POC Conf. Call 8-18-10

POC meeting, Webex Conference Call; Date: Aug 18th, 2010 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the 8-11-10 meeting? All in favor?

Status and Update of Progress: PO Release

. Beta Browser is Up!- Notices sent out and posted:

Aug 2010 Beta PO.

A. Notices posted on "What's New" on both the live site and the dev site and on the Jaiswal Lab web page.

• Should also be on the Beta site- when we update it next time* Post updated version of index.html to beta branch

B. Announcements sent to: po-dev, po-announce, po-internal.

C. Announcement for Plant Sciences Bulletin: Note that this is not for the beta version but the live version due to the timing. Sent to PJ for review 8/12/10

Dennis will also send this to the BSA for posting on their website.

Announcements sent to user groups

• TAIR email: curator@arabidopsis.org

• NASC sent to: email: bioinfo@arabidopsis.info

(not really clear who to send it to here)

• Gramene email: gramene@gramene.org

• MaizeGDB Carolyn Lawrence, Mary Schaeffer, Jack Gardiner. No generic contact address

• VirtualPlant Posted to their "contact us" form

• SoyBase Sent to: Rex Nelson and posted to their "contact us" form.

• Genevestigator Sent to:support@genevestigator.com

• SGN Sent to: Lukas Mueller + Naama Menda and posted to their "contact us"

• OryzaBase Sent to: Yukiko Yamazaki and posted on their "contact us" page.

• PlantTribes Sent to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu

• TraitNet Ramona contacted??

• CIMMYT, Mexico Generation Challenge Program Sent to: Rosemary Shrestha

• BRENDA Sent to:project leader Prof. Dr. Dietmar Schomburg

• UniProt Posted on their "contact us" page

• BAR Sent to Nicholas Provert and Rohan Patel

Feedback on the Beta Release

A. Feedback Box:

New link to feedback box on beta site- emails will go to po-internal

• We can customize this with additional fields and boxes for more directed responses

B. Response emails

On the notices, we ask the users to respond to po-dev@plantontology. Do we really want people responding to po-dev??

That goes out to 68 people, many of who, I suspect would rather not take part in lengthy discussions of user feelings about the ontologies. Maybe we should set up a new email such as po-feedback that would just go to the internal group?

(Note: We need to define the function of each of the mailing lists: po, po-dev, po-announce, po-internal). I think po-announce, po-internal are fine, but what are the other 2 supposed to be for?

Annotations that have no term associated with them

-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

A. TAIR - 8/13/10 message sent to Donghui, Kate and Tanya: "The main issues are with the annotations associated with the following PO terms which were obsoleted in the beta version: PO:0009003: sporophyte 1 (from: po_anatomy_gene_arabidopsis_tair.assoc) PO:0000056: floral bud 54: (from: po_anatomy_gene_arabidopsis_tair.assoc) PO:0008037: seedling 16 (from po_anatomy_gene_arabidopsis_tair.assoc) The first three will need to be looked at to determine where to beat put them. We have put our recommendations or suggestions on the spreadsheet

PO:0008034: leaf whorl 15,802: (from po_anatomy_gene_arabidopsis_tair.assoc) These ones are pretty straightforward- we recommend to move them all to the new term collective leaf structure PO:0025022

Spreadsheet: File:TAIR dangling annotations (LC 8-13-10).pdf

B. Gramene - 8/13/10 message sent to gramene@gramene.org contact email. Ken replied and said that Pankaj was the best person to look at these.

File:Gramene dangling annotations (LC 8-13-10).pdf

Contacting potential Reviewers:

At the last couple of meetings, we discussed what aspects of the ontology we should ask each reviewer to focus on.

See comments in parentheses, below, in italics.

• Laurel prepared and distributed (to po-internal) a general letter to go to all reviewers, which can be customized for the specific reviewer. We are looking for some feedback on it before sending it out this week.

Laurel and Ramona will send the letters to Dennis, so he can contact the reviewers that he knows personally (those marked with an asterix).

• So the reviewers can access the obo, flat files and OWL files, they should be made available on the download page (http://www.plantontology.org/download/download.html#download).

On all three sites or just on the beta site??**

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 Museum (overall look at the ontology?)

Systematics, solanaceae

s.knapp@nhm.ac.uk

Also to consider:

Richard Halse, Oregon State University (overall look at the ontology?)

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

Austin Mast Robert K. Godfrey Herbarium, Florida State University (which area of the ontology?)

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

amast@bio.fsu.edu

Documentation page

Posted on the POwiki Summary_of_changes_to_the_Plant_Ontology page with link from the PO web page with details of the changes made in the new release.

Could everyone please review this for accuracy and completeness? Thanks a lot

Next meeting scheduled for: Weds, Aug 25th, 10am

Who is going to be able to attend? On Vacation: Pankaj (till sept 3rd) but may still take part by skype, Ramona (till sept 9th), Laurel Aug 27th-Sept 8th.