POC Conf. Call 4-16-13

POC meeting, Webex Conference Call; Date: Tuesday April 16th, 2013 10am PST/1pm EST

In attendance:Laurel Cooper (OSU), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), Marie Alejandra Gandolfo (Cornell)

Absent: Dennis W Stevenson (NYBG)

accessory branch or accessaory paraclade

Request from JL for the Plant Phenotype project for the term 'accessory branch' or accessory paraclade:

Suggested term and def'n: accessory branch (new PO:ID): A shoot axis (PO:00025029) that develops from a shoot node (PO:0005004) that has produced at least one axillary branch (PO:0006343)

Literature citation: The term 'accessory branch' is used in the description of the different types of phytomers (pg. 2724, top of left column):

"...In both of these phytomer types, a second branch (accessory branch) may later develop between the axillary branch and its subtending leaf (Fig. 1A)." Talbert et al, 1995

This figure is actually referring to an accessory paraclade, not simply an accessory branch.

We have the term paraclade, but it needs to be refined:

Current def'n: paraclade (PO:0004720)- An inflorescence branch (PO:0009081) that ends in an inflorescence that repeats the main inflorescence.

Question: are they both from the same axillary bud meristem (PO:0000232)or is there more than one bud?

Comments: from SF: DWS: Accessory bud is the term used when more than one axillary bud occurs at a node as in many cacti and legumes.

Need to differentiate between the accessory paraclade in the rosette and cauline positions

A paraclade is a second

inflorescence branch (PO:0009081): An inflorescence axis (PO:0020122) that is a branch forming from a primary or higher order inflorescence axis.

see this paper for additional information

http://aob.oxfordjournals.org/content/early/2011/03/01/aob.mcr039.full

branch

branch (PO:0025073): revised definition: A shoot axis (PO:00025029) that develops from an axillary bud meristem (PO:0000232) or from equal divisions of a meristematic apical cell (PO:0030007).

revised comment: In vascular plants, branches arise from an axillary bud meristem (PO:0000232) and from divisions of the meristematic apical cell (PO:0030007) in non-vascular plants.

trichome tip

The problem with this is that sometimes a trichome is unicellular and sometimes it is multicellular. Direct child of plant structure. Part of a trichome is not a cardinal organ part.

multicellular trichome (PO:0025162) A portion of plant tissue that forms a non-sclerified outgrowth from the epidermis. [source: POC:curators]

So the tip would be a portion of plant tissue

multicellular trichome tip (new): A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162).

part_of multicellular trichome

petal nanoridges

Suggested Definition: Microscopic, often parallel, ridges composed of cutin occurring on the surface of petals. Parent/relationship: part_of petal epidermis (PO:0006041)

Reference: PMID 19959665

These are composed of cutin.

plant cuticle ridge A portion of plant cuticle (PO:000022) that forms a ridge, may be overlayed with epicuticluar wax (PO:0025388).

epicuticular wax PO:0025388

A portion of cuticular wax that forms crystalloids or a smooth film on the exterior of a cuticle. [source: PMID:12467640, PO_Ref:00010]

Comment: Epicuticular waxes may take a variety of forms, such as plates, ribbons, tubes, and rods.

Image annotations

Update on the progress on the image annotations:

• New dropbox has been set up for the Po-Images

- DWS has original images (higher res), sending 2 copies, labelled and unlabelled (lower res versions), needs help converting the pdfs into tab-delimited files

- DWS is providing the data for ~3 dozen images (tab delimited file), will be incorporated into the new database

- Sample images from DWS, NYBG (~2 dozen) can be used as a test set for segmenting and labeling with PO terms

• AISO to segment and label images with PO terms

- Data submission template for bulk uploads for whole images with keywords

- import script for whole images, can be used for any images with keyword associations, pull in stuff from Plantsystematics.org

- first whole images, then segmented ones

- image annotation tool, keywords, uses tab delimited file

- database and schema has been built to hold the whole images and the parts, along with the keyword annotations

- Need to prioritize which terms need images: PJ: Physco terms, grass florets, root anatomy, SAM (fern and flowering plant), different kinds of veins in leaves, part of ATOL project

- DWS has images of thorns and prickles, septum, locule, pericarp,

-DWS wants LC to look at the spreadsheet??

Other Items

Chelsea Specht (http://spechtlab.berkeley.edu/) will be visiting OSU to give the Templeton Lecture. Her talk is entitled Petaloidy, polarity, and pollination: the evolution and diversification of floral form in the Zingiberales.

She will be on campus all day Thursday(4/25) and Friday morning (4/26). Should we plan to meet with her?

Upcoming meetings and Presentations 2013:

NCBO Hackathon April 29-30, 2013

The NCBO Hackathon will take place at Stanford University on April 29-30, 2013. This event will focus on projects in biomedical or clinical informatics that can benefit from use of ontology-based technology.

The entire NCBO Team will be available to brainstorm application ideas and to answer development questions. We will also have separate sessions to provide training on the NCBO Web services, the BioPortal SPARQL endpoint, and other topics of interest requested by participants.

If you are thinking of incorporating semantics into your software application, the Hackathon will provide a great opportunity to get a head start on your project.

Phenotype RCN Plant Group Meeting- Ames, Iowa April 30th-May 3rd

We will be meeting to work on the Plant Phenotype Pilot Project, LC is going

PR-PO-GO meeting, May 15-16th 2013

Please see this page for more information: PRO-PO-GO_Meeting

Location: Buffalo, NY

Dates: May 15-16th, 2013.

• 1. To inform members of the Protein, Plant, Gene Ontology communities of developments in each of these ontologies, and in related ontologies such as the CL (Cell), TO (Plant Trait), ENVO (Environment), PATO (Phenotype) and IDO-Plant (Plant Infectious Disease) ontologies. Specifically:
  • a. To enhance the PO treatment of plant-related proteins
  • b. To address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages
• 2. To contribute to the cROP (Common Reference Ontologies for Plants) initiative
• 3. To contribute to the ontological understanding of phenotype and disease in all model organisms.
• 4. To identify potentially fruitful applications which enhanced ontology coordination might bring.

1st International Workshop on Semantics for Biodiversity (S4BIODIV), Montpellier, 26-30 May 2013

S4BIODIV

Registration Information ESWC 2013

Early Registration deadline March 17th

Agropolis Montpellier, the University of Montpellier and Bioversity are collaborating to organize a one-day workshop entitled 'Agrobiodiversity semantics' as part of the larger conference.

Held in parallel with the 10th Extended Semantic Web Conference (ESWC 2013)

Workshop date: May 27, 2013

IMPORTANT DATES:

• Pre-submission inquiry deadline: February 24, 2013 (Abstract up to 500 words)
• Submission Deadline: March 4, 2013
• Notification: April 1, 2013
• Camera ready: April 15, 2013

Note: May be able to send abstract on March 11th and then the final paper by April 15th

TOPICS:

Scientific themes of interest (include but are not limited to):

• sustainable agriculture
• plant
• health and habitat
• relationship between plant-pests/pathogens
• usages of plants by community
• biodiversity conservation
• ecosystems services
• quality of biodiversity data

Informatics technologies of interest (include but are not limited to):

• ontology applications
• knowledge engineering
• linked biodiversity data
• remote sensors
• mobile devices
• vizualization tools
• data mining

MONOCOTS V Meeting at NYBG, July 5th - 14th, 2013

MONOCOTS V:

5th International Conference on Comparative Biology of Monocotyledons Friday, July 05, 2013 7:00 AM - Sunday, July 14, 2013 12:00 PM (Eastern Time)

The New York Botanical Garden & Fordham University

ICBO 2013, Concordia University, Montreal, Quebec July 7th - 9th 2013

4th International Conference on Biomedical Ontologies 2013 (ICBO2013)

Concordia University, Montreal, Quebec, July 7th - 9th 2013 call for papers

The conference aim is to foster discussion, exchange, and innovation in research and development in the areas Biomedical Ontology. Researchers and professionals from biology, medicine, computer science and engineering are invited to share their knowledge and experience.

The event is part of the Semantic Trilogy 2013 featuring:

• International Conference on Biomedical Ontologies (ICBO 2013)
• Canadian Semantic Web Symposium (CSWS 2013)
• Data Integration in the Life Sciences (DILS 2013)

Workshop on Semantic Systems Biology 2013 (SSB2013) will be held as part of the International Conference on Biomedical Ontologies (ICBO2013) at Concordia University, Montreal, Quebec, on July 7th, 2013. The event is part of the Semantic Trilogy 2013 (above)

Topics of interest include, but are not limited to:

• ontologies & terminologies for modeling computational biology
• ontologies & terminologies for simulation (and result data) in computational biology/medicine/neuroscience
• semantic web technologies for description, integration, query and discovery of models, simulations and result data
• semantic web technologies for biological data and analysis
• semantic annotations of bio-models
• applications of ontologies in computational systems biology/medicine/neuroscience
• semantic platforms for undertaking and visualizing simulation results

We welcome four types of submissions:

• short papers, up to 4 pages.
• long papers, up to 7 pages.
• position papers, up to 1 page.
• late breaking reports, up to 1 page.

See the ICBO website for further information on the submission types.

All submission are due on Monday, April 15 2013. Notification of acceptance: May 6th, 2013

Botanical Society Meeting July 27-31st New Orleans

BSA 2013

- MAG is planning to present the work she has been doing with the images and slides, will circulate the abstract