POC Conf. Call 4-5-11

POC meeting, Webex Conference Call; Date: Tuesday Apr 5th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_3-29-11?

Issues arising from previous meetings:

mega/microspore

Unresolved question from 3-22-11:

Is is more accurate to say:

mega/microspore develops_from tetrad of mega/microspores

or

tetrad of mega/microspores has_part mega/microspore

embryonic plant structures

Definition of embryonic plant structure:

embryonic plant structure (PO:0025099): A plant structure that is part of an embryo.

Comment: Includes organs, tissues and cell types that are unique to embryos, not plant structures that can occur in both embryos and mature plant structures.

(changed definition from "proper part of" to "part of", so it would be consistent with the intersection of term. Think part_of is better anyway)

Questions about these structures:

embryonic leaf (PO:0006338): One of the first few leaves to develop from the embryonic shoot apical meristem [GR:pj].

Is this an embryonic plant structure, that is, is it always part of the embryo? Probably better off as just a leaf.

embryonic root (PO:0000045): An embryonic plant structure that is a root that is initiated in a developing embryo. [TAIR:ki]

Suggest that this should be is_a root instead of is_a embryonic plant structure, b/c it is not necessarily part of an embryo.

Proposed definition: A root that is initiated in a developing embryo.

radicle (PO:0020031): The radicle is the basal continuation of the hypocotyl in an embryo and gives rise to the root system of the adult plant; sometimes more or less abortive. is_a embryonic root [APWeb:Glossary]

Proposed definition: A root that is the basal continuation of a hypocotyl in an embryo and may develop into the root system of an adult plant.

Comment: Sometimes abortive.

remove part_of embryo axis, add embryo axis has_part radical

hypocotyl (PO:0020100): The part of the stem below the cotyledonary node and transitional to a root, found in a young sporophyte. [APWeb:Glossary]

currently is_a cardinal organ part, propose is_a shoot internode

Proposed definition: A stem internode that is the part of a stem below the cotyledonary node and transitional to a root.

Comment: Found in some young sporophytes. is_a shoot internode; embryo axis has_part hypocotyl

epicotyl (PO:0020035): The first internode of a stem above the hypocotyl. In literature also used for the entire embryonic axis, consisting of several internodes, above the cotyledonary node. [APWeb:Glossary]

currently is_a embryonic plant structure, propose is_a stem internode (PO:0005005). Also, the second part of the current definition only adds ambiguity. Need to define it more precisely.

Proposed definition: The first stem internode above a hypocotyl.

part_of stem

New Physcomitrella and related terms

Collective plant structures:

vascular and non-vascular shoot systems

The Moss Ontology did not request these terms, but suggest adding them in order to classify shoot systems.

non-vascular shoot system: A shoot system that does not have as part a vascular system (or vascular tissue?).

comment: Does not have any xylem of phloem, but may have other conducting cells, such hydroids or leptoids. Can occur in both the gametophytic and sporophytic phases of non-vascular plants.

subsets for bryophytes and pteridophytes

Could we use the relation "lacks_part"? Then we could define this class using intersection_of relations, which would be better. CL has used this (lack_plasma_membrane_part). Works better in OWL; translates into something like has_part exactly 0 (some ?Y) [need to check this].

Children of non-vascular shoot system will be gametophore (see below) and thallus. If we used the lacks_part relation and intersection_of relations, we could make gameotophore a child of shoot system, and the reasoner would infer it was a non-vascular shoot system.

Can't use participates_in gametophyric phase, because the sporophyte of a bryphyte is also a non-vascular shoot system (since it doesn't have roots or vascular tissue).

vascular shoot system: A shoot system that has as part a vascular system (or vascular tissue?).

comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.

participates_in sporophytic phase, has_part vascular system

If we accept these terms, suggest changing definitions of leaf and non-vascular leaf to "A leaf that is part of a non-vascular/vascular shoot system. This would be better than the current definitions which reference their taxonomy (part of a vascular or non-vascular plant) and would help with reasoning.

root-bourne shoot system (PO:0004544) should be is_a vascular shoot system

gametophore

Definition supplied by Moss Ontology: The leafy moss plant. The gametophore is the adult form of the moss gametophyte and bearer of the sex organs (gametangia). Ref: Reski (1998): Development, genetics and molecular biology of mosses. Botanica Acta 111, 1-15.

Suggest is_a shoot system.

Proposed def.: A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase. participates_in gametophytic phase

Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. In mosses, gametophores develop from buds that form on the caulonema. Antheridia and archegonia arise on the gametophore.

This will work as long as we can call the shoot system in leafy liverworts a gametophore as well.

gametophore bud

The term "bud" has been requested: Def'n supplied by Moss Ontology: A structure produced by a caulonema and able to develop into a gametophore or a stem that includes an apical cell able to develop into a gametophore. The earliest recognizable stage of gametophore development. Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered by David Cove

Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).

Proposed def'n: A bud that develops into a gametophore.

Comment: Occurs in mosses (and leaf liverworts?). Develops from a caulonema cell in mosses.

participates_in gametophytic phase, has_part shoot axis apical cell

Thallus

From Parihar: A simple vegetative plant body not differentiated into root, stem and leaf, and lacking vascular tissues.

From Schofeld: A flattened gametophore in which no leaf-like organs dominate the structure.

Saying a thallus is a gametophore implies that it is a shoot system and therefore a collective plant structure (CPS). As a CPS, it must have more that one organ. This is not always true for a thallus (sometime they branch, so you could say they have multiple axes, but it is a stretch. Maybe better to classify it as a whole plant.

alternative proposed definitions:

1) A flat gametophore with no distinct organs.

Comment: A thallus is a whole plant in the gametophytic phase in liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.

or

2) A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.

Comment: A thallus is a gametophyte of liverworts and pteridophytes and develops from a short-lived protonema. Roughly two dimensional growth results from division of a single apical cell. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.

Add prothallium (for ferns) as a synonym?

apical cell

Moss Ontology has requested the term apical cell. Apical growth in byrophytes is via division of a single cell at the tip of the shoot apical meristem. They also requested shoot apical cell and phyllid apical cell.

Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.

We already have the term apical cell (PO:0004000), which is an embryonic cell: "An embryonic plant cell that is the uppermost cell formed after the first division of the zygote." The embryonic apical cell can also be found in non-angiosperms. Suggest renaming PO:0004000 embryonic apical cell for clarity and using the name apical cellfor the term described below. May want to obsolete PO:0004000 and replace with the two new terms, to avoid confusion in the names.

Definition of apical cell from Esau: The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.

Definition of apical cell from Crum: A single cell at the tip of a stem, leaf, leaf or other structure that divides repeatedly to form new cells; also known as an apical intial. a Is apical cell more consistent with meristematic cell (A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall) or with initial cell (A meristematic cell that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body)? Probably meristematic cell, because the apical cell can give rise to more than two cells (because it can have three or four cutting faces).

Proposed def. of apical cell: A single meristematic cell at the tip of a shoot apex, leaf apex, root apex, or gametophore apex.

Comment: Occurs in bryophytes and some pteridophytes, where apical growth results from division of a single meristematic cell located at the tip of the apical meristem, rather than from a population of meristematic cells located at the tip of the apical meristem. May be tetrahedral shaped, with three (in shoots) or four (in roots) cutting faces, or wedge shaped with two cutting faces (in non-vascular leaves). An apical cell is established upon the first cell division of an embryo or germination of a spore.

-note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.

Suggested ontology structure for the children of apical cell:

The dotted lines represent relations inferred by the reasoner.

Includes two ways of classifying: by structure and by gametophyte/sporophyte. Structural relations are asserted as is_a relations. The relations to gametophyte or sporophyte are inferred by the intersection_of terms.

New terms and definitions for apical cells

gametophytic apical cell: An apical cell that is part of a whole plant in the gametophytic phase.

Comment: Occurs in mosses and other bryophytes.

intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase

sporophytic apical cell: An apical cell that is part of a whole plant in the sporophytic phase.

Comment: Occurs in pteridophytes and the sporophyte of bryophytes.

intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase

root apical cell: A sporophytic apical cell that is part of a root apical meristem.

comment: Only occurs in the sporophytic phase of vascular plants.

part_of root apical meristem

shoot apical cell: An apical cell that is part of a shoot system.

comment: May occur in shoot axes or leaves of bryophytes or ferns.

part_of shoot system

gametophore apical cell: A shoot apical cell that is part of a gametophore.

comment: Occurs in the non-vascular shoot system of the gametophyte of mosses.

intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore

thallus apical cell: A gametophore apical cell that is part of a thallus.

comment: We still need to add the term thallus.

part_of thallus (once we add it)

leaf apical cell: A shoot apical cell that is part of a leaf apex.

comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some mosses. Only in plants where leaf growth is apical.

part_of leaf

non-vascular leaf apical cell: A leaf apical cell that is part of a leaf apex of a non-vascular leaf.

comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.

part_of non-vasucular leaf; synonym: phyllid apical cell

vascular leaf apical cell: A leaf apical cell that is part of the leaf apex of a vascular leaf.

comment: Occurs in vascular leaves of some ferns in their sporophytic phase.

part_of vascular leaf

shoot axis apical cell: An apical cell at the tip of a shoot apical meristem.

Comment: Divides to produces leaf initial cells and other stem tissues.

part_of shoot apical meristem

gametophore axis apical cell: A shoot axis apical cell at the tip of a gametophore axis.

Comment: Occurs at the tips of the stems and branches of bryophytes.

part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell

vascular shoot axis apical cell: A shoot axis apical cell at the tip of a shoot apical meristem in a vascular shoot system.

Comment: Occurs in some ferns in their sporophytic phase.

part_of vascular_shoot system; synonym: fern shoot axis apical cell

Also:

embryonic apical cell (PO:0004000): A shoot axis apical cell that is part of an embryo and is the uppermost cell formed after the first division of the zygote.

Comment: For plants that grow via an apical cell in their sporophytic phase, the embryonic apical cell may remain an apical cell throughout the plant's life.

Plant organs:

cauloid

- This is the term used for the gametophore stem or axis.

Suggest using gametophore axis as primary name, cauloid as synonym.

Proposed def'n: A shoot axis that is part of a gametophore.

Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.

intersection_of: is_a plant axis, intersection_of: part_of gametophore

-Also suggest adding terms for gametophore stem and gametophore branch.

gametophore stem: A stem that is part of a gametophore.

is_a stem, part_of gametophore

gametophore branch: A branch that is part of a gametophore.

is_a branch, part_of gametophore

-If the intersection_of relations are asserted in the end user's version (e.g. Amigo), users will see dual parentage (is_a gametophore axis and is_a stem or branch).

perigonial bract

- The specialized phyllids surrounding the antheridia.

Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

A bract (PO:0009055) is defined as: A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure. [source: POC:curators] Comment: Often used to refer to what is called here floral bract.

Proposed def'n: A bract that subtends an antheridium. part_of gametophore, participates in gametophytic phase

Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.

foot

Moss Ontology definition: The base of the sporophytes in mosses

Proposed name and def.: sporophyte foot: A plant organ (?) that is the base of a whole plant in the sporophytic phase, below the seta, that attaches it to the gametophore. (ref: Schofeld)

Comment: Found in bryophytes. The sprophyte foot serves for both attachment and absorption. The outer portion of the foot is the absorptive haustorium. (From Crum)

participates_in sporophytic phase, has_part transfer cell, only_in_taxon bryophytes (I know this isn't a clade, will have to create a pseudo-clade).

- Should we add a term for sporophyte foot haustorium when we deal with portions of plant tissue or is the whole foot the haustorium?

Additional organ related moss terms:

These were not requested by the Physcomitrella group, but they are related to the terms above and are commonly used to describe mosses, so we should add them now.

perichaetal bract

Proposed def'n: A bract that subtends an archegonium. part_of gametophore

Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts. The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.

gametophytic perianth

Proposed def'n: A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on a gametophore axis and surround the calyptra (capsule?).

Should it be surrounds the capsule, in case no calyptra is present?

-has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)

Comment: The parachaetal bracts may fuse laterally in the gametophytic perianth. The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.

seta

-The stalk of a moss sporophyte.

Proposed def.: A plant axis that that holds up a spore capsule. participates_in sporophytic phase

Comment: Found in mosses.

antheridiophore and archeginiophore

These are stalks that hold up the antheridia or archegonia in Marchantiales

Proposed definitions:

antheridiophore: A plant axis that bears antheridia.

participates_in gametophytic phase

Comment: Found in Marchantiales.

archeginiophore: A plant axis that bears archegonia.

participates_in gametophytic phase

Comment: Found in Marchantiales.

Upcoming meetings 2011:

* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC contributed to the workshop proposal "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" Authors: Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland and Laurel Cooper (Accepted)

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO. Invite other plant people?

-BS suggested we might want to submit a short paper which could be published in longer form later- see above

*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

Abstract deadlines: Your abstract must be submitted by March 11 if you want it to be considered for a minisymposium talk.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.

* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

Early bird registration deadline - Extended 1 March 2011 Deadline for registration by presenters 1 March 2011

See IBC 2011 Bio-Ontologies Symposium wiki page for more details