POC Outreach Events

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Workshops, Presentations, Posters, etc

Year 2014

Year 2013

PAG 2013 San Diego, CA

- Organizers: Laurel Cooper and Pankaj Jaiswal

  • Jaiswal, P. 2013. A Resource for a Common Reference Ontology for Plants. Available at: abstract.
  • Elizabeth Arnaud, Laurel Cooper, Pankaj Jaiswal,, et al. [ The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes
  • Uberon, An Integrative Gross Anatomy Ontology For Animals

Christopher Mungall, Berkeley Bioinformatics Open-Source Projects

  • Application of Ontologies to Plant Gene Function and Phenotype Data

Eva Huala, Carnegie Institution for Science

  • Status Of The Draft Potato Ontology

Reinhard Simon, International Potato Center (CIP); Merideth Bonierbale, International Potato Center

Posters:

  • Laurel D. Cooper. 2013. Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics. Available at: abstract.
  • Lingutla N, Preece J, Todorovic S, Jaiswal P. 2013 AISO: Annotation of Image Segments using Ontologies AISO demo Abstract and AISO poster abstract.

Phenotype RCN Plant Working Group Meeting Ames, Iowa, May 1-2, 2013

- LC of the Plant Ontology met with other members of the Plant Working Group to continue the development of the phenotype annotation files using the PO, GO, ChEBI, PATO and EO ontologies consistently and correctly to describe phenotypes from Medicago, rice, maize, Arabidopsis, tomato and soybean.

- The goal is the analysis of the full phenotype annotation set which should include ~6400 phenotype annotation statements made to 2750 mutant genes across the 6 plant species.

- Analysis possibilities include investigating the extent to which a mutant phenotype can be predicted from protein similarity or vice versa, and whether this can be used as a basis for selecting candidate genes underlying QTL or genetic loci.


PRO-PO-GO_Meeting Buffalo NY, May 15-16, 2013

A workshop to promote the coordination of the Gene, Protein, and Plant Ontologies and of other reference ontologies used in plant biology.

Co-organized by: The Plant Ontology, The Protein Ontology, National Center for Biomedical Ontology, and the National Center for Ontological Research.

Oral Presentations by members of the PO group:

  • Laurel Cooper: The Plant Ontology: A Resource for Plant Genomics
  • Pankaj Jaiswal: Outline of the cROP Framework
  • Pankaj Jaiswal: The Trait Ontology
  • Laurel Cooper: Plant Phenotype Pilot Project
  • Justin Preece: AISO: Annotation of Image Segments using Ontologies (remotely via webex)


Botany 2013, July 27 - 31, 2013, New Orleans

- Annual Botanical Society of America Meeting

Poster Presentation:

- Brian Atkinson* and Laurel Cooper et al. Plant Ontology, a controlled and structured plant vocabulary for all botanical disciplines.

Oral Paper Presentation: Developmental and Structural Section

- Dennis Stevenson* et al. The Plant Ontology (PO)

Year 2012

Phenotype RCN Working Group meeting, Oct 26-29th 2012

Asilomar Conference Grounds, Pacific Grove, California

Second RCN working group meeting

- LC of the Plant Ontology met with other members of the Plant Working Group to continue the development of the phenotype annotation files using the PO, GO, ChEBI, PATO and EO ontologies consistently and correctly to describe phenotypes from Medicago, rice, maize, Arabidopsis, tomato and soybean.

- developed plans and templates for the project

PO/TO Crop Annotation Workshop at OSU; Sept. 13-15th, 2012

For more information see the wiki page: Plant_Ontology_and_Crop_Annotation_Workshop_OSU_2012

Dates: Sept. 13-15th

The focus of the workshop will be on mostly development stages and traits for the crop plants


Genome Informatics 2012

Genome Informatics 2012

September 6th-9th, Robinson College, Cambridge, UK

Abstract

JP attended and presented a poster: The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Abstract: Poster Number: P28002

Media:Poster_ASPB_2012_(LC_7-18-12).pdf

Plant Informatics Workshop was held with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 9:00 PM

Link to Plant Ontology workshop presentation: Media:Cooper_PO_ASPB_2012.pdf‎

LC attended

Outreach booth- ASPB Plant Biology 2012

ICBO 2012

International Conference on Biomedical Ontologies, July 22nd-25th, Graz, Austria, co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012).

A paper describing a plant disease extension of the Infectious Disease Ontology was presented at this meeting, as well as a poster on the PO-FNA collaboration.

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

The PO hosted a Plant Ontology workshop on Sunday, July 8th, 9:00AM - 12:00PM, to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.


The PO participated in an outreach booth at the Botany Meeting, which was hosted by the NYBG Press.

5th International Biocuration Conference

April 2-4, 2012, Washington DC

Poster Presentation: File:Abs Biocuration 2012 (LC 12-9-11).pdf

Maize Genetics Meeting 2012

March 15-18, 2012 in Portland, OR

LC submitted an abstract for a short talk abstract Friday March 16th, 5:45pm, which was presented by PJ.

File:Maize meeting 2012 v2.pdf

Phenotype RCN 2012 annual meeting, 23-25 February 2012

Annual RCN meeting held at NESCent.

RW attended

PAG 2012 San Diego, CA

PO was represented at the following events:

PO organized an Ontology workshop: Using Ontologies for Organizing Plant and Animal Genomics Data, Saturday January 14th from 10:20am-12:30pm.

We had 5 speakers and a panel discussion at the end.

File:Cooper PO (LC 4-4-12).pdf

For more info, see the PAG 2012 Ontology workshop wiki page

Link to abstract and presentation:

Link to abstract and presentation: Media: Cooper_Phenos_PAG2012.pdf.

  • Computer demo Monday 12:50 pm for the PO.

Link to abstract and presentation:

Year 2011

JP will present a poster entitled "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes". (abstract: SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf). He will also participate in a "hackathon" software development session meant to spur innovation in semantic web applications.

Preece, Justin. “Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotype.” Poster presented at the 4th International Workshop on Semantic Web Applications and Tools for Life Sciences, Univ. of London and the Wellcome Trust Collection Conference Center, London, UK. December 6, 2011. http://dl.acm.org/citation.cfm?doid=2166896.2166921.


RW will present a poster entitled "Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets". (link to abstract: Media:PO_abstract_PGB_CSHL2011.pdf


  • Departmental seminar: Facultad de Ciencis Naturales y Museo , Universidad Nacional de La Plata, Argentina, Nov. 1, 2011

MAG presented: 'El valor de las fosiles para descrifar la historia evolutiva de las angiospermas y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany Laboratory- Dr. Ari Iglesias.

  • Departmental seminar: Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, Argentina, Oct. 31, 2011

MAG presented: "Paleobotanica en la era de la Biologia Molecular y breve introduccion a la Ontologia de Plantas"; Hosted by the Paleobotany and Palynology laboratory- Dr. Maria del Carmen Zamaloa.


  • 12th Genomic Standards Consortium Meeting (GSC 12), Max Planck Institute for Marine Microbiology, Bremen, September 28-29, 2011

Barry Smith addressed Plant Ontology issues in two presentations, on “An Introduction to Ontology as a Strategy for Data Integration”, and on “The Structure of the Environment Ontology”)


  • Syngenta Presentation. Global webinar, September 26, 2011

PJ and JP presented our current work on the Planteome Annotation Wiki to the IT Research and Development Dept. at Syngenta. (presentation: Jaiswal Lab - Semantic Wiki Presentation - 2011.pdf)


Two posters related to the Plant Ontology were presented.

LC presented the poster: "Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa".

JP presented a poster: "Planteome Annotation Wiki: A Semantic Application for the Community Curation of Plant Genotypes and Phenotypes". This explains the development of a semantic web application for annotation curation. This web application makes use of PO data via a newly created web service and includes an initial data set built from PO GAF (.assoc) files for Oryza sativa.




  • ASPB Plant Biology meeting 2011, PB2011, Minneapolis, Minn. Aug 6th-10th, 2011

PO and Gramene hosted a Data Curation Workshop

LC presented a PO poster and we took part in an Plant Biology 2011 Outreach Booth


  • International Botanical Congress (IBC2011),Melbourne, Australia. July 23rd – 30th 2011

Symposium hosted: Bio-Ontologies for the Plant Sciences under the Genetics, Genomics and Bioinformatics theme.

Please see the IBC 2011 Bio-Ontologies Symposium wiki page for more details.

Press release about the PO at IBC 2011: Media:IBC_2011_Congress_News_Thursday_28_July_WEB.pdf‎

POC presented talks:

Pankaj Jaiswal, Oregon State University, Ontologies for Plant Biology - IBC 2011

Dennis Stevenson, Genomics of Seed Plants and Ontologies.

Ramona Walls, The New York Botanical Garden, The Plant Ontology: an updated tool for all plant biologists - IBC 2011. Link to PDF of presentation: Media:Walls_PO_presentation_IBC11.pdf


  • International Conference on Biomedical Ontologies IBCO 2011 Buffalo, NY. July 26-30, 2011

LC co-organized the session on "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability" and presented a flash talk "The Plant Ontology: Development of a Reference Ontology for all Plants"

LC also presented the PO in the OBO Foundry session as part of the application for OBO Foundry Membership link


*Plant Working Group Meeting of the Phenotype Ontology RCN, Google Campus in Boulder, CO; June 1-3, 2011 RCN, June 2011

All four (Plants, Arthropoda, Vertebrates and Bioinformatics) Working Group sessions ran concurrently to maximize the benefits of emerging results, group experiences and collective synergy.


*Semantic Web Workshop, June 6-7, 2011, Santa Fe, NM.

The Plant Ontology was represented at the 2011 Semantic Web Workshop. Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop focused on biological applications for semantic web services. JP and JE attended.


* Presentation to Physcomitrella Collaborators May 2011 Plant Ontology Webinar- May 2011 release


  • Phenotype RCN Meeting Durham, NC, February 25-27, 2011 [1]

The Plant Ontology attended the inaugural meeting of the newly-funded Phenotype Ontology RCN at the National Evolutionary Synthesis Center in Durham, NC.



Plant and Animal Genome XIX Conference

PAG 2011, San Diego, CA. January 15-19, 2011

LC, RW, JP and DWS presented a PO poster and a computer demo.

LC took part in the Plant Phenotypes workshop and panel discussion

We also hosted a PAG_2011_Collaborators_Workshop on Sunday, Jan 16th, 2011.

Year 2010

Justin Preece presented the poster: A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species" File:NETTAB 2010 poster proposal.pdf

  • Seminar, Department of Botany and Plant Pathology, Oregon State University- Thurs, Oct 14th, 2010.

Laurel presented a seminar: Bridging Plant Anatomy and Genomics in the Digital Era: Recent Advances at The Plant Ontology File:Cooper BPP final (LC 10-14-10).pdf

  • Seminar, New York Botanical Garden. October 6, 2010. Ramona Walls presented a seminar 'Plant Ontology: A tool for structural, developmental and molecular plant biologists'

Laurel Cooper and Pankaj Jaiswal attended. Laurel presented a poster:The Plant Ontology: A Database for Plant Genomics.

Cooper, L., Elser, J., Walls, R., Stevenson, Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Database for Plant Genomics. American Society of Plant Biologists, Quebec, Montreal, Canada


We also organized a Plant Biology 2010 Outreach Booth: Plant Genome Resources Outreach Booth.

A workshop to demonstrate the Phenote Annotation Tool was held at the ASPB Plant Biology Meeting in Montreal, Quebec, Canada.

You can find a link to the workshop page at: Phenote Workshop

  • Botany 2010, Providence, RI. Jul. 31 - Aug. 4, 2010. Dennis Stevenson, Alejandra Gandolfo, and Ramona Walls attended.

Ramona Walls gave a presentation for the Developmental and Structural Section Abstract-BSA2010 File:Presentation-BSA2010.pdf

Walls, R., Cooper, L., Elser, J., Stevenson Dennis W., Smith, B., Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: a tool for structural, developmental, and molecular plant biologists. Providence, RI.


Laurel Cooper and Ramona Walls attended and presented a poster and a one page write-up that was presented as a 'flash update talk'

File:PO Poster BioOntologies2010.pdf

File:PO FlashTalk BioOntologies2010.pdf

File:Walls Cooper BioOntologies29.pdf

Walls, R., Cooper, L., Elser, J., Dennis W. Stevenson, Mungall, C. J., Gandolfo, M. A., and Jaiswal, P. (2010). The Plant Ontology: A Common Reference Ontology for Plants. Boston, MA.


Laurel Cooper and Ramona Walls attended and Laurel presented a talk "Introduction to the Plant Ontology™"

Laurel Cooper and Justin Elser Poster and Computer Demonstration

Elser, J., Cooper, L., and Jaiswal, P. (2010). Plant Ontology: Databases And Applications. San Diego, CA.

Year 2009

  • GCP Ontology Workshop Rome, Italy, April 20-22, 2009
    • Chih-Wei Tung, Gave a talk on "Plant and Trait Ontology"

Year 2008

Year 2007

  • AGRONOMICS workshop " Ontologies, Standards and Best Practices", Gent, Belgium, May 21-23
  • ITMI Israel, April 16-20, 2007
    • Shuly Avraham, poster

Year 2006

Year 2005

  • The 16th International Conference on Arabidopsis Research, Madison, WI, June 18, 2005
  • Frontiers in Plant Biology, MO, April 2005 Poster

Year 2004

Year 2002

  • PAG X Bioinformatics: Database
    • Leszek Vincent: The POC and Plant ontologies (poster)
    • Leszek Vincent: The POC and Plant ontologies - silk purpose from a maize ear (workshop: ontology)
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