POC Conf. Call 4-19-11
POC meeting, Webex Conference Call; Date: Tuesday Apr 19th, 2011 10am (PDT)
In attendance:
POC members:
Absent:
Collaborators:
Acceptance of the minutes from the POC_Conf._Call_4-12-11?
Tech issues:
Report from JE about OBO to OWL conversion, and progress on has_parts?
Other items:
*Changing the namespace from Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO) This was discussed at the POC_Conf._Call_3-29-11
Action taken: -LC talked with CM, we all agreed that it would not be too much of an issue to do so.
-Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group"
-Still needs to be changed on the PO webpage and in other spots where the individual files are linked to (such as Bioportal)- so it should also change in those places.
-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?
Issues arising from last week's meeting:
gametophytic phase and sporophytic phase
sporophytic phase (PO:0028002)
Current definition: A plant life cycle phase that is the product of fertilization. [source: POC:rw]
Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis.
Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with fertilization or the division of a non-fertilized embryogenic cell.
Comment: During the sporophtyic phase, a plant may produce meiospores by meiosis. A whole plant in the sporophytic phase usually has twice the chromosome complement of a plant in the gametophytic phase, but not in the case of apogamy or in vitro culture of haploid embryos.
gametophytic phase (PO:0028003)
Current definition: A plant life cycle phase that arises through meiosis. [source: POC:rw]
Comment: During the gametophytic phase, a plant may produce gametes by mitosis.
Proposed definition: A plant life cycle phase (or a whole plant growth stage) that begins with meiosis.
Comment: During the gametophytic phase, a plant may produce gametes by mitosis. In bryophytes and pteridophytes, a gametophytic phase may begin without meiosis by apospory, when damage to a plant in the sporophytic phase leads directly to the growth of a plant that is in the gametophytic phase but bears the chromosome complement that would normally be found in the sporophytic phase. A whole plant in the gametophytic phase usually has half the chromosome complement of a plant in the sporophytic phase, but not in the case of apospory.
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 (PO:0030017): A shoot system that does not have as part 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
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).
Child of non-vascular shoot system will be gametophore (see below). A moss sprophyte could also be called a non-vascular shoot system. 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 gametophytic phase, because the sporophyte of a bryophyte might also be considered a non-vascular shoot system.
vascular shoot system (PO:0030016): A shoot system that has as part 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 vascular leaf (PO:0009025) and non-vascular leaf (PO:0025075) to "A leaf that is part of a vascular/non-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 (PO:0030018)
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, develops_from gametophore bud
Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.
subset for bryophytes
gametophore bud (PO:0030026)
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 vegetative bud that develops into a gametophore.
Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.
participates_in gametophytic phase, has_part gametophore apical cell
synonym: brown bud
thallus (PO:0030027)
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 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.
proposed def: 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. Thalli may be ribbon or heart shaped or almost filamentous. Although there are no distinct organs, there may be tissue differentiation and dichotomous branching.
Add prothallium as a broad synonym of thallus and as a narrow synonym of whole plant.
Other gametophyte terms
We need to keep in mind terms for other types of gametophytes, such as the subterranean, heterotrophic gametophytes of some ferns. RW, DWS, and MAG will maintain a list of terms that we don't need to add yet, but may want to add as time allows or need demands. Can use this list, for example, for writing a renewal of things that still need to be done.
