POC Conf. Call 1-24-12

POC meeting, Webex Conference Call; Date: Tuesday Jan 24th, 2012 10am (PST)

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

Absent: Ramona Walls (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_1-17-12?

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Interim Data Release 16A, January 2012

The Plant Ontology is pleased to announce the availability of the January 2012, Interim Data Release 16A on our web page.

Through a collaborative effort with the Moss Computational Biology Resource (COSMOSS and University of Freiburg), this interim data release adds approximately 82,000 new annotations for genes expressed in the model moss species; Physcomitrella patens.

Links from annotations on the PO terms; gametophore (PO:0030018), spore (PO:0025017), protonema (PO:0030003) and protoplast (PO:0030003) will take you to the Cosmoss site (cosmoss.org) for further info.

This work is the result of a process that has been undergone for the past year, adding more than 80 new terms and revising the structure of the Plant Anatomy branch of the ontology to accommodate non-vascular plants.

There are no changes to the ontology file relative to version #16.

Demonstration of Image Annotation Tool

JP and Nikhil (CS student) will demonstrate an image annotation application currently under development. It is intended to be used by curators for segmenting and tagging images of plant specimens with PO terms.

Background comments from PJ: Idea is to label the images, and to create a training set for the computer to learn to annotate the new images before an annotator starts working on it. That is learn to recognize specific parts. Needs active learning algorithm for this to work.

They showed how the user can select portions of the plant images and label them as either the foreground (left click line) or background (right click line) colors. This is how the computer recognizes the sections

To create the labels, select from the drop down list of PO terms after entering what you think the correct term is; ie: petal, linked by web services to the PO live database. Can zoom in and out to help with making the annotations. High resolution images work better ?

Image info is saved as an HTML file, Metadata will be displayed on the right hand side: image IDs, taxonomic info, PO definition, links to websites, curators ID.

Other info needed to annotate: MAG: species and family (through UBIO), magnification, bar code (linked to image and sample ID)

To transfer to the images to OSU, MAG will give us a hard disk with images at the Wood meeting

Updates from PAG 2012

January 14-18, 2012, San Diego, California

PO was represented at the following events:

• Ontology workshop, Saturday January 14th from 10:20am-12:30pm: Use of Ontologies for Organizing Plant and Animal Genomics Data.

We had 5 speakers and a panel discussion at the end

For more info, see the PAG 2012 Ontology workshop wiki page.

LC will summarize comments from the panel discussion, will post on wiki. MAG suggests that we encourage writers to refer to the PO when reviewing papers and at workshops, demos etc.

• Non-Seed Plant Workshop on Saturday, Jan 14th, (3:50pm-6pm)
• Plant Phenotypes workshop on Sunday, Jan. 15th, (8:00am - 10:10am)
• Computer demo Monday 12:50 pm for the PO.

• The PO also took part in an Outreach booth organized by MaizeGDB

Wood Anatomy Ontology Meeting

Please see the Wood_Anatomy and the Wood anatomy ontology meeting, 2012 at NYBG, agenda wiki pages for more information.

Confirmed dates are Feb. 5th-7th, 2012 (Sun-Tues)

Update and status:

Attendees:

• Frederic Lens: Netherlands Centre for Biodiversity Naturalis
• Barb Lachenbruch link
• Elisabeth Wheeler (paleobotanist and wood anatomist at NC State
• Rachel Spicer Connecticut College
• John Carlson (jec16@psu.edu) link
• Meg (Margeret) Staton (mestato@yahoo.com) Clemson University (the lead on both the hardwoods website and the Fagaceae Genomics Web)

Hotel is booked and flights have been arranged for all except for Rachel spicer, who is driving

BS will give his presentation on Sunday morning (see: Wood anatomy ontology meeting, 2012 at NYBG, agenda). This will be open to the public and notices have been sent out.

LC will send out reminder and post on the PO front page

Vascular tissues and cell types

These terms will need to be fixed before the Wood Ontology meeting in February.

vascular tissue types

See SF tracker for: vascular tissue and vascular bundle

For vascular plants, we have the class:

portion of vascular tissue (PO:0009015): A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]

Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.

part_of vascular bundle (which is part_of vascular system)

This is okay, but suggest that we change definition to include xylem or phloem, and it may not always be part_of vascular bundle.

Proposed definition: A portion of plant tissue that has as parts tracheary elements or sieve elements.

Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or as scattered vascular bundles. May include other types of tissues or cells, such as parenchyma or fibers.

part_of vascular system (should add vascular system participates_in sporophytic phase)

We looked at the def'n of 'portion of plant tissue': A plant structure that consists predominantly of similarly specialized cells of one or more types.

ok

vascular bundle (PO:0005020) current def.: A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]

This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.

proposed definition: A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.

Comment: Usually contains both xylem and phloem. May also contain other types of cells or tissue such as fibers, vascular cambium, or portions of ground tissue.

part_of vascular system

add vein as exact synonym -- can be in any organ

Should add a comment that bundle sheath (PO:0006023) can also be part of the vascular bundle, if it is present

Remember to include the PO ids with the PO terms in the definition and comments.

primary and secondary vascular tissue

See SF tracker for: primary and secondary vascular tissue

primary vascular tissue: A portion of vascular tissue that develops from a procambium. (ref: Esau)

comment: Forms as part of primary growth (GO:xxxx).

secondary vascular tissue: A portion of vascular tissue that develops from a vascular cambium. (ref: Esau)

comment: Forms as part of secondary growth (GO:0080117) in vascular plants. Often differentiated into the axial system and ray system.

If we set both of these up as a cross products, then primary and secondary xylem and phloem will be inferred children.

phloem

See SF tracker for: phloem and its children

phloem (PO:0005417) current def.: A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]

proposed definition: A portion of vascular tissue that has as parts sieve elements.

Comment: Functions in the conduction of organic substances in vascular plants.

Note: currently, sieve element is listed as a synonym of sieve tube member, but this does not correctly follow Esau's usage. It was okay when we only had angiosperms in PO, but is no longer valid. Suggest we make a new term for sieve element, rather than have it as synonym. See below under conductive_and_related_cell_types.

metaphloem (PO:0006076) current def.: Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

proposed definition: A portion of primary phloem that differentiates after the protophloem.

Comment: Differentiates before the secondary phloem, if any is formed.

protophloem (PO:0006077) current def.: The first-formed elements of the primary phloem.

proposed definition: A portion of primary phloem tissue that has as parts the first-formed sieve elements of the primary phloem.

Discussion about the use of 'first-formed'. Morphological differences differentiate the proto- and metaphloem tissues- should note in comment at least. Xylem and phloem development stages need to be addressed in the PSDS branch. Can be used to clarify these tissues.

is 'first-formed' equivalent to 'initial'? It is not the very 1st instance of primary phloem, just the first instance in a particular location, but protophloem and metaphloem continues to form during development, even in the same location.

Can we specify these morphological differences? - they have differences in maturity; during maturation secondary metabolites accumulate in the cell wall, moves towards apoptosis. Development of the companion cell occurs

We will discuss this and revisit next week. There will probably be more interest in the xylem terms from the wood anatomists, as the 2' phloem is completely crushed by the 2' xylem.

primary phloem (PO:0006075) current def.: A portion of phloem tissue of the primary plant body.

proposed definition: A portion of phloem tissue that develops from the procambium.

Comment: Primary phloem develops as part of GO:xxxx primary growth. (see below)

develops_from PO:0025275 procambium

secondary phloem (PO:0005043) current def.: A portion of phloem tissue formed by the activity of the vascular cambium.

proposed definition: A portion of phloem tissue that develops from the vascular cambium.

Comment: Secondary phloem develops as part of GO:0080117 secondary growth.

develops_from PO:0005598 vascular cambium

Again this is specific to a particular location

The following items were postponed until next week's discussion

Details moved to Items for future meetings

Upcoming meetings and Presentations 2012:

Phenotype RCN meeting, February 23rd-25th, 2012

The dates: February 23-25, 2012 (Thursday, Friday, 1/2 Saturday) have been confirmed for the next annual Phenotype RCN meeting.

It will be held again at NESCent (Durham, NC).

RW has a friend there she can stay with and is interested in going.

This meeting will focus on bringing in new people and training them on how to develop and use anatomy ontologies. RW offered to help with the training.

The projects of the Plant Working Group that we started in CO will be worked on during the next meeting.

Eva said that they can cover RW's plane fare from NY.

Maize Genetics Meeting, March 15-18, 2012

The maize meetings are being held in Portland, OR this year.

For more info see: Maize Genetics Meeting 2012

Registration Link: 2012 Maize Genetics Conference Registration Page will open on December 30, 2011.

Deadlines: Advance meeting registration is due by January 31, 2012.

The PO and Gramene will most likely be co-hosting a workshop. Details TBA....

5th International Biocuration Conference

April 2-4, 2012, Washington DC

• Abstract was submitted December 9, 2011 for consideration for a talk (or else a poster). MS was co-author.

See link: File:Abs Biocuration 2012 (LC 12-9-11).pdf

• Notification date: February 3, 2012

From 9-27-11: PJ is planning to attend and will be running a biocuration workshop- is this happening?

SPNHC 2012

Annual meeting of the Society for the Preservation of Natural History Collections

Yale University, New Haven Connecticut June 11-16, 2012

Any interest in making a PO presentation at this meeting? Perhaps RW and/or DWS could just go for the day of the presentation, since it is local (New Haven, CT).

The theme for the meeting is "Emerging Technology and Innovation in Natural History Collections Management" (focus on the tools, innovative methods and collaborations that will move the natural history collections community forward).

From PJ: If we can show progress in the FNA work or Morphobank yes we should

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

Call for Symposia, Colloquia and Workshops:

RW, DWS and MAG put together a proposal for a half day hands-on workshop. The goal will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

Proposal was submitted, waiting for news.

PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrixes.

exhibitor's booth

We should also consider hosting an outreach booth.

Not a bad deal for non-profits: $500 for A 10 x 10 Booth Space at Botany 2012, and 2 complimentary registrations for the conference. (plus all the extras!)

• 2 months of Rotating Banner Ads in the online American Journal of Botany

• A Rotating Banner Ad in one edition of the online Plant Science Bulletin

• A Rotating Banner Ad on the Botany 2012 abstract submission site

• A Rotating Banner Ad on the 2012 Conference Registration site.

PJ will check with Gramene and Doreen Ware to see if they want to co-host a booth.

Annotation wiki

JP may also give a talk on the new annotation wiki at this meeting, as part of the genomics section.

ASPB Plant Biology 2012

July 20 - 24, 2012 - Plant Biology 2012, Austin, TX

Registration scheduled to open first week in January.

Early Bird Registration: by May 11

Advance Discounted: May 12-June 15

ICBO 2012

International Conference on Biomedical Ontologies (ICBO 2012), July 22nd-25th, Graz, Austria

co-located with the 7th International Conference on Formal Ontologies in Information Systems (FOIS 2012)

Relevant dates

• Jan. 31st, 2012: Paper submission deadline
• Feb. 28th, 2012: Notification of paper acceptance
• March 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
• April 15th, 2012: Notification of poster, early career symposium, software demonstrations and workshop paper acceptance
• June 30th 2012: Deadline for all camera-ready copies for the proceedings

BS would like to collaborate on a preliminary paper on Plant Disease Ontology. RW will review IDO and summarize what is there already for plants, what is needed, how it will link to PO. LC will also collaborate.

RW will circulate a draft of a manuscript for a plant disease extension of the Infectious Disease Ontology. Must be submitted by Jan. 31, 2012.

RW is working on an abstract summarizing the PO-FNA collaboration, with the folks from FNA. Will circulate soon. This will be either for a poster or a short talk in the Early Career Researcher session.

BS will be organizing an OBO Foundry meeting the afternoon of the day before the conference starts