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

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This came up as the need to describe things that are part of a seed, along with some other problems.
 
This came up as the need to describe things that are part of a seed, along with some other problems.
  
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Will fill in more details.
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==New and revised collective terms==
 +
===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.
 +
 +
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'''. This would be parent to CPS, but also plant organ, cardinal organ part, and things like arilloid.
 +
 +
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''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.
 +
 +
===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.
 +
 +
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.
 +
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===[https://sourceforge.net/tracker/?func=detail&aid=3530843&group_id=76834&atid=835555 mulit-tissue plant structure]===
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'''proposed definition:''' A plant structure that has as parts two or more portions of planttissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit.
 +
 +
Comment: maybe give some examples
 +
 +
This includes plant organs, collective plant structures, cardinal organ parts, and those wierd, unclassifiable things like arilloid or ovary.
 +
 +
 +
'''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. This is basically the same as PO plant organ.
 +
 +
We probably do not want to constrain our term to have bona-fide boundaries (otherwise, we can't include most cardinal organ parts or things like ovaries). RW has written to CARO to ask if they can modify this, but no specific response.
 +
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3530834&group_id=76834&atid=835555 collective plant structure (new)]===
 +
 +
''needs work''
 +
 +
A multi-tissue plant structure that has as parts two or more other multi-tissue plant structures.
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=2954382&group_id=76834&atid=835555 collective plant organ structure]===
 +
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
 +
(PO:0009007).
 +
 +
comment: A collective plant 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
 +
(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:'''
 +
 +
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 structure" and "cardinal part of 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 lope 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===
 +
 +
This is really just to cover the parts of a seed plus a few fruit parts, because most other structures are a cardinal part of an organ or a collective organ part structure.
  
 
=Upcoming meetings and Presentations 2012:=
 
=Upcoming meetings and Presentations 2012:=

Revision as of 15:55, 30 May 2012

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

In attendance:

POC members:

Absent:


Collaborators: none


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

Back to POC Meetings Minutes


Preparations for Botany meeting workshop

Website refresh

There was discussion of a refresh to the PO website (see Plant Ontology Web Site Update: Winter 2012). RW: I need to know if this will happen before the BSA meeting (July 8), so I can make slides that will match the live browser.

Updated 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.

Presentations/tutorials that need to be updated:

There is a problem opening or downloading both quicktime movies and the ppt files. They are probably out of date. Includes the following links:

Introduction to ontologies: http://plantontology.org/docs/presentations/tutorials/poc_intro.mov, http://plantontology.org/docs/presentations/tutorials/poc_intro.ppt Powerpoint slides

Development of ontologies: http://plantontology.org/docs/presentations/tutorials/ontology.mov, http://plantontology.org/docs/presentations/tutorials/ontology.ppt

Annotations: http://plantontology.org/docs/presentations/tutorials/annotation.mov, http://plantontology.org/docs/presentations/tutorials/annotation.ppt

Plant ontology browser and POC web site: http://plantontology.org/docs/presentations/tutorials/website.mov, http://plantontology.org/docs/presentations/tutorials/website.ppt

From the wiki:

Principles, Rationales and Key Organizing Rules of the PO:

  • Wiki page with instructions on How to use the Source Forge tracker. Need to add details and images.
  • wiki home page: under Formats of the Ontology Files, needs info on OWL (provide link).

Mistakes on website

Pages that should be fixed before the workshop:

Less important fixes:

Booklet

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.

New upper level terms for PO

This came up as the need to describe things that are part of a seed, along with some other problems.

New and revised collective terms

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.

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. This would be parent to CPS, but also plant organ, cardinal organ part, and things like arilloid.


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.

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.

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.

mulit-tissue plant structure

proposed definition: A plant structure that has as parts two or more portions of planttissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit.

Comment: maybe give some examples

This includes plant organs, collective plant structures, cardinal organ parts, and those wierd, unclassifiable things like arilloid or ovary.


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. This is basically the same as PO plant organ.

We probably do not want to constrain our term to have bona-fide boundaries (otherwise, we can't include most cardinal organ parts or things like ovaries). RW has written to CARO to ask if they can modify this, but no specific response.


collective plant structure (new)

needs work

A multi-tissue plant structure that has as parts two or more other multi-tissue plant structures.

collective plant organ structure

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 (PO:0009007).

comment: A collective plant 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 (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:

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 structure" and "cardinal part of 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 lope 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

This is really just to cover the parts of a seed plus a few fruit parts, because most other structures are a cardinal part of an organ or a collective organ part structure.

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.

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

Botany 2012

July 7 - 11, 2012 - Columbus, Ohio

see: Botany 2012 workshops

This is a half-day (morning) workshop. The schedule now links to the correct abstract.

An announcement has been posted on the PO home page and FB page.

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.

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.

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.

We should do the booth. PJ will attend to host the booth for both Gramene and PO.

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)

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

See: POC_Conf._Call_6-12-12

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