POC Conf. Call 8-11-10

POC meeting, Webex Conference Call; Date: Aug 11th, 2010 10am (PDT)

Agenda and Minutes

In attendance:

POC members: Laurel Cooper, Justin Elser, Justin Preece, Dennis Stevenson, Ramona Walls

Absent: Alejandra Gandolfo, Pankaj Jaiswal, Chris Mungal, Barry Smith

Collaborators: none

Acceptance of the minutes from the 7-21-10 meeting? All in favor? no changes

Reports from Meetings: ASPB Plant Biology 2010 and BSA

Plant Biology 2010

The dev.plantontology.org version was demo’d at the Plant Genome resources Outreach Booth and through the poster and brochures.

PO-Gramene workshop

More details of the presentations are available on the Outreach Page.

Botanical Society of America meeting:

Ramona and Dennis met briefly with Sandra Knapp of the British Museum, who is interested in putting together an EU grant to use the Plant Ontology for species descriptions.

After Ramona's presentation, Bruce Kirchoff expressed some concerns about ontologies. Below is an excerpt from his email:

'I feel that there are still serious problems with any attempt to bring all aspects of plant morphology together under a unifying ontology. Perhaps the word 'ontology' was coined for these controlled vocabularies with tongue-in-cheek, but the attempts to extend the ontology beyond their use in databases tends to remove the jest, at least in my opinion.

I very much believe in open discussion as a way of advancing science. It was for this reason that I convinced the Botanical Society to institute the discussion sections that now are a standard part of the annual program. I would be interested in continuing the discussion of plant trait ontology at the next botanical society meetings, in a discussion session. Perhaps you and your colleagues would be interested in organizing one of these sessions with me.'

We will set up a conference call with Bruce in late September (he is available after September 20th).

Status and Update of Progress: PO Release

See the timeline and plan sent out 7-19-10 File:Plan PO Release (LC 7-19-10).pdf

1. Progress and Modifications to the Plan

-Since the last conference call on July 21st, We have reviewed the most recent changes and made some additional fixes. Plans did not proceed as laid out since Justin E was on leave. but this week we have gotten it loaded onto the Beta browser ( http://beta.plantontology.org:8080/amigo/go).

This is the same version as on the dev site, but also includes the annotations.

Note from PJ: Once these files are loaded, along with the annotations/associations we will need to assess if there were any dropped out as a result of the changes we have made to the Ontology. Any annotations that have dropped out will need to be reassigned to terms in the PO.

Laurel compiled a list of the terms that have been obsoleted and how many annotations that are associated with them. There were only 11 and only 5 of them are problematic: floral bud, gametophyte, leaf whorl, seedling and sporophyte. File:Obseleted terms (LC 8-10-10).pdf

From Justin E (Thanks!)

PO:0009003: sporophyte 117:

po_anatomy_gene_arabidopsis_tair.assoc

po_anatomy_gene_oryza_gramene.assoc

po_anatomy_qtl_oryza_gramene.assoc

PO:0000056: floral bud 54:

po_anatomy_gene_arabidopsis_tair.assoc

PO:0009004:gametophyte 1:

po_anatomy_gene_oryza_gramene.assoc

PO:0008034: leaf whorl 15802:

po_anatomy_gene_arabidopsis_tair.assoc

PO:0008037: seedling 16:

po_anatomy_gene_arabidopsis_tair.assoc

Justin confirmed that the 100 annotation associated with sporophyte that look the same are actually different. We discussed possibly re-configuring the PO web page so that more information shows up for each annotation, so it is clearer to the users how annotations differ from one another.

We discussed whether or not it would be better for the user groups who made the annotations to decide where to move the terms we are uncertain about. In any case, we will need to prepare a list for them including the terms that were moved automatically (because there was only one replacement term), and our suggestions for terms that could be replaced by multiple terms. They will need to approve any movement of annotations.

2. Notices will be posted on the PO mail lists: po-announce, po-dev, the PO web page and the Jaiswal lab web page that the beta version is available for review.

Ramona and Lol will work on an announcement. Dennis will also send this to the BSA for posting in their Plant Sciences Bulletin. Needs to get to BSA by the end of the week.

3. The documentation page will be posted on the POwiki page and the PO webpage with details of the changes made in the new release.

-wiki page has been created. We will load documentation of changes as we go along.

Ramona and Lol will discuss what needs to go on this page, and get it posted.

An announcement will be sent directly to the direct user groups listed on the 6-29-10 Conference Call page.

• TAIR email: curator@arabidopsis.org
• NASC ??? email: bioinfo@arabidopsis.info

(not really clear who to send it to here)

• Gramene email: gramene@gramene.org
• MaizeGDB Carolyn Lawrence
• VirtualPlant
• SoyBase Rex Nelson
• Genevestigator
• SGN Lukas Mueller+Naama Menda ?
• OryzaBase Yukiko Yamazaki?
• PlantTribes
• TraitNet
• Generation Challenge Program, CIMMYT, Mexico Rosemary Shrestha
• BRENDA
• UniProt

We will send the email to the 'contact' email address at each of these groups, if we do not have contact people at these groups.

Feedback on the Ontology: Over the next ~ 3 weeks we will take feedback for our direct user groups through a feedback box on the PO-beta.plantontology.org page and of course, through emails. Note: We can use the same feedback page that is on the main PO site, we will ask Justin E to make a link to it from the header on beta.plantontology.org browser. The feedback box captures the context of the comment ( ie: which page you are looking at).

Ramona and Lol will discuss how customize the feedback page for the beta browser, and work with Justin E to reconfigure it. This will be done in conjunction with the letter we send to users and reviewers.

Aug 8-26- The beta version will be ready to send it out to our panel of experts and also to the user groups for final review.

-The letter and review template will be sent out to the panel of experts (along with the user groups) that were identified on the 6-29-10 Conference Call.

-Reviewers will be asked to send their comments by Aug 26th. This will give them about 2 weeks to respond.

-We will follow the way the reviews were done in 2005, where the reviewers will be asked to look at specific sections or branches of the ontology.

- Laurel will send out an email inquiry (copied to DWS and PJ) to the reviewers asking them if they would be willing to do it.

-Once we all get back from vacation, we will make the required changes and prepare the release.

(Ramona out Aug 21th- Sept 7th, Laurel out Aug 27th- Sept 8th, Pankaj gone Aug 11th- Sept 3rd, then Sept )

To do: Identify reviewers for specific branches of the ontology:

We discussed what aspects of the ontology we should ask each reviewer to focus on. See comments in parentheses, in italics. We will prepare a general letter to go to all reviewers, with a place where each letter can be customized for the specific reviewer. Lol and Ramona will send the letters to Dennis, so he can contact the reviewers that he knows personally (those marked with an asterix).

Potential reviewers, areas of expertise, and contact information (suggestions for portions to review in italics):

Sarah Hake* UC Berkeley, The Plant Gene Expression Center (floral terms, plant tissue or plant cell)

Maize inflorescence development

“Our laboratory is interested in plant morphology. We are taking a genetic approach to understand the processes that regulate form and function. We are primarily interested in how shoot meristems initiate organs. The knotted1 gene and related knox (knotted1-like homeobox) genes appear to play a critical role in this process. We are studying what regulates knox genes and what genes are regulated by KNOX proteins.”

hake@berkeley.edu

Quentin Cronk* Biodiversity Research Center, University of British Columbia (whole plant, collective plant structure, plant tissue)

“Our lab integrates comparative genomics, molecular developmental biology and evolutionary biology to study plant form. We are interested in the how different morphologies evolve in plants, as well as the functional significance of morphological differences between species. Our main model organisms for this include the Leguminosae (floral morphology) and black cottonwood, Populus trichocarpa (adaptive evolution of trees).”

Quentin.cronk@ubc.ca

Paula Rudall* Head of Micromorphology Section, Royal Botanic Garden, Kew (overall ontology structure, plant cell, male and female gametophyte)

plant anatomy expert, monocot systematics

“Use of micromorphology as a source of data in assessments of homology and phylogeny. Focused analytical studies on systematic morphology, anatomy, embryology and palynology in a phylogenetic and developmental-genetic context. A primary focus is to address questions about the evolutionary origin of flowers, including targeted comparative ontogenetic studies on a phylogenetically broad range of angiosperms in which the inflorescence–flower boundary is ambiguous, especially the monocot family Triuridaceae, the eudicot family Euphorbiaceae and the early-divergent angiosperm family Hydatellaceae. A second key research focus is on plant embryology and pollen morphology, including the developmental bases for key innovations in the seed-plant megagametophyte and microgametophyte. Research portfolio of over 200 research papers and books, including a textbook, Anatomy of Flowering Plants. Collaborative research includes year-out placement students and PhD students, plus a broad international network. Kew’s Micromorphology lab attracts collaborations and research visits from considerable numbers of international researchers.”

p.rudall@kew.org

Sarah Mathews* Harvard University, Arnold Arboretum (shoot system, plant organ, plant tissue; how does our terminology relate to gene annotation, especially with respect to gymnosperms)

Phytochromes and phylogeny, gymnosperm tree of life

“Evolution in the plant kingdom is marked by the successive origin of new forms, including the land plants, tracheophytes, seed plants, and flowering plants. The origin of these forms was followed by a period of remarkable innovation, diversification, and extinction, leading to the establishment of the modern land flora. We are interested in the patterns and mechanisms of plant diversification.”

smathews@oeb.harvard.edu

Elena Kramer* Harvard University, Organismic and Evolutionary Biology (plant organ, reproductive structures, flower)

Floral morphology and development

“My lab is very broadly interested in the evolution of floral morphology. We use molecular, morphological, and phylogenetic approaches to study how flowers have changed over the course of evolutionary time. Research projects in the lab cover a diverse set of topics, including gene lineage evolution and the effects of gene duplication, the morphological diversification of floral parts such as petals and fruits, and the evolutionary and ecological significance of pollinator interactions. Within this context, one of our major focus areas is the development of Aquilegia (columbine) as a new system for studying evolutionary and ecological questions.”

ekramer@oeb.harvard.edu

Neelima Sinha UC Davis (plant organ, phyllome)

Leaf evolution and development

“Sinha Lab at the University of California, Davis focuses on studying fundamental mechanisms of leaf development, using model organisms such as tomato and maize. In order to understand how leaves evolved we are also looking at other organisms like Welwitschia mirabilis, ferns, cycads and basal and derived Angiosperms. Our website will let visitors learn about not only the projects we are working on, but also about the people working on these projects.”

nrsinha@ucdavis.edu

Chelsea Specht* UC Berkeley, Plant and Microbial Biology (reproductive terminology, plant organ, collective plant structure)

plant systematics, Zingiberales, plant anatomy expert

“The Specht Lab focuses on studies in Plant form and function. We use traditional morphological techniques combined with molecular and evolutionary biology to study the natural diversity of plants and to help better understand the forces creating and sustaining this diversity.”

cdspecht@berkeley.edu

Rob Martienssen* Cold Spring Harbor Laboratory (ow does our terminology relate to gene annotation, collective plant structure, root system, shoot system)

“… a plant geneticist, working on transposons, genome biology, and developmental genetics of maize and the model plant Arabidopsis thaliana…”

martiens@cshl.edu

Peter Raven* Missouri Botanical Garden (whole plant, plant organ, collective plant structure)

“General Research Interests: Onagraceae, conservation, sustainable development, plant geography Research Emphases: To summarize the relationships among the species and genera of Onagraceae using the precise definitions and methodologies of phylogenetic systematics. Investigate the biogeography of plants, especially in the tropics and Southern Hemisphere” peter.raven@mobot.org

Gar Rothwell* Ohio University, Department of Environmental and Plant Biology (overall structure of the ontology, especially how it relates to fossil taxa; any terms were might be missing for fossils?)

Phylogenetic Systematics, 
Evolutionary Developmental Plant Biology, Fossil Plants

“Studies of fossil and living land plants are directed toward a fuller understanding of phylogeny and evolution. These are explored using data from morphological, anatomical, ultrastructural, developmental, and molecular characters. Evaluations of ontogeny, reproductive biology, and organismal interactions are emphasized in interpreting development of the modern flora within the context of evolutionary ecology.”

rothwell@ohio.edu

Peter Linder* Universität Zürich, Institut für Systematische Botanik, director of botanical garden (plant tissue, plant organ, vascular system; review the ontology from an ecological perspective)

plant anatomy expert

Evolution of the Cape flora,
Systematics of Restionaceae, Diseae (Orchidaceae) Danthonioideae (Poaceae), Evolution of Wind Pollination
Biogeography in particular phytogeography, of Africa and the Southern Hemisphere generally

peter.linder@systbot.uzh.ch

Chris Hardy* Millersville University, Herbarium (collective plant structure, plant organ; review ontology from a teaching perspective; how will it appeal to the next generation of plant scientists)

plant anatomy expert

Plant Systematics & Phylogenetics Floral Morphogenesis & Anatomy Botanical Illustration

Rob Last Michigan State University, Biochemistry and Molecular Biology (plant cell, trichomes)

Plant genomics, Trichomes project

“Our group uses genetic, genomic and biochemical approaches to understand the regulation of biosynthetic pathways of importance to flowering plants and the animals that depend on plants for sustenance.”

lastr@msu.edu

Robert Stevens University of Manchester, Bio and Health Informatics Group (entire ontology, upper level structure)

Ontology expert- needs OWL format

robert.stevens@manchester.ac.uk

Farshid Ahrestani Columbia University, TraitNet (shoot system, plant organ, or entire ontology with reference to the particular structures his group is interested in)

Bioinformatics, Semantic web applications using PO. Post-doc in Shahid Naeem's lab.

Sandy Knapp* British Musem

Systematics, solanaceae

s.knapp@nhm.ac.uk

Also to consider:

Richard Halse, Oregon State

Rich Zobel <Rich.zobel@ars.usda.gov> (Roots)

Austin Mast Robert K. Godfrey Herbarium, Florida State University

Using PO to code USDA key for legumes. Involved with Morphbank.

amast@bio.fsu.edu

7. Update documentation on web page and wiki:

-what we did and why we did it

-highlight things we want people to review

-wiki page has been created. We will load documentation of changes as we go along.

8. Week of Sept 9th-15th

- Laurel and Ramona will compile the feedback and comments from expert reviewers and user groups, make final changes, complete any additional documentation needed.

Sept 15th- Release live version

Mid Oct: Submit update paper to Plant Physiology as discussed at 6-29-10 Conference Call.

Other Items

• Using Skype for the conference call-

Pankaj would like to try this while he is in India through Sept 3rd. Does everyone have a skype account?

My skype contact: cooperlol910

• New curator hire at NYBG: She has been hired and will be a split appointment between Genomics of Seed Plants project (with Gloria Coruzzi Virtual Plant) and the PO (?). She will spend part of her time NYBG and rest at NYU.

• Fall exhibition at NYBG- DWS: ask PJ about the details of this? Look for details in the grant.

Next meeting scheduled for: Weds, Aug 18th, 10am