Difference between revisions of "POC Conf. Call 4-19-11"

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In attendance:  
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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:
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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.''
  
−
=Issues arising from last week's meeting:=
 
  
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=New Physcomitrella and related terms=
+
=Tech issues:=
−
==Collective plant structures:==
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3244685&group_id=76834&atid=835555 vascular and non-vascular shoot systems]===
 
  
−
The Moss Ontology did not request these terms, but suggest adding them in order to classify shoot systems.
+
'''*Update on the OBO to OWL conversion:'''
  
−
'''non-vascular shoot system:''' A shoot system that does not have as part vascular tissue.
+
''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''
  
−
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.
+
''Still working with Damon and Shuly on getting the SSWAP components to work properly from their end.''
  
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subsets for bryophytes
+
'''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).
+
'''* 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.''
  
−
Child of non-vascular shoot system will be gametophore (see below). A moss sprophyte could also be called a non-vascular shoot system. If we used the lacks_part relation and intersection_of relations, we could make gameotophore a child of shoot system, and the reasoner would infer it was a non-vascular shoot system.
 
  
−
Can't use participates_in gametophytic phase, because the sporophyte of a bryphyte doesn't have roots or vascular tissue.
+
'''*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"
  
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'''vascular shoot system:'''  A shoot system that has as part vascular tissue.
+
-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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comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.
+
-Will also need to be changed on the AmiGO Browser (eg search page)- how difficult is this?
  
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participates_in sporophytic phase, has_part vascular system
+
''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.
+
'''*Review for OBO Foundry Acceptance'''
  
−
'''root-bourne shoot system''' (PO:0004544) should be is_a vascular shoot system
+
''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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===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore]===
+
''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.''
  
−
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.
+
''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]]''
  
−
Suggest is_a shoot system.
+
=Issues arising from last week's meeting:=
  
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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.
+
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo (PO:0009009)]==
  
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participates_in gametophytic phase, develops_from gametophore bud
+
'''current definition:''' A whole plant in the post-zygotic stage that does not yet consist of fully differentiated tissues.
  
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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.
+
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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subset for bryophytes
 
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud]===
+
This is not really consistent with the fact that we have tissues like embryonic epidermis and embryonic cortex.
  
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The term "bud" has been requested:
+
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.
−
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.  
+
'''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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Comment: Occurs in mosses and leaf liverworts. Develops from a caulonema cell in mosses.
+
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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participates_in gametophytic phase, has_part gametophore apical cell
 
  
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synonym: brown bud
+
''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''
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3257063&group_id=76834&atid=835555 thallus]===
+
''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.''
  
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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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''Can we say when the embryonic phase ends for cultured embryos? Yes, when roots and shoots form''
  
 +
[[File:embryo terms 4-14-11.jpg]]
  
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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.
 
  
 +
'''Other issues:'''
  
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'''proposed def:''' A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
+
*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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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.
+
''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.''
  
−
Add '''prothallium''' as a broad synonym of thallus and as a narrow synonym of whole plant.
+
''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.''
  
−
===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.
+
'''*adventitious embryo''' (PO:0004537): Embryo derived directly from nucellus cells without involving embryo sac cells
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3234956&group_id=76834&atid=835555 apical cell]==
+
Is this always true?  Need to check on it.
  
−
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'''.
+
''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'.'' 
  
−
Non-seed vascular plants can also have an apical cell, that is, a single dividing cell at the apex of a root or shoot.  
+
''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.
  
−
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.
+
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:
  
 +
==[https://sourceforge.net/tracker/?func=add&group_id=76834&atid=835555 cultured plant embryo and its children]==
  
−
'''Definition of apical cell from Esau:''' The single initial cell in an apical meristem of root or shoot. Characteristic of many lower vascular plants.
+
'''*cultured plant embryo (PO:0000010):'''
  
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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.
+
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
  
−
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).
+
Rename: cultured plant embryo (PO:0000010)
  
 +
Proposed def’n: A plant embryo that is grown or maintained in vitro.
  
−
'''Proposed def. of apical cell:''' A single meristematic cell at the tip of a shoot axis apex, leaf apex, root apex, or thallus apex.
+
Comment: Includes isolated and maintained mature or immature zygotic embryos, somatic embryos or haploid embryos (derived from male gametophyte).
  
−
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 maybe established upon germination of a spore or upon the first cell division of an embryo or later.
+
parentage: is_a plant embryo (PO:0009009) and is_a in vitro plant structure
  
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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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PJ: We should we have a cultured zygotic embryo, any annotation to cultured ZE should go there
  
 +
''see the discussion above about this''
  
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Suggested ontology structure for the children of apical cell:
 
  
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[[File:apical_cell1.jpg]]
+
'''*cultured somatic embryo: (PO:0000011):'''  Child of cultured plant embryo
  
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The dotted lines represent relations inferred by the reasoner.
+
Current Def’n: An embryo arising from previously differentiated somatic cells in vitro, rather than from fused haploid gametes, i.e., zygote.
  
−
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.
+
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.
  
−
===New terms and definitions for apical cells===
+
''is_a: plant embryo, and need a new term "somatic (plant) embryo"''
  
  
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'''gametophytic apical cell:''' An apical cell that is part of a whole plant in the gametophytic phase.
+
''See new proposed definition of embryo above.''
  
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Comment: Occurs in mosses and other bryophytes.  
+
==[http://sourceforge.net/tracker/index.php?func=detail&aid=3132547&group_id=76834&atid=835555 embryonic plant structures]==
  
−
intersection_of: is_a apical cell, intersection_of: participates_in gametophytic phase
+
===Definition of embryonic plant structure:===
  
 +
'''embryonic plant structure''' (PO:0025099): A plant structure that is part of an embryo.
  
−
'''sporophytic apical cell:''' An apical cell that is part of a whole plant in the sporophytic phase.
+
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.
  
−
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
+
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.''
  
−
'''thallus apical cell''': An apical cell that is part of a thallus.  
+
''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.''
  
−
part_of thallus
+
''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:===
  
−
'''root apical cell''': A sporophytic apical cell that is part of a root apical meristem.
+
'''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: Only occurs in the sporophytic phase of vascular plants.
+
'''scutellum''' (PO:0020110): An embryonic plant structure that is a more or less shield-shaped and absorptive portion of an embryo of Poaceae.
  
−
part_of root apical meristem
+
'''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
  
−
'''shoot apical cell''': An apical cell that is part of a shoot system.
+
'''[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.
  
−
comment: May occur in shoot axes or leaves of bryophytes or ferns.
+
is_a embryonic plant structure, intersection_of: is_a plant cell, intersection_of: part_of embryo
  
−
part_of shoot system
 
  
 +
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
  
−
'''gametophore apical cell''': A shoot apical cell that is part of a gametophore.
+
Made basal cell (PO:0002002, now embryonic basal cell) is_a plant cell, part of embryo (still dev_from zygote)
  
−
comment: Occurs in the non-vascular shoot system of the gametophyte of mosses.
+
Made hypophysis (PO:0020109, now embryonic hypophysis) is_a plant cell, part_of embryo.
  
−
intersection_of: is_a shoot apical cell, intersection_of: part_of gametophore
 
  
 +
'''(portion of) embryonic plant tissue''' (PO:0025233): A portion of plant tissue that is part of an embryo.
  
−
'''leaf apical cell''': A shoot apical cell that is part of a leaf apex.
+
is_a embryonic plant structure, intersection_of: is_a portion of plant tissue, intersection_of: part_of embryo
  
−
comment: Occurs in the non-vascular leaves of bryophytes and the vascular leaves of some mosses. Only in plants where leaf growth is apical.
+
Should we add the '''portion of''' prefix to the name?
  
−
part_of leaf
+
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.
  
  
−
'''non-vascular leaf apical cell''': A leaf apical cell that is part of a leaf apex of a non-vascular leaf.
+
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.
  
−
comment: Occurs in the non-vascular leaves of bryophytes, which grow by division of a single, wedge-shaped apical cell with two cutting faces.
 
  
−
part_of non-vasucular leaf; synonym: phyllid apical cell
+
Here is a picture of some plant tissues, to show how it works:
  
 +
[[File:Embryonic plant structure2.jpg]]
  
−
'''vascular leaf apical cell''': A leaf apical cell that is part of the leaf apex of a vascular leaf.
+
===Proposed changes/questions for structures that were is_a embryonic plant structure:===
  
−
comment: Occurs in vascular leaves of some ferns in their sporophytic phase.
+
''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]''
  
−
part_of vascular leaf
+
'''coleoptile''' (PO:0020033)
  
 +
'''coleorhiza''' (PO:0020034)
  
−
'''shoot axis apical cell:''' An apical cell at the tip of a shoot apical meristem.
+
'''hypocotyl''' (PO:0020100)
  
−
Comment: Divides to produces leaf initial cells and other stem tissues.
+
'''epicotyl''' (PO:0020035)
  
−
part_of shoot apical meristem
+
'''mesocotyl''' (PO:0020037)
  
 +
'''hypocotyl-root junction''' PO:0004724
  
−
'''gametophore axis apical cell''': A shoot axis apical cell at the tip of a gametophore axis.
+
'''plumule'''(PO:0020032)
  
−
Comment: Occurs at the tips of the stems and branches of bryophytes.
+
'''scutellar node''' (PO:0004708)
  
−
part_of gametophore axis; synonym: cauloid apical cell, non-vascular shoot axis apical cell
+
'''embryonic root''' (PO:0000045)
  
 +
'''radicle''' (PO:0020031)
  
−
'''vascular shoot axis apical cell''': A shoot axis apical cell at the tip of a shoot apical meristem in a vascular shoot system.
+
'''embryonic leaf''' (PO:0006338)
  
−
Comment: Occurs in some ferns in their sporophytic phase.
+
=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]''
  
−
part_of vascular_shoot system; synonym: fern shoot axis apical cell
+
===[https://sourceforge.net/tracker/?func=detail&aid=3244685&group_id=76834&atid=835555 vascular and non-vascular shoot systems]===
  
 +
The Moss Ontology did not request these terms, but we may want to add them in order to classify shoot systems.
  
−
Also:
+
'''non-vascular shoot system (PO:0030017):''' A shoot system that does not have as part vascular tissue.
  
−
'''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.
+
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.
  
−
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.
 
  
−
==Plant organs:==
+
'''vascular shoot system (PO:0030016):'''  A shoot system that has as part vascular tissue.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185162&group_id=76834&atid=835555 cauloid]===
+
comment: Has xylem and/or phloem. Occurs only in the sporophytic phase of vascular plants.
−
- This is the term used for the gametophore stem or axis.
 
  
−
Suggest using '''gametophore axis''' as primary name, cauloid as synonym.
+
participates_in sporophytic phase, has_part vascular system
  
−
'''Proposed def'n:''' A shoot axis that is part of a gametophore.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3185093&group_id=76834&atid=835555 gametophore (PO:0030018)]===
  
−
Synonyms: cauloid, gametophyte axis, non-vascular shoot axis (broad, because it can also apply to the seta); participates_in gametophytic phase.
+
'''Proposed def.:''' A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.  
  
−
intersection_of: is_a plant axis, intersection_of: part_of gametophore
+
participates_in gametophytic phase, develops_from gametophore bud
  
−
Add caulome as synonym of shoot axis
+
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.
  
−
-Also suggest adding terms for '''gametophore stem''' and '''gametophore branch'''.
+
subset for bryophytes
  
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3185097&group_id=76834&atid=835555 gametophore bud (PO:0030026)]===
  
−
'''gametophore stem''': A stem that is part of a gametophore.
+
Suggest a new term '''gametophore bud'''. This could be a child of bud (PO:0000055: An undeveloped shoot system).
  
−
is_a stem, part_of gametophore
+
'''Proposed def'n:''' A vegetative bud that develops into a gametophore.
−
 
  
−
'''gametophore branch''': A branch that is part of a gametophore.
+
Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.
  
−
is_a branch, part_of gametophore
+
participates_in gametophytic phase, has_part gametophore apical cell
  
 +
synonym: brown bud
  
−
-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).
+
===[https://sourceforge.net/tracker/?func=detail&aid=3257063&group_id=76834&atid=835555 thallus (PO:0030027)]===
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perigonial bract]===
+
'''proposed def:''' A whole plant in the gametophytic phase that has a flat growth form and no distinct organs.
  
−
- The specialized phyllids surrounding the antheridia.  
+
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.
  
−
Ref: Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
+
===Other gametophyte terms===
  
−
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.
+
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.
−
 
 
−
'''Proposed def'n:''' A bract that subtends an antheridium.
 
−
 
 
−
part_of gametophore, participates in gametophytic phase
 
−
 
 
−
Comment: When an antheridium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually perigonial bracts. If an antheridium occurs on a main axis of the gametophore, usually only the terminal phyllomes are perigonial bracts.
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3234965&group_id=76834&atid=835555 foot]===
 
−
 
 
−
Moss Ontology definition: The base of the sporophytes in mosses
 
−
 
 
−
'''Proposed name and def.: sporophyte foot:''' A plant organ that is the base of a whole plant in the sporophytic phase and attaches it to the gametophore. (ref: Schofeld)
 
−
 
 
−
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)
 
−
 
 
−
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).
 
−
 
 
−
==Additional organ related moss terms:==
 
−
 
 
−
These were not requested by the Physcomitrella group, but they are related to the terms above and are commonly used to describe mosses, so we should add them now.
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185168&group_id=76834&atid=835555 perichaetal bract]===
 
−
 
 
−
'''Proposed def'n:''' A bract that subtends an archegonium. part_of gametophore
 
−
 
 
−
Comment: When an archegonium occurs on a specialized lateral branch of the gametophore, all of the phyllomes on that branch are usually parichaetal bracts. If an archegonium occurs on a main axis of the gametophore, only the terminal phyllomes are usually parichaetal bracts.  The two or three terminal-most perichaetal bracts may fuse to form a gametophytic perianth.
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3185171&group_id=76834&atid=835555 gametophytic perianth]===
 
−
 
 
−
'''Proposed def'n:'''  A collective phyllome structure that consists of two or more of the most distal parachaetal bracts on a gametophore axis and surround the calyptra (capsule?).
 
−
 
 
−
Should it be surrounds the capsule, in case no calyptra is present?
 
−
 
 
−
-has_part parachaetal bract, part_of gametophore, disjoint_from perianth (PO:0009058)
 
−
 
 
−
Comment: The parachaetal bracts may fuse laterally in the gametophytic perianth. The gametophytic perianth is not the same structure as a perianth (PO:0009058) in angiosperms.
 
−
 
 
−
===[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
 
−
 
 
−
Comment: Found in some bryophytes, especially mosses.
 
−
 
 
−
===[https://sourceforge.net/tracker/?func=detail&aid=3272612&group_id=76834&atid=835555 antheridiophore and archegoniophore]===
 
−
 
 
−
These are stalks that hold up the antheridia or archegonia in Marchantiales (liverworts)
 
−
 
 
−
'''Proposed definitions:'''
 
−
 
 
−
'''antheridiophore:''' A plant axis that bears two or more antheridia.
 
−
 
 
−
participates_in gametophytic phase
 
−
 
 
−
Comment: Found in Marchantiales.
 
−
 
 
−
'''archegoniophore:''' A plant axis that bears two or more archegonia.
 
−
 
 
−
participates_in gametophytic phase
 
−
 
 
−
Comment: Found in Marchantiales.
 
−
 
 
−
 
 
−
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
 
−
 
 
−
==Cardinal organ parts==
 
−
Terms requested by MO:
 
−
 
 
−
* '''[https://sourceforge.net/tracker/?func=detail&aid=3234979&group_id=76834&atid=835555 calyptra]'''
 
−
 
 
−
Moss Ontology definition: A membranous or hairy cap or hood that forms from the wall of the archegonium and protects the embryonic sporophyte. It is formed from the archegonium by mitotic divisions, and hence it is haploid. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition and altered from David Cove.
 
−
 
 
−
We also have a request (from PJ) for calyptra, which 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.
 
−
 
 
−
'''Proposed name and def.: spore capsule calyptra:''' A cardinal organ part that develops from the wall of an archegonium and surrounds a sporangium.
 
−
 
 
−
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.
 
−
 
 
−
participates_in gametophytic phase, develops_from venter (more specific) or archegonium (more general)?
 
−
 
 
−
subsets for bryophytes, pteridophytes
 
−
 
 
−
[From Smith p. 39: calyptra develops from venter in Corsiniaceae (also has an involucre); also p. 52, p. 67, See picture on p. 77
 
−
 
 
−
 
 
−
* '''[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.
 
−
 
 
−
'''proposed def.:''' A cardinal organ part that is the enlarged basal part of an archegonium and has an egg cell located in it.
 
−
 
 
−
part_of archegonium
 
−
 
 
−
subsets for bryophytes, pteridophytes, gymnosperms
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3234985&group_id=76834&atid=835555 archegonium neck]'''
 
−
 
 
−
This term was not suggested by Moss Ontology, but perhaps we should add it.
 
−
 
 
−
'''proposed def.:''' A cardinal organ part that is the elongated apica part of an archegonium.
 
−
 
 
−
Comment: Early in development, the neck is occluded by a single row of neck canal cells. At maturity, the neck canal cells disintegrate, creating a canal for the sperm to enter the archegonium.
 
−
 
 
−
part_of archegonium
 
−
 
 
−
(can also add term for neck canal cell when we deal with cells)
 
−
 
 
−
subsets for bryophytes, pteridophytes, gymnosperms
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241725&group_id=76834&atid=835555 base]'''
 
−
 
 
−
'''Proposed name and def.: sporangium base''': A cardinal organ part that is the basal part of a sporangium.
 
−
 
 
−
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)
 
−
 
 
−
part_of sporangium; Synonyms: sporangium neck, apophysis, hypophysis
 
−
 
 
−
subsets for bryophytes
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241737&group_id=76834&atid=835555 theca]'''
 
−
 
 
−
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
 
−
 
 
−
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:'''.
 
−
 
 
−
'''Proposed name and def.: sporangium theca:''' A cardinal organ part that is the main body of a sporangium and has spores located in it.
 
−
 
 
−
Comment: Term used in mosses and other bryophytes (what about pteridophytes?)
 
−
 
 
−
part_of sporangium
 
−
 
 
−
subsets for bryophytes, maybe pteridophytes
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241747&group_id=76834&atid=835555 peristome]'''
 
−
 
 
−
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
 
−
 
 
−
'''proposed definition:''' A cardinal organ part that is a single or double circle of teeth inside a spore capsule mouth.
 
−
 
 
−
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.
 
−
 
 
−
part_of sporangium
 
−
 
 
−
subsets for bryophytes
 
−
 
 
−
 
 
−
*'''peristome tooth'''
 
−
 
 
−
Not requested by Moss Ontology, but should add it.
 
−
 
 
−
'''Proposed def:''' A cardinal organ part that is a single lobe or tooth of a peristome.
 
−
 
 
−
Comment: Peristome teeth may be simple or compound, and may be attached by their tips to the epiphragm.
 
−
 
 
−
part_of peristome
 
−
 
 
−
subsets for bryophytes
 
−
 
 
−
 
 
−
*Add term for peristome cell? Are they dead at maturity? What kind of cells are they?
 
−
 
 
−
 
 
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241767&group_id=76834&atid=835555 lid/operculum]'''
 
−
 
 
−
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.
 
−
 
 
−
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.
 
−
 
 
−
'''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.
 
−
 
 
−
Comment: Found in mosses. May remain partly attached to the rest of the capsule.
 
−
 
 
−
Synonym: sporangium lid
 
  
−
part_of sporangium
+
=Upcoming meetings 2011:=
  
−
subsets for bryophytes
+
'''[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.
 +
'''
  
−
===Also add these terms for angiosperms:===
+
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.
  
−
'''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 fruit operculum]:''' A collective organ part structure that is the apical part of a circumsesile capsular fruit that separates from the rest of the capsule during dehiscence.
+
-JE and JP will be attending
  
−
Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.  
+
-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.  
  
−
part_of fruit
+
For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
  
−
Is is a cardinal organ part (formed from a single carpel) or collective organ part structure (formed from parts of multiple carpels)?
 
  
 +
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York
  
−
'''[https://sourceforge.net/tracker/?func=detail&aid=3241802&group_id=76834&atid=835555 perianth calyptra]:''' A perianth that is composed of fused perianth parts and located on tops of a gynoecium that contains an inferior ovary.
+
[http://icbo.buffalo.edu ICBO]
  
−
Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. May separate from the plant at maturity, exposing the capsular fruit and fruit operculum. Sometimes erroneously referred to as part of a fruit.
+
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.
  
−
==Other related terms for mosses, not from Moss Ontology==
+
'''Full-Day Workshops Schedule:'''
  
−
*'''[https://sourceforge.net/tracker/?func=detail&aid=3241816&group_id=76834&atid=835555 spore capsule mouth]'''
+
'''July 26 9am-6pm''' The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
−
'''Proposed definition:''' A plant anatomical space that is the opening on the apical end of a spore capsule.
+
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
−
Comment: The mouth is formed when the operculum separates from the capsule. The mouth may be covered by a peristome.
+
'''July 26 6.30pm-9pm'''  Evening Workshop: Common Logic
  
−
part_of sporangium
+
'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
  
−
subsets for bryophytes
+
- LC will attend and represent the PO.  Invite other plant people?
  
  
−
*'''[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)."
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
−
From Crum: "A circular membrane at the tip of the columella to which the peristome teeth of the prolytrichaceae are attached."
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
−
'''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.  
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
  
−
Comment: Present in some moss species of the family Polytrichaceae.
+
Gramene will be putting together a workshop again, focusing on pathways.  PJ will present a PO poster.
  
−
Synonym: tympanum, epiphram
+
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
  
−
subsets for bryophytes
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
  
−
*'''[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."
+
'''* International Botanical Congress (IBC2011)'''
  
−
From Schofeld: "An elongated mass of leafless gametophore tissue that pushes the sporophyte beyond the perichaetial leaves (in Andreaea and Sphagnum)."
+
July 23rd-30th 2011, Melbourne, Australia'''
  
−
'''Proposed definition:''' A plant axis that is a leafless extension of a gametophore axis on which a sporophyte is borne.
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]
  
−
Comment: Raises the sporophyte above the perichaetial bracts. Found in Sphagnum and Andreaea.
+
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.  
  
−
participates_in gametophytic phase
+
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
  
−
subsets for bryophytes
+
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=

Latest revision as of 23:49, 25 April 2011

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:

plant embryo (PO:0009009)

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

Embryo terms 4-14-11.jpg


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 and its children

*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.

embryonic plant structures

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:

Embryonic plant structure2.jpg

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

vascular and non-vascular shoot systems

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

gametophore (PO:0030018)

Proposed def.: A non-vascular shoot system that consists of the shoot axes and non-vascular leaves of a plant in the gametophytic phase.

participates_in gametophytic phase, develops_from gametophore bud

Comment: A gametophore is the leafy part of the gametophyte of mosses and leafy liverworts, excluding the protonema. Develop from buds that form on the protonema. Antheridia and archegonia arise on the gametophore.

subset for bryophytes

gametophore bud (PO:0030026)

Suggest a new term gametophore bud. This could be a child of bud (PO:0000055: An undeveloped shoot system).

Proposed def'n: A vegetative bud that develops into a gametophore.

Comment: Occurs in mosses and leafy liverworts. Develops from a caulonema cell in mosses.

participates_in gametophytic phase, has_part gametophore apical cell

synonym: brown bud

thallus (PO:0030027)

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

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