Difference between revisions of "POC Conf. Call 6-5-12"

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Justin Preece will give an updated demo of the ontology-enabled image annotation desktop application and also review these '''[[POC_Conf._Call_4-10-12#Demo_-_Integrating_Annotated_Images_with_PO_terms|HTML mock-ups]]''' (intended for future database and web development) for those who missed the previous demos.
 
Justin Preece will give an updated demo of the ontology-enabled image annotation desktop application and also review these '''[[POC_Conf._Call_4-10-12#Demo_-_Integrating_Annotated_Images_with_PO_terms|HTML mock-ups]]''' (intended for future database and web development) for those who missed the previous demos.
  
−
=Preparations for Botany meeting workshop=
+
''JP demo'd the OEIA desktop application for the group. Thanks to all for their good questions and helpful feedback.''
−
We will have a separate meeting to go over web site changes. Please fill out Doodle Poll:
 
−
http://www.doodle.com/vcpdceau6maratsp
 
  
−
The notes below are just for everyone's information -- no need to discuss them at today's meeting
+
* '''Main idea:''' Markup and annotate images of botanical species w/ ontology terms, and store that data in such a way (structured zip files) that we can transfer it to a database in the future and serve it out to other applications. The application allows you to open an image, highlight individual parts of that image, label those parts with Plant Ontology terms, and save the annotated image accompanied by add'l metadata such as a curator, independent identifier, species, etc.
 +
* '''Future use-case example:''' Build a database to store this annotated image data and write an import utility to pull in .zip files and other annotated images (i.e. from ''plantsystematics.org''). Integrate this database with external web applications, such as the Plant Ontology AmiGO browser.
 +
* '''Usage and testing:''' The Cornell group is invited to begin using the app and providing feedback when it's ready (in a couple of weeks). We will set up a feature request and bug report submission system.
 +
* '''Presentation:''' RW has graciously agreed to demo it at the Botany 2012 conference (July 7-11)
 +
* ''Credits:'' Nikhil Lingutla: software adaptation and development, Justin Preece: software and systems architecture, design, development, and technical oversight. Pankaj: The bright ideas and the funding to make it happen.
  
−
==Updated tutorials and presentations==
+
There are many UI and usability improvements we would like to make -- we already have a long list of things we look forward to adding or enhancing -- but we've been very focused on getting the fundamental image segmentation functionality, web service integration and data architecture ready. We welcome your feedback and suggestions, and we will prioritize those and implement them in incremental releases. - JP
−
We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.
 
  
−
See [[Plant_Ontology_Web_Site_Update:_2012#Tutorials_and_Demos_out-of-date]]
+
=Updating the pages on the PO website=
 +
Some of these changes like the tutorials are nb for the BSA workshop
  
−
==Mistakes on website and wiki==
+
We will have a separate meeting to go over web site changes. Please fill out
−
See [[Plant_Ontology_Web_Site_Update:_2012#High_priority_fixes]]
+
[http://www.doodle.com/vcpdceau6maratsp Doodle Poll]
  
−
==Booklet==
+
''This poll will be updated- maybe the week of June 18th we should follow-up on the changes''
−
MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website.  Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.
 
  
−
Might be good to make it as a PDF, so it can include web links if people open it on screen.
+
==Tutorials and presentations:==
 +
We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.
  
−
=New upper level terms for PO=
+
See [[Plant_Ontology_Web_Site_Update:_2012#Tutorials_and_Demos_out-of-date]]
−
This came up with the need to describe things that are part of a seed (and therefore not cardinal organ parts), along with some other problems.
 
−
==structures that are located other organisms==
 
−
The located_in relation has been to the PO file. Right now it is only used for embryo sac located in plant ovary ovule, but should be applied whenever there are two plant structures that are parts of different organisms.
 
  
−
Located_in replaces contained_in. Located_in can be used for both part_of and contained_in.
+
''JE fixed the files so that they can be downloaded now.''
  
−
Could also add the "inverse located in" relation. For example, we now have seed has_part plant embryo, but this should really be inverse_located_in. This is a terrible name for the relation.
+
==Mistakes on website and wiki==
 +
See [[Plant_Ontology_Web_Site_Update:_2012#High_priority_fixes]]
  
−
Need to check with CM about correct xrefs for located_in.
+
''The website refresh (change to Drupal6) will probably take place late summer, early fall 2012, but in the meantime, we will start fixing the out of date pages''
−
==Background==
 
−
At the [[POC Conf. Call 5-8-12]] we discussed the need for a general term for collective plant structures that are collections of things other than organs. This general term would be parent of collective plant organ structure, collective organ part structure and other types of collective structures.
 
  
−
If we want this term to be parent to seed, we need to define it broadly. What is a seed? It has as parts a mature ovule, some accessory structures like an aril, and parts derived from the ovule like the seed funicle. It also contains endosperm and an embryo. (See below about located in relation.) Is this a collective plant structure? What does it collect? Maybe seed coat, endosperm, and embryo.
+
''RW will work on content of some pages and post to SVN, so we can review them on the beta or dev browser.''
  
−
We also need a term to cover structures that are part of a seed (like arilloid and seed funicle) and terms like ovary that are parts of a plant, but do not fit any of the other categories. These are not necessarily collections. Could use something like CARO term '''multi-tissue structure'''.
+
''PJ will write up something about the [http://plantontology.org/docs/otherdocs/charter.html PO consortium charter], and how it stands now. This page is a priorty to update. Will also provide feedback on changes to the [http://plantontology.org/docs/otherdocs/principles_rationales.html principles and rationale page].''
  
 +
''RW will merge and update the pages for growth stage and development ontologies.''
  
−
''Note from earlier meeting:'' If we include seed under the new CPS, we should mention that some of the parts of this new CPS are part of the mother plant and some are new organism. Some of the cells may be from the mother plant, but they take on a new developmental pathways, function, etc.
+
''The developers' guide, which is currently on both the web and wiki pages, can move to just the wiki page. Also, we will add link to wiki page from the "Documentation" table. (Note: should also add a link to the curator page, as requested by Barry).''
  
−
==New proposed term [https://sourceforge.net/tracker/?func=detail&aid=3530843&group_id=76834&atid=835555 multi-tissue plant structure]==
+
==Booklet for the BSA Workshop==
−
'''CARO:multi-tissue structure:''' Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. -- Examples are simple organ and compound organ component.  
+
MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website.  Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.
  
−
This is very similar to PO plant organ, but does not come with the baggage of being called an organ so it can be applied more broadly. See below for definition of plant organ.
+
Might be good to make it as a PDF, so it can include web links if people open it on screen.
  
 +
''We did not discuss this on today's call.''
  
−
'''proposed definition, multi-tissue plant structure:''' A plant structure that has as parts two or more portions of plant tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
+
=New upper level terms for PO=
−
 
+
This section has moved back to [[Items_for_future_meetings#background_-_CARO]]- will go on the next meeting agenda.
−
Not sure about the bona-fide boundaries part.
 
−
 
 
−
Seed could be a child of multi-tissue plant structure, as would plant organ, or we could make plant organ a synonym of multi-tissue plant structure.
 
−
 
 
−
If we keep a separate term for plant organ, we could also add a term for "cardinal part of a multi-tissue structure", to go along with "cardinal organ part". If we decide to merge plant organ with multi-tissue structure, then cardinal organ part should be merged with cardinal part of a multi-tissue structure. Even if we keep plant organ (because it is such a commonly used term), we could still merge cardinal organ part with cardinal part of a multi-tissue structure. It seems confusing to have them as two separate classes.
 
−
 
 
−
RW: I think this terms could be interpreted to be a parent to collective plant organ structure (CPOS), since CPOS's have two or more tissue and form a distinct structural unit (think of a flower or a gynoecium or a shoot system as a structural unit). In that case, if we create the term "cardinal part of multi-tissue structure", it could include things like ovary, which are part of either an organ or a CPOS. Cardinal organ part (and/or cardinal part of multi-tissue structure), however, would be outside this class, because not all cardinal organ parts are distinct structural units and have bona-fide boundaries.
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3530834&group_id=76834&atid=835555 collective plant structure (new)]===
 
−
 
 
−
Do we still want a general term for collective plant structure, parent to collective plant organ structure and collective organ part structure?
 
−
 
 
−
The important part of a collective plant structure is that it is a collection of two or more similar structures that are not tissues (e.g., two organs, two cardinal organ parts). If we add multi-tissue structure to cover seed, we may not need a new term for collective plant structure.
 
−
 
 
−
proposed definition: A plant structure that is a proper part of a whole plant...
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=2954382&group_id=76834&atid=835555 collective plant organ structure] (PO:0025007)===
 
−
This is currently named '''collective plant structure'''. At the POC meeting on 5-?-12, we discussed renaming it "collective plant organ structure", which is clearer.
 
−
 
 
−
Changed name, and slight change to clarify that the two organs must be adjacent, not one part of the other. Otherwise, a sporophyll would be a collective plant organ structure.
 
−
 
 
−
New proposed def.: A collective plant structure (PO:id) that is a proper
 
−
part of a whole plant (PO:0000003) and is composed of two or more '''adjacent'''
 
−
plant organs (PO:0009008) and the associated portions of plant tissue
 
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(PO:0009007).
 
−
 
 
−
comment: A collective plant organ structure must have as parts at least two
 
−
organs that do not have a part of relation between them, that is, one must
 
−
be adjacent to the other, rather than one part of the other. The organs in
 
−
a collective plant structure can be of the same type, such as a corolla
 
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(PO:0009059) composed of multiple petals (PO:0009032), or of different
 
−
types, such as a shoot system (PO:0009006) composed of shoot axes
 
−
(PO:0025029) and phyllomes (PO:0006001). Other examples include flower
 
−
(PO:0009046), perianth (PO:0009058), and inflorescence (PO:0009049). See
 
−
also collective organ part structure (PO:0025269), for collective plant
 
−
structures composed of parts of multiple organs, but no complete organs.
 
−
 
 
−
===Modified comment for plant organ:===
 
−
 
 
−
plant organ (PO:0009008), current def.: A plant structure that is a functional unit, is a proper part of a plant, and includes portions of tissues of at least two different types that derive from a common developmental path.
 
−
 
 
−
new proposed def. for plant organ (PO:0009008): A plant structure (PO:0009011) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.
 
−
 
 
−
comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an ovule.
 
−
 
 
−
 
 
−
===Slight modification to cardinal organ part===
 
−
 
 
−
Add comment to see also COPS, add ids:
 
−
 
 
−
'''cardinal organ part (PO:0025001), proposed def.:''' A plant structure (PO:0009011) that is a proper part of a plant organ (PO:0009008) and includes portions of plant tissue (PO:0009007) of at least two different types.
 
−
 
 
−
comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include petiole (PO:0020038), lamina (PO:0025060), and leaflet (PO:0020049). See also collective organ part structure (PO:0025269), for plant structures composed of parts of multiple organs.
 
−
 
 
−
'''From discussion on 5-8-12:'''
 
−
 
 
−
Maybe it would be better to say '''cardinal part of collective plant organ'''.
 
−
 
 
−
FMA has "regional parts". It is like a "zone", which PO uses in a few terms. We also have terms like leaf tip or leaf lobe that are regional parts.
 
−
 
 
−
This is what we call a cardinal part. BS: Biological significance is not all of the story for cardinal parts. They should also have their own boudaries on all sides (??), as opposed to regional parts, which just have a boundary on one side.
 
−
 
 
−
===collective organ part structure===
 
−
 
 
−
Current def.: A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.
 
−
 
 
−
comment: A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type (e.g., petioles, carpel walls), but may be of different types. Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths. Unlike a collective plant structure, a collective organ part structure does not contain any complete organs.
 
−
 
 
−
Add PO ids. Say "plant organs" instead of "organs".
 
−
 
 
−
===cardinal part of collective plant structure===
 
−
 
 
−
Do we still need this term? Maybe replace with cardinal part of multi-tissue plant structure.
 
  
 
=Upcoming meetings and Presentations 2012:=
 
=Upcoming meetings and Presentations 2012:=
Line 161: Line 88:
 
July 7 - 11, 2012 - Columbus, Ohio
 
July 7 - 11, 2012 - Columbus, Ohio
  
−
* [http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on Sunday, July 8th, 9:00AM - 12:00PM
+
[http://www.botanyconference.org/engine/search/index.php?func=detail&aid=31 PO workshop] on '''Sunday, July 8th, 9:00AM - 12:00PM'''
−
 
 
−
see: [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops]
 
  
−
This is a half-day (morning) workshop. The schedule now links to the correct abstract.
+
see: link on [http://www.2012.botanyconference.org/info/Workshops.php Botany 2012 workshops schedule] to view the abstract.
  
−
An announcement has been posted on the PO home page and FB page.
+
Wiki page for workshop: [[Plant Ontology Workshop, Botany 2012]]
−
 
+
 
−
Goal of workshop:  Will be to teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.
+
Goal of workshop:  To teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.
  
 
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices.   
 
PJ: suggest that we go there with a 'draft' version of the Plant Phenotype Ontology and show them how to use these in character matrices.   
  
 
''A desktop version of the image annotation software should be ready to demo at this meeting.''
 
''A desktop version of the image annotation software should be ready to demo at this meeting.''
 +
 +
Announcement has been posted on the PO home page and FB page.
  
 
===exhibitor's booth===
 
===exhibitor's booth===
−
We had considered hosting an '''[http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf outreach booth].''' 
+
We had considered hosting an [http://www.2011.botanyconference.org/info/ExhibitorInfo2.pdf 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)
−
 
 
−
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.
 
  
 
''We decided that there were not enough people at the conference to man a booth and we could put up a display at the NYBG booth''
 
''We decided that there were not enough people at the conference to man a booth and we could put up a display at the NYBG booth''

Latest revision as of 12:24, 6 June 2012

POC meeting, Webex Conference Call; Date: Tuesday June 6th, 2012 10am PDT/1pm EDT

In attendance:

POC members:Laurel Cooper (OSU), Ramona Walls (NYBG), Marie Alejandra Gandolfo (Cornell), Pankaj Jaiswal (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG)

Absent:Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab)


Collaborators: none

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=65565392&rKey=0c7d839ea1cb7310

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=65565392&rKey=8aee18c021fa41e0

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_5-29-12?

Back to POC Meetings Minutes


Image annotation software demo

Justin Preece will give an updated demo of the ontology-enabled image annotation desktop application and also review these HTML mock-ups (intended for future database and web development) for those who missed the previous demos.

JP demo'd the OEIA desktop application for the group. Thanks to all for their good questions and helpful feedback.

  • Main idea: Markup and annotate images of botanical species w/ ontology terms, and store that data in such a way (structured zip files) that we can transfer it to a database in the future and serve it out to other applications. The application allows you to open an image, highlight individual parts of that image, label those parts with Plant Ontology terms, and save the annotated image accompanied by add'l metadata such as a curator, independent identifier, species, etc.
  • Future use-case example: Build a database to store this annotated image data and write an import utility to pull in .zip files and other annotated images (i.e. from plantsystematics.org). Integrate this database with external web applications, such as the Plant Ontology AmiGO browser.
  • Usage and testing: The Cornell group is invited to begin using the app and providing feedback when it's ready (in a couple of weeks). We will set up a feature request and bug report submission system.
  • Presentation: RW has graciously agreed to demo it at the Botany 2012 conference (July 7-11)
  • Credits: Nikhil Lingutla: software adaptation and development, Justin Preece: software and systems architecture, design, development, and technical oversight. Pankaj: The bright ideas and the funding to make it happen.

There are many UI and usability improvements we would like to make -- we already have a long list of things we look forward to adding or enhancing -- but we've been very focused on getting the fundamental image segmentation functionality, web service integration and data architecture ready. We welcome your feedback and suggestions, and we will prioritize those and implement them in incremental releases. - JP

Updating the pages on the PO website

Some of these changes like the tutorials are nb for the BSA workshop

We will have a separate meeting to go over web site changes. Please fill out Doodle Poll

This poll will be updated- maybe the week of June 18th we should follow-up on the changes

Tutorials and presentations:

We agreed that updating the PO tutorial videos/ppt presentations was a priority for the next release. RW will need these for the Botany workshop.

See Plant_Ontology_Web_Site_Update:_2012#Tutorials_and_Demos_out-of-date

JE fixed the files so that they can be downloaded now.

Mistakes on website and wiki

See Plant_Ontology_Web_Site_Update:_2012#High_priority_fixes

The website refresh (change to Drupal6) will probably take place late summer, early fall 2012, but in the meantime, we will start fixing the out of date pages

RW will work on content of some pages and post to SVN, so we can review them on the beta or dev browser.

PJ will write up something about the PO consortium charter, and how it stands now. This page is a priorty to update. Will also provide feedback on changes to the principles and rationale page.

RW will merge and update the pages for growth stage and development ontologies.

The developers' guide, which is currently on both the web and wiki pages, can move to just the wiki page. Also, we will add link to wiki page from the "Documentation" table. (Note: should also add a link to the curator page, as requested by Barry).

Booklet for the BSA Workshop

MAG suggested that we create a booklet for participants to take with them. Some people prefer to have printed guidelines, rather than relying on the website. Maybe two double sided pages, folded in half and stapled in the middle. Just enough to explain the basics of the PO and the website.

Might be good to make it as a PDF, so it can include web links if people open it on screen.

We did not discuss this on today's call.

New upper level terms for PO

This section has moved back to Items_for_future_meetings#background_-_CARO- will go on the next meeting agenda.

Upcoming meetings and Presentations 2012:

MOSS 2012 and The 3rd International Symposium on Molecular Systematics of Bryophytes

Thursday, June 14, 2012 - Friday, June 22, 2012

The New York Botanical Garden

Attendees have the option of registering for MOSS 2102 ($225), the Symposium on Molecular Systematics of Bryophytes ($225) or both ($400).

RW submitted an abstract for a poster File:PO poster Moss 2012.pdf.

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

PO workshop on Sunday, July 8th, 9:00AM - 12:00PM

see: link on Botany 2012 workshops schedule to view the abstract.

Wiki page for workshop: Plant Ontology Workshop, Botany 2012

Goal of workshop: To teach people (mostly botanists) how to access and use the PO, including how to send feedback, suggest new terms, etc.

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

A desktop version of the image annotation software should be ready to demo at this meeting.

Announcement has been posted on the PO home page and FB page.

exhibitor's booth

We had considered 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)

We decided that there were not enough people at the conference to man a booth and we could put up a display at the NYBG booth

RW will look into purchasing a TV/monitor (~22") that could display a rotating slideshow. Could also be used for future presentations

Bio-Ontologies SIG 2012

Where: July 13 - 14, 2012, Long Beach, CA. Co-located with ISMB 2012

When: Submissions Due: April 13th, 2012 (Fri)

See: Bio-Ontologies SIG 2012

Three types of submissions.

- Short papers, up to 4 pages. - Poster abstracts, up to 1 page. - Flash updates, up to 1 page

Successful papers will be presented at the Bio-Ontologies SIG.

Poster abstracts: time will be allocated during the 2 days for at least one poster session.

Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Authors of posters can also provide a flash update. Unsuccessful papers will automatically be considered for poster presentation.

ASPB Plant Biology 2012

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

Link to meeting page: ASPB2012

Abstract was submitted for submission for minisymposia consideration.

Joint workshop is planned with PO, Gramene and TAIR

Registration is open, 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)

RW and BS (with JE, AG, DWS and PJ) submitted a short paper describing a plant disease extension of the Infectious Disease Ontology. This paper was accepted. Wiki page for notes on Plant Disease Ontology.

Relevant dates

  • Feb. 28th, 2012: Notification of paper acceptance
  • April 15th, 2012: Poster, early career symposium, software demonstrations and workshop papers submission deadline
  • May 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

RW will present the IDO-Plant paper and a poster on the PO-FNA collaboration.

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

Anatomy Ontology Course at NESCent, July 30th- Aug 3rd, 2012

Link to: Anatomy Ontology course

from Paula Mabee: Opening are available the Anatomy Ontology course.

Link to Course materials

This course aims to teach proper ontology design principles and practices such that anatomical interoperability across evolutionarily disparate taxa is achieved. It further seeks to promote community growth and adoption of ontology-based methods and tools. The subsequent benefit is in the form of shared access to the unique data store of each community (e.g. genetic, genomic, developmental, and evolutionary data).

Apply here: [1]

Application deadline is April 4th, 2012 (extended through mid-April)

Crop Ontology Workshop

For more information see the wiki page: Crop_Ontology_Workshop_at_OSU,_2012

Dates TBA: probably Sept. 13-15th

The focus of the workshop will be on mostly development stages and traits for the crop plants

Next meeting scheduled for Tuesday, June 12, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_6-12-12

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