Planteome Outreach

Conferences and Workshops

This page is currently under construction....

For 2013-2014: Please see: POC_Outreach_Events

2015:

Plant and Animal Genome Meeting, January 9-13, 2015 San Diego, CA

Link to Conference program: Plant and Animal Genome Meeting XXIII

• DivSeek Meeting- Friday January 9th from 8am-5pm
• Systems Biology and Ontologies Workshop, Saturday January 10th from 8:00-10:10 AM. Organizers: Laurel Cooper, Sushma Naithani and Pankaj Jaiswal
• Plant Phenotypes Workshop, Sunday, January 11, 2015. Organizers: Mary Schaeffer and Chi-Ren Shyu
• Crop Ontology Meeting Monday, January 12, 2015. Organizers: Elizabeth Arnaud and Rex Nelson

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2015 Maize Genetics Conference- March 12-15, 2015, St. Charles, Illinois, USA

• Link to Conference site: 2015 Maize Genetics
• Link to program: 2015 Maize Genetics

Poster presentation: # P235 Comparative Phenomics in Plants.

Harper, Lisa¹; Oellrich, Anika²; Walls, Ramona³; Cannon, Ethy⁴; Cannon, Steven⁵; Cooper, Laurel⁶; Gardiner, Jack⁴; Gkoutos, George⁷; He, Mingze⁴; Hoehndorf, Robert⁸; Jaiswal, Pankaj⁶; Lloyd, Johnny⁹; Kalberer, Scott⁵; Meinke, David¹⁰; Menda, Naama¹¹; Moore, Laura⁶; Nelson, Rex⁵; Pujar, Anuradha¹²; Lawrence, Carolyn⁴; Huala, Eva¹³

1. USDA ARS Albany, CA 2. Wellcome Trust Sanger Institute, Hinxton, United Kingdom 3. The iPlant Collaborative, Tucson, AZ 4. Iowa State University, Ames, IA 5. USDA-ARS-CICGRU, Ames, IA 6. Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 7. Computer Science Department, Aberystwyth University, Aberystwyth, United Kingdom 8. King Abdullah University of Science & Technology, Thuwal, Saudi Arabia 9. Michigan State University, East Lansing, MI 10. Oklahoma State University, Stillwater, OK 11. Boyce Thompson Institute for Plant Research, Ithaca, NY 12. Cornell Univer sity, Ithaca, NY 13. Phoenix Bioinformatics, Redwood City, CA

Plant phenotype comparisons enable us to expl ore the relationship between gene function, sequence similarity and consequently to ma ke predictions for crop improvements. Plant phenotypes are described primarily using free text and are inconsistent between species, making computer facilitated queries difficult; however, asse ssing this data manually is impossible due to the ever increasing plethora of available phenotype data. To address this issue, we undertook a pilot project to formalize phenotype descriptors for six plant species, focusing on mutant phenotypes associated with sequenced genes. To do this, we selected free text descriptions of 1742 unique phenotypes for 2741 genes from maize, rice, Arabidopsis, soybean, tomato, and Medicago and manually converted them into a common Entity-Quality format using taxonomically broad ontologies; e.g., the Plant Ontology and the Gene Ontology. The power of this method lies in the fact that hierarchical ont ologies allow even distantly related phenotypes to be identified computationally. Similarity scores were calculated for each pair of phenotypes and the resulting associations were loaded into a database and query tool called PhenomeNet (http://phenomebrowser.net/plant/ query.php). PhenomeNet enables researchers to query these associations with locus names, gene identifiers, and phenotypic descriptions. To the user, this is roughly similar to using BLAST to identify si milar sequences. Although the phenotype dataset must be greatly expanded to be a useful research tool, our work demonstrates that comparing phenotypes among divergent plant species can be automated. Funding acknowledgement: National Science Foundation (NSF), United States Department of Agriculture (USDA)

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Data Harmonization Workshop, Beltsville, MD. June 11-12th 2015

AgMIP and USDA have organized a for the crop modeling research community

Data Harmonization

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Big Data + Bio-imaging Workshop: May 14-15, UC-Santa Barbara

Attendees:

• Jaiswal Lab (OSU, BPP): Justin Preece
• Todorovic Group (OSU, EECS): Xu Xu
• iPlant-Bisque Group (UCSB): Kris Kvilekval, Dmitri Fedorov, B.S. Manjunath, Nirav Merchant, Martha Narro

• Link to: Meeting Agenda
• Link to: Report

• Attended this workshop as collaborators with the iPlant Bisque group
• Presentations: AISO software demo (JP): File:AISO Bisque Workshop Final.pdf
  • Described the Planteome project and our efforts to port AISO to iPlant Bisque

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Upcoming Meetings of Interest:

• Botanical Society of America- http://2015.botanyconference.org/
• ICBO 2015 http://icbo2015.fc.ul.pt/
• http://www.bio-ontologies.org.uk/