POC Conf. Call 4-23-13

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POC meeting, Webex Conference Call; Date: Tuesday April 23rd, 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), Dennis W Stevenson (NYBG)

Absent: none


Update from Cornell

Ale is doing editing on the images, no tech help now. Poster is in the Cornell images dropbox.

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?

Image annotations

The image annotation "dual-track" plan:

1) Import keyword-annotated whole images (from DWS) into our image annotation database.
2) Segment and annotate DWS-contributed images with AISO; then import those newer, annotated versions into the image annotation database as an update for

Annotation progress

  • DWS has provided over a dozen images (in both unlabeled and labeled versions) and has filled out the image data submission data template. Thanks, Dennis!
  • Lol and Laura have received basic training on using AISO and have begun annotating images
  • Let's 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 (NOTE: DWS has images of thorns and prickles, septum, locule, pericarp)

Database development

  • We have designed and built a database for holding annotated image data, with ontology terms and/or keywords
  • Nikhil is currently developing a data import script to bring Dennis' images and annotations into this db (whole image annotations first, segmented annotations next)

AISO Software Updates

New Requests:

Request from DWS for terms to describe root protoxylem development

*protoxylem (PO:0000272): A portion of primary xylem (PO:0005849) tissue that has as parts tracheary elements (PO:0000290) with only annular or helical secondary wall thickening that are the first formed tracheary elements at a particular location. [source: ISBN:047125208]

Comment: Develops while the vascular tissue (PO:0009015) is still elongating. Tracheary elements in protoxylem are smaller than in metaxylem (PO:0000372). Tracheary elements have lignified cell walls with secondary thickening and are dead at maturity.

These are patterns of xylem development see: http://en.wikipedia.org/wiki/Xylem Add a comment (or synonym) to the child terms: also called xylem system

Extended discussion about whether or not these are actually plant structures: BS: they are portions of xylem tissue, that are classified according to their patterns of development. PJ: are these actually a phenotype or a trait?

Proposed terms and def'ns

Definitions adapted from Esau, 1977 except for centarch protoxylem:

These ones are only in the shoot system: centarch and mesarch

* centarch protoxylem (new PO:0025552): A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem of the shoot system progresses centripedally, the oldest elements (protoxylem) are farthest from the center of the axis. (ref: wikipedia)

comment from DWS on SF: the definition of of centrach is opposite of what we have so I corrected it with a reference:

centarch protoxylem (new PO:0025552): A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem of the shoot system progresses centrifugally with the oldest elements (protoxylem) in the center of the axis.

Added dbxref to ISBN:9780716719465 Gifford, E.M., and A.S. Foster. 1989. Morphology and Evolution of Vascular Plants. W. H. Freeman.

* mesarch protoxylem (new PO:0025553): A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem (PO:0005849) of the shoot system (PO:0009006) progresses both centripetally and centrifugally from the center.

Comment: found in ferns and cycads stems

added dbxrefs OBO_SF_PO:3610599

ref: wikipedia: mesarch: used when there is more than one strand of primary xylem in a stem or root, and the xylem develops from the middle of a strand in both directions. The metaxylem is thus on both the peripheral and central sides of the strand with the protoxylem between the metaxylem (possibly surrounded by it). The leaves and stems of many ferns have mesarch development.[24]

need to clarify the cells - primary xylem cells or protoxylem cells. Cells are produced continuously, the original cell that differentiates is the protoxylem (pole), then subsequent ones are actually metaxylem.'


Endarch- only in shoot system, so define as in shoots

* endarch protoxylem (new PO:0025557): - A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem (PO:0005849) progresses centrifugally, with the oldest elements (protoxylem) are towards the center of the axis.

Comment: Endarch protoxylem is typically found in stems of seed plants, and also in leaves in which the protoxylem is on the adaxial side.

Exarch is in root and shoot- will make a generic one and add an instance for each shoot system and root system protoxylem. leaves can have a variety of patterns, exarch, endarch, mesarch etc. Roots always exarch, not the other classes

* exarch protoxylem (new PO:0025554): - A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem (PO:0005849) of the shoot system (PO:0009006) progresses centripetally, the oldest elements (protoxylem) are farthest from the center of the axis.

    • shoot system exarch protoxylem (PO:0025556): A portion of exarch protoxylem (PO:002554) tissue in which the maturation of primary xylem (PO:0005849) of the shoot system (PO:0009006) progresses centripetally, the oldest elements (protoxylem) are farthest from the center of the axis.

Protoxylem terms 4-24-13.png

These ones are only in root:

  • root system exarch protoxylem (PO:0025555): A portion of exarch protoxylem (PO:002554) tissue in which the maturation of primary xylem (PO:0005849) of the root system (PO:0025025) progresses centripetally, the oldest elements (protoxylem) are farthest from the center of the axis.
    • monarch protoxylem (new PO:0025558): A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has only one protoxylem strand or pole, and differentiation progresses centripetally, with the oldest element (protoxylem) farthest from the center of the axis.
    • diarch protoxylem (new PO:0025559): A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has two protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.
    • triarch protoxylem (new PO:0025560): A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has three protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.
    • tetrarch protoxylem (new PO:0025561): A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has four protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.
    • pentarch protoxylem (new PO:0025562): A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has five protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.
    • polyarch protoxylem (new PO:0025563): A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has more than five protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.

Other Items for discussion

- moved back to Items_for_future_meetings page

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

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

Next meeting scheduled for Tuesday, May 7th, 2013 at 10am Pacific/1pm Eastern

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