POC Conf. Call 4-2-13

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

In attendance:Laurel Cooper (OSU), Dennis W Stevenson (NYBG),Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU).

Absent: Marie Alejandra Gandolfo (Cornell)

New CROP Website available

- put announcement about PRO-PO-GO meeting on the new site and on the blog

- create log ins and then you can post on blog

New Requests on SourceForge

tapetum 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

We will add the terms suggested above (anther wall tapetum cell, tapetum cell and microsporangium tapetum cell) and recommend that the GO adjust their term name and definitions to match. This might be a good example to illustrate in Bufalo, but TB will not be there.

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)

plant sap (new PO:00255380): A portion of plant substance (PO:0025161) that is an aqueous solution which may contain sugars, hormones, mineral elements and/or other nutrients.

Comment: plant sap should not be confused with latex or resins.

xylem sap (new PO:0025539): A plant sap (PO:0025538) that is an aqueous solution which may contain mineral elements, nutrients, and plant hormones, and is transported from the root system (PO:0025025) toward the leaves through the tracheary elements (PO:0000290) of the xylem.

Transport of sap in xylem is characterized by movement from the roots toward the leaves.

Phloem sap (new PO:0025539): A plant sap (new PO:0025538) that is an aqueous solution which may contain sugars, mineral elements, and plant hormones, and is transported through the phloem sieve elements (PO:0025406).

PJ: We will need to have a root xylem sap and shoot xylem sap as they are different. Could add those later when we need them

Image Annotations

Update on the progress on the image annotations:

- AISO to segment and label images with PO terms

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

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

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

- 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,

- New dropbox will be set up for the Po-Images

- Will set up a separate call to discuss further

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.

Need to share the PO with representatives from the ontologies and resources such as PRO, PIR (Claire O'Donovan), Uniprot. Annotations to newly sequenced plant genomes are going into Plant Ensemble, Uniprot etc. Want to build early relationship with them to develop quality measures for plant-based ontology annotations. Section on annotations is needed.

JB wanted to explore genotype and phenotype connections, can only stay for part of the day on Thursday

Need to know who will speak about what. Looking for volunteers.

Separate the sessions on disease and phenotype, include TO discussion to there?

RW presentation on Plant-IDO?, interest in new Plant DO, existing DO is no good (?), Split phenotype and diseases into separate sessions.

Reference ontologies need to know how to deal with terms that are used by both plants and animals, e.g. senescence.

Alert attendees to bring applications for the users, biological examples

Notices could be posted in advance of the meeting, send out on PO-announce, will do IBC article later. Idea for future meeting- plants, human nutrition, toxicity, to include more NIH type people

Travel to Amherst: Need to book our rooms, plan to fly out Thursday afternoon.

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