POC Conf. Call 6-12-12

POC meeting, Webex Conference Call; Date: Tuesday June 12th, 2012 10am PDT/1pm EDT

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY).

Absent: Marie Alejandra Gandolfo (Cornell), Chris Mungall (Lawrence Berkeley National Lab)'

Collaborators: none

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=65751172&rKey=6c81e7a9c537c42b

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=65751172&rKey=7fe6151ae7f2c9eb

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_6-5-12?

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New upper level terms for Plant Anatomical Entity branch of the PO

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.

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.

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.

New proposed hierarchy:

plant ovary should be a subtype of the new term cardinal part of multi-tissue structure

Collective plant structure (new term) should be a subtype of plant structure. Some discussion of whether or not CPS's are "distinct structural units". Probably not all are, so better to keep under plant structure

New proposed term: multi-tissue plant structure (MTPS) (PO:0025496)

proposed def'n: 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.

This is derived from the CARO term: multi-tissue structure (CARO:0000055): 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 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).

• Not sure about the bona-fide boundaries part.

Comment from RW: I think this term 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).

We decided that CPS (and its children CPOS and CPOP) should not be subtypes of MTPS, because they are not always distinct structural units.

We discussed the difference between bona-fide and fiat boundaries. Bona-fide boundaries include things like the boundary between epidermis and air or between two tissue types. Fiat boundaries are more or less arbitrary, such as the boundary between a hand and wrist. In reality, organs are not completely separated by bona fide boundaries, but are often connected to other organs by pipe-like structures.

CARO has terms for "organism subdivision", which includes things like appendages that are separated by fiat boundaries, and "multi-tissue structure", which includes things like organs that are separated by bona-fide boundaries. However, it does not appear to have any terms of for organ parts.

We need to check with CARO to found out how they plan to deal with organ parts.

FMA has the following hierarchy for organ parts (definitions paraphrased):

anatomical structure

>cardinal organ part: any part of an organ that has two or more tissues

>>organ component: a cardinal organ part which is bounded predominantly by bonafide boundaries

>>organ region: a cardinal organ part which is a fiat subdivision of an organ (includes organ segments and organ zones)

>>region of organ component: a cardinal organ part which is a fiat subdivision of an organ component. (RW: This seems redundant with organ region to me)

Sub-classes of MTPS:

-what about rhizoid (PO:0030078) and trichome (PO:0000282) and vascular system??

rhizoid and trichome don't fit under MTPS, because they are either a cell or a tissue.

Vascular system should maybe move to be subtype of portion of vascular tissue (see tracker).

seed (PO:0009010):

Current def'n: A plant structure that develops from an ovule and has as parts an embryo enclosed in a seed coat.

propose revised def'n: A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).

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.

comment: Examples: stem, leaf, root. May include individual cell types that are not part of tissues (e.g.: idioblasts).

new proposed def'n: plant organ (PO:0009008): A multi-tissue plant structure (PO:0025496) 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.

new proposed 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 (PO:0000283)). 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 plant ovule (PO:0020003).

plant ovary (PO:0009072):

current def'n: A plant structure that is the basal portion of a carpel or group of fused carpels and encloses the ovule(s).

note: An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc

revised def'n: A cardinal part of multi-tissue plant structure (PO:0025498) that is the basal portion of a carpel (PO:0009030) or group of fused carpels and encloses the plant ovule(s) (PO:0020003).

does this mean that carpel should be a MTPS?, currently it is a plant organ Plant organ is a MTPS.

This does not work as a subtype of cardinal part of MTPS, because ovary can be part of either carpel (a MTPS) or gyneocium (a CPS). If CPS were a subtype of MTPS, this would work, but the current working hierarchy doesn't solve the problem of parentage of ovary.

New term: collective plant structure (PO:0025497)

This would be a general term, parent to collective plant organ structure (PO:0025007) and collective organ part structure (PO:0025269); see below.

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).

proposed definition: A multi-tissue plant structure (PO:0025496) that is a proper part of a whole plant (PO:0000003) and includes two or more different plant organs (PO:0009008), or cardinal organ parts (PO:0025001), along with any associated portions of plant tissue (PO:0009007).

Should say "adjacent plant organs" and "adjacent cardinal organ parts".

Sub-classes of collective plant structure (PO:)

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:PO:0025497) that is a proper part of a whole plant (PO:0000003), and is composed of two or more adjacentplant organs (PO:0009008) and the associated portions of plant tissue (PO:0009007).

comment: A collective plant organ structure must have as parts at least two plant organs (PO:0009008) 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 plant organs in a collective plant structure can be of the same type, such as the 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.

We need to look at the existing sub-classes of the current CPS class and ask if they fit this definition: eg: fruit, anther, shoot system, root system

fruit should be a sub-class of multi-tissue plant structure

collective organ part structure (PO:0025269)

This is the existing term that is currently defined as: "A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue." examples are septum, pseudostem etc.

propose revised def'n: A collective plant structure (PO:0025497) composed of two or more cardinal organ parts (PO:0025001) from adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007).

Sub-classes for the parts of the various multi-tissue plant structures

These are subclasses of plant structure, not of multi-tissue plant structure, since they do not necessarily for "distinct structural units" (although maybe some, like leaflet, do).

cardinal organ part (PO:0025001)

current def'n: A plant structure that is a proper part of an organ and includes portions of tissues of at least two different types.

comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Examples include lobe (PO TBD), operculum (PO TBD), neck (PO TBD), petiole PO:0020038, leaflet PO:0020049.

proposed new 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.

revised 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.

decided this should be a subclass of cardinal part of multi-tissue plant structure (PO:0025498)

Revised def'n: A cardinal part of multi-tissue plant structure (PO:0025498) 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.

From discussion on 5-8-12:

Maybe it would be better to say 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 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 boundaries on all sides (??), as opposed to regional parts, which just have a boundary on one side.

cardinal part of multi-tissue plant structure (PO:0025498)

If we decide to add a new term for multi-tissue plant structure, which would be parent to plant organ but also things like seed, we could use a term for "cardinal part of multi-tissue plant structure".

This would be similar to "cardinal plant organ" (or cardinal part of plant organ) but could multi-tissue parts of multi-tissue plant structures that are not organs (e.g., aril, which is part of seed). It would also serve as parent to things like ovary, which can be part of either an organ or a collective plant structure.

Proposed def.: A plant structure (PO:0009011) that is a proper part of a multi-tissue plant structure (PO:0025496) and includes portions of plant tissues (PO:0009007) of at least two different types.

Comment: Cardinal refers to the fact that these are biologically meaningful parts, not arbitrary. Includes cardinal parts of plant organs. (add examples)

Decided that cardinal organ part and ovary should be a subclasses of this...

cardinal part of collective plant structure (PO:xxxxxxx)

Do we still need this term? Maybe replace with cardinal part 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.

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: Plant Ontology Crop Annotation Workshop at OSU, 2012

Dates: 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 19, 2012 at 10am PDT/1pm EDT

See: POC_Conf._Call_6-19-12