Difference between revisions of "POC Outreach Events"

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Workshops, Presentations, Posters, etc
 
Workshops, Presentations, Posters, etc
  
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=Year 2012=
+
=Year 2014=
 +
 
 +
==Presentations on the Phenotype RCN monthly Webex Call- Jan 6th 2014==
 +
 
 +
http://www.phenotypercn.org/?page_id=2039
 +
 
 +
* RW:  http://www.slideshare.net/rlwalls2008/po-development-stages-jan2014
 +
 
 +
This is an abbreviated version of the talk that includes only the slides on development stages, so it can  be linked to from the development stage ontology wiki (http://code.google.com/p/developmental-stage-ontologies/)
 +
 
 +
* LC: cROP_RCN talk (LC_1-5-14).pptx
 +
 
 +
==[http://www.intlpag.org/ PAG 2014]==
 +
Plant and Animal Genome XXII Meeting, January 11-15, 2014 San Diego, CA
 +
 
 +
* [https://pag.confex.com/pag/xxii/webprogram/Session2103.html "Systems Biology and Ontologies Workshop:"], Saturday January 11th from 8:00-10:10 AM.
 +
 
 +
- Organizers: Laurel Cooper, Sushma Naithani and Pankaj Jaiswal
 +
 
 +
* [https://pag.confex.com/pag/xxii/webprogram/Paper9799.html Common Reference Ontologies for Plant Biology (cROP)]: A Platform for Integrative Plant Genomics: Laurel Cooper et al.
 +
 
 +
==[http://www.phenotypercn.org/?page_id=2287  Fourth Annual Summit of the Phenotype Ontology Research Coordination Network]==
 +
 
 +
February 21-23, 2014 at the University of Arizona’s Biosphere2 about 40 miles north of Tucson, AZ,
 +
 
 +
* Presentations:
 +
** Plant Environmental Condition Ontology (EO), Pankaj Jaiswal*, Laurel Cooper and Laura Moore.
 +
 
 +
==[https://sites.google.com/a/cgxchange.org/cropontologycommunity/ Workshop on Crop Ontology and Phenotyping Data Interoperability]==
 +
 
 +
Date: 31 March-4th April 2014, Montpellier France
 +
 
 +
Presentations:
 +
* The Plant Ontology and the Trait Ontology: Resources for Plant Genomics; presented by: Laurel Cooper
 +
 
 +
* Harmonizing trait classes in the Crop Ontology & aligning with Plant and Trait Ontologies; Harold Duruflé*, Laurel Cooper*, Marie-Angelique Laporte & Elizabeth Arnaud
 +
 
 +
* AISO- Annotation of Image Segments using Ontologies; presented by: Laurel Cooper
 +
 
 +
* Plant Phenotype Pilot Project; presented by: Laurel Cooper
 +
 
 +
==[http://www.ibc-montpellier.fr Institute of Computational Biology] Invited Guest Seminar==
 +
 
 +
Host Institute: Institute of Computational Biology (IBC) in Montpellier, France, Weds. March 26th, 2014
 +
 
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Presentation: Common Reference Ontologies for Plants and Tools for Integrative Plant Genomics: Presented by: Laurel Cooper
 +
 
 +
 
 +
==Botanical Ontologies: A Cross-Disciplinary Forum on Human-Plant Relationships, 2014, Oxford==
 +
 
 +
Helen Ougham et al. (Aberystwyth University): Enriching online content of a scientific journal using the Plant Ontology
 +
 
 +
 
 +
The increasing availability of scientific journals in online format offers new opportunities to enrich the content of articles. Content enrichment can include the provision of additional terms for indexing, definitions of specialised terms, links to relevant content in bioinformatics and other databases, suggestions for further reading and much more. We are developing a process for enriching the content of papers published in New Phytologist, one of the world's leading plant science journals (impact factor 6.736). A key component of this process is the Plant Ontology (PO; http://www.plantontology.org/), a botanical ontology that describes plant anatomy and stages in plant development. The PO, which has been developed by international experts in these domains with considerable and ongoing input from the research community, provides a structured controlled vocabulary of defined terms. We describe how we are using the PO to increase the amount of knowledge readers of New Phytologist papers can access, and how this approach can facilitate botanical research and education.
 +
 
 +
Keywords: content enrichment, New Phytologist, plant ontology, text mining
 +
 
 +
May 16-17 2014, Oxford, UK
 +
 
 +
==ASPB Plant Biology 2014, Portland, OR, July 12-16th, 2014==
 +
 
 +
The [http://plantontology.org Plant Ontology] will be represented at the [http://my.aspb.org/page/Oregon2014 ASPB Plant Biology 2014] meeting in Portland, Oregon July 12th-16th.
 +
 
 +
Representatives of the PO, along with several other plant genome databases, will be present at the Plant Genome Resources Outreach Booth: (# 415) throughout the meeting to answer questions and interact with users.  You can find a schedule at the booth in Exhibit Hall A-B.
 +
 
 +
Visit our poster (P41006-C) to learn more about recent developments in Reference Ontologies for Plants and Tools for Integrative Plant Genomics.
 +
 
 +
Also, plan to attend the Special Minisymposium: Bioinformatic Resources for Plant Biology Research, Sunday July 13th, from 7:45 PM to 10:00 PM in room A106.
 +
This workshop will provide an overview of a variety of tools and resources of interest to plant biology researchers.
 +
 
 +
=Year 2013=
 +
==[http://www.intlpag.org/2013/ PAG 2013] San Diego, CA==
 +
Plant and Animal Genome XXI Meeting, January 11-16, 2013 San Diego, CA
 +
 +
*Ontology workshop: [https://pag.confex.com/pag/xxi/webprogram/Session1596.html "Applications of Ontologies to Plant and Animal Genomics"], Saturday January 14th from 8:00-10:10 AM.
 +
 
 +
- Organizers: Laurel Cooper and Pankaj Jaiswal
 +
 
 +
* Jaiswal*, P.,  B. Smith, R. Bastow, P.J. Kersey, E. Arnaud, L. Cooper, C. Rawlings, 2013. [https://pag.confex.com/pag/xxi/webprogram/Paper5587.html A Resource for a Common Reference Ontology for Plants].
 +
 
 +
* Elizabeth Arnaud*, Laurel Cooper,  Pankaj Jaiswal,, et al.  [https://pag.confex.com/pag/xxi/webprogram/Paper5002.html The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes].
 +
 +
* Chris Mungall [https://pag.confex.com/pag/xxi/webprogram/Paper5577.html Uberon, An Integrative Gross Anatomy Ontology For Animals].
 +
 
 +
* Eva Huala [https://pag.confex.com/pag/xxi/webprogram/Paper5804.html Application of Ontologies to Plant Gene Function and Phenotype Data].
 +
 
 +
* Reinhard Simon. [https://pag.confex.com/pag/xxi/webprogram/Paper4937.html Status Of The Draft Potato Ontology].
 +
 
 +
 
 +
'''PAG Posters:'''
 +
 
 +
* Laurel D. Cooper*, et al. 2013. [https://pag.confex.com/pag/xxi/webprogram/Paper7640.html Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics]. Poster presentation. PAG 2013 meeting, San Diego, CA.
 +
 
 +
* Elizabeth Arnaud*, Laurel Cooper,  Pankaj Jaiswal,, et al.  [https://pag.confex.com/pag/xxi/webprogram/Paper6588.html The Species-Specific Crop Ontology (Generation Challenge Programme): Application and Integration into the Reference Plant Trait Ontology to Enable Data Mining on Phenotypes].
 +
Poster presentation. PAG 2013 meeting, San Diego, CA.
 +
 
 +
* Eva Huala*,  Laurel Cooper, Pankaj Jaiswal, Laura Moore, et al. [https://pag.confex.com/pag/xxi/webprogram/Paper5616.html Development of a Unified Phenotype Dataset for Plants.] Poster presentation. PAG 2013 meeting, San Diego, CA.
 +
 
 +
* Lingutla, N, Preece*, J, Todorovic, S, Jaiswal P. 2013 AISO: Annotation of Image Segments using Ontologies [https://pag.confex.com/pag/xxi/webprogram/Paper7520.html AISO demo Abstract] and [https://pag.confex.com/pag/xxi/webprogram/Paper7632.html AISO poster] abstract. Poster presentation and computer Demo. PAG 2013 meeting, San Diego, CA.
 +
 
 +
== [http://www.phenotypercn.org/?cat=128 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: [http://www.plantontology.org/ The Plant Ontology], [http://pir.georgetown.edu/pro/ The Protein Ontology], [http://bioontologies.org National Center for Biomedical Ontology], and the [http://ncor.buffalo.edu 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)
 +
 
 +
 
 +
==[http://jaiswallab.cgrb.oregonstate.edu/node/107 STEM Class], July 15-19, 2013 Oregon State University==
 +
The [http://academy.engr.oregonstate.edu/ STEM Academy] and [http://jaiswallab.cgrb.oregonstate.edu/ Jaiswal laboratory] at Oregon State University co-organized a week long (July 15-19, 2013) DNA Biology and Bioinformatics Summer Camp for high school students. The course was heavily subscribed, with 12 students (4 boys and 8 girls).
 +
 +
Subjects: The course involved a mix of lectures and hands-on exercises to learn about plant DNA and bioinformatics:
 +
* Basics of the genome, DNA, RNA, protein, genetic mutations, genetic markers (SNPs and SSRs), molecular structures, and the genetics and scoring of agronomic traits.
 +
 
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* The students worked with DNA modeling kits to learn about its structure, components, assembly of the molecule and how mutations occur in the DNA chain.
 +
 
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Hands-on Lab Activity:
 +
*Students isolated DNA from two varieties of Einkorn wheat (''Triticum monococcum''), a diploid wheat which is a close relative of the modern bread wheat and assayed a wheat genetic marker, (recently-discovered in the Jaiswal laboratory) using PCR amplification followed by gel electrophoresis to illustrate differences between the varieties and learned about the applications of genetic markers in genetic and forensic studies including plant breeding and variety development.
 +
 
 +
Hands-on Computer Activity:
 +
* Using the rice chloroplast genome sequence available from the EMBL data archive as a starting point, students explored bioinformatics software, tools, and databases (including Artemis, Pfam, Cn3D, etc.) scientists use to import and annotate genome sequences to find genes, gene products (proteins), assign function to proteins, compare to other well-known homologous proteins, and model protein 3D structures.
 +
 
 +
The course ended with a lecture and hands-on exercise focusing on genetics, plant breeding and scoring differences in important agronomic traits (characters/phenotypes) such as the spike structures (seed-bearing parts/fruits) of plants from the Oregon Wolfe Barley population
 +
 
 +
== [http://www.2013.botanyconference.org/  Botany 2013]==
 +
Annual Botanical Society of America Meeting, July 27 - 31, 2013, New Orleans
  
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==[http://www.intl-pag.org/ PAG 2012] San Diego, CA==
+
* Oral Paper Presentations:
 +
**[http://www.2013.botanyconference.org/engine/search/index.php?func=detail&aid=465 The Plant Ontology (PO)] Presented by: Dennis Stevenson (Developmental and Structural Section)
 +
** [http://www.2013.botanyconference.org/engine/search/index.php?func=detail&aid=104 CUPAC- The Cornell University Plant Anatomy Collection: a web-based tool for the Plant Sciences teachers and researchers] presented by: Maria Alejandra Gandolfo (Teaching section)  http://cupac.bh.cornell.edu/
  
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PO was represented at the following events:
+
* Poster Presentation:  
 +
**[http://www.2013.botanyconference.org/engine/search/index.php?func=detail&aid=1337 Plant Ontology, a controlled and structured plant vocabulary for all botanical disciplines]. Presented by Brian Atkinson
  
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PO organized an Ontology workshop: Using Ontologies for Organizing Plant and Animal Genomics Data, Saturday January 14th from 10:20am-12:30pm.
+
==[http://www.ibima.med.uni-rostock.de/IBIMA/symposium/2013/ Rostock Symposium on Systems Biology and Bioinformatics in Aging Research], September 20-21, 2013, Rostock, Germany==
  
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We had 5 speakers and a panel discussion at the end.
 
  
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* [http://pag.confex.com/pag/xx/webprogram/Session1272.html Ontology Workshop page]
+
Location: Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany,
  
−
[http://pag.confex.com/pag/xx/webprogram/Paper1716.html Expanding the Plant Ontology: Linking Plant Anatomy and Development to Genomics Across Plant Taxa ]
+
Barry Smith presented the Keynote address: [http://www.slideshare.net/BarrySmith3/ontology-of-aging-and-death “Ontology of Aging and Death”], where the Plant Ontology played a central role.
  
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For more info, see the [[PAG 2012 Ontology workshop]] wiki page
+
=Year 2012=
 +
==[https://pag.confex.com/pag/xx/webprogram/start.html PAG 2012], January 14-18, 2012, San Diego, CA==
 +
PO was represented at the following events:
 +
* Ontology workshop: Using Ontologies for Organizing Plant and Animal Genomics Data, Saturday January 14th from 10:20am-12:30pm.
 +
** [http://pag.confex.com/pag/xx/webprogram/Session1272.html Ontology Workshop page]; 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
  
 
* [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1046.html Non-Seed Plant Workshop] on Saturday, Jan 14th, (3:50pm-6pm)  
 
* [http://pag.confex.com/pag/xx/webprogrampreliminary/Session1046.html Non-Seed Plant Workshop] on Saturday, Jan 14th, (3:50pm-6pm)  
Line 21: Line 167:
  
 
* [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html Plant Phenotypes] workshop on Sunday, Jan. 15th, (8:00am - 10:10am)
 
* [http://pag.confex.com/pag/xx/webprogrampreliminary/Symposium56.html Plant Phenotypes] workshop on Sunday, Jan. 15th, (8:00am - 10:10am)
−
Link to [http://pag.confex.com/pag/xx/webprogram/Paper1878.html abstract] and presentation: [[Media: Cooper_Phenos_PAG2012.pdf]]
+
Link to [http://pag.confex.com/pag/xx/webprogram/Paper1878.html abstract] and presentation: [[Media: Cooper_Phenos_PAG2012.pdf]].
  
 
* Computer demo Monday 12:50 pm for the PO.
 
* Computer demo Monday 12:50 pm for the PO.
Line 28: Line 174:
 
* The PO also took part in an [http://www.agron.missouri.edu/mnl/pgoPAG.htm Outreach booth] organized by MaizeGDB
 
* The PO also took part in an [http://www.agron.missouri.edu/mnl/pgoPAG.htm Outreach booth] organized by MaizeGDB
  
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==[http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference]==
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==[http://www.phenotypercn.org/?page_id=628 Phenotype RCN 2012 annual meeting], 23-25 February 2012==
 +
RW attended annual RCN meeting held at NESCent
 +
 
 +
==Maize Genetics Meeting 2012, Portland, OR, March 15-18, 2012==
 +
[http://www.maizegdb.org/maize_meeting/2012/index.php Maize Genetics Meeting 2012]
 +
 
 +
LC submitted an abstract for a short talk [http://maizemeeting.maizegdb.org/mm2012/see_abstract.php?id=302 abstract] Friday March 16th, 5:45pm, which was presented by PJ.
 +
 
 +
[[File:Maize_meeting_2012_v2.pdf]]
 +
 
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==[http://pir.georgetown.edu/biocuration2012.html 5th International Biocuration Conference], April 2-4, 2012, Washington DC==
 +
Poster Presentation: [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf‎]]
 +
 
 +
==Semantics of Biodiversity Workshop, University of Kansas Biodiversity Institute, Lawrence, Kansas. May 16-18, 2012==
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Website with On-line videos at http://biocodecommons.org/workshops/sob.html
  
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April 2-4, 2012, Washington DC
+
==[http://www.botanyconference.org/ Botany 2012], July 7 - 11, 2012 - Columbus, Ohio==
 +
The PO hosted a [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 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.
  
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Abstract submitted 12-9-11, [[File:Abs_Biocuration_2012_(LC_12-9-11).pdf‎]]
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* Wiki page for workshop: [[Plant Ontology Workshop, Botany 2012]]
  
 +
The PO participated in an '''outreach booth''' at the Botany Meeting, which was hosted by the NYBG Press.
  
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==[http://www.maizegdb.org/maize_meeting/2012/index.php Maize Genetics Meeting 2012]==
+
==ASPB Plant Biology 2012, Austin, TX, July 20 - 24, 2012==
 +
Abstract: [http://precis.preciscentral.com/utils/ip/SearchResults.asp?EventId=d64a340b Poster Number: P28002]
  
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March 15-18, 2012 in Portland, OR 
+
[[Media:Poster_ASPB_2012_(LC_7-18-12).pdf]]
  
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LC will present a short talk [http://maizemeeting.maizegdb.org/mm2012/see_abstract.php?id=302 abstract] Friday March 16th, 5:45pm
+
[http://my.aspb.org/default.asp?page=Meetings_PB12Wrkshps Plant Informatics Workshop] was held with TAIR, Gramene and PO : Saturday, July 21, 2012, 7:30 PM - 9:00 PM
  
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Attach pdf of ppt?
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Link to Plant Ontology workshop presentation: [[Media:Cooper_PO_ASPB_2012.pdf‎]]
  
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=Year 2011=
+
LC attended
  
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* '''[http://www.swat4ls.org/workshops/london2011/ Semantic Web Applications and Tools for Life Sciences Workshop]''' Univ. of London and the Wellcome Trust Collection Conference Center (London, UK), Dec 6-9
+
[[Outreach booth- ASPB Plant Biology 2012]]
  
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JP will present a poster entitled "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes". (abstract: [[Media:SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf|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.
+
==[http://purl.bioontology.org/ICBO/ ICBO 2012], July 22nd-25th, Graz, Austria==
 +
International Conference on Biomedical Ontologies, , co-located with the 7th International Conference on Formal Ontologies in Information Systems [http://www.kr-med.org/icbofois2012/ (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.
  
−
* '''[http://meetings.cshl.edu/meetings/plants11.shtml Plant Genomes & Biotechnology: from Genes to Networks]''' Cold Spring Harbor Laboratory, November 30 - December 3, 2011
+
*Link to IDOPlant paper: [[Media:idoplant_paper.pdf]]
 +
*Link to IDOPlant presentation [[Media:IDOPlant_ICBO2012.pdf]]
 +
*Wiki page for notes on [[Plant Disease Ontology]]
 +
*Link to abstract for PO-FNA mapping poster: [[Media:PO_FNA_ICBO_abstract.pdf]]
 +
*Link to PO-FNA mapping poster: [[Media:PO_FNA_ICBO_poster.pdf]]
 +
*Link to PO-FNA mapping: http://tinyurl.com/FNAPOmapping
  
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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]]
+
==Genomic Standards Consortium 14th Annual Conference, September 18-20, 2012==
  
 +
[http://gensc.org/?title=GSC_14 Genomic Standards Consortium 14th Annual Conference], Biocode Commons Hackathon, Oxford, September 18-20, 2012
  
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* '''Departmental seminar: Facultad de Ciencis Naturales y Museo , Universidad Nacional de La Plata, Argentina''', Nov. 1, 2011
+
Presentation by BS: “Sample Ontology for Biodiversity Genomics”
−
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''' ([http://gensc.org/gc_wiki/index.php/GSC_12 GSC 12]), Max Planck Institute for Marine Microbiology, Bremen, September 28-29, 2011
+
==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]]
  
−
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”)
+
Dates: Sept. 13-15th
  
 +
The focus of the workshop will be on mostly development stages and traits for the crop plants
  
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* '''Syngenta Presentation'''. Global webinar, September 26, 2011
+
==Genome Informatics 2012, Robinson College, Cambridge, UK, September 6th-9th, 2012 ==
 +
[https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=296 Genome Informatics 2012]
  
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PJ and JP presented our current work on the Planteome Annotation Wiki to the IT Research and Development Dept. at Syngenta. (presentation: [[Media:Jaiswal_Lab_-_Semantic_Wiki_Presentation_-_2011.pdf|Jaiswal Lab - Semantic Wiki Presentation - 2011.pdf]])
+
[http://wiki.plantontology.org/index.php/File:Abstract_GI_2012_PO_poster.pdf Abstract]
  
 +
JP attended and presented a poster: The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa
  
−
* '''[http://conference.cgrb.oregonstate.edu/ 2011 CGRB Fall Conference]''' Oregon State University, September 18th-19th, 2011.
+
==[http://www.phenotypercn.org/?page_id=1396 Phenotype RCN Working Group meeting], Oct 26-29th 2012==
  
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Two posters related to the Plant Ontology were presented.
+
Asilomar Conference Grounds, Pacific Grove, California
−
 
−
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''.
+
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
  
−
* '''Moss 2011 PO presentation''' (Black Forest, September 11th - 15th, 2011, done via Webex) [[Moss 2011 Meeting- PO presentation]] Sept 12, 2011
+
=Year 2011=
 +
==Plant and Animal Genome XIX Conference, San Diego, CA, January 15-19, 2011==
 +
[http://intl-pag.org/ PAG 2011], 
 +
LC, RW, JP and DWS presented a [http://www.intl-pag.org/19/abstracts/C01_PAGXIX_887.html PO poster and a computer demo].
  
 +
LC took part in the [http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes workshop] and panel discussion
  
−
* '''NSF Plant Genome Awardee meeting''' Sept, 2011. Washington, DC. Submission: [[Media:2-pager_plant_ontology-2011.pdf]]
+
We also hosted a [[PAG_2011_Collaborators_Workshop]] on Sunday, Jan 16th, 2011.
  
 +
* [http://www.phenotypercn.org/?page_id=289 Phenotype RCN Meeting], Durham, NC''', February 25-27, 2011
 +
The Plant Ontology attended the inaugural meeting of the newly-funded [http://phenotypercn.org Phenotype Ontology RCN] at the National Evolutionary Synthesis Center in Durham, NC.
  
−
* '''ASPB Plant Biology meeting 2011,'''  [http://my.aspb.org/?page=Meetings_PB2011 PB2011], Minneapolis, Minn. Aug 6th-10th, 2011
+
==Presentation to Physcomitrella Collaborators, May 2011==
 +
May 2011 [[Plant Ontology Webinar- May 2011 release]]
  
−
PO and [http://www.gramene.org/ Gramene] hosted a [http://outreach.gramene.org/gramene-outreach/index.php/Main_Page Data Curation Workshop] 
+
==Plant Working Group Meeting of the Phenotype Ontology RCN', Google Campus in Boulder, CO; June 1-3, 2011==
 +
[http://www.phenotypercn.org/?page_id=542 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.
  
−
LC presented a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster] and we took part in an [[Plant Biology 2011 Outreach Booth]]
+
==Semantic Web Workshop, June 6-7, 2011, Santa Fe, NM==
 +
The Plant Ontology was represented at the 2011 [http://www.iplantcollaborative.org/learn/events/2011/04/22/2011-semantic-web-workshop 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.
  
 +
==International Botanical Congress, Melbourne, Australia. July 23rd – 30th  2011==
 +
[http://www.ibc2011.com/Default.htm (IBC2011)]
  
−
* '''International Botanical Congress''' [http://www.ibc2011.com/Default.htm (IBC2011)],Melbourne, Australia. July 23rd – 30th  2011
 
 
Symposium hosted: [[Bio-Ontologies for the Plant Sciences]] under the Genetics, Genomics and Bioinformatics theme.  
 
Symposium hosted: [[Bio-Ontologies for the Plant Sciences]] under the Genetics, Genomics and Bioinformatics theme.  
  
Line 103: Line 286:
  
 
POC presented talks:
 
POC presented talks:
 +
* Pankaj Jaiswal, Oregon State University, [[Ontologies for Plant Biology - IBC 2011]]
 +
* Dennis Stevenson, Genomics of Seed Plants and Ontologies.
  
−
Pankaj Jaiswal, Oregon State University, [[Ontologies for Plant Biology - IBC 2011]]
+
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]]
  
−
Dennis Stevenson, Genomics of Seed Plants and Ontologies.
+
==ASPB Plant Biology meeting 2011, [http://my.aspb.org/?page=Meetings_PB2011 PB2011], Minneapolis, Minn. Aug 6th-10th, 2011==
  
−
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]]
+
PO and [http://www.gramene.org/ Gramene] hosted a [http://outreach.gramene.org/gramene-outreach/index.php/Main_Page Data Curation Workshop]
  
 +
LC presented a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster] and we took part in an [[Plant Biology 2011 Outreach Booth]]
  
 +
==International Conference on Biomedical Ontologies, Buffalo, NY.  July 26-30, 2011==
 +
[http://icbo.buffalo.edu IBCO 2011]
  
−
* '''International Conference on Biomedical Ontologies''' [http://icbo.buffalo.edu IBCO 2011] Buffalo, NY.  July 26-30, 2011
 
 
LC co-organized the session on [http://icbo.buffalo.edu/2011/WorkshopD_Program.pdf "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability"]
 
LC co-organized the session on [http://icbo.buffalo.edu/2011/WorkshopD_Program.pdf "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"
 
and presented a flash talk "The Plant Ontology: Development of a Reference Ontology for all Plants"
Line 118: Line 305:
 
LC also presented the PO in the OBO Foundry session as part of the application for OBO Foundry Membership [http://icbo.buffalo.edu/2011/slides/Thursday%20OBO_Foundry_Panel/ link]
 
LC also presented the PO in the OBO Foundry session as part of the application for OBO Foundry Membership [http://icbo.buffalo.edu/2011/slides/Thursday%20OBO_Foundry_Panel/ link]
  
 +
==2011 CGRB Fall Conference, Oregon State University, September 18th-19th, 2011==
 +
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''.
  
 +
==Moss 2011, Black Forest,  September 11th - 15th, 2011==
 +
PO presentation, done via Webex, Sept 12, 2011: [[Moss 2011 Meeting- PO presentation]]
  
−
'''*Plant Working Group Meeting of the Phenotype Ontology RCN''', Google Campus in Boulder, CO; June 1-3, 2011  
+
==NSF Plant Genome Awardee meeting''' Sept, 2011. Washington, DC. Submission: [[Media:2-pager_plant_ontology-2011.pdf]]==
−
[http://www.phenotypercn.org/?page_id=542 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.
 
  
 +
==12th Genomic Standards Consortium Meeting, ([http://gensc.org/gc_wiki/index.php/GSC_12 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==
  
−
'''*Semantic Web Workshop''', June 6-7, 2011, Santa Fe, NM.
+
PJ and JP presented our current work on the Planteome Annotation Wiki to the IT Research and Development Dept. at Syngenta. (presentation: [[Media:Jaiswal_Lab_-_Semantic_Wiki_Presentation_-_2011.pdf|Jaiswal Lab - Semantic Wiki Presentation - 2011.pdf]])
  
−
The Plant Ontology was represented at the 2011 [http://www.iplantcollaborative.org/learn/events/2011/04/22/2011-semantic-web-workshop 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.  
+
==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.
  
−
'''* Presentation to Physcomitrella Collaborators''' May 2011 [[Plant Ontology Webinar- May 2011 release]]
+
==[http://meetings.cshl.edu/meetings/plants11.shtml Plant Genomes & Biotechnology: from Genes to Networks], Cold Spring Harbor Laboratory, November 30 - December 3, 2011==
 +
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]]
  
−
 
+
==[http://www.swat4ls.org/workshops/london2011/ Semantic Web Applications and Tools for Life Sciences Workshop], Univ. of London and the Wellcome Trust Collection Conference Center (London, UK), Dec 6-9==
−
*'''Phenotype RCN Meeting Durham, NC''', February 25-27, 2011  [http://www.phenotypercn.org/?page_id=289]
+
JP will present a poster entitled "Planteome Annotation Wiki: A Semantic Web Application for the Community Curation of Plant Genotypes and Phenotypes". (abstract: [[Media:SWAT4LS_2011_Proceedings-Planteome_Annotation_Wiki.pdf|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.
−
The Plant Ontology attended the inaugural meeting of the newly-funded [http://phenotypercn.org Phenotype Ontology RCN] at the National Evolutionary Synthesis Center in Durham, NC.
+
* 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.
−
 
 
−
 
 
−
 
 
−
 
 
−
==Plant and Animal Genome XIX Conference==
 
−
[http://intl-pag.org/ PAG 2011], San Diego, CA. January 15-19, 2011
 
−
 
 
−
LC, RW, JP and DWS presented a [http://www.intl-pag.org/19/abstracts/C01_PAGXIX_887.html PO poster and a computer demo].
 
−
 
 
−
LC took part in the [http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes workshop] and panel discussion
 
−
 
 
−
We also hosted a [http://wiki.plantontology.org:8080/index.php/PAG_2011_Collaborators_Workshop PO Collaborators workshop] on Sunday, Jan 16th, 2011.
 
  
 
=Year 2010=
 
=Year 2010=
 +
==[http://intl-pag.org/ Plant and Animal Genome XVIII Conference], San Diego, CA. Jan. 9-13, 2010==
 +
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.''
  
−
* [http://www.nettab.org/2010/ NETTAB 2010 conference on Biological Wikis], Nov 29-Dec 1, 2010, Naples, Italy
+
==[http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology Workshop],Jackson Laboratory, Bar Harbor, Mass. May 18th-19th, 2010==
−
Justin Preece presented the poster: A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species" [[File:NETTAB 2010 poster proposal.pdf]]
+
Laurel Cooper and Ramona Walls attended and Laurel presented a talk [http://obofoundry.org/wiki/images/9/95/Plant_Ontology_CL_Workshop.ppt "Introduction to the Plant Ontology™"]
−
 
+
==[http://www.aspb.org/pb-2010/ American Society of Plant Biologists], Quebec, Montreal, Canada. Jul. 31 - Aug. 4, 2010==
−
* 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'
 
−
 
 
−
*[http://www.aspb.org/pb-2010/ American Society of Plant Biologists], Quebec, Montreal, Canada. Jul. 31 - Aug. 4, 2010
 
 
Laurel Cooper and Pankaj Jaiswal attended.  Laurel presented a poster:[http://abstracts.aspb.org/pb2010/public/P14/P14010.html The Plant Ontology: A Database for Plant Genomics].
 
Laurel Cooper and Pankaj Jaiswal attended.  Laurel presented a poster:[http://abstracts.aspb.org/pb2010/public/P14/P14010.html 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''
 
''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]].
 
We also organized a Plant Biology 2010 Outreach Booth: [[Plant Genome Resources Outreach Booth]].
  
−
*PO-Gramene Annotation Workshop at Plant Biology 2010  [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop PO-Gramene Annotation Workshop]
+
* PO-Gramene Annotation Workshop at Plant Biology 2010  [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop PO-Gramene Annotation Workshop].  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: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop Phenote Workshop]  
−
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: [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2010_Workshop Phenote Workshop]  
 
  
−
*[http://www.botanyconference.org/ 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.''
+
==[http://sites.google.com/site/bioontologiessig2010/ Bio-Ontologies 2010: Semantic Applications in Life Sciences] July 9th-10th, 2010==
−
 
 
−
 
 
−
*[http://sites.google.com/site/bioontologiessig2010/ Bio-Ontologies 2010: Semantic Applications in Life Sciences] July 9th-10th, 2010
 
 
Laurel Cooper and Ramona Walls attended and presented a poster and a one page write-up that was presented as a 'flash update talk'  
 
Laurel Cooper and Ramona Walls attended and presented a poster and a one page write-up that was presented as a 'flash update talk'  
  
Line 189: Line 361:
 
[[File:Walls_Cooper_BioOntologies29.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.''
+
** ''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.''
  
  
−
*[http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology Workshop],Jackson Laboratory, Bar Harbor, Mass. May 18th-19th, 2010  
+
==[http://www.botanyconference.org/ Botany 2010], Providence, RI. Jul. 31 - Aug. 4, 2010==
−
Laurel Cooper and Ramona Walls attended and Laurel presented a talk [http://obofoundry.org/wiki/images/9/95/Plant_Ontology_CL_Workshop.ppt "Introduction to the Plant Ontology™"]
+
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.''
 +
==Seminar, New York Botanical Garden. October 6, 2010==
 +
Ramona Walls presented a seminar 'Plant Ontology: A tool for structural, developmental and molecular plant biologists'
 +
==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]]
 +
==[http://www.nettab.org/2010/ NETTAB 2010 conference on Biological Wikis], Nov 29-Dec 1, 2010, Naples, Italy==
 +
Justin Preece presented the poster: A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species" [[File:NETTAB 2010 poster proposal.pdf]]
  
−
*[http://intl-pag.org/ Plant and Animal Genome XVIII Conference], San Diego, CA. Jan. 9-13, 2010
+
Conference paper: Preece, J., J. Elser, and P. Jaiswal. (2010). A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species. NETTAB-BBCC 2010 Biological Wikis Proceedings. Naples, Italy.
−
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=
 
=Year 2009=
Line 209: Line 385:
 
* [http://www.intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 10-14, 2009
 
* [http://www.intl-pag.org/ Plant & Animal Genome Conference] San Diego, Jan 10-14, 2009
 
** Chih-Wei Tung, [http://www.intl-pag.org/17/abstracts/P08a_PAGXVII_807.html/ POC poster presentation]
 
** Chih-Wei Tung, [http://www.intl-pag.org/17/abstracts/P08a_PAGXVII_807.html/ POC poster presentation]
 +
 +
 +
From Year 1 Report:
 +
 +
* ASPB Plant Biology 2009, Hawaii
 +
* BSA Botany and Mycology 2009, Utah
 +
* Systematics Association, Leiden, The Netherlands, August 10-14
 +
* International Society for Plant Molecular Biology 2009 St. Louis (presentation and hands on training)
 +
* Center for Genome Research and Biocomputing conference 2009 Corvallis, OR
 +
* NSF Plant Genome PIs meeting 2009, Washington DC.
  
 
=Year 2008=
 
=Year 2008=

Latest revision as of 19:56, 2 February 2015

Workshops, Presentations, Posters, etc

Year 2014

Presentations on the Phenotype RCN monthly Webex Call- Jan 6th 2014

http://www.phenotypercn.org/?page_id=2039

This is an abbreviated version of the talk that includes only the slides on development stages, so it can be linked to from the development stage ontology wiki (http://code.google.com/p/developmental-stage-ontologies/)

  • LC: cROP_RCN talk (LC_1-5-14).pptx

PAG 2014

Plant and Animal Genome XXII Meeting, January 11-15, 2014 San Diego, CA

- Organizers: Laurel Cooper, Sushma Naithani and Pankaj Jaiswal

Fourth Annual Summit of the Phenotype Ontology Research Coordination Network

February 21-23, 2014 at the University of Arizona’s Biosphere2 about 40 miles north of Tucson, AZ,

  • Presentations:
    • Plant Environmental Condition Ontology (EO), Pankaj Jaiswal*, Laurel Cooper and Laura Moore.

Workshop on Crop Ontology and Phenotyping Data Interoperability

Date: 31 March-4th April 2014, Montpellier France

Presentations:

  • The Plant Ontology and the Trait Ontology: Resources for Plant Genomics; presented by: Laurel Cooper
  • Harmonizing trait classes in the Crop Ontology & aligning with Plant and Trait Ontologies; Harold Duruflé*, Laurel Cooper*, Marie-Angelique Laporte & Elizabeth Arnaud
  • AISO- Annotation of Image Segments using Ontologies; presented by: Laurel Cooper
  • Plant Phenotype Pilot Project; presented by: Laurel Cooper

Institute of Computational Biology Invited Guest Seminar

Host Institute: Institute of Computational Biology (IBC) in Montpellier, France, Weds. March 26th, 2014

Presentation: Common Reference Ontologies for Plants and Tools for Integrative Plant Genomics: Presented by: Laurel Cooper


Botanical Ontologies: A Cross-Disciplinary Forum on Human-Plant Relationships, 2014, Oxford

Helen Ougham et al. (Aberystwyth University): Enriching online content of a scientific journal using the Plant Ontology


The increasing availability of scientific journals in online format offers new opportunities to enrich the content of articles. Content enrichment can include the provision of additional terms for indexing, definitions of specialised terms, links to relevant content in bioinformatics and other databases, suggestions for further reading and much more. We are developing a process for enriching the content of papers published in New Phytologist, one of the world's leading plant science journals (impact factor 6.736). A key component of this process is the Plant Ontology (PO; http://www.plantontology.org/), a botanical ontology that describes plant anatomy and stages in plant development. The PO, which has been developed by international experts in these domains with considerable and ongoing input from the research community, provides a structured controlled vocabulary of defined terms. We describe how we are using the PO to increase the amount of knowledge readers of New Phytologist papers can access, and how this approach can facilitate botanical research and education.

Keywords: content enrichment, New Phytologist, plant ontology, text mining

May 16-17 2014, Oxford, UK

ASPB Plant Biology 2014, Portland, OR, July 12-16th, 2014

The Plant Ontology will be represented at the ASPB Plant Biology 2014 meeting in Portland, Oregon July 12th-16th.

Representatives of the PO, along with several other plant genome databases, will be present at the Plant Genome Resources Outreach Booth: (# 415) throughout the meeting to answer questions and interact with users. You can find a schedule at the booth in Exhibit Hall A-B.

Visit our poster (P41006-C) to learn more about recent developments in Reference Ontologies for Plants and Tools for Integrative Plant Genomics.

Also, plan to attend the Special Minisymposium: Bioinformatic Resources for Plant Biology Research, Sunday July 13th, from 7:45 PM to 10:00 PM in room A106. This workshop will provide an overview of a variety of tools and resources of interest to plant biology researchers.

Year 2013

PAG 2013 San Diego, CA

Plant and Animal Genome XXI Meeting, January 11-16, 2013 San Diego, CA

- Organizers: Laurel Cooper and Pankaj Jaiswal


PAG Posters:

Poster presentation. PAG 2013 meeting, San Diego, CA.

  • Lingutla, N, Preece*, J, Todorovic, S, Jaiswal P. 2013 AISO: Annotation of Image Segments using Ontologies AISO demo Abstract and AISO poster abstract. Poster presentation and computer Demo. PAG 2013 meeting, San Diego, CA.

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)


STEM Class, July 15-19, 2013 Oregon State University

The STEM Academy and Jaiswal laboratory at Oregon State University co-organized a week long (July 15-19, 2013) DNA Biology and Bioinformatics Summer Camp for high school students. The course was heavily subscribed, with 12 students (4 boys and 8 girls).

Subjects: The course involved a mix of lectures and hands-on exercises to learn about plant DNA and bioinformatics:

  • Basics of the genome, DNA, RNA, protein, genetic mutations, genetic markers (SNPs and SSRs), molecular structures, and the genetics and scoring of agronomic traits.
  • The students worked with DNA modeling kits to learn about its structure, components, assembly of the molecule and how mutations occur in the DNA chain.

Hands-on Lab Activity:

  • Students isolated DNA from two varieties of Einkorn wheat (Triticum monococcum), a diploid wheat which is a close relative of the modern bread wheat and assayed a wheat genetic marker, (recently-discovered in the Jaiswal laboratory) using PCR amplification followed by gel electrophoresis to illustrate differences between the varieties and learned about the applications of genetic markers in genetic and forensic studies including plant breeding and variety development.

Hands-on Computer Activity:

  • Using the rice chloroplast genome sequence available from the EMBL data archive as a starting point, students explored bioinformatics software, tools, and databases (including Artemis, Pfam, Cn3D, etc.) scientists use to import and annotate genome sequences to find genes, gene products (proteins), assign function to proteins, compare to other well-known homologous proteins, and model protein 3D structures.

The course ended with a lecture and hands-on exercise focusing on genetics, plant breeding and scoring differences in important agronomic traits (characters/phenotypes) such as the spike structures (seed-bearing parts/fruits) of plants from the Oregon Wolfe Barley population

Botany 2013

Annual Botanical Society of America Meeting, July 27 - 31, 2013, New Orleans

Rostock Symposium on Systems Biology and Bioinformatics in Aging Research, September 20-21, 2013, Rostock, Germany

Location: Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany,

Barry Smith presented the Keynote address: “Ontology of Aging and Death”, where the Plant Ontology played a central role.

Year 2012

PAG 2012, January 14-18, 2012, San Diego, CA

PO was represented at the following events:

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:

Phenotype RCN 2012 annual meeting, 23-25 February 2012

RW attended annual RCN meeting held at NESCent

Maize Genetics Meeting 2012, Portland, OR, March 15-18, 2012

Maize Genetics Meeting 2012

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

5th International Biocuration Conference, April 2-4, 2012, Washington DC

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

Semantics of Biodiversity Workshop, University of Kansas Biodiversity Institute, Lawrence, Kansas. May 16-18, 2012

Website with On-line videos at http://biocodecommons.org/workshops/sob.html

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.

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

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, July 22nd-25th, Graz, Austria

International Conference on Biomedical Ontologies, , 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.

Genomic Standards Consortium 14th Annual Conference, September 18-20, 2012

Genomic Standards Consortium 14th Annual Conference, Biocode Commons Hackathon, Oxford, September 18-20, 2012

Presentation by BS: “Sample Ontology for Biodiversity Genomics”


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, Robinson College, Cambridge, UK, September 6th-9th, 2012

Genome Informatics 2012

Abstract

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

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

Year 2011

Plant and Animal Genome XIX Conference, San Diego, CA, January 15-19, 2011

PAG 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.

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

Presentation to Physcomitrella Collaborators, May 2011

May 2011 Plant Ontology Webinar- May 2011 release

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.

International Botanical Congress, Melbourne, Australia. July 23rd – 30th 2011

(IBC2011)

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:

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

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

IBCO 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

2011 CGRB Fall Conference, Oregon State University, September 18th-19th, 2011

Two posters related to the Plant Ontology were presented:

Moss 2011, Black Forest, September 11th - 15th, 2011

PO presentation, done via Webex, Sept 12, 2011: Moss 2011 Meeting- PO presentation

NSF Plant Genome Awardee meeting Sept, 2011. Washington, DC. Submission: Media:2-pager_plant_ontology-2011.pdf

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)

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.

Plant Genomes & Biotechnology: from Genes to Networks, Cold Spring Harbor Laboratory, November 30 - December 3, 2011

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

Semantic Web Applications and Tools for Life Sciences Workshop, Univ. of London and the Wellcome Trust Collection Conference Center (London, UK), Dec 6-9

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.

Year 2010

Plant and Animal Genome XVIII Conference, San Diego, CA. Jan. 9-13, 2010

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.

Cell Ontology Workshop,Jackson Laboratory, Bar Harbor, Mass. May 18th-19th, 2010

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

American Society of Plant Biologists, Quebec, Montreal, Canada. Jul. 31 - Aug. 4, 2010

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.

  • PO-Gramene Annotation Workshop at Plant Biology 2010 PO-Gramene Annotation Workshop. 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


Bio-Ontologies 2010: Semantic Applications in Life Sciences July 9th-10th, 2010

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.


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.

Seminar, New York Botanical Garden. October 6, 2010

Ramona Walls presented a seminar 'Plant Ontology: A tool for structural, developmental and molecular plant biologists'

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

NETTAB 2010 conference on Biological Wikis, Nov 29-Dec 1, 2010, Naples, Italy

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

Conference paper: Preece, J., J. Elser, and P. Jaiswal. (2010). A Semantic Wiki for Genotype/Phenotype Annotation in Plant Species. NETTAB-BBCC 2010 Biological Wikis Proceedings. Naples, Italy.

Year 2009

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


From Year 1 Report:

  • ASPB Plant Biology 2009, Hawaii
  • BSA Botany and Mycology 2009, Utah
  • Systematics Association, Leiden, The Netherlands, August 10-14
  • International Society for Plant Molecular Biology 2009 St. Louis (presentation and hands on training)
  • Center for Genome Research and Biocomputing conference 2009 Corvallis, OR
  • NSF Plant Genome PIs meeting 2009, Washington DC.

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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