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.
We agreed to change the name to Plant Anatomy Ontology. Since this name or PAO does not actually occur in the ontology anywhere, and it is just a name for one branch of the PO, changing it is not a problem. Also, in the separate versions of the files, the PAO branch file is already called plant_anatomy.obo, so this name is more consistent.
We should check with CM to see if we should change the namespace, which is currently Plant Structure, and what the ramifications of such a change would be.
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.
For the top level PAO terms that reference CARO, we should remove the ID from the definition and add it as a definition dbxref. We should put the definition and ID of the CARO term into the comment, like we have done with GO for plant cell.
As a general guideline, whenever we use a definition from another ontology for a term, but alter it to fit PO, we should put the other onotlogy ID plus POC:curators into the definition dbxrefs.
Add text explaining this to our developer's guide.
embryonic plant structure
Do we want dual parentage for embryonic structures? Should we use intersection_of relations, instead of asserting dual parentage?
Will the intersection of relations be displayed by AmiGO?
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:
pi represents participates_in relation
dotted lines are relations that are inferred by the reasoner.
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. Similar relations could be used for other embryonic plant structures.
This allows us to classify cells as plant cells, tissues as plant tissues, etc., but still lets them have a relationship to embryonic plant structure, while other structures, like embryo proper, could remain as is_a children of embryonic plant structure. This is the method specified as the best_practice for OBO foundry (at least orally, if not actually in their principals).
embryonic cell
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
Report from JE @ tests and annotations etc:
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. (in OboEdit by default)
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:
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: The embryo sac and pollen replace the function of gametangia of producing gametes in gymnosperms (for antheridia) and angiosperms (for both antheridia and archegonia).
-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.
-Added new relation participates_in.
This definition of gametangium works for algae. Could add a child term oogonium. Do we want to add a subset for algae? At this point, we don't have any terms specific to algae, but several that apply.
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
Should add antheridial initial as a synonym of generative cell.
archegonium: A plant gametangium that produces an archegonial 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 dioicous 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 ovule 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.
For the time being, any annotations for these two genera should just be placed under microgametophyte or megagamethopyte.
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.
will add pollen grain as an exact synonym
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 microgametophyte: 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 cells and sperm cells from last week's meeting
archegonial 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, part_of egg apparatus
For Gnetum and Weltwischia, should just use parent terms (egg cell or sperm cell).
antheridial sperm cell (PO:0025120): A sperm cell that is produced by 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 a pollen grain.
Comment: A pollen sperm cell consists of a nucleus without a cell wall.
only_in_taxon seed plants, part_of pollen
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?
Upcoming meetings 2011:
* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York
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 10th).
*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn
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
