POC Conf. Call 3-29-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 29th, 2011 10am (PDT)

In attendance:

POC members:

Absent:

Collaborators:

Acceptance of the minutes from the POC_Conf._Call_3-22-11?

Issues with the ontology arising during writing:

This section is for questions about the PO that came up while were writing the manuscript. These are issues that need to be addressed by the curators, preferably before publication and the next release.

Rename Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO)?

Reason: better reflects the new upper structure, highlights the changes we have done over the past year

PAO is consistent with other anatomical entities in OBO foundry, like HAO.

Use of ontology id's in definitions

We have been inconsistent in where we put ID's for terms from other ontologies that we reference in the PO.

For the top level PSO terms, we have CARO ID's in the definitions, but also have them as xrefs.

For plant cell, we reference GO ID in the comment, but also have it as an xref.

embryonic plant structure

Do we want dual parentage for embryonic structures? Should we use intersection_of relations, instead of asserting dual parentage?

Here is a figure of how it would work, if the is_a relation to the "normal" plant structure were asserted, and the relation to embryonic plant structure were inferred using intersection_of relations, using embryonic apical cell as an example:

This method defined embryonic plant cell as is_a: embryonic plant structure, intersection_of: is_a plant structure, intersection_of: part_of embryo.

Because the intersection_of relations specify sufficient conditions, any plant cell that has a part_of relation to embryo will be classified as an embryonic plant cell whenever the reasoner is on.

This allows us to classify cells as plant cells, etc. This is the method specified as the best_practice for OBO foundry (at least orally, if not in their documents).

in vitro plant structures

What are the boundaries for an in vitro structure?

What about a whole plant or parts thereof that are grown in culture? Suppose someone had an annotation for a leaf from an in vitro grown plant. Where should they put it?

Also, we talked about using derived_from relations for in vitro structures (e.g., cultured cell derived_from plant cell). Do we still want to do that? How to assure that the derives from relations always hold?

has_part relation

How will we deal with has_part relation? for this release? for future releases?

We confirmed that the reciprocal part_of and has_part relations were what was actually cause the problem with loading the obo file onto our browser:

-JE tried to load the dev browser with the current plant_ontology.obo file with only one reciprocal part_of/has_part relation, but no other known problems, and it would not load.

-Then he loaded the dev browsers with a file that had only has_part relations but no reciprocals, and it worked fine.

-Still have to test loading it onto beta browser with annotations

participates_in relation

Need to get these in. Should we make a test file to see if these are going to cause issues?

RW- I have been putting them in the developer's file. Don't seem to interfere with loading. Show up on the dev browser, but need an icon.

Question: If a parent term (e.g., plant gametangium) has a participates_in relation, do we need to specify participates_in relation for all its children (e.g., archegonium and antheridium), or will the reasoner know to apply the relation to the children?

Should not need it for children if it is transitive:

A is_a B, and B participates_in C, then A participates_in C

and

A part_of B, and B participates_in C, then A participates_in C

Answer (from Chris Mungall): participation isn't transitive.

what you want to say is that a is part of b, and b participates in c, then a participates in c

unfortunately you can't do this in OE yet - use a text editor and add the following line to the declaration for participates_in:

[Typedef]

id: participates_in

holds_over_chain: part_of participates_in

this gives the reasoner the information that an apical cell participates in gametophyte phase via the part_of relation

(really this axiom should be in RO, and there should be some mechanism where you can just import it but things are a bit primitive right now)

RW: I did this and it worked.

Issues arising from last week's meeting:

Recap of Gametangium, antheridium, archegonium and related terms

Proposed new definitions from last week's meeting:

plant gametangium (PO:0025124): A plant organ that produces one or more gametes that are located in it and is part of a whole plant in the gametophytic phase.

participates in gametophytic phase, only_in_taxon bryophytes plus pteridophytes plus gymnosperms (=never_in_taxon angiosperms)

comment: never used in angiosperms, not the same as not occuring in angiosperms

-Should not say disjoint_from megagametophyte, because we will define megagametophyte such that archegonium is a part of it (see below).

-We used "located in" rather than "contained in." Contained_in is used when an organism has a cavity or space that contains some material object that is not part of it (such as a fetus in a womb). Located_in is used when one class located in another is also part of the class it is located in. We will use located in for the same reason a human mother's egg is part of the mother rather than contained in the mother. Also, we can put pictures on Plantsystematics.org that show gametangium development, and show how the egg cell derives from one of the same population of cells as the rest of the gametangium.

-New subsets were added for bryophytes, pteridophytes, and gymnosperms, in addition to the subset for angiosperms. Will put terms in proper subset(s) until we can use the only_in taxon relation.

Could work for algae. do we want to add a subset for them? Add oogonium?

-Added new relation participates_in.

antheridium: A plant gametangium that produces antheridial sperm cells that are located in it.

Comment: A antheridium has a single outer layer of non-sperm producing cells called the sterile jacket layer and sporagenous cells on the interior. There are no antheridia in seed plants.

only_in_taxon bryophytes plus pteridophytes (or never_in taxon seed plants), add relation sterile jacket layer part_of antheridium

archegonium: A plant gametangium that produces an archegonium egg cell that is located in it.

Comment: There are no archegonia in angiosperms or Gnetum or Weltwischia.

only_in_taxon bryophytes plus pteridophytes plus gymnosperms (never_in taxon angiosperms, Gnetum and Weltwischia)

Note: there are no examples of unicellular archegonia in the green algae or land plants, so we don't need to worry about it

New terms and proposed definitions from last week's meeting

We should obsolete PO:0020092 megagametophyte and PO:0020091 microgametophyte, and create new terms that can encompass dioecious bryophyte gametophytes as well as the gametophytes in angiosperms. Embryo sac and pollen grain will be children of these terms, as well as archegonial megagatephyte and antheridial microgametophyte.

megagametophyte: A whole plant in the gametophytic phase that produces only egg cells.

Comment: Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores. In angiosperms, Gnetum and Weltwischia the megagametophyte is greatly reduced. The megagametophyte in angiosperms is an embryo sac.

microgametophyte: A whole plant in the gametophytic phase that produces only sperm cells.

Comment: Microgametophytes in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In some pteridophytes, microgametophytes develop from microspores. In seed plants the male gametophyte is reduced to a pollen grain.

embryo sac (existing term, PO:0025074): A megagametophyte that is contained in an ovary.

Comment: Produces an embryo sac egg cell.

develops_from megaspore, only_in_taxon angiosperm

Do we need a separate class for the microgametophytes in Gnetum and Weltwischia? Usually don't use "embryo sac" for these taxa.

pollen: A microgametophyte that is located in a pollen sac.

Comment: Produces pollen sperm cells.

develops_from microspore, only_in_taxon seed plants

-Would pollen grain be a better name for this? Pollen implies all of the pollen grains, collectively.

archegonial megagametophyte: A megagametophyte that has as parts one or more archegonia.

Comment: Megagametophytes in bryophytes only produce egg cells, but do not develop from megaspores, because there is no heterospory in bryophytes. In some pteridophytes, megagametophytes develop from megaspores.

only_in_taxon bryophyte plus pteridophytes

antheridial microgametophute: A microgametophyte that has as parts one or more antheridia.

comment: Microgametophytes in bryophytes only produce sperm cells, but do not develop from microspores, because there is no heterospory in bryophytes. In some pteridophytes, microgametophytes develop from microspores.

only_in_taxon bryophyte plus pteridophytes

New definitions for egg and sperm cells from last week's meeting

archegonium egg cell (PO:0025122): An egg cell that is produced by and located in an archegonium.

only_in_taxon bryophytes plus pteridophytes plus gymnosperms (or never_in taxon angiosperms), part_of archegonium

embryo sac egg cell (PO:0025123): An egg cell that is produced by and located in an embryo sac.

only_in_taxon angiosperm plus Gnetum plus Weltwischia, part_of egg apparatus

need to find out if this is appropriate for Gnetum and Weltwischia. Usually don't use "embryo sac" for these taxa.

antheridium sperm cell (PO:0025120): A sperm cell that is produced by and located in an antheridium.

only_in_taxon bryophytes plus pteridophytes (or never_in seed plants), part of antheridium

pollen sperm cell (PO:0025121): A sperm cell that is produced by and located in a pollen grain.

only_in_taxon seed plants, part_of pollen

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

proposed definition: A flattened gametophore with no leaves.

Comment: A thallus is a whole plant in the gametophytic phase (a gametophyte) in liverworts, pteridophytes.

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.

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.

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 shoot apex, root apex, or gametophore apex or thallus 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 shoot apical cell that is part of a thallus. (or maybe 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.

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) LC is working with the other organizers to develop the workshop plans and a call for papers.

call for papers

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, will submit a short paper/poster for the workshop (deadline April 10th).

*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.

TAIR is organizing an Outreach Booth and we are invited to take part.

* 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