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| − | In attendance: | + | In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG), |
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| − | POC members:
| + | Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab), |
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| − | Absent:
| + | Collaborators: none |
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| − | Collaborators:
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| − | Acceptance of the minutes from the [[POC_Conf._Call_4-12-11]]? | + | Acceptance of the minutes from the [[POC_Conf._Call_4-14-11]]? ''There were no changes, additions or deletions.'' |
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| − | =Issues arising from last week's meeting:=
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| − | =New Physcomitrella and related terms=
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| − | ==Collective plant structures:==
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3244685&group_id=76834&atid=835555 vascular and non-vascular shoot systems]===
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| − | The Moss Ontology did not request these terms, but suggest adding them in order to classify shoot systems.
| + | =Tech issues:= |
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| − | '''non-vascular shoot system:''' A shoot system that does not have as part vascular tissue. | + | '''*Update on the OBO to OWL conversion:''' |
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| − | 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.
| + | ''JE now has an owl version of the live plant_ontology file that has the definitions and other information. It is available at: http://palea.cgrb.oregonstate.edu/svn/Poc/tags/live/plant_ontology.owl'' |
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| − | subsets for bryophytes
| + | ''Still working with Damon and Shuly on getting the SSWAP components to work properly from their end.'' |
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| | + | '''PO will host the owl file and the SSWAP components of it (?), they have software that enables us to do it. (need more accurate details)'' |
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| − | 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).
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| | + | '''* progress on has_parts?''' |
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| − | 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.
| + | ''Currently, the existing has parts in the ontology do not seem to be causing any problems, now that we removed the reciprocal relations. The problem still exists that the annotations do not flow in the right direction. '' |
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| | + | ''JE still needs a test file that has fewer terms and annotations, because testing with the live version takes about 10 hours to load.'' |
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| − | Can't use participates_in gametophytic phase, because the sporophyte of a bryphyte doesn't have roots or vascular tissue.
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| | + | '''*Changing the namespace from Plant Structure Ontology (PSO) to Plant Anatomy Ontology (PAO)''' |
| | + | This was discussed at the [[POC_Conf._Call_3-29-11]] |
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| | + | Action taken: |
| | + | -LC talked with CM, we all agreed that it would not be too much of an issue to do so. |
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| − | '''vascular shoot system:''' A shoot system that has as part vascular tissue.
| + | -Change was made in the plant_ontology.OBO development file, version #1068 and on the SourceForge term tracker "group" |
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| − | comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.
| + | -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. |
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| − | participates_in sporophytic phase, has_part vascular system
| + | -Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this? |
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| | + | ''JE was able to modify the drop down menu on the Amigo browser to say "plant anatomy" instead of "plant structure" while we spoke.'' |
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| − | 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.
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| − | '''root-bourne shoot system''' (PO:0004544) should be is_a vascular shoot system | + | '''*Review for OBO Foundry Acceptance''' |
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore]===
| + | ''BS brought up the topic of review for OBO Foundry acceptance. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks'' |
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| − | 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.
| + | ''Asked if we have one ontology or two? We have one, because all have same id space (PO). We have been using the word 'namespace' to mean a branch of the ontology, which is really a line in the obo stanza generated by OboEdit. Namespace may mean something different in the Obo Foundry. The default namespace for the PO is still plant ontology. We should be careful in how we refer to parts of the PO. For example, GO has been merged into one file, but old literature says there were three ontologies, so that is how people still talk about it. BS will send a copy of OBO foundry principles so we can check if we are in compliance and what needs to be done.'' |
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| − | Suggest is_a shoot system.
| + | ''By email after the call: BS sent us a link to the list of principles: [[http://www.obofoundry.org/wiki/index.php/OBO_Foundry_Principles OBO_Foundry_Principles]] and then CM sent:"Use the list here": [[http://www.obofoundry.org/wiki/index.php/Category:Accepted Accepted]]'' |
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| − | '''Proposed def.:''' A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.
| + | =Issues arising from last week's meeting:= |
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| − | participates_in gametophytic phase, develops_from gametophore bud
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| − | 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.
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| − | subset for bryophytes
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud]===
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| − | The term "bud" has been requested:
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| − | 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
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| − | Suggest a new term '''gametophore bud'''. This could be a child of bud (PO:0000055: An undeveloped shoot system).
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| − | '''Proposed def'n:''' A bud that develops into a gametophore.
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| − | Comment: Occurs in mosses and leaf liverworts. Develops from a caulonema cell in mosses.
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| − | participates_in gametophytic phase, has_part gametophore apical cell
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| − | synonym: brown bud
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3257063&group_id=76834&atid=835555 thallus]===
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| − | From Parihar: A simple vegetative plant body not differentiated into root, stem and leaf, and lacking vascular tissues.
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| − | From Schofeld: A flattened gametophore in which no leaf-like organs dominate the structure.
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| − | 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.
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| − | '''proposed def:''' A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
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| − | 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.
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| − | Add '''prothallium''' as a broad synonym of thallus and as a narrow synonym of whole plant.
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| − | ===Other gametophyte terms===
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| − | 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.
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| − | ==[https://sourceforge.net/tracker/?func=detail&aid=3234956&group_id=76834&atid=835555 apical cell]==
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| − | 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'''.
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| − | Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.
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| − | 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 obsoleting PO:0004000 and replacing it with the new term'''embryonic apical cell''' for clarity, and using the name '''apical cell''' for the general class of apical cells described below.
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| − | '''Definition of apical cell from Esau:''' The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.
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| − | '''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.
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| − | 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).
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| − | '''Proposed def. of apical cell:''' A single meristematic cell at the tip of a shoot axis apex, leaf apex, root apex, or thallus apex.
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| − | Comment: Occurs in bryophytes and some pteridophytes, where apical growth results from division of a single meristematic cell located at the tip of an apical meristem or plant organ, rather than from a population of meristematic cells located at the tip of an 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 or thalli). An apical cell is established upon the first cell division of an embryo or germination of a spore.
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| − | -note: the last sentence of the comment allows us to classify an embryonic apical cell as an apical cell.
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| − | Suggested ontology structure for the children of apical cell:
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| − | [[File:apical_cell1.jpg]]
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| − | The dotted lines represent relations inferred by the reasoner.
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| − | 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.
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| − | ===New terms and definitions for apical cells===
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| − | '''gametophytic apical cell:''' An apical cell that is part of a whole plant in the gametophytic phase.
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| − | Comment: Occurs in mosses and other bryophytes.
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| − | intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase
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| − | '''sporophytic apical cell:''' An apical cell that is part of a whole plant in the sporophytic phase.
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| − | Comment: Occurs in pteridophytes and the sporophyte of bryophytes.
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| − | intersection_of: is_a apical cell, intersection_of: participates_in sporophytic phase
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| − | '''thallus apical cell''': An apical cell that is part of a thallus.
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| − | part_of thallus
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| − | '''root apical cell''': A sporophytic apical cell that is part of a root apical meristem.
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| − | comment: Only occurs in the sporophytic phase of vascular plants.
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| − | part_of root apical meristem
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| − | '''shoot apical cell''': An apical cell that is part of a shoot system.
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| − | comment: May occur in shoot axes or leaves of bryophytes or ferns.
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| − | part_of shoot system
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| − | '''gametophore apical cell''': A shoot apical cell that is part of a gametophore.
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| − | comment: Occurs in the non-vascular shoot system of the gametophyte of mosses.
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| − | intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore
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| − | '''leaf apical cell''': A shoot apical cell that is part of a leaf apex.
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| − | comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some mosses. Only in plants where leaf growth is apical.
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| − | part_of leaf
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| − | '''non-vascular leaf apical cell''': A leaf apical cell that is part of a leaf apex of a non-vascular leaf.
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| − | comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.
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| − | part_of non-vasucular leaf; synonym: phyllid apical cell
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| − | '''vascular leaf apical cell''': A leaf apical cell that is part of the leaf apex of a vascular leaf.
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| − | comment: Occurs in vascular leaves of some ferns in their sporophytic phase.
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| − | part_of vascular leaf
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| − | '''shoot axis apical cell:''' An apical cell at the tip of a shoot apical meristem.
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| − | Comment: Divides to produces leaf initial cells and other stem tissues.
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| − | part_of shoot apical meristem
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| − | '''gametophore axis apical cell''': A shoot axis apical cell at the tip of a gametophore axis.
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| − | Comment: Occurs at the tips of the stems and branches of bryophytes.
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| − | part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell
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| − | '''vascular shoot axis apical cell''': A shoot axis apical cell at the tip of a shoot apical meristem in a vascular shoot system.
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| − | Comment: Occurs in some ferns in their sporophytic phase.
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| − | part_of vascular_shoot system; synonym: fern shoot axis apical cell
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| − | Also:
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| − | '''embryonic apical cell (replaces PO:0004000)''': An apical cell that is part of an embryo and is the uppermost cell formed after the first division of the zygote.
| + | ==[http://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo (PO:0009009)]== |
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| − | Comment: For plants that grow via an apical cell in their sporophytic phase, the embryonic apical cell may remain meristematic throughout the plant's life.
| + | '''current definition:''' A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues. |
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| − | ==Plant organs:==
| + | Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants. |
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185162&group_id=76834&atid=835555 cauloid]===
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| − | - This is the term used for the gametophore stem or axis.
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| − | Suggest using '''gametophore axis''' as primary name, cauloid as synonym.
| + | This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex. |
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| − | '''Proposed def'n:''' A shoot axis that is part of a gametophore.
| + | Logically, an embryo could be treated like a sporophyte or gametophyte, that is, a whole plant in the embryonic life cycle phase. However, since we don't have embryonic phase yet, and so much research is done on embryos, it seems appropriate to pre-compose the term embryo and use that for now. |
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| − | Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.
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| − | intersection_of: is_a plant axis, intersection_of: part_of gametophore
| + | '''Proposed definition of plant embryo:''' A whole plant in the early part of a sporophytic phase after the first cell division. |
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| − | Add caulome as synonym of shoot axis
| + | Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa. |
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| − | -Also suggest adding terms for '''gametophore stem''' and '''gametophore branch'''.
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| | + | ''Proposed definition is workable for now. In the comment, we should be more specific about the end of the embryonic phase in different taxa, to the extent that we know about it. We discussed that the word 'early' is quite vague, but we can't say pre-seedling stage- restricted to seed plants'' |
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| − | '''gametophore stem''': A stem that is part of a gametophore. | + | ''We discussed the possibility of describing the end of the embryonic phase as 'before any organs or non-embryonic organs are formed'. Problems: Cotyledons are formed in pteridophyte embryos (and many seed plants too), and they are organs. Also, the foot in a bryophyte or pteridophyte organ.'' |
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| − | is_a stem, part_of gametophore
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| | + | ''new proposed comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.'' |
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| − | '''gametophore branch''': A branch that is part of a gametophore.
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| − | is_a branch, part_of gametophore
| + | ''Can we say when the embryonic phase ends for cultured embryos? Yes, when roots and shoots form'' |
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| | + | [[File:embryo terms 4-14-11.jpg]] |
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| − | -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).
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perigonial bract]===
| + | '''Other issues:''' |
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| − | - The specialized phyllids surrounding the antheridia. | + | *on 4-12-11, PJ suggested we could add zygotic embryo- the one in the seed and also a cultured one. Also, we need haploid embryo as child of cultured embryo? Do haploid embryos ever form in nature? |
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| − | Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
| + | ''We discussed whether or not the original intent was to describe an embryo derived from a zygote and grown in culture? BS suggested it would be better to call it: "cultured zygote-derived (plant) embryo", as the name 'zygotic embryo' is a little misleading, because it implies that it is an embryo that is a zygote. May want to rename "zygote-derived embryo" or similar, but should keep (cultured) zygotic embryo as synonym because it is widely used.'''' |
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| − | 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.
| + | ''Need to add the term: zygotic (plant) embryo, is_a plant embryo, then 'cultured zygote-derived (plant) embryo' is_a zygotic (plant) embryo, and is_a cultured embryo.'' |
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| − | '''Proposed def'n:''' A bract that subtends an antheridium. | + | ''We will also add 'haploid embryo' (microspore-derived HE?) as child of cultured embryo. Needs to be defined. Can add the naturally arising one later if needed.'' |
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| − | part_of gametophore, participates in gametophytic phase
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| − | 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.
| + | '''*adventitious embryo''' (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells |
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3234965&group_id=76834&atid=835555 foot]===
| + | Is this always true? Need to check on it. |
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| − | Moss Ontology definition: The base of the sporophytes in mosses
| + | ''It was suggested that adventitious embryo should be a synonym for somatic embryo, or maybe a child of somatic embryo. LC pointed out that adventitious embryos are really those embryos that arise where embryos normally would not arise, i.e.: on the edges of leaves on Kalanchoe or ferns. There was general agreement on this.'' |
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| − | '''Proposed name and def.: sporophyte foot:''' A plant organ that is the base of a whole plant in the sporophytic phase and attaches it to the gametophore. (ref: Schofeld) | + | ''DS pointed out that somatic or adventitious embryos are all embryos that are derived from apogamy, so we could use the word apogamy in the definition for clarity.'' |
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| | + | ''Adventitious embryo should be merged into the new term 'somatic plant embryo' Need to work on the definition of 'somatic plant embryo'.'' |
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| − | Comment: Found in bryophytes and some pteridophytes. In mosses, the foot is located below the seta. In ferns, the foot is formed from the upper hypobasal quandrant of the embryo. The sporophyte foot serves for both attachment and absorption. The outer portion of the foot is composed of absorptive transfer cells. (ref: Crum)
| + | ''Note: BS: We need to remember to put 'plant' in the all these names.'' |
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| − | 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).
| + | *Note: Adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization. |
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| − | ==Additional organ related moss terms:== | + | Suggest that we rework the definition of [https://sourceforge.net/tracker/index.php?func=detail&aid=3030027&group_id=76834&atid=835555 sporophytic phase] with a comment about apogamy. see SF tracker and/or future meeting: |
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| − | 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.
| + | ==[https://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555 cultured plant embryo and its children]== |
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| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perichaetal bract]===
| + | '''*cultured plant embryo (PO:0000010):''' |
| | | | |
| − | '''Proposed def'n:''' A bract that subtends an archegonium. part_of gametophore
| + | Current Def’n: In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). [source: TAIR:ki] Comment: None |
| | | | |
| − | 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.
| + | Rename: cultured plant embryo (PO:0000010) |
| | | | |
| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185171&group_id=76834&atid=835555 gametophytic perianth]===
| + | Proposed def’n: A plant embryo that is grown or maintained in vitro. |
| | | | |
| − | '''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?).
| + | Comment: Includes isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). |
| | | | |
| − | Should it be surrounds the capsule, in case no calyptra is present?
| + | parentage: is_a plant embryo (PO:0009009) and is_a in vitro plant structure |
| | | | |
| − | -has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)
| + | PJ: We should we have a cultured zygotic embryo, any annotation to cultured ZE should go there |
| | | | |
| − | 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.
| + | ''see the discussion above about this'' |
| | | | |
| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3185175&group_id=76834&atid=835555 seta]===
| |
| − | -The stalk of a moss sporophyte.
| |
| | | | |
| − | '''Proposed def.:''' A plant axis that that holds up a spore capsule. participates_in sporophytic phase | + | '''*cultured somatic embryo: (PO:0000011):''' Child of cultured plant embryo |
| | | | |
| − | Comment: Found in some bryophytes, especially mosses.
| + | Current Def’n: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote. |
| | | | |
| − | ===[https://sourceforge.net/tracker/?func=detail&aid=3272612&group_id=76834&atid=835555 antheridiophore and archegoniophore]===
| + | Proposed def’n: A plant somatic embryo that is grown or maintained in vitro. |
| | | | |
| − | These are stalks that hold up the antheridia or archegonia in Marchantiales (liverworts)
| + | new proposed def’n: A plant embryo arising from previously differentiated somatic cells ''in vitro'', rather than from the zygote or from gametes. |
| | | | |
| − | '''Proposed definitions:''' | + | ''is_a: plant embryo, and need a new term "somatic (plant) embryo"'' |
| | | | |
| − | '''antheridiophore:''' A plant axis that bears two or more antheridia.
| |
| | | | |
| − | participates_in gametophytic phase
| + | ''See new proposed definition of embryo above.'' |
| | | | |
| − | Comment: Found in Marchantiales.
| + | ==[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]== |
| | | | |
| − | '''archegoniophore:''' A plant axis that bears two or more archegonia.
| + | ===Definition of embryonic plant structure:=== |
| | | | |
| − | participates_in gametophytic phase
| + | '''embryonic plant structure''' (PO:0025099): A plant structure that is part of an embryo. |
| | | | |
| − | Comment: Found in Marchantiales. | + | 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. |
| | | | |
| | | | |
| − | Will also add terms for '''antheridium stalk''' and '''archegonium stalk''' for stalks that hold up a single antheridium or archegonium. part_of antheridium or archegonium
| + | 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, because technically an embryo is an embryonic plant structure. |
| | | | |
| − | ==Cardinal organ parts==
| + | ''We discussed how to deal with structures that are part of an embryo when the plant is in the embryonic phase but are also part of a plant after it passes out of the embryonic phase, like hypocotyl root junction or coleorhiza.'' |
| − | Terms requested by MO:
| |
| | | | |
| − | * '''[https://sourceforge.net/tracker/?func=detail&aid=3234979&group_id=76834&atid=835555 calyptra]'''
| + | ''Ideally, we would define embryonic plant structure as "A plant structure that is part of an embryo when a plant is in the embryonic phase," but we don't have a mechanism whereby the reasoner could infer that. Humans may know that a radicle is part of an embryo when the plant is an embryo and part of a seedling when a plant is a seedling, but the reasoner could only infer it after an annotation is made, and only if the user specified the phase that the structure was taken from. Since we can't count on that, and we don't yet have embryonic phase and seedling phase, it is not a practical solution for now.'' |
| | | | |
| − | 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.
| + | ''An alternative solution is to specify sibling terms like embryonic radicle and seedling radicle, with the correct part_of or participates_in relations. We will try this, because there are only 5-10 terms where this should be necessary. We should add appropriate develops from relations (e.g., seedling radicle develops_from embyronic radicle).'' |
| | | | |
| − | We also have a request (from PJ) for calyptra, which encloses the fruit in Eucalyptus. That term should be named '''perianth calyptra''' (see below under operculum), and this term should be named '''spore capsule calyptra''', to distinguish them.
| + | ===Some terms were left as is_a children of embryonic plant structure:=== |
| | | | |
| − | '''Proposed name and def.: spore capsule calyptra:''' A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium. | + | '''embryo proper''' (PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor. |
| | | | |
| − | Comment: Found in bryophytes and pteridophytes (''according to Parihar''). The calyptra ia a membranous or hairy cap or hood 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.
| + | '''scutellum''' (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae. |
| | | | |
| − | participates_in gametophytic phase, develops_from venter (more specific) or archegonium (more general)?
| + | '''suspensor''' (PO:0020108): An embryonic plant structure at the base of an embryo that develops from a basal cell and connects an embryo proper to the wall of a megagametophyte. |
| | | | |
| − | subsets for bryophytes, pteridophytes
| + | ===New definitions for embryonic plant cells and tissues=== |
| | + | Both now have cross-product definitions, and no asserted is_a children |
| | | | |
| − | [From Smith p. 39: calyptra develops from venter in Corsiniaceae (also has an involucre); also p. 52, p. 67, See picture on p. 77 | + | '''[http://sourceforge.net/tracker/index.php?func=detail&aid=3177665&group_id=76834&atid=835555 embryonic plant cell]''' (PO:0025028): A plant cell that is part of an embryo. |
| | | | |
| | + | is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo |
| | | | |
| − | * '''[https://sourceforge.net/tracker/?func=detail&aid=3234981&group_id=76834&atid=835555 venter]'''
| |
| | | | |
| − | This term was not suggested by Moss Ontology, but perhaps we should add it.
| + | Made apical cell (PO:0004000, now embryonic apical cell) is_a apical cell part_of embryo (still dev_from zygote). Should probably obsolete and replace with new term to avoid confusion |
| | | | |
| − | '''proposed def.:''' A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.
| + | Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote) |
| | | | |
| − | part_of archegonium | + | Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo. |
| | | | |
| − | subsets for bryophytes, pteridophytes, gymnosperms
| |
| | | | |
| | + | '''(portion of) embryonic plant tissue''' (PO:0025233): A portion of plant tissue that is part of an embryo. |
| | | | |
| − | *'''[https://sourceforge.net/tracker/?func=detail&aid=3234985&group_id=76834&atid=835555 archegonium neck]'''
| + | is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo |
| | | | |
| − | This term was not suggested by Moss Ontology, but perhaps we should add it.
| + | Should we add the '''portion of''' prefix to the name? |
| | | | |
| − | '''proposed def.:''' A cardinal organ part that is the elongated apica part of an archegonium.
| + | coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049) are now inferred children of embryonic plant tissue. |
| | | | |
| − | 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
| + | Technically, we could get rid of the is_a embryonic plant structure relation for both, because it would be inferred, but is makes it easier to work with the reasoner off when the relations are there. |
| | | | |
| − | (can also add term for neck canal cell when we deal with cells)
| |
| | | | |
| − | subsets for bryophytes, pteridophytes, gymnosperms
| + | Here is a picture of some plant tissues, to show how it works: |
| | | | |
| | + | [[File:Embryonic plant structure2.jpg]] |
| | | | |
| − | *'''[https://sourceforge.net/tracker/?func=detail&aid=3241725&group_id=76834&atid=835555 base]'''
| + | ===Proposed changes/questions for structures that were is_a embryonic plant structure:=== |
| | | | |
| − | '''Proposed name and def.: sporangium base''': A cardinal organ part that is the basal part of a sporangium. | + | ''Discussion of specific terms was postponed until the next meeting. For more details please see [http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_4-26-11#embryonic_plant_structures next week's agenda]'' |
| | | | |
| − | Comment: Term used in mosses and other bryophytes (what about pteridophytes?). The sporangium base is the sterile part of the sporangium below the theca. If swollen and distinct from the rest of the sporangium, it is called an apophysis or hypophysis. (ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition)
| + | '''coleoptile''' (PO:0020033) |
| | | | |
| − | part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis
| + | '''coleorhiza''' (PO:0020034) |
| | | | |
| − | subsets for bryophytes
| + | '''hypocotyl''' (PO:0020100) |
| | | | |
| | + | '''epicotyl''' (PO:0020035) |
| | | | |
| − | *'''[https://sourceforge.net/tracker/?func=detail&aid=3241737&group_id=76834&atid=835555 theca]'''
| + | '''mesocotyl''' (PO:0020037) |
| | | | |
| − | Moss Ontology definition: The main body (urn) of a sporangium. Altered from Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
| + | '''hypocotyl-root junction''' PO:0004724 |
| | | | |
| − | We already have the term theca (PO:0009069) to describe paired microsporangia in angiosperms. Maybe we should call that '''anther theca''' and call this term '''sporangium theca:'''.
| + | '''plumule'''(PO:0020032) |
| | | | |
| − | '''Proposed name and def.: sporangium theca:''' A cardinal organ part that is the main body of a sporangium and has spores located in it. | + | '''scutellar node''' (PO:0004708) |
| | | | |
| − | Comment: Term used in mosses and other bryophytes (what about pteridophytes?)
| + | '''embryonic root''' (PO:0000045) |
| | | | |
| − | part_of sporangium
| + | '''radicle''' (PO:0020031) |
| | | | |
| − | subsets for bryophytes, maybe pteridophytes
| + | '''embryonic leaf''' (PO:0006338) |
| | | | |
| | + | =New Physcomitrella and related terms= |
| | + | ==Collective plant structures:== |
| | + | ''Discussion of specific terms was postponed until the next meeting. For more details please see [http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_4-26-11#Collective_plant_structures: next week's agenda]'' |
| | | | |
| − | *'''[https://sourceforge.net/tracker/?func=detail&aid=3241747&group_id=76834&atid=835555 peristome]'''
| + | ===[https://sourceforge.net/tracker/?func=detail&aid=3244685&group_id=76834&atid=835555 vascular and non-vascular shoot systems]=== |
| | | | |
| − | Moss Ontology definition: A single or double circle of teeth inside the mouth of a moss sporangium. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition | + | The Moss Ontology did not request these terms, but we may want to add them in order to classify shoot systems. |
| | | | |
| − | '''proposed definition:''' A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth. | + | '''non-vascular shoot system (PO:0030017):''' A shoot system that does not have as part vascular tissue. |
| | | | |
| − | Comment: The peristome is located under the operculum, if an operculum is present. Upon maturity of a capsule, the teeth of the peristome open to release the spores.
| + | 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. |
| | | | |
| − | part_of sporangium
| |
| | | | |
| − | subsets for bryophytes
| + | '''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. |
| | | | |
| − | *'''peristome tooth'''
| + | participates_in sporophytic phase, has_part vascular system |
| | | | |
| − | Not requested by Moss Ontology, but should add it.
| + | ===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore (PO:0030018)]=== |
| | | | |
| − | '''Proposed def:''' A cardinal organ part that is a single lobe or tooth of a peristome. | + | '''Proposed def.:''' A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase. |
| | | | |
| − | Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
| + | participates_in gametophytic phase, develops_from gametophore bud |
| | | | |
| − | part_of peristome
| + | 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. |
| | | | |
| − | subsets for bryophytes
| + | subset for bryophytes |
| | | | |
| | + | ===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud (PO:0030026)]=== |
| | | | |
| − | *Add term for peristome cell? Are they dead at maturity? What kind of cells are they?
| + | 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. |
| | | | |
| − | *'''[https://sourceforge.net/tracker/?func=detail&aid=3241767&group_id=76834&atid=835555 lid/operculum]'''
| + | Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses. |
| | | | |
| − | Moss Ontology definition: Either the lid that blocks the capsule mouth or the apical portion of a sporangium that opens during dehiscence. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition.
| + | participates_in gametophytic phase, has_part gametophore apical cell |
| | | | |
| − | We also have a request (from PJ) for operculum, which is part of the fruit in Eucalyptus. That term should be named fruit operculum, and this term should be named spore capsule operculum, to distinguish them.
| + | synonym: brown bud |
| | | | |
| − | '''Proposed name and def.: spore capsule operculum:''' A cardinal organ part that is the apical part of a spore capsule that separates from the rest of the capsule during dehiscence.
| + | ===[https://sourceforge.net/tracker/?func=detail&aid=3257063&group_id=76834&atid=835555 thallus (PO:0030027)]=== |
| | | | |
| − | Comment: Found in mosses. May remain partly attached to the rest of the capsule.
| + | '''proposed def:''' A whole plant in the gametophytic phase that has a flat growth form and no distinct organs. |
| | | | |
| − | Synonym: sporangium lid
| + | 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. |
| | | | |
| − | part_of sporangium
| + | ===Other gametophyte terms=== |
| | | | |
| − | subsets for bryophytes
| + | 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. |
| − | | |
| − | ===Also add these terms for angiosperms:===
| |
| − | | |
| − | '''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 fruit operculum]:''' A cardinal organ part that is the apical part of a capsular fruit that separates from the rest of the capsule (the fruit calyptra) during dehiscence. apical part of a circumsesile fruit.
| |
| − | part_of fruit
| |
| − | | |
| − | The top part of the bud where the perianth (petals) is fused. Leaves fruit underneath it. Operculum is underneath that
| |
| − | | |
| − | Comment: Found in Eucalyptus.
| |
| − | | |
| − | Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?
| |
| − | | |
| − | '''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 perianth calyptra]:''' A collective plant structures that is composed of fused perianth parts and located on tops of a gynoecium that contains an inferior ovary.
| |
| − | | |
| − | Comment: Found in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit.
| |
| − | | |
| − | ==Other related terms for mosses, not from Moss Ontology==
| |
| − | | |
| − | *'''[https://sourceforge.net/tracker/?func=detail&aid=3241816&group_id=76834&atid=835555 spore capsule mouth]'''
| |
| − | | |
| − | '''Proposed definition:''' A plant anatomical space that is the opening on the apical end of a spore capsule.
| |
| − | | |
| − | Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.
| |
| − | | |
| − | part_of sporangium
| |
| − | | |
| − | subsets for bryophytes
| |
| − | | |
| − | | |
| − | *'''[https://sourceforge.net/tracker/?func=detail&aid=3241820&group_id=76834&atid=835555 epiphragm]'''
| |
| − | | |
| − | Schofeld says it is a "membranelike expansion of the columella covering most of the mouth of the sporangium in Polytrichidae (hair cap mosses)."
| |
| − | | |
| − | From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."
| |
| − | | |
| − | '''Proposed definition:''' A portion of parenchyma tissue that forms a circular membrane extending from a spore capsule collumella and attached to the ends of the peristome teeth that covers a spore capsule mouth.
| |
| − | | |
| − | Comment: Present in some moss species of the family Polytrichaceae.
| |
| − | | |
| − | Synonym: tympanum, epiphram
| |
| − | | |
| − | subsets for bryophytes
| |
| − | | |
| − | | |
| − | *'''[https://sourceforge.net/tracker/?func=detail&aid=3241827&group_id=76834&atid=835555 pseudopodium]'''
| |
| − | | |
| − | From Crum: "An elongation of the gametophytic axis on which the capsule is borne in Sphagnum and Andreaea."
| |
| − | | |
| − | From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
| |
| − | | |
| − | '''Proposed definition:''' A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.
| |
| − | | |
| − | Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
| |
| − | | |
| − | participates_in gametophytic phase
| |
| − | | |
| − | subsets for bryophytes
| |
| − | | |
| − | | |
| − | ==[https://sourceforge.net/tracker/index.php?func=detail&aid=3132600&group_id=76834&atid=835555 Sporangium]==
| |
| − | | |
| − | We currently have the class '''sporangium''' (PO:0025094), which is a cardinal organ part. | |
| − | | |
| − | In bryophytes, the sporangium is a plant organ. In seed plants, it is a cardinal organ part (part of a sporophyll). In ferns, it grows on the surface of a leaf. Would it be legitimate to say that in seed plants, the sporangium is a reduced organ that is located in another organ?
| |
| − | | |
| − | Current def: A hollow cardinal organ part in which spores are produced. [source: ISBN:0716710072]
| |
| − | | |
| − | Comment: May be multicellular or unicellular. In bryophytes, particularly in mosses, a sporangium is referred to as a capsule
| |
| − | | |
| − | | |
| − | We also have:
| |
| − | | |
| − | '''megasporangium''' (PO:0025201): A sporangium in which megaspores are produced. [source: ISBN:0716710072]
| |
| − | | |
| − | '''microsporangium''' (PO:0025202): A sporangium in which microspores are produced. [source: ISBN:0716710072]
| |
| − | | |
| − | '''nucellus''' (PO:0020020): A megasporangium in a seed plant, composed of fleshy subepidermal tissue inside an ovule and surrounding a megasporocyte. [source: POC:rw]
| |
| − | | |
| − | Comment: In seed plants, the megaspores and megagametophyte are retained within the nucellus.
| |
| − | | |
| − | '''pollen sac''' (PO:0025277): A microsporangium that is part of a sporophyll where the pollen grains developed and are contained after they develop. [source: POC:curators]
| |
| − | | |
| − | Comment: A pollen sac is a microsporangium in seed plants. In angiosperms, a single, unfused pollen sac may contain an anther locule or several pollen sacs may fuse so they contain a single anther locule.
| |
| − | | |
| − | | |
| − | '''Proposed def. nucellus:''' A megasporangium in a seed plant, composed of fleshy subepidermal tissue ''located in'' an ovule and surrounding a megasporocyte.
| |
| − | | |
| − | '''Proposed def. pollen sac:''' A microsporangium that is ''located in'' a sporophyll and where the pollen grains developed and are ''located'' after they develop. [source: POC:curators]
| |
| − | | |
| − | (comments stay the same)
| |
| − | | |
| − | We could continue to use the more general part_of relation for located_in
| |
| − | | |
| − | ==Sporangium parts==
| |
| − | | |
| − | This is continued from our discussion at the [[POC_Conf._Call_3-8-11]]
| |
| − | | |
| − | Currently classes like exothecium, endothecium, primary parietal cell layer and tapetum are part of anther wall (PO:0000002). However, these layers and their constituent cell types can be part of any sporangium, not just an anther. Proposed making them part of a general class sporangium wall (as we did for parts of leaf).
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| − | | |
| − | From Smith:
| |
| − | | |
| − | Liverworts: Embryo divides to form outer layer (ampithecium) that gives rise to jacket layer and inner mass (endothecium) that gives rise to archesporium (cells of which divide to produce sporocytes and nurse cell, may also produce elators).
| |
| − | | |
| − | Hornworts: Embryo divides to form ampithecium that gives rise to jacket layer and primiary sporogenous layer, and endothecium that gives rise to sterile columella in all but one species (where it gives rise to sporagenous tissue). Jacket layer is 4-6 cells thick, and outer layer develops into epidermis. Sporagenous tissue gives rise to sporocytes and filaments of sterile cells called pseudoelators.
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| − | | |
| − | Sphagnum: Upper tier of cells in the embryo divides to form endothecium that gives rise to sterile columella and ampithecium that gives rise to outer sterile layer and inner archesporium. Archesporium gives rise to sporogenous layer two to four cells thick. Outer sterile layer gives rise to jacket layer 3 or 4 cells thick.
| |
| − | | |
| − | Eubrya: Early division of capsule gives rise to multilayered ampithecium and endothecium (with ampithecial cells and endothecial cells). Endothecium (usually) gives rise to archesporium and columella. Columella cells adjacent to archesporium remain small and develop into inner spore sac. Ampithecium develops into a multilayered structure, including layers with and without chloroplasts and an epidermis.
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| − | | |
| − | Psilophyta: Paired sporangia (a synangium or maybe a reduced sporangiophore) develop from a single cell. First cell division leads to a jacket initial and an archesporial (primary sporogenous) cell. Repeated periclinal divisions of jacket initial lead to jacket layer four or five cells thick and divisions of archesporial cell lead to many sporogenous cells. No tapetum develops. Near maturity, irregular clumps of sporogenous tissue divide to give rise to spore mother cells, remainder disintegrate
| |
| − | | |
| − | Lycopods: Sporangia borne on sporophylls.
| |
| − | | |
| − | ==Plant Cells==
| |
| − | | |
| − | Terms requested by MO:
| |
| − | | |
| − | ===archesporial cell===
| |
| − | | |
| − | We have the terms:
| |
| − | | |
| − | '''female archesporial cell''' (PO:0006015): In the majority of flowering plants including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]
| |
| − | | |
| − | '''male archesporial cell''' (PO:0006014): It undergoes periclinal divisions, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]
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| − | | |
| − | | |
| − | | |
| − | Suggest new term for archesporial cell (for homosporous plants), plus revised definitions of male and female archesporial cell.
| |
| − | | |
| − | Proposed definitions:
| |
| − | | |
| − | '''archesporial cell''' A plant cell that gives rise to a sporocyte.
| |
| − | | |
| − | Comment: May be part of an archesporium.
| |
| − | | |
| − | | |
| − | '''female archesporial cell''' (PO:0006015): A plant cell that is part of a megasporangium and divides to give rise to a megasporocyte.
| |
| − | | |
| − | Comment: Found in heterosporous ferns and seed plants. In the majority of flowering plants, including Arabidopsis, the female archesporial cell elongates and polarizes longitudinally, and directly differentiates into the megasporocyte or megaspore mother cell (MMC). In some flowering plants, it undergoes a periclinal division, and subsequently the inner cell differentiates into the megasporocyte. [source: PMID:10465788]
| |
| − |
| |
| − | | |
| − | '''male archesporial cell''' (PO:0006014): A plant cell that is part of a microsporangium and divides to gives rise to a microsporocyte.
| |
| − | | |
| − | Comment: Male archesporial cell may undergo periclinal division, giving rise to an inner primary sporogenous cell (PSC) layer and an outer primary parietal cell (PPC). [source: GR:pj, PMID:10465788]
| |
| − | | |
| − | ===alar cell===
| |
| − | | |
| − | ===brachycyte===
| |
| − | | |
| − | chloronema cell - done
| |
| − | | |
| − | caulonema cell - done
| |
| − | | |
| − | ===tmema cell===
| |
| − | | |
| − | ===jacket layer cell===
| |
| − | | |
| − | ===axillary hair terminal cell===
| |
| − | | |
| − | ===axillary hair base cell===
| |
| − | | |
| − | ===neck canal cell===
| |
| − | | |
| − | ===side branch initial===
| |
| − | | |
| − | | |
| − | ===Other cell types, not requested by MO:===
| |
| − | | |
| − | hyrdoid
| |
| − | | |
| − | leptoid
| |
| − | | |
| − | rhizoid initial
| |
| − | | |
| − | ==Plant Tissues==
| |
| − | | |
| − | ===paraphyllium=== Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
| |
| − | | |
| − | Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."
| |
| − | | |
| − | Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.
| |
| − | | |
| − | Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.
| |
| − | | |
| − | '''Proposed definition:''' A plant organ/portion of plant tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.
| |
| − | | |
| − | Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.
| |
| − | | |
| − | [[File:Paraphyllia.jpg]] The paraphyllia are the small, dark structures between the leaves.
| |
| − | | |
| − | | |
| − | ===midrib/costa===
| |
| − | Moss Ontology definition: The nerve of a phyllid. Altered from Bill and Nancy Malcolm (2006)
| |
| − | | |
| − | We have term midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary] (which, by the way, should just say phyllome, instead of leaf or leaf-like organ). However, midvein is_a leaf vein, which is a portion of vascular tissue, so it cannot apply to mosses.
| |
| − | | |
| − | We should have a term that groups conductive tissue together for both vascular and non-vascular plants, kind of like we have axial cell for vascular and non-vascular conductive cells.
| |
| − | | |
| − | New child of portion of plant tissue: portion of axial tissue:
| |
| − | | |
| − | | |
| − | (also, we need to redefine phloem to be more like definition of xylem, and not based on function)
| |
| − | (need to redefine axial cell so it doesn't say vascular cell)
| |
| − | | |
| − | ===rhizoid===
| |
| − | | |
| − | archesporium
| |
| − | | |
| − | amphithecium
| |
| − | | |
| − | endothecium
| |
| − | | |
| − | jacket layer
| |
| − | | |
| − | paraphysis
| |
| − | | |
| − | axilliary hair
| |
| − | | |
| − | tmema
| |
| − | | |
| − | =Continuing User requests: for PSO=
| |
| − | | |
| − | - Deal with and complete the list of user requests on SourceForge-
| |
| − | | |
| − | ==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]==
| |
| − | | |
| − | submitted by Austin Mast
| |
| − | | |
| − | Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
| |
| − | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3165981&group_id=76834&atid=835555 fascicle] The term fascicle can refer to different structures in different taxa. Suggest we use the term '''floral fascicle''' or '''flower fascicle''' in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.
| |
| − | | |
| − | From Tucker, 2003, Flora:
| |
| − | (in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in
| |
| − | that two to several flowers are initiated in each bract axil rather than
| |
| − | just one as in a raceme. '''The cluster of flowers at each node is called a fascicle.''' The order of initiation among flowers at a node (Fig. 5B, Psoralea macrostachys DC) shows
| |
| − | '''the fascicle to be a short shoot topped by a second order inflorescence apical meristem'''. This meristem initiates
| |
| − | flowers in a bilaterally symmetrical order: a single abaxial flower, then
| |
| − | two lateral flowers, another median abaxial, then two more laterals. The
| |
| − | number of flowers per fascicle depends on the duration of the axillary
| |
| − | inflorescence apex of the short shoot, which ceases activity after
| |
| − | initiating the few flowers in the fascicle. No flowers are initiated
| |
| − | adaxially (toward the first order axis) on the short shoot (Tucker, 1987b;
| |
| − | Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be
| |
| − | distinguished from a cyme in that every flower is bract subtended in a
| |
| − | pseudoraceme."
| |
| − | | |
| − | '''Proppsed def:''' A second order inflorescence in which the second order inflorescence branch bears two or more flowers but is not elongated. Comment: A fascilce appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Common in some sections of the Fabaceae.
| |
| − | | |
| − | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle] (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
| |
| − | | |
| − | We added the term stipule spine. Could also add the term '''stipule bristle''': A stipule that has a brush-like appearance.
| |
| − | | |
| − | Alternative is to suggest bristled to PATO
| |
| − | | |
| − | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]
| |
| − | | |
| − | '''Proppsed def:''' A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
| |
| − | | |
| − | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]
| |
| − | | |
| − | '''Banner''' (as in a legume flower) - suggest using name 'banner petal'
| |
| − | | |
| − | '''Proppsed def:''' A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.
| |
| − | | |
| − | | |
| − | '''Wing''' (as in a legume flower) - suggest using name 'wing petal'
| |
| − | | |
| − | '''Proppsed def:''' One of two petals that is adjacent to the banner petal in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner petal and the corolla keel.
| |
| − | | |
| − | | |
| − | '''Keel''' (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name 'corolla keel'
| |
| − | | |
| − | Suggest three new terms:
| |
| − | | |
| − | '''fused petal:''' A petal that is fused to another petal.
| |
| − | | |
| − | Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).
| |
| − | | |
| − | | |
| − | '''fused corolla:''' A corolla in which the petals are fused.
| |
| − | | |
| − | Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.
| |
| − | | |
| − | | |
| − | '''corolla keel:''' A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae.
| |
| − | | |
| − | Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.
| |
| − | | |
| − | ==TraitNet requests==
| |
| − | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]
| |
| − | | |
| − | proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
| |
| − | | |
| − | child of stem (PO:0009047).
| |
| − | | |
| − | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]
| |
| − | | |
| − | Their comment: is synonym to Tubercle
| |
| − | | |
| − | podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
| |
| − | | |
| − | tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
| |
| − | | |
| − | proposed def:
| |
| − | | |
| − | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]
| |
| − | | |
| − | definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
| |
| − | | |
| − | proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.
| |
| − | | |
| − | | |
| − | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore]
| |
| − | | |
| − | definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.
| |
| | | | |
| − | We could add this term as a kind of upper level bin term (similar to trichome)
| + | =Upcoming meetings 2011:= |
| | | | |
| | + | '''[http://www.iplantcollaborative.org/2011/02/09/2011-semantic-web-workshop-june-6-7-santa-fe-nm 2011 Semantic Web Workshop] June 6th and 7th, Santa Fe, NM. |
| | + | ''' |
| | | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone]
| + | Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services. |
| | | | |
| − | Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
| + | -JE and JP will be attending |
| | | | |
| | + | -JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward. |
| | | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3080922&group_id=76834&atid=835555 sorus] | + | For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web]. |
| | | | |
| − | from Crum (2001): a cluster of fern sporangia
| |
| − | from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
| |
| | | | |
| − | Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.
| + | '''* ICBO 2011 Second International Conference on Biomedical Ontology''' |
| | + | July 26-30, 2011 |
| | + | Buffalo, New York |
| | | | |
| − | Part_of vascular leaf, has_part sporangium
| + | [http://icbo.buffalo.edu ICBO] |
| | | | |
| | + | LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" |
| | + | along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland. |
| | | | |
| − | [https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]
| + | '''Full-Day Workshops Schedule:''' |
| | | | |
| − | Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
| + | '''July 26 9am-6pm''' The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies |
| | | | |
| − | tendrils can derived from multiple types of structures. Suggest we make separate terms:
| + | '''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability |
| | | | |
| − | branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.
| + | '''July 26 6.30pm-9pm''' Evening Workshop: Common Logic |
| | | | |
| − | leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
| + | '''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium |
| | | | |
| − | leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.
| + | - LC will attend and represent the PO. Invite other plant people? |
| | | | |
| − | leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.
| |
| | | | |
| − | Can add other types of tendrils if they come up or users need them.
| |
| | | | |
| − | ==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
| + | '''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn''' |
| | | | |
| − | submitted by Rich Zobel (Nov 2009)
| + | [http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011] |
| | | | |
| − | ==User requests still open on Source Forge; PGDSO ==
| + | Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13. |
| − | ===[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]===
| |
| | | | |
| − | This item has been open on SF since 6/2009
| + | Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster. |
| | | | |
| − | I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
| + | TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part. |
| | | | |
| − | Suggested stages:
| + | For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''. |
| | | | |
| − | -sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
| |
| | | | |
| − | -tuber initiation
| |
| | | | |
| − | -tuber growth
| + | '''* International Botanical Congress (IBC2011)''' |
| | | | |
| − | -tuber maturation | + | July 23rd-30th 2011, Melbourne, Australia''' |
| | | | |
| − | How we work these in will depend on restructuring of PGDSO
| + | Registration is open [http://www.ibc2011.com/Dates.htm Important dates] |
| | | | |
| − | l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
| + | Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30. |
| | | | |
| − | ===[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed development stages]===
| + | Dennis, Alejandra, Pankaj and Ramona are planning to attend. |
| | | | |
| − | This is a fairly new request for terms for cotton
| + | See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details |
| | | | |
| | =Next meeting scheduled for Tues, Apr. 26th, 2011 at 10am PDT= | | =Next meeting scheduled for Tues, Apr. 26th, 2011 at 10am PDT= |
POC meeting, Webex Conference Call; Date: Tuesday Apr 19th, 2011 10am (PDT)
In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Barry Smith (University at Buffalo, NY), Justin Preece (OSU), Justin Elser (OSU), Dennis Stevenson (NYBG),
Absent: Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University), Chris Mungall (Lawrence Berkeley National Lab),
Collaborators: none
Acceptance of the minutes from the POC_Conf._Call_4-14-11? There were no changes, additions or deletions.
Tech issues:
*Update on the OBO to OWL conversion:
JE now has an owl version of the live plant_ontology file that has the definitions and other information. It is available at: http://palea.cgrb.oregonstate.edu/svn/Poc/tags/live/plant_ontology.owl
Still working with Damon and Shuly on getting the SSWAP components to work properly from their end.
'PO will host the owl file and the SSWAP components of it (?), they have software that enables us to do it. (need more accurate details)
* progress on has_parts?
Currently, the existing has parts in the ontology do not seem to be causing any problems, now that we removed the reciprocal relations. The problem still exists that the annotations do not flow in the right direction.
JE still needs a test file that has fewer terms and annotations, because testing with the live version takes about 10 hours to load.
*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?
JE was able to modify the drop down menu on the Amigo browser to say "plant anatomy" instead of "plant structure" while we spoke.
*Review for OBO Foundry Acceptance
BS brought up the topic of review for OBO Foundry acceptance. He suggested that the PO can be submitted for OBO Foundry membership within the next weeks
Asked if we have one ontology or two? We have one, because all have same id space (PO). We have been using the word 'namespace' to mean a branch of the ontology, which is really a line in the obo stanza generated by OboEdit. Namespace may mean something different in the Obo Foundry. The default namespace for the PO is still plant ontology. We should be careful in how we refer to parts of the PO. For example, GO has been merged into one file, but old literature says there were three ontologies, so that is how people still talk about it. BS will send a copy of OBO foundry principles so we can check if we are in compliance and what needs to be done.
By email after the call: BS sent us a link to the list of principles: [OBO_Foundry_Principles] and then CM sent:"Use the list here": [Accepted]
Issues arising from last week's meeting:
current definition: A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.
Comment: Adventitious embryos and somatic embryos do not arise from zygotes. Cultured embryos (PO:0000010), including haploid embryos, are in vitro plant structures. Embryos occur prior to germination in vascular plants.
This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.
Logically, an embryo could be treated like a sporophyte or gametophyte, that is, a whole plant in the embryonic life cycle phase. However, since we don't have embryonic phase yet, and so much research is done on embryos, it seems appropriate to pre-compose the term embryo and use that for now.
Proposed definition of plant embryo: A whole plant in the early part of a sporophytic phase after the first cell division.
Comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, embryos that arise through apogamy and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. In seed plants, the embryonic phase ends with germination. In non-seed plants and cultured embryos of seed plants, the end of the embryonic phase is less clearly defined and varies among taxa.
Proposed definition is workable for now. In the comment, we should be more specific about the end of the embryonic phase in different taxa, to the extent that we know about it. We discussed that the word 'early' is quite vague, but we can't say pre-seedling stage- restricted to seed plants
We discussed the possibility of describing the end of the embryonic phase as 'before any organs or non-embryonic organs are formed'. Problems: Cotyledons are formed in pteridophyte embryos (and many seed plants too), and they are organs. Also, the foot in a bryophyte or pteridophyte organ.
new proposed comment: An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryonic phase varies among taxa. In seed plants, the embryonic phase ends with germination. In pteridophytes, the embryonic phase ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryonic phase ends when the apical cell stops dividing and the sporangium begins to develop.
Can we say when the embryonic phase ends for cultured embryos? Yes, when roots and shoots form
Other issues:
- on 4-12-11, PJ suggested we could add zygotic embryo- the one in the seed and also a cultured one. Also, we need haploid embryo as child of cultured embryo? Do haploid embryos ever form in nature?
We discussed whether or not the original intent was to describe an embryo derived from a zygote and grown in culture? BS suggested it would be better to call it: "cultured zygote-derived (plant) embryo", as the name 'zygotic embryo' is a little misleading, because it implies that it is an embryo that is a zygote. May want to rename "zygote-derived embryo" or similar, but should keep (cultured) zygotic embryo as synonym because it is widely used.''
Need to add the term: zygotic (plant) embryo, is_a plant embryo, then 'cultured zygote-derived (plant) embryo' is_a zygotic (plant) embryo, and is_a cultured embryo.
We will also add 'haploid embryo' (microspore-derived HE?) as child of cultured embryo. Needs to be defined. Can add the naturally arising one later if needed.
*adventitious embryo (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells
Is this always true? Need to check on it.
It was suggested that adventitious embryo should be a synonym for somatic embryo, or maybe a child of somatic embryo. LC pointed out that adventitious embryos are really those embryos that arise where embryos normally would not arise, i.e.: on the edges of leaves on Kalanchoe or ferns. There was general agreement on this.
DS pointed out that somatic or adventitious embryos are all embryos that are derived from apogamy, so we could use the word apogamy in the definition for clarity.
Adventitious embryo should be merged into the new term 'somatic plant embryo' Need to work on the definition of 'somatic plant embryo'.
Note: BS: We need to remember to put 'plant' in the all these names.
- Note: Adventitious embryos, somatic embryos, embryos that arise through apogamy, and cultured haploid embryos, embryos cannot be considered in the sporophytic phase (as it it defined now), since they are not the product of fertilization.
Suggest that we rework the definition of sporophytic phase with a comment about apogamy. see SF tracker and/or future meeting:
*cultured plant embryo (PO:0000010):
Current Def’n: In vitro isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte). [source: TAIR:ki] Comment: None
Rename: cultured plant embryo (PO:0000010)
Proposed def’n: A plant embryo that is grown or maintained in vitro.
Comment: Includes isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte).
parentage: is_a plant embryo (PO:0009009) and is_a in vitro plant structure
PJ: We should we have a cultured zygotic embryo, any annotation to cultured ZE should go there
see the discussion above about this
*cultured somatic embryo: (PO:0000011): Child of cultured plant embryo
Current Def’n: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.
Proposed def’n: A plant somatic embryo that is grown or maintained in vitro.
new proposed def’n: A plant embryo arising from previously differentiated somatic cells in vitro, rather than from the zygote or from gametes.
is_a: plant embryo, and need a new term "somatic (plant) embryo"
See new proposed definition of embryo above.
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, because technically an embryo is an embryonic plant structure.
We discussed how to deal with structures that are part of an embryo when the plant is in the embryonic phase but are also part of a plant after it passes out of the embryonic phase, like hypocotyl root junction or coleorhiza.
Ideally, we would define embryonic plant structure as "A plant structure that is part of an embryo when a plant is in the embryonic phase," but we don't have a mechanism whereby the reasoner could infer that. Humans may know that a radicle is part of an embryo when the plant is an embryo and part of a seedling when a plant is a seedling, but the reasoner could only infer it after an annotation is made, and only if the user specified the phase that the structure was taken from. Since we can't count on that, and we don't yet have embryonic phase and seedling phase, it is not a practical solution for now.
An alternative solution is to specify sibling terms like embryonic radicle and seedling radicle, with the correct part_of or participates_in relations. We will try this, because there are only 5-10 terms where this should be necessary. We should add appropriate develops from relations (e.g., seedling radicle develops_from embyronic radicle).
Some terms were left as is_a children of embryonic plant structure:
embryo proper (PO:0000001): An embryonic plant structure that is the body of a developing embryo attached to the maternal tissue in an ovule by a suspensor.
scutellum (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.
suspensor (PO:0020108): An embryonic plant structure at the base of an embryo that develops from a basal cell and connects an embryo proper to the wall of a megagametophyte.
New definitions for embryonic plant cells and tissues
Both now have cross-product definitions, and no asserted is_a children
embryonic plant cell (PO:0025028): A plant cell that is part of an embryo.
is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo
Made apical cell (PO:0004000, now embryonic apical cell) is_a apical cell part_of embryo (still dev_from zygote). Should probably obsolete and replace with new term to avoid confusion
Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)
Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.
(portion of) embryonic plant tissue (PO:0025233): A portion of plant tissue that is part of an embryo.
is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo
Should we add the portion of prefix to the name?
coleorhiza (PO:0020034), embryo cortex (PO:0005014), embryo epidermis (PO:0005015), embryonic shoot apical meristem (PO:0006362), epiblast (PO:0020036), scutellar epithelium (PO:0008048), and scutellum epidermis (PO:0006049) are now inferred children of embryonic plant tissue.
Technically, we could get rid of the is_a embryonic plant structure relation for both, because it would be inferred, but is makes it easier to work with the reasoner off when the relations are there.
Here is a picture of some plant tissues, to show how it works:
Proposed changes/questions for structures that were is_a embryonic plant structure:
Discussion of specific terms was postponed until the next meeting. For more details please see next week's agenda
coleoptile (PO:0020033)
coleorhiza (PO:0020034)
hypocotyl (PO:0020100)
epicotyl (PO:0020035)
mesocotyl (PO:0020037)
hypocotyl-root junction PO:0004724
plumule(PO:0020032)
scutellar node (PO:0004708)
embryonic root (PO:0000045)
radicle (PO:0020031)
embryonic leaf (PO:0006338)
New Physcomitrella and related terms
Collective plant structures:
Discussion of specific terms was postponed until the next meeting. For more details please see next week's agenda
The Moss Ontology did not request these terms, but we may want to add 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.
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
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
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
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.
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.
Upcoming meetings 2011:
2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
-JE and JP will be attending
-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.
For more Workshop details: Semantic web.
* ICBO 2011 Second International Conference on Biomedical Ontology
July 26-30, 2011
Buffalo, New York
ICBO
LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability"
along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
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?
*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.
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
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 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
See IBC 2011 Bio-Ontologies Symposium wiki page for more details
Next meeting scheduled for Tues, Apr. 26th, 2011 at 10am PDT
