POC Conf. Call 4-2-13

POC meeting, Webex Conference Call; Date: Tuesday April 2nd, 2013 10am PST/1pm EST

In attendance:

New Requests on SourceForge

tapetal cell

Needed for cross-product with GO terms:

tapetal cell differentiation, GO:0048657

tapetal cell fate specification, GO:0010234

Suggested definition (TB) (needs help): A plant cell that is part of the tapetum.

Proposed name and def'n: anther wall tapetum cell: A plant cell (PO:0009002) that is part of the anther wall tapetum (PO:0009071).

Should probably also add the corresponding terms for a tapetum cell and microsporangium tapetum cell.

Existing terms in the PO:

• tapetum (PO:0025313): A portion of ground tissue that is the inner-most layer of a sporangium wall

• microsporangium tapetum (PO:0025314):

• anther wall tapetum; (PO:0009071): A microsporangium tapetum that is part of an anther wall.

• megasporangium tapetum; PO:0025315

• E tapetum degeneration initiated stage; PO:0001032

References:

• Regulation of Arabidopsis tapetum development and function by DYSFUNCTIONAL TAPETUM1 (DYT1) encoding a putative bHLH transcription factor.

Zhang etal, 2006 PMID:16831835

• The Arabidopsis U-box/ARM repeat E3 ligase AtPUB4 influences growth and degeneration of tapetal cells, and its mutation leads to conditional male sterility.

Wang et al, 2013 PMID:23398263

• The excess microsporocytes1 gene encodes a putative leucine-rich repeat receptor protein kinase that controls somatic and reproductive cell fates in the Arabidopsis anther.

Zhao et al, 2002 PMID:12154130

Niu N, Liang W, Yang X, Jin W, Wilson ZA, Hu J, Zhang D. 2013. EAT1 promotes tapetal cell death by regulating aspartic proteases during male reproductive development in rice. abstract Nat Commun 4, 1445.

xylem sap

Suggested Definition: The mixture of water and solutes existing in a xylem vessel

Parent/relationship: part_of xylem (PO:0005352)

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

floral node

suggested definition: A cardinal organ part of a shoot axis where one or more flower may arise

Parent/relationship: is_a shoot node (PO:0005004)

Submitted: Johnny Lloyd

adventitious branch

Definition: A shoot axis (PO:00025029) that develops in an unusual place

Parent/relationship: is_a shoot axis (PO:0025029)

Image Annotations

- AISO to segment and label images with PO terms

- images from DWS, NYBG

- import script for whole images- from Plantsystematics

- image annotation tool, parts and keywords

- database

-original images, 2 copies, labelled and unlabelled

Upcoming meetings and Presentations 2013:

Biocuration 2013 conference, Cambridge, 7-10th April 2013

submission deadline for abstracts for posters is Jan 31st.

website and registration are now open: Biocuration 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.

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.

Tentative participant list:

PO Consortium members: Pankaj Jaiswal and Laurel Cooper (OSU), Dennis Stevenson (NYBG), Barry Smith (Buffalo), others?

GO Consortium members: Jane Lomax (EBI), Judith Blake (JAX), Alex Diehl (Buffalo) who else?

PRO Consortium members: Cathy Wu, Alan Ruttenberg (Buffalo)

BS would like a list of who we would like to include in the meeting and whose costs can be covered by PO

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