done? *Who will do what? *Timeline for meeting our goals ==Action items== ===Plant anatomical entities and development stages=== *RW (with DWS and MAG) will prepare list of anatomical terms, plus definitions, for PO and GO, and send to group for review. (See [[Goal_1._Anatomical_Entities]] for more details) *Secondary xylem development stage terms are nearly complete (see [[Goal_2._Plant_Structure_Development_Stages#wood_development_stages]] ). These will go in the PO now, along with general terms for secondary phloem development stage, and bark development stage, which can be fleshed out as needed. *Need to talk to GO about their term for "lignin network" -- is it in or out of cell, should it be in PO or GO? *Need to talk to POC about whether/how to include specialized terms like storied cambium, vascular bundle types. *RW will be responsible for getting anatomy and development terms into PO and GO by September, 2012. ===Traits=== See [[Goal_3._Wood_qualities_and_phenotypes]] for more details * Wood traits for which genomic data are currently being collected -- add these to the TO by September 2012 (LC) * Work with GO and ChEBI to get terms needed for wood traits (LC, others?) * What about concerns over TO general structure? ===Data integration=== LC will work with MS and JW to integrate the PO with their Wood databases and develop association data sets for the PO. Some of this can be done in the short term, as the [http://www.hardwoodgenomics.org/ Hardwood Genomics] group has been using PO terms to annotate gene expression sets. ===Outreach=== 1. press item for IAWA journal (Rachel, Frederic, Barb, Andrew) Frederic will write draft of announcement and send it to group for review. 2. Contact groups developing high throughput and genome data (Jill) -for advertizing and getting them to send us data 3. Write a research paper (Whole group) Need to make sure that ontologies are in pretty good shape first so when we send people to it, they will find it useful. RW is willing to take the lead on writing. Use case: make sure PO and Hardwood Genomics.org are linking effectively to each other (Meg) Data and analysis (LC, Andrew and/or Jill?) Submit by fall 2012. 4. Ontology workshop at IAWA meeting -- in Japan in 2013 5. Participation in Forest Tree workshop at PAG next year. All day Sunday. (Lol and Jill. Jill can talk to coordinators) Can be very competitive to get in it. Alternative is to have our own workshop and have the forest tree workshop group advertise it to their list * Contact PAG forest tree workshop organizers about possible talk at their workshop- Sunday of PAG =Useful References= Glosary: IAWA Multilingual Glossary of Terms Used in Wood Anatomy Link to references from EW on [http://insidewood.lib.ncsu.edu/links#general Inside Wood] Texts: Metcalfe and Chalk "Anatomy of the Dicotyledons" 1st edition 1950 + the more recent recent volumes Carlquist's Comparative Plant Anatomy Larson's "The Vascular Cambium" Panshin, A. J. and C. de Zeeuw. 1980. Textbook of Wood Technology: Structure, Identification, Properties, and Uses of the Commercial Woods of the United States, McGraw-Hill. * Wiedenhoeft & Miller. 2002. BRIEF COMMENTS ON THE NOMENCLATURE OF SOFTWOOD AXIAL RESIN CANALS AND THEIR ASSOCIATED CELLS. IAWA Journal, Vol. 23 (3), 2002: 299–303 * Wilson, B. F. and R. R. Archer. 1977. Reaction wood: induction and mechanical action. Annual Review of Plant Physiology 28: 23-43.y; reviews others' comments that normal wood may be on a continuum from opposite wood to reaction wood. * Wilson, B. F. and R. R. Archer. 1979. Tree design: some biological solutions to mechanical problems. Bioscience 29: 293-298.y; desing problems: as tree grows the forces causing bending stresses increase so beams have to be stiffended to avoid breakage or excessive bending; also stiffening will reduce the amt of bending but can't reverse the direction of bending; discusses gradient of cw, opp. wood, etc. * Pickard, W. F. 2008. Laticifers and secretory ducts: two other tube systems in plants. New Phytologist 177: 877-888(12) * Sanchez, P., Nehlin, L., and Greb, T. (2012). From thin to thick: major transitions during stem development. Trends in Plant Science 17, 113–121.

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