POC Conf. Call 3-22-11

POC meeting, Webex Conference Call; Date: Tuesday Mar 22nd, 2011 10am (PDT)

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo; (Cornell University, Barry Smith (University at Buffalo, NY), Dennis Stevenson (NYBG),

Absent: Chris Mungall (Lawrence Berkeley National Lab)

Collaborators: None

Acceptance of the minutes from the POC_Conf._Call_3-15-11? There were no changes, additions, or deletions.

POC 'Technical Issues' Conf Call 3-17-11 Problems discussed:

Updates from the "Technical Issues" Conference call meeting we had on Thursday Mar 17th.

Please see:POC Technical Issues Page for more details.

Webex Conference Call; Date: Thursday Mar 17th, 2011 4pm (PDT) In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Chris Mungall (Lawrence Berkeley National Lab)

has_parts problem

• We discussed the has_parts problem, that some of the has_parts relations we have been using are causing the ontology file to "hang up" during loading into the database.

• Based on our tests last week, it appears that the problems arise when we have reciprocal part_of and has_part relations (or reciprocal part_of and develops_from relations)

Action Items since the meeting:

1. Confirm that the reciprocal part_of and has_part relations were what was actually cause the problem with loading the obo file onto our browser. To do this, we should:

    a) Try loading the file without the reciprocal relations but with some has_part relations onto the beta browser with annotations (this will require an edited a version of the live file, since the annotation files currently match the live file)

done

    b) Try loading a version of the file that has maybe one or two reciprocal relations, but no annotations on to the dev browser (to see if the reciprocal relations cause a problem when there are no annotations).

2. If the reciprocal relations are causing the problem, we can deal with them in one of two ways:

    a) remove all reciprocal relations from the ontology file, that is, only use part_of or has_part, but not both

    b) include reciprocal relations when they are appropriate, but write a script that searches the files for reciprocal relations and removes the has_part relation from classes that have both.

3. For cases where a class has two children that differ in structural characteristics and also occur in separate taxa, we should create the children, but not propagate the part_of children from the parent to the specific children (i.e., what we did for leaf and what have talked about for microsporangium).

In these cases, we could add "only_in_taxon" relations to the specific children. Then we can use the only_in_taxon relations in a script that will examine the annotation for the part_of children of the parent class and assign them to the child class if they come from the correct taxon.

Action item: We should send CM an example file with the only_in_taxon relations so that he can send us an example of how the script would work

We may be able to use Gramene's taxonomic ontology (check if it is for all plants) rather than editing the slim CM et al. created for GO.

LC: Gramene's taxonomic ontology is limited in its scope- focuses on the Poaceae (Gramineae) family of plant taxonomy only

Items carried over from last week's meeting: Physcomitrella terms

Gametangium, antheridium, archegonium and related terms

May want to use the name plant gametangium, to make it clear that we are not including algae.

Current definitions:

plant gametangium (PO:0025124): A cardinal organ part that is part of a whole plant in the gametophytic phase and produces gametes.

antheridium (PO:0025125): A gametangium that produces antheridium sperm cells.

archegonium (PO:0025126): A gametangium that produces archegonium egg cells.

megagametophyte (PO:0020092): A gametophyte that produces female gametes.

microgametophyte (PO:0020091): A gametophyte that produces pollen sperm cells.

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

embryo sac egg cell (PO:0025123): An egg cell that is produced by a megagametophyte.

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

pollen sperm cell (PO:0025121): A sperm cell that is produced by a microgametophyte.

Problems with these defintions:

-Definitions of mega/microgametophyte don't work, because we no longer have the term gametophyte to use as a genus.

-Need definitions that distinguishes gametangia from megagametophyte (embryo sac) and microgametophyte (pollen). Could use only in taxon/never in taxon relations here.

-The definitions are circular (see e.g., definitions of archegonium egg cell and archegonium):

-Finally, having both sets of egg and sperms cells seems redundant. They were put in to satisfy the part_of relations. We could get around this by using has_part relations, but maybe we don't want to?

Here is an image of the current PO, showing only female parts:

Here is how it would look using has_part relations:

In this image, archegonium egg cell and embryo sac egg cell have been merged with egg cell.

On the other hand, keeping the separate types of egg cells in this case would not cause too much term inflation, because they don't have any part_of children.

May want to merge embryo sac with female gametophyte. It is the only child of female gametophyte, suggesting they are redundant. This would be analogous to our current situation of having pollen grain as a synonym of microgametophyte.

OR, maybe we need the terms mega- and microgametophyte for bryophytes (and ferns?) that produce separate male and female plants in the gametophytic stage. Should there be classes for that, or is it better to post-compose whole plant in gametophytic phase with male or female from PATO (like for flowers)?

We decided to keep embryo sac egg cell, pollen sperm cell, archegonium egg cell and antheridium sperm cell for now. Although they are not strictly different structures (aside from where they occur), being able to use the part_of relations to pass on annotations outweighs the cost of having them in the ontology.

Also, will not merge embryo sac with female gametophyte (see more below).

Proposed new definitions:

plant gametangium (PO:0025124)

From Raven et al.: A cell or multicelluar structure in which gametes are formed.

Proposed definition: A plant organ that produces gametes and is part of a whole plant in the gametophytic phase (This is to distinguish it from a stamen or carpel).

Note: the comment in parenthesis is only for this discussion. It is not part of the definition.

New proposed definition: 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); can we say disjoint_from megagametophyte if it is part_of a megagametophyte (depends on how we define megagametophyte)

Should not say disjoint_from megagametophyte, because we will define megagametophyte such that archegonium is a part of it.

Need to add subsets for bryophytes, pteridophytes, and gymnosperms, in addition to the subset for angiosperms. Put terms in proper subset(s) until we can use the only_in taxon relation.

We will use "located in" rather than "contained in." Contained-in is used when an organism has a cavity or space that contains some material object (such as a fetus in a womb). Located_in is used when one class located in another is also part of the other class. 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.

antheridium

From Schofeld: The multicellular male sex organ of bryphytes that consist of a stalked sac containing many sperms enclosed by a unistratose sterile jacket of cells.

From Parihar: The male sex organ of the cryptograms

proposed definition: A gametangium that produces sperm cells.

new proposed definition: A plant gametangium that produces antheridium sperm cells that are located in it.

Comment: A antheridium has a sterile jacket layer that does not produce sperm cells.

only_in_taxon bryophytes plus pteridophytes (or never_in taxon seed plants), has_part sterile jacket layer

archegonium

From Schofeld: The flask-shaped multicellular sex organ that conatins a single egg.

From Parihar: The female sex organ of bryophytes, pteridophytes and gymnosperms.

proposed definition: A gametangium that produces an egg cell.

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

only_in_taxon bryophytes plus pteridophytes plus gymnosperms (or never_in taxon angiosperms)

Comment about how it can be unicellular in some algae?

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

embryo sac (currently is_a megagametophyte PO:0020092) (PO:0025074): A whole plant in the gametophytic phase that is contained in an ovary and produces an egg cell.

pollen grain (currently synonym of microgametophyte) (PO:0020091): A whole plant in the gametophytic phase that develops from a microspore within a pollen sac and produces pollen cells.

What about microgametophyte and megagametophyte?

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

New terms and proposed definitions from today's meeting

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

Comment: Megagametophytes in bryopytes only produce egg cells, but do not arise from megaspores, because there is no heterospory in bryophytes. In angiosperms, Gnetum, (and Weltwischia?) the megagametophyte is reduced to the embryo sac.

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

Comment: Microgametophytes in bryopytes only produce sperms cells, but do not arise from microspores, because there is no heterospory in bryophytes. In seed plants the male gametophyte is reduced to pollen.

embryo sac (existing term, PO:0025074): A female gametophyte that is located in a nucellus (does this work for Gnetum?)

Comment: Produces an embryo sac egg cell.

develops_from megaspore, only_in_taxon angiosperm plus Gnetum (plus Weltwischia?)

pollen: A male gametophyte that is located in a pollen sac.

Comment: Produces pollen sperm cells.

develops_from microspore, only_in_taxon seed plants

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

only in taxon bryophyte (need to check about pteridophytes)

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

only in taxon bryophyte (need to check about pteridophytes)

New definitions for egg and sperm cells from today'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

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

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.

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 tip of a shoot apex or root 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).

Do we need separate terms for sporophytic apical cell and gametophytic apical cell?

gametophytic apical cell: A meristematic cell at the apex of a gametophore or non-vascular leaf.

Comment: Occurs in mosses and other bryophytes. participates_in gametophytic phase

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

Comment: Occurs in Pteridophytes (and in the sporophyte of bryophytes?). participates_in sporophytic phase

Moss ontology also requested shoot apical cell and phyllid apical cell.

Proposed names and definitions:

gametophore apical cell: A gametophytic apical cell at the tip of a gametophore.

OR shoot axis apical cell: An apical cell at the tip of a shoot apical meristem. (could apply to mosses and ferns)

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

part_of shoot apical meristem

phyllid apical cell: A gametophytic apical cell at the tip of a non-vascular leaf.

Comment: Divides to produce non-vascular leaf tissues.

part_of non-vascular leaf

(ref: C. Jill Harrison et al. (2009): Local Cues and Asymmetric Cell Divisions Underpin Body Plan Transitions in the Moss Physcomitrella patens.)

Collective plant structures:

Discussion of the items below was postponed until next week.

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 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 a moss gametophyte, without the protonema. Gametophores develop from buds that form on the caulonema. Antheridia and archegonia arise on the gametophore.

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 on a caulonema that develops into a gametophore. participates_in gametophytic phase

Comment: Occurs in mosses.

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 plant axis that is part of a gametophore. is_a plant axis, part_of gametophore

Synonyms: cauloid, gametophyte axis

Also suggest adding terms for gametophore stem and gametophore branch (similar to stem and 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 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.

Cardinal organ parts

Terms requested by MO:

• calyptra

Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.

We also have a request (from PJ) for calyptra, which is part of the fruit in Eucalyptus. That term should be named fruit calyptra (see below under operculum), and this term should be named spore capsule calyptra, to distinguish them.

Proposed name and def.: spore capsule calyptra: A cardinal organ part that develops from a venter and surrounds a sporangium.

Comment: Found in mosses and pteridophytes. The calyptra ia a membranous or hairy cap composed of gametophytic tissue that protects the embryonic sporophyte within the archegonium. In some species, the calyptra may persist after the sporophyte develops and gets carried upward as the seta elongates.

participates_in gametophytic phase, develops_from venter

• venter

This term was not suggested by Moss Ontology, but perhaps we should add it.

proposed def.: A cardinal organ part that is the enlarged basal part of an archegonium and contains an egg cell.

part_of archegonium

• archegonium neck

This term was not suggested by Moss Ontology, but perhaps we should add it.

proposed def.: A cardinal organ part that is the elongated apica part of an archegonium.

Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.

part_of archegonium

(can also add term for neck canal cell when we deal with cells)

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.

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 1st).

*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