Difference between revisions of "Crop Plant Trait Ontology Workshop Agenda"

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'''Location:''' Oregon State University
 
'''Location:''' Oregon State University
  
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This page has a Tiny Url: TBA
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Return to the main [[Crop_Plant_Trait_Ontology_Workshop_OSU_2012]] page
  
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=Attendees=
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=Weds Sept. 12th, 6-8pm=
 +
Dinner on your own those who arrive early
  
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==Organizing Committee:==
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Snack and refreshments will be available at Finley Hall or Arnold dining center will be open until 7pm
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* Laurel Cooper- Plant Ontology and Trait Ontology Projects, Oregon State University, Corvallis, Oregon (cooperl@science.oregonstate.edu)
 
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* Pankaj Jaiswal, Plant Ontology, Trait Ontology and Gramene Projects, Oregon State University, Corvallis, Oregon (jaiswalp@science.oregonstate.edu)
 
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* Ruth Bastow, GARNet Coordinator,  University of Warwick (ruth@garnetcommunity.org.uk)
 
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* Elizabeth Arnaud, Crop Ontology, Generation Challenge Program, Bioversity International, Rome, Italy (e.arnaud@cgiar.org)
 
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* Naama Menda, Sol Genomics Network, Boyce Thompson institute for Plant Research, Ithaca NY (nm249@cornell.edu)
 
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* Rex Nelson, SoyBase, USDA-ARS, Ames, IA (nelsonrt@iastate.edu)
 
  
 +
=Thursday September 13=
 +
Location: [http://oregonstate.edu/conferences/ch2m-hill-alumni-center CH2M Hill Alumni Center]  Williamette Room
  
−
==From the Plant Ontology Consortium:==
 
−
Tentatively:
 
  
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* Dennis Stevenson, Vice President for Laboratory Research, New York Botanical Garden
+
'''* 8:00- 9am Continental Breakfast in Williamette Room'''
  
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* Ramona Walls, Post-doctoral researcher and Plant Ontology curator, New York Botanical Garden
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* 9:00- 9:15  Welcome and Introductions - Pankaj Jaiswal, OSU
  
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* Maria Alejandra Gandolfo, Cornell University
+
== Ruth Bastow:  Insights and follow-up from [http://transplantdb.eu/node/68 EBI Crop Ontology Meeting]==
 +
[[Media:Bastow_GARNet-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Improve current ontologies for UK/EU crops''
 +
** ''Improve community uptake and use''
 +
** ''Widen participation and involvement''
 +
** ''Make the best of funding and resources (build on PO and GCP)''
  
−
* Barry Smith, University at Buffalo [http://ontology.buffalo.edu/smith/ Ontology site], [http://philosophy.buffalo.edu/people/faculty/smith/ Department of Philosophy site]
+
== Melissa Haendel; "Introduction to Ontologies" [http://www.ohsu.edu/library/ OHSU Library]==
 +
[[Media:Haendel_OHSU-9-13-12.pdf]]
 +
**''Main points:''
 +
** ''Ontology- A formal conceptualization of a specified domain of interest.''
 +
** ''Terms are defined''
 +
** ''Relationships between terms are defined''
 +
** ''Terms are arranged in a structured hierarchy''
 +
** ''The true path rule- The pathway from a subClass all the way to its top level parent must be universally true.''
  
−
Others?
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==Laurel Cooper, OSU [http://www.plantontology.org/ Plant Ontology] and the [http://www.gramene.org/plant_ontology/ontology_browse.html#to/ Trait Ontology]==
 +
[[Media:Cooper_PO+TO-9-13-13.pdf]]
 +
**''Goals:''
 +
** ''Revise and expand the existing Trait Ontology''
 +
** ''Refer Plant Trait Ontology to link the crop- and clade- specific ontologies''
 +
** ''Develop a reference set of ontologies for all plants''
 +
** ''CROP- Common Reference Ontology for Plants''
  
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* Justin P
+
   
 +
'''* 10:30- 10:45 coffee break'''
  
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* Justin E
+
==Organizing Committee Talks==
  
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==Invited Experts:==
+
===Elizabeth Arnaud, Bioversity /[http://www.generationcp.org/ Generation Challenge Program]===
−
+
[[Media:Arnaud_GCP-9-13-12.pdf]]
−
Invitees: EU/Int'l
+
**''Goals for Crop Ontology:''
−
* Manuel Spannagl: MIPS, Munich, potato genome, TRansplant project, bioinformatics, and potato traits, wheat; [http://mips.helmholtz-muenchen.de/plant/static/gen/plantProjects.html MIPS]
+
** ''Add new crops: barley, pigeon pea, sweet potato, yam''
 +
** ''Add translations''
 +
** ''Add the Crop wild relative ontology''
 +
** ''Cross reference with main data sources''
 +
** ''Use as search tool for Integrated Breeding Platform''
 +
** ''Automatic submission to PO and TO''
 +
** ''Contribute to Reference Plant Trait Ontology''
  
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*Pawel Krajewski Leading the standards WP in transPLANT
 
−
 
−
* Reinhard Simon CIP potato trait ontology [http://www.cropontology.org/ontology/CO_330]
 
  
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* Cristobal Uauy wheat, traits, anatomy
+
[[File:Arnaud_GCP-9-13-12.pdf]]
  
−
* Yukiko Yamazaki Oryzabase, Japan- not able to attend
+
===Naama Menda- [http://solgenomics.net/ Sol Genomics Network]===
−
+
[[Media:Menda_sol-9-13-12.pdf]]
−
* Cyril Pommier INRA France,  Ephesis
+
**''Goals:''
 +
** ''Complete mapping to PO''
 +
** ''Map terms to TO''
 +
** ''Annotate expression data with PO terms''
 +
** ''Generate EQ statements for Solanaceae known genes''
  
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* Jacques Legouis curator of the Wheat trait lists for INRA, France;
+
===Rex Nelson- [http://soybase.org/ SoyBase]===
−
+
[[Media:Nelson_SoyBase-LIS-9-13-12.pdf]]
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* Alexandra Viel Syngenta, France
+
**''Goals:''
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* Rosemary Shrestha maize and wheat traits, CIMMYT, Mexico
+
** ''Soybean specific ontology – SOY''
−
+
** ''Integrate PO, TO, GO, CHEBI, and PATO into SOY''
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Invitees: UK
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** ''Soybean QTL and traits annotated with SOY, PO, TO identifiers''
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* Dan Bosler EBI, Ensembl Plants Project Leader, potato genomics
+
** ''Annotate gene functions/ mutations with PO, TO, GO, CHEBI, PATO identifiers as part of PhenotypeRCN project''
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* Peter Jack plant breeders, cereals
+
** ''Search SoyBase by TO and GO annotations and produce full report of all major data and classes''
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* John Doonan UK phenomics centre, all crops, EU phenomics network linkIain Donnison miscanthus, bioenergy grasses
 
−
 
−
Invitees: USA
 
−
* Mary Schaeffer MaizeGDB, USDA, Missouri [http://www.maizegdb.org/]
 
−
* Victoria Carollo GrainGenes, USDA-  CA
 
−
* Dave Matthews GrainGenes; Cornell University
 
−
 
−
local experts:
 
−
 
−
* Pat Hayes Crop and Soil Science, OSU, barley breeding, genomics
 
−
 
−
* Jennifer Kling Crop and Soil Science, OSU, Barley/ Wheat CAP
 
  
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=Lodging and Transportation=
+
===Mary Schaeffer- [http://www.maizegdb.org/ MaizeGDB]===
 +
[[Media:Schaeffer_maizeGDB_9-13-12.pdf]]
 +
 
 +
* 11:45- 12:00 0pen time for questions and discussion
 +
 
 +
'''* 12:00- 1:00 Lunch: Soup and Salad Buffet; Elle/Burlingham Room #111'''
 +
 
 +
==Flash Talks- Session 1==
 +
 
 +
===Bob Benson, Syngenta traits===
 +
[[Media:Bensen_syngenta-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''The “Native Trait” approach to discovering and developing improved performing products.''
 +
** ''(DNA sequence info => Mapped genetic elements => Polymorphisms => Germplasm panels => Marker trait associations => Create directed novel gene combinations)''
 +
** ''Range phenotypic expression across germplasm in water limited growing conditions''
 +
** ''Manage the drought stress environment''
 +
 
 +
===Sharon Lewis; Syngenta- Information governance===
 +
[[Media:Lewis_syngenta-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Raise productivity in sustainable ways''
 +
** ''Improve farm productivity''
 +
** ''Reduce agriculture's environmental footprint''
 +
** ''Build rural prosperity''
 +
** ''Create continued sales growth across all regions''
 +
** ''Innovate across technologies to transform the way plants are grown''
 +
** ''Need to move ahead with EO,
 +
** ''Need an "Agronomic Practices Ontology: e.g. plowing, irrigation, planting, fertilizer regimes, compare to CO, have lists''
 +
** ''Use BBCH scale- prefer over stage terms, also used in Europe and EU- need to make sure to BBCH are synonyms are used in the PSDS''
 +
 
 +
===Alice Clara Augustine, Monsanto===
 +
(No slides presented)
 +
 
 +
**Discovery- testing genes, starts with ontology, esp TO
 +
**put genes into crops in the field to test -> develop product
 +
**change in languages- the 'Tower of Babel'
 +
**Trait Ontology terms are part of the hypothesis and are used in the regulatory package
 +
 
 +
===Sonia Dias- [http://agrobiodiversityplatform.org/database/?expert=sonia-dias Trait Information Portal]===
 +
[[Media:Dias_PGRSecure-9-13-12.pdf]]
 +
 
 +
**Ontologies for Agrobiodiversity Conservation and Use
 +
**[http://www.pgrsecure.org/ PGR secure]: characterization of crop wild relative and landrace resources
 +
 
 +
''PGR Secure Goals:''
 +
** To produce a web-based crop wild relative (CWR) and landrace (LR) Trait Information Portal (TIP)
 +
** Case study genera: Avena, Beta, Brassica and Medicago
 +
** Triontology: crop wild relative (CWR) and landrace (LR) and CO for case study genera
 +
** Should be available mid-October- link up to external ontologies
 +
 
 +
''Needs:
 +
** An ontology that describes the crops, themes, traits, anatomical and morphological structures and growth and  developmental stages, etc
 +
** Describe crops, CWR and LR structures and entities and the relationships between them
 +
** A semantic framework for meaningful cross-species queries across crops, inventories and traits (genotyping and phenotype datasets)
 +
 
 +
**[http://eurisco.ecpgr.org/home_page.html EURISCO]:a web-based catalogue that provides information on more than 1.1M accessions of ex situ plant collections maintained in Europe
 +
** ''Develop a staging area for inclusions of characterization and evaluation data using ontologies''
 +
** ''Up-grade staging for passport data''
 +
 
 +
** ''Collaborate for integration of other ontologies''
 +
** ''Contribute to existing ontologies i.e. CO, TO, GO...''
 +
** ''Analysis tools''
 +
** ''Visualization for cross – species/domain search''
 +
 
 +
===Pawel Krajewski, [http://www.transplantdb.eu/ transPLANT]===
 +
[[Media:Pawel_transPLANT-9-13-12.pdf]]
 +
 
 +
Head, Laboratory of Biometry, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
 +
 
 +
[http://www.polapgen.eu POLAPGEN-BD]- Biotechnological tools for breeding cereals with increased resistance to drought
 +
**''Goals:''
 +
** ''Generate and describe genetic diversity''
 +
** ''Phenotypic expression of drought tolerance''
 +
** ''Data analysis and integration''
 +
** ''Describe and predict environmental conditions''
 +
** GERMINATE schema- with JHI
 +
** mainly focused on spring barley
 +
 
 +
===Jacques Legouis; [http://www4.clermont.inra.fr/umr1095_eng/Staff/Business-cards/LE-GOUIS-Jacques INRA], France===
 +
[[Media:Legouis_INRA-9-13-12.pdf]]
 +
 
 +
*''Goals:''
 +
** ''PHENOME – high-throughput phenotyping network''
 +
 
 +
** ''Various scales:  field platforms (plot/farm), field semi-controlled platforms(plot scale), greenhouse platforms (plant/organ), metabolomic/structural (Scale: organ)''
 +
 
 +
**''BREEDWHEAT – breeding for sustainable wheat varieties''
 +
 
 +
** Interested in a diverse list of traits (see slides):
 +
 
 +
#At different scales: – plot, plant, tiller, organ, tissue
 +
# At different stages - times, Biomass at flowering, harvest, stem nitrate content at sunrise / sunset
 +
# With different units- Flowering time (d, das, °Cd,…)
 +
# In different ways- Canopy temperature
 +
# infrared thermometer/ infrared camera
 +
# Measured/ calculated traits – Grain protein deviation
 +
# Response across treatments/locations – Joint regression
 +
 
 +
===Cyril Pommier, INRA France; [http://urgi.versailles.inra.fr/Projects/URGI-softwares/Ephesis Ephesis]===
 +
[[Media:Pommier_URGI-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Data standardization -''
 +
*** ''Inside species groups''
 +
*** ''Help new projects''
 +
*** ''Recommended for international collaboration and publications''
 +
*** ''Ease data interoperability and re-usability''
 +
** ''Ease inclusion of INRA's traits to international standards''
 +
 
 +
===John Doonan, UK Phenomics Center [http://www.aber.ac.uk/en/ibers/staff/staff-list/doonan,-prof.-john/ IBERS, Aberystwyth University, Wales]===
 +
[[Media:Doonan_OR_ontology_WS-new.pdf]]
 +
**''Goals:''
 +
** ''Integration of biological and chemical phenomics''
 +
** ''Development of laser scanning technologies''
 +
** ''Calibrating technology for grasses and perennial crops''
 +
** ''Providing transnational access to NCCP''
 +
** ''Establishing data standards and ref expt''
 +
 
 +
===Dan Bolser, EBI, [http://plants.ensembl.org/index.html Ensembl], potato genomics===
 +
[[Media:Bolser_CPTO-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Species specific vs. species independent anatomical ontologies.''
 +
*** ''Mapping?''
 +
** ''Overview of ontologies...''
 +
*** ''Whats well/poorly represented?''
 +
*** ''What does the ontology think a plant looks like?''
 +
*** ''Can I learn about plant biology from an ontology?''
 +
** ''Composing terms to describe phenotypes''
 +
** ''OBO/OBF/OLS''
 +
*** ''REST services?''
 +
 
 +
 
 +
'''* 2:30- 2:40 coffee break'''
 +
 
 +
==Flash Talks- Session 2==
 +
 
 +
===Reinhard Simon,  [http://cipotato.org/  International Potato Center] ===
 +
 
 +
Integrated IT and Computational Research, CIP
 +
[[Media:Simon_CIP-9-13-12.pdf]]
 +
 
 +
[http://www.cropontology.org/ontology/CO_330 potato trait ontology]
 +
**''Goals:''
 +
** ''Help build the institutional memory of research data''
 +
** ''Make data accessible and providing tools for scientists''
 +
** ''Statistics, GIS, database and application development, bioinformatics, data curation''
 +
** ''Key central data store organized around germplasm using biomart''
 +
**  ''Using ontologies for improving quality, data exchange and data mining for germplasm resources''
 +
** ''Traits of interest in potato breeding:
 +
*** Tuber yield and related phenology (stolons, tuber initiation, tuber filling, plant senescence, flowering, earliness)
 +
*** Reaction to abiotic stress (drought, salinity)
 +
*** Reaction to biotic stress (late blight, bacterial wilt, virus)
 +
*** Reproductive biology
 +
*** Quality (processing & nutritional)
 +
 
 +
===Victoria Blake, USDA, ARS, CA [http://wheat.pw.usda.gov/GG2/index.shtml GrainGenes] TCAP project===
 +
[[Media:Blake_T3-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Combine genotype/phenotype data for associated analysis with TASSEL''
 +
** ''Create genotype data for graphical genotyping with FlapJack''
 +
** ''Create two independent databases for barley and wheat to support the T-CAP project''
 +
 
 +
 
 +
===Luke Ramsay, Barley traits [http://www.hutton.ac.uk/staff/luke-ramsay Hutton Institute]===
 +
[[Media:Ramsay_Hutton_Institute-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Manipulating recombination distribution and frequency in barley''
 +
** ''Add malting quality traits to TO''
 +
 
 +
 
 +
===C Tom Hash, ICRISAT, sorghum===
 +
[[Media:Hash_ICRISAT-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Prioritization of breeding targets''
 +
** ''Use of appropriate experimental designs''
 +
** ''Generation of high quality phenotype data''
 +
** ''Thorough statistical analysis of the resulting data sets''
 +
 
 +
 
 +
===Ken McNally, [http://irri.org/ International Rice Research Institute]===
 +
[[Media:McNally_ASPIR-9-13-12_ed.pdf‎]]
 +
**''Goals:''
 +
** ''Harnessing genetic diversity to chart new productivity, quality, and health horizons''
 +
** ''Characterizing genetic diversity and creating novel gene pools''
 +
 
 +
===Michael Dingkuhn, [http://irri.org/ International Rice Research Institute]===
 +
[[Media:Dingkuhn_IRRI_CIRAD-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Multi-phenotyping on shared reference panels''
 +
** ''Yield potential and abiotic stresses''
 +
** ''Multi-environment field phenomics for trait GxE''
 +
** ''Complementary HTP platforms''
 +
 
 +
===Sunita Kumari, [http://genomicscience.energy.gov/compbio/ KBase]===
 +
[[Media:Kumari_Kbase-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Integration of the data to extract knowledge from the wealth of high-throughput data in plant biology''
 +
** ''Establish a framework for developing capability that will allow interactive, data-driven analysis and exploration across multiple-omics experiments''
 +
** ''Provide researchers access to comprehensive data sets from high-throughput experiments together with relevant analytical tools and resources''
 +
** ''Provide a platform for researchers to analyze their own experimental data and have these results incorporated into the data exploration framework''
 +
 
 +
==Plant Ontology Tools for Annotation: Live Software Demo==
 +
===Justin Preece, OSU===
 +
 
 +
:*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
 +
 
 +
:*Plant Annotation Wiki
 +
 
 +
:*[http://www.plantontology.org/docs/otherdocs/web_services_guide.html PO Web Services]
 +
 
 +
* 4:30- 5:00  Open time for questions and discussion
 +
 
 +
'''* 5:00- 6:00 break, free time'''
 +
 
 +
'''* 6:00- 7:00 Pizza dinner- Elle/Burlingham Room #111'''
 +
 
 +
* 7:00 to 9:00pm 'Hands-on' Session
 +
 
 +
==Ontology editing: Using OBO Edit- tutorial and practice==
 +
 
 +
* You can download and install OBO-Edit from here: [http://oboedit.org/ OBO-Edit]
 +
 
 +
Note: the newest version of Mac OS Mountain Lion appears to have a default setting blocking installations from sites other than Apple Apps store.  This can be turned off.
 +
 
 +
 
 +
Steps to setting up the OBO-Edit after doing download and install:
 +
 
 +
# Select "New Ontology"
 +
# Set up save profile
 +
# set up a number space using ID Manager
 +
# Set auto commit text edits
 +
# Create a root class
 +
# Create a root relation- part_of
 +
# Populate the ontology
 +
 
 +
===Requesting terms using the SourceForge trackers===
 +
Please see the link: [[How to use the Source Forge tracker]]
 +
 
 +
Before using the PO Source Forge tracker you should:
 +
 
 +
# Register (create a login)
 +
# Log in to your account
 +
# Search the tracker for existing items on the same topic
 +
 
 +
=Friday September 14=
 +
'''* 8:00- 9am Continental Breakfast in Williamette Room'''
 +
 
 +
9:00- 9:10 Welcome and Announcements
 +
 
 +
==Sushma Naithani, OSU Horticulture==
 +
[[Media:Naithani-9-13-12.pdf]]
 +
**''Goals:''
 +
**''Genome annotation and curation of metabolic pathways''
 +
 
 +
 
 +
==Laurent DeLuc, OSU Horticulture, grape research==
 +
[[Media:Deluc-9-13-12.pdf]]
 +
**''Goals:''
 +
** ''Create an integrative approach to identify the mechanisms that govern grape berry ripening''
 +
** ''Development of new traits to describe the enhancement with non destructive measurement''
 +
** ''Imaging tools to capture the fruit growth and ripening''
 +
 
 +
 +
9:30-9:40 Pankaj
 +
 
 +
'''* 9:50- 10:50 coffee break'''
 +
 
 +
* 10:00- 11:00 Creating the 'CROP Initiative' (Common Reference Ontologies for Plants)
 +
** Pankaj: Introduction
 +
==[http://ontology.buffalo.edu/smith/ Barry Smith]: Webex presentation [http://ontology.buffalo.edu/smith/ Ontology site], [http://philosophy.buffalo.edu/people/faculty/smith/ Department of Philosophy site]==
 +
[[Media:Smith_CROP-9-13-12.pdf]]
 +
***[http://ontology.buffalo.edu/12/CROP.ppt slides]
 +
*** [http://wiki.plantontology.org/index.php/Crop_Plant_Trait_Ontology_Workshop_OSU_2012#CROP:_Common_Reference_Ontology_for_Plants List of Ontologies]
 +
*** [http://obofoundry.org/ OBO Foundry website]
 +
*** [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf Background reading on the OBO Foundry]
 +
 
 +
**''Goals:''
 +
** ''Support the annotation of meta-data related to:''
 +
*** ''Data about biological samples produced from various technologies''
 +
*** ''Data produced from remote sensing equipment''
 +
*** ''Images''
 +
*** ''Physical holdings''
 +
*** ''Anything that has an environment''
 +
 
 +
 
 +
[https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=68286512&rKey=138dd3cb991f2096 Streaming recording link]
 +
 
 +
[https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=68286512&rKey=a7e12ce89b2a9e0d Download recording link]
 +
 
 +
 
 +
11:00- 12:00 discussion
 +
   
 +
'''* 12:00-1:00 Lunch: Assorted Wraps with Soup and Salad; Elle/Burlingham Room #111'''
 +
 
 +
==1:00- 1:30 Breakout Groups are organized and tasks are explained==
 +
 
 +
1:30- 3:00 '''Breakout Group Session: "Find your trait of Interest"'''
 +
 
 +
* Groups will explore the TO and find out if the traits they are interested in are represented
 +
 
 +
- Creating name, defining the trait, assigning a place in the hierarchy
 +
 
 +
- Can also be 'Hands-on' using OBO-Edit
 +
 
 +
* Breakout Groups:
 +
 
 +
Quality: Pawel, Luke, Rex, Melissa, Sharon
 +
 
 +
Yield: Jaques, Mary, Ruth, Tom, Cyril, Michael, Laurel
 +
 
 +
Stress: Sunita, Sonia, Pankaj, Bob
 +
 
 +
Anatomy and Morphology: Victoria, Ken, Elizabeth, Alice Clara, Laura
 +
 
 +
Growth and Develoment:  John, Laurent, Naama, Reinhard
 +
 
 +
Informatics: Justin E, Justin P, Dan, Alok?, Rex
 +
 +
'''3:00 coffee break and group photo'''
 +
 
 +
3:30- 5:00- Breakout Groups report on progress, discussion, questions
 +
 
 +
===Informatics===
 +
Amigo - Ontology Browser used by plant ontology
 +
 
 +
Amigo problems- upload to a new version
 +
 
 +
Amigo not many other solution
 +
 
 +
Amigo can load multiple ontologies at the same time and deal with parent child relationships from separate ontologies
 +
 
 +
Questions does Omego support OWL - yes new version should do
 +
 
 +
OBO vs OWL
 +
 
 +
OWL still hard for humans
 +
 
 +
OBO easier to edit
 +
 
 +
Likely that everything will move to OWL
 +
 
 +
Annotations
 +
 
 +
Some we get bulk uploads
 +
 
 +
Need incremental ways to add these in
 +
 
 +
using annotation wiki for smaller numbers would be useful
 +
 
 +
===Quality===
 +
need to write a real good request so it could be understood eg acronyms need to defined or not used
 +
 
 +
cooking and brewing quality - relationship to OBI ontologies processing. probably needs a re think
 +
 
 +
Some were assays
 +
 
 +
===Yield ===
 +
Needs a lot of work.
 +
 
 +
Defined a new yield term
 +
 
 +
Moved through levels
 +
 
 +
Fruit yield
 +
 
 +
Grain needs to be a separate area not just a synonymn - need to know how to use tracker
 +
 
 +
Do we need above or below ground biomass
 +
 
 +
Need botanical/ontological first in many cases would be great if this was present now
 +
 
 +
pper level terms are really hard to define
 +
 
 +
===Stress===
 +
Need to start at the top first!
 +
 
 +
Abiotic (temp water, light etc) and Biotic stress
 +
 
 +
Stress is a response
 +
 
 +
Decide upon 'Response to ………' this removes the idea of a negative response that is associated with stress
 +
 
 +
Biotic due to a specific agent with varied responses
 +
 
 +
Outcome of biotic stress e.g. rust or brown spot are shared by many different pathogens
 +
 
 +
Specturm of response needs to be taken into account e.g. resistant to susceptible
 +
 
 +
Need community standards on how to collect and store information re specific biotic stress to help people collect data. Should these be associated with the ontology?
 +
 
 +
Water
 +
 
 +
Response to sub optimal water conditions
 +
 
 +
Phenological, morphological conditions
 +
 
 +
Should it be 'response to' or should it be 'adaptation' instead as some plants are 'pre determined' to deal with this from day one this is not a response it is genetic.
 +
 
 +
Developmental conditions also need to be taken into account.
 +
 
 +
GO looks at abiotic/biotic stimulus.
 +
GO should be at molecular
 +
 
 +
===Growth and Development===
 +
Sprout should be before after tuberisation.
 +
 
 +
Tuber is after shoot in the ontology
 +
 
 +
Days to tuberisation
 +
 
 +
Tuber growth rate - don't usually measure this is it needed
 +
 
 +
All in the tracker but need to be added into PO and TO
 +
 
 +
Incompatibility- needs to be defined
 +
 
 +
partial incompatibility needs to be added in
 +
 
 +
morphological incompatibility- in some wild species of tomato
 +
 
 +
No term for fruit development?
 +
 
 +
 
 +
Soybean - terms for nodulation
 +
 
 +
nodule developmental stages should be in PO
 +
 
 +
Need to check how nodule formation and step there under are described in GO
 +
 
 +
Need to define between a process leading to a condition at the end point which is the trait.
 +
 
 +
The end point needs to be a measurable trait to go into to TO.
 +
 
 +
Discussion over not putting a unit in the description. agreed that the ontologies need to be changed to remove units such as days
 +
 
 +
Flowering time or time to flowering - needs to be divided into days to flowering from sowing, days to flowering from emergence, days to heading each should be a separate child not a synonym.
 +
 
 +
There should be a set of description known as field term e.g. 50% flowering
 +
 
 +
===Anatomy and Morphology===
 +
trait descriptions were not specific enough in many case need more information in most cases and a domain expert!
 +
 
 +
How are time series dealt with in PO/TO etc
 +
 
 +
Melissa - What are the use cases - build to our needs
 +
 
 +
Concrete queries for the new ontologies
 +
 
 +
 
 +
 
 +
'''* 5:00- 6:00 break, free time'''
 +
 
 +
* 6:00- 6:30 Gathering
 +
 
 +
'''* 6:30- 9:00 Dinner and Social -Elle/Burlingham Room #111'''
 +
 
 +
=Saturday September 15=
 +
 
 +
'''* 8:00- 9am Continental Breakfast in Williamette Room'''
 +
 
 +
9:00- 9:30 Biological examples and ontology applications; Pankaj Jaiswal, OSU
 +
 
 +
9:30- 10:30  Group discussion
 +
 
 +
'''* 10:30- 10:45 Coffee break'''
 +
   
 +
10:45 Summary and conclusions
 +
   
 +
Wrap and to-do lists for follow-up
 +
 
 +
'''12:00 Boxed Lunches'''

Latest revision as of 21:18, 22 October 2012

Dates: Sept 13-15th, 2012 (Thursday through Saturday)

Location: Oregon State University

Return to the main Crop_Plant_Trait_Ontology_Workshop_OSU_2012 page

Weds Sept. 12th, 6-8pm

Dinner on your own those who arrive early

Snack and refreshments will be available at Finley Hall or Arnold dining center will be open until 7pm

Thursday September 13

Location: CH2M Hill Alumni Center Williamette Room


* 8:00- 9am Continental Breakfast in Williamette Room

  • 9:00- 9:15 Welcome and Introductions - Pankaj Jaiswal, OSU

Ruth Bastow: Insights and follow-up from EBI Crop Ontology Meeting

Media:Bastow_GARNet-9-13-12.pdf

    • Goals:
    • Improve current ontologies for UK/EU crops
    • Improve community uptake and use
    • Widen participation and involvement
    • Make the best of funding and resources (build on PO and GCP)

Melissa Haendel; "Introduction to Ontologies" OHSU Library

Media:Haendel_OHSU-9-13-12.pdf

    • Main points:
    • Ontology- A formal conceptualization of a specified domain of interest.
    • Terms are defined
    • Relationships between terms are defined
    • Terms are arranged in a structured hierarchy
    • The true path rule- The pathway from a subClass all the way to its top level parent must be universally true.

Laurel Cooper, OSU Plant Ontology and the Trait Ontology

Media:Cooper_PO+TO-9-13-13.pdf

    • Goals:
    • Revise and expand the existing Trait Ontology
    • Refer Plant Trait Ontology to link the crop- and clade- specific ontologies
    • Develop a reference set of ontologies for all plants
    • CROP- Common Reference Ontology for Plants


* 10:30- 10:45 coffee break

Organizing Committee Talks

Elizabeth Arnaud, Bioversity /Generation Challenge Program

Media:Arnaud_GCP-9-13-12.pdf

    • Goals for Crop Ontology:
    • Add new crops: barley, pigeon pea, sweet potato, yam
    • Add translations
    • Add the Crop wild relative ontology
    • Cross reference with main data sources
    • Use as search tool for Integrated Breeding Platform
    • Automatic submission to PO and TO
    • Contribute to Reference Plant Trait Ontology


File:Arnaud GCP-9-13-12.pdf

Naama Menda- Sol Genomics Network

Media:Menda_sol-9-13-12.pdf

    • Goals:
    • Complete mapping to PO
    • Map terms to TO
    • Annotate expression data with PO terms
    • Generate EQ statements for Solanaceae known genes

Rex Nelson- SoyBase

Media:Nelson_SoyBase-LIS-9-13-12.pdf

    • Goals:
    • Soybean specific ontology – SOY
    • Integrate PO, TO, GO, CHEBI, and PATO into SOY
    • Soybean QTL and traits annotated with SOY, PO, TO identifiers
    • Annotate gene functions/ mutations with PO, TO, GO, CHEBI, PATO identifiers as part of PhenotypeRCN project
    • Search SoyBase by TO and GO annotations and produce full report of all major data and classes

Mary Schaeffer- MaizeGDB

Media:Schaeffer_maizeGDB_9-13-12.pdf

  • 11:45- 12:00 0pen time for questions and discussion

* 12:00- 1:00 Lunch: Soup and Salad Buffet; Elle/Burlingham Room #111

Flash Talks- Session 1

Bob Benson, Syngenta traits

Media:Bensen_syngenta-9-13-12.pdf

    • Goals:
    • The “Native Trait” approach to discovering and developing improved performing products.
    • (DNA sequence info => Mapped genetic elements => Polymorphisms => Germplasm panels => Marker trait associations => Create directed novel gene combinations)
    • Range phenotypic expression across germplasm in water limited growing conditions
    • Manage the drought stress environment

Sharon Lewis; Syngenta- Information governance

Media:Lewis_syngenta-9-13-12.pdf

    • Goals:
    • Raise productivity in sustainable ways
    • Improve farm productivity
    • Reduce agriculture's environmental footprint
    • Build rural prosperity
    • Create continued sales growth across all regions
    • Innovate across technologies to transform the way plants are grown
    • Need to move ahead with EO,
    • Need an "Agronomic Practices Ontology: e.g. plowing, irrigation, planting, fertilizer regimes, compare to CO, have lists
    • Use BBCH scale- prefer over stage terms, also used in Europe and EU- need to make sure to BBCH are synonyms are used in the PSDS

Alice Clara Augustine, Monsanto

(No slides presented)

    • Discovery- testing genes, starts with ontology, esp TO
    • put genes into crops in the field to test -> develop product
    • change in languages- the 'Tower of Babel'
    • Trait Ontology terms are part of the hypothesis and are used in the regulatory package

Sonia Dias- Trait Information Portal

Media:Dias_PGRSecure-9-13-12.pdf

    • Ontologies for Agrobiodiversity Conservation and Use
    • PGR secure: characterization of crop wild relative and landrace resources

PGR Secure Goals:

    • To produce a web-based crop wild relative (CWR) and landrace (LR) Trait Information Portal (TIP)
    • Case study genera: Avena, Beta, Brassica and Medicago
    • Triontology: crop wild relative (CWR) and landrace (LR) and CO for case study genera
    • Should be available mid-October- link up to external ontologies

Needs:

    • An ontology that describes the crops, themes, traits, anatomical and morphological structures and growth and developmental stages, etc
    • Describe crops, CWR and LR structures and entities and the relationships between them
    • A semantic framework for meaningful cross-species queries across crops, inventories and traits (genotyping and phenotype datasets)
    • EURISCO:a web-based catalogue that provides information on more than 1.1M accessions of ex situ plant collections maintained in Europe
    • Develop a staging area for inclusions of characterization and evaluation data using ontologies
    • Up-grade staging for passport data
    • Collaborate for integration of other ontologies
    • Contribute to existing ontologies i.e. CO, TO, GO...
    • Analysis tools
    • Visualization for cross – species/domain search

Pawel Krajewski, transPLANT

Media:Pawel_transPLANT-9-13-12.pdf

Head, Laboratory of Biometry, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland

POLAPGEN-BD- Biotechnological tools for breeding cereals with increased resistance to drought

    • Goals:
    • Generate and describe genetic diversity
    • Phenotypic expression of drought tolerance
    • Data analysis and integration
    • Describe and predict environmental conditions
    • GERMINATE schema- with JHI
    • mainly focused on spring barley

Jacques Legouis; INRA, France

Media:Legouis_INRA-9-13-12.pdf

  • Goals:
    • PHENOME – high-throughput phenotyping network
    • Various scales: field platforms (plot/farm), field semi-controlled platforms(plot scale), greenhouse platforms (plant/organ), metabolomic/structural (Scale: organ)
    • BREEDWHEAT – breeding for sustainable wheat varieties
    • Interested in a diverse list of traits (see slides):
  1. At different scales: – plot, plant, tiller, organ, tissue
  2. At different stages - times, Biomass at flowering, harvest, stem nitrate content at sunrise / sunset
  3. With different units- Flowering time (d, das, °Cd,…)
  4. In different ways- Canopy temperature
  5. infrared thermometer/ infrared camera
  6. Measured/ calculated traits – Grain protein deviation
  7. Response across treatments/locations – Joint regression

Cyril Pommier, INRA France; Ephesis

Media:Pommier_URGI-9-13-12.pdf

    • Goals:
    • Data standardization -
      • Inside species groups
      • Help new projects
      • Recommended for international collaboration and publications
      • Ease data interoperability and re-usability
    • Ease inclusion of INRA's traits to international standards

John Doonan, UK Phenomics Center IBERS, Aberystwyth University, Wales

Media:Doonan_OR_ontology_WS-new.pdf

    • Goals:
    • Integration of biological and chemical phenomics
    • Development of laser scanning technologies
    • Calibrating technology for grasses and perennial crops
    • Providing transnational access to NCCP
    • Establishing data standards and ref expt

Dan Bolser, EBI, Ensembl, potato genomics

Media:Bolser_CPTO-9-13-12.pdf

    • Goals:
    • Species specific vs. species independent anatomical ontologies.
      • Mapping?
    • Overview of ontologies...
      • Whats well/poorly represented?
      • What does the ontology think a plant looks like?
      • Can I learn about plant biology from an ontology?
    • Composing terms to describe phenotypes
    • OBO/OBF/OLS
      • REST services?


* 2:30- 2:40 coffee break

Flash Talks- Session 2

Reinhard Simon, International Potato Center

Integrated IT and Computational Research, CIP Media:Simon_CIP-9-13-12.pdf

potato trait ontology

    • Goals:
    • Help build the institutional memory of research data
    • Make data accessible and providing tools for scientists
    • Statistics, GIS, database and application development, bioinformatics, data curation
    • Key central data store organized around germplasm using biomart
    • Using ontologies for improving quality, data exchange and data mining for germplasm resources
    • Traits of interest in potato breeding:
      • Tuber yield and related phenology (stolons, tuber initiation, tuber filling, plant senescence, flowering, earliness)
      • Reaction to abiotic stress (drought, salinity)
      • Reaction to biotic stress (late blight, bacterial wilt, virus)
      • Reproductive biology
      • Quality (processing & nutritional)

Victoria Blake, USDA, ARS, CA GrainGenes TCAP project

Media:Blake_T3-9-13-12.pdf

    • Goals:
    • Combine genotype/phenotype data for associated analysis with TASSEL
    • Create genotype data for graphical genotyping with FlapJack
    • Create two independent databases for barley and wheat to support the T-CAP project


Luke Ramsay, Barley traits Hutton Institute

Media:Ramsay_Hutton_Institute-9-13-12.pdf

    • Goals:
    • Manipulating recombination distribution and frequency in barley
    • Add malting quality traits to TO


C Tom Hash, ICRISAT, sorghum

Media:Hash_ICRISAT-9-13-12.pdf

    • Goals:
    • Prioritization of breeding targets
    • Use of appropriate experimental designs
    • Generation of high quality phenotype data
    • Thorough statistical analysis of the resulting data sets


Ken McNally, International Rice Research Institute

Media:McNally_ASPIR-9-13-12_ed.pdf‎

    • Goals:
    • Harnessing genetic diversity to chart new productivity, quality, and health horizons
    • Characterizing genetic diversity and creating novel gene pools

Michael Dingkuhn, International Rice Research Institute

Media:Dingkuhn_IRRI_CIRAD-9-13-12.pdf

    • Goals:
    • Multi-phenotyping on shared reference panels
    • Yield potential and abiotic stresses
    • Multi-environment field phenomics for trait GxE
    • Complementary HTP platforms

Sunita Kumari, KBase

Media:Kumari_Kbase-9-13-12.pdf

    • Goals:
    • Integration of the data to extract knowledge from the wealth of high-throughput data in plant biology
    • Establish a framework for developing capability that will allow interactive, data-driven analysis and exploration across multiple-omics experiments
    • Provide researchers access to comprehensive data sets from high-throughput experiments together with relevant analytical tools and resources
    • Provide a platform for researchers to analyze their own experimental data and have these results incorporated into the data exploration framework

Plant Ontology Tools for Annotation: Live Software Demo

Justin Preece, OSU

  • Semantic Image Annotator (SIA)- pre-release; the public release will be announced on the PO mailing list and available for download at the Jaiswal Lab web site soon
  • Plant Annotation Wiki
  • 4:30- 5:00 Open time for questions and discussion

* 5:00- 6:00 break, free time

* 6:00- 7:00 Pizza dinner- Elle/Burlingham Room #111

  • 7:00 to 9:00pm 'Hands-on' Session

Ontology editing: Using OBO Edit- tutorial and practice

  • You can download and install OBO-Edit from here: OBO-Edit

Note: the newest version of Mac OS Mountain Lion appears to have a default setting blocking installations from sites other than Apple Apps store. This can be turned off.


Steps to setting up the OBO-Edit after doing download and install:

  1. Select "New Ontology"
  2. Set up save profile
  3. set up a number space using ID Manager
  4. Set auto commit text edits
  5. Create a root class
  6. Create a root relation- part_of
  7. Populate the ontology

Requesting terms using the SourceForge trackers

Please see the link: How to use the Source Forge tracker

Before using the PO Source Forge tracker you should:

  1. Register (create a login)
  2. Log in to your account
  3. Search the tracker for existing items on the same topic

Friday September 14

* 8:00- 9am Continental Breakfast in Williamette Room

9:00- 9:10 Welcome and Announcements

Sushma Naithani, OSU Horticulture

Media:Naithani-9-13-12.pdf

    • Goals:
    • Genome annotation and curation of metabolic pathways


Laurent DeLuc, OSU Horticulture, grape research

Media:Deluc-9-13-12.pdf

    • Goals:
    • Create an integrative approach to identify the mechanisms that govern grape berry ripening
    • Development of new traits to describe the enhancement with non destructive measurement
    • Imaging tools to capture the fruit growth and ripening


9:30-9:40 Pankaj

* 9:50- 10:50 coffee break

  • 10:00- 11:00 Creating the 'CROP Initiative' (Common Reference Ontologies for Plants)
    • Pankaj: Introduction

Barry Smith: Webex presentation Ontology site, Department of Philosophy site

Media:Smith_CROP-9-13-12.pdf

    • Goals:
    • Support the annotation of meta-data related to:
      • Data about biological samples produced from various technologies
      • Data produced from remote sensing equipment
      • Images
      • Physical holdings
      • Anything that has an environment


Streaming recording link

Download recording link


11:00- 12:00 discussion

* 12:00-1:00 Lunch: Assorted Wraps with Soup and Salad; Elle/Burlingham Room #111

1:00- 1:30 Breakout Groups are organized and tasks are explained

1:30- 3:00 Breakout Group Session: "Find your trait of Interest"

  • Groups will explore the TO and find out if the traits they are interested in are represented

- Creating name, defining the trait, assigning a place in the hierarchy

- Can also be 'Hands-on' using OBO-Edit

  • Breakout Groups:

Quality: Pawel, Luke, Rex, Melissa, Sharon

Yield: Jaques, Mary, Ruth, Tom, Cyril, Michael, Laurel

Stress: Sunita, Sonia, Pankaj, Bob

Anatomy and Morphology: Victoria, Ken, Elizabeth, Alice Clara, Laura

Growth and Develoment: John, Laurent, Naama, Reinhard

Informatics: Justin E, Justin P, Dan, Alok?, Rex

3:00 coffee break and group photo

3:30- 5:00- Breakout Groups report on progress, discussion, questions

Informatics

Amigo - Ontology Browser used by plant ontology

Amigo problems- upload to a new version

Amigo not many other solution

Amigo can load multiple ontologies at the same time and deal with parent child relationships from separate ontologies

Questions does Omego support OWL - yes new version should do

OBO vs OWL

OWL still hard for humans

OBO easier to edit

Likely that everything will move to OWL

Annotations

Some we get bulk uploads

Need incremental ways to add these in

using annotation wiki for smaller numbers would be useful

Quality

need to write a real good request so it could be understood eg acronyms need to defined or not used

cooking and brewing quality - relationship to OBI ontologies processing. probably needs a re think

Some were assays

Yield

Needs a lot of work.

Defined a new yield term

Moved through levels

Fruit yield

Grain needs to be a separate area not just a synonymn - need to know how to use tracker

Do we need above or below ground biomass

Need botanical/ontological first in many cases would be great if this was present now

pper level terms are really hard to define

Stress

Need to start at the top first!

Abiotic (temp water, light etc) and Biotic stress

Stress is a response

Decide upon 'Response to ………' this removes the idea of a negative response that is associated with stress

Biotic due to a specific agent with varied responses

Outcome of biotic stress e.g. rust or brown spot are shared by many different pathogens

Specturm of response needs to be taken into account e.g. resistant to susceptible

Need community standards on how to collect and store information re specific biotic stress to help people collect data. Should these be associated with the ontology?

Water

Response to sub optimal water conditions

Phenological, morphological conditions

Should it be 'response to' or should it be 'adaptation' instead as some plants are 'pre determined' to deal with this from day one this is not a response it is genetic.

Developmental conditions also need to be taken into account.

GO looks at abiotic/biotic stimulus. GO should be at molecular

Growth and Development

Sprout should be before after tuberisation.

Tuber is after shoot in the ontology

Days to tuberisation

Tuber growth rate - don't usually measure this is it needed

All in the tracker but need to be added into PO and TO

Incompatibility- needs to be defined

partial incompatibility needs to be added in

morphological incompatibility- in some wild species of tomato

No term for fruit development?


Soybean - terms for nodulation

nodule developmental stages should be in PO

Need to check how nodule formation and step there under are described in GO

Need to define between a process leading to a condition at the end point which is the trait.

The end point needs to be a measurable trait to go into to TO.

Discussion over not putting a unit in the description. agreed that the ontologies need to be changed to remove units such as days

Flowering time or time to flowering - needs to be divided into days to flowering from sowing, days to flowering from emergence, days to heading each should be a separate child not a synonym.

There should be a set of description known as field term e.g. 50% flowering

Anatomy and Morphology

trait descriptions were not specific enough in many case need more information in most cases and a domain expert!

How are time series dealt with in PO/TO etc

Melissa - What are the use cases - build to our needs

Concrete queries for the new ontologies


* 5:00- 6:00 break, free time

  • 6:00- 6:30 Gathering

* 6:30- 9:00 Dinner and Social -Elle/Burlingham Room #111

Saturday September 15

* 8:00- 9am Continental Breakfast in Williamette Room

9:00- 9:30 Biological examples and ontology applications; Pankaj Jaiswal, OSU

9:30- 10:30 Group discussion

* 10:30- 10:45 Coffee break

10:45 Summary and conclusions

Wrap and to-do lists for follow-up

12:00 Boxed Lunches

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