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| − | This page is under construction.....
| + | ==Release announcements== |
| | + | '''January 21, 2011''' |
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| | + | The latest release (Version #14) of the Plant Ontology is now available on our [http://plantontology.org Ontology Browser]. |
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| − | [[Summary of Changes to PO Jan2011]]
| + | This release is aimed at restructuring the Plant Structure Ontology to accommodate all plants. |
| − | ==List of Obsoleted Terms==
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| − | * pollen tube (PO:0006345) [http://www.plantontology.org/amigo/go.cgi?session_id=5689b1294171797&view=assoc&search_constraint=terms&query=PO:0006345&page=94 97 pages of annotations:all from ''Arabidopsis'']
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| − | * pollen tube tip (PO:0000028) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=8476b1294171984&view=assoc&query=PO%3A0000028&search_constraint=terms 9 annotations from ''Arabidopsis'']
| + | For more information about the release and details on the changes made to the ontology, please visit: [[Summary of Changes to PO Jan2011]] |
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| − | * root hair (PO:0000256) [http://www.plantontology.org/amigo/go.cgi?session_id=9177b1294172354&view=assoc&search_constraint=terms&query=PO:0000256&page_size=all ~100 annotations from various sources]
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| − | * root hair tip (PO:0000029) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=4940b1294172538&view=assoc&query=PO%3A0000029&search_constraint=terms 1 annotation from ''Arabidopsis'']
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| − | * floral epidermis (PO:0008043) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=158b1294173248&view=assoc&query=PO%3A0008043&search_constraint=terms 1 annotation from ''Arabidopsis'']
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| − | * floral stomatal complex (PO:0008044) No Annotations
| + | '''January 7, 2011''' |
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| − | * elongation zone (PO:0020125) (replaced by root elongation zone (PO:0025181) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=1646b1294179675&view=assoc&query=PO%3A0020125&search_constraint=terms ~40 annotations, all from ''Arabidopsis'']
| + | A [http://beta.plantontology.org:8080/amigo/go.cgi beta version] of the new Plant Ontology file is available for internal review. For this release, the former plant_anatomy.obo and plant_structure.obo files have been merged into one file (plant_ontology.obo). |
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| − | *papillae (PO:0002001) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=1797b1294180398&view=assoc&query=PO%3A0002001&search_constraint=terms 6 annotations from ''Arabidopsis'']
| + | About 10 terms have been obsoleted or renamed/redefined. This may impact annotations from TAIR, MaizeGBD, Gramene and SGN . See [[New_terms_and_obsolete_terms_for_Jan2011_release]], where it is possible to review the changes, with links to the annotation pages and suggestions as to where the annotations should be moved to. |
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| − | * trichome branch (PO:0008031) (replaced by 'multicellular trichome branch cell' in PO plus unicellular trichome branch in GO):No Annotations
| + | ==Summary of Changes== |
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| − | *differentiation zone (PO:0020135)-(replaced by root differentiation zone; PO:0020135)
| + | For more information about the release, please visit our wikipage with a [[Summary of Changes to PO Jan2011]]. |
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| − | *basal endosperm transfer layer (PO:0009019) (created new term with same name, but new def'n and id) No annotations
| + | You can also view a list of [[new terms and obsolete terms for Jan2011 release]] |
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| | + | ==How to Provide Feedback== |
| | | | |
| | + | You can send feedback via email from our [http://beta.plantontology.org:8080/db/feedback/send_feedback Feedback link]. This is available in the upper left corner of any page on the beta browser. If you have comments on a specific page or term, please include the url of the page/term you are referring to in the appropriate box of the feedback form. Be sure to include your email on the feedback form, so we can contact you with any questions. |
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| | + | You can also contact us at po-discuss@plantontology.org. |
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| − | | + | All comments from the feedback page go to the po-discuss mailing list. Archives of this list are available at the [http://mailman.cgrb.oregonstate.edu/pipermail/po-discuss/ po-discuss archive]. |
| − | "Got rid of pore and slit, and made their chilren direct children of plant anatomical space" were these terms- can't find them on live site or on dev
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| − | '''To be Obsoleted?:'''
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| − | *primary root elongation zone (PO:0003003) [http://www.plantontology.org/amigo/go.cgi?taxid=all&species_db=all&ev_code=aca&show_associations=direct&session_id=4638b1294180703&view=assoc&query=PO%3A0003003&search_constraint=terms ~40 annotations from ''Arabidopsis'', 1 from ''Oryza'']
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| − | *Lateral root elongation zone (PO:0003014) [http://www.plantontology.org/amigo/go.cgi?view=assoc&search_constraint=terms&depth=0&query=PO:0003014&session_id=5563b1294180915&show_associations=list 4 annotations from ''Arabidopsis'']
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| − | * leaf abaxial epidermis ?
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| − | * leaf adaxial epidermis?
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| − | ==List of New Terms-general:==
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| − | * '''plant anatomical entity''' (PO:0025131): An anatomical entity (CARO:0000000) that is or was part of a plant.
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| − | *''' plant anatomical space''' (PO:0025117): An anatomical space (CARO:0000005) that is part of a plant.
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| − | * '''axil''' (child of plant anatomical space) , made
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| − | * '''leaf axil''' (PO:0009023)
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| − | * '''branch axil''' (PO#)
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| − | * '''bract axil''' (PO#) (children of axil).
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| − | * '''reproductive shoot system''' (PO:0025082): A shoot system in the sporophytic phase that has as part at least one sporangium.
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| − | * '''gynoecium ridge''' (PO:0025088): A gynoecium in the early stages of development, characterized as a ridge on the abaxial surface of the floral meristem that develops from a gynoecium primordium.
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| − | * '''dehiscence zone''' (PO:0025092): A portion of plant tissue that is part of a plant structure and consists of a narrow band of cells that undergoes dehiscence upon maturation of the structure.
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| − | * '''primordium''' (PO:0025127)
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| − | * '''phyllome primordium'''
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| − | * '''root parenchyma''' (PO:0025095): A portion of parenchyma tissue that is part of a root system.
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| − | * '''stele'''
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| − | * '''shoot axis stele'''
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| − | * '''branch stele'''
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| − | * '''stem stele'''
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| − | Added new terms sporangium (already there, but didn’t have definition), microsporangium, megasporangium. Made nucellus child of megasporangium. Renamed old microsporangium pollen sac and made it a child of new microsporangium. May need to obsolete old term and add new one.
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| − | | |
| − | ==New terms- cells==
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| − | * '''pollen tube cell''' (PO:0025195): A plant cell that develops from a vegetative cell and forms a tubular extension of the pollen grain. [source: POC:rw] Comment: Carries the male gametes to into or near the ovule. May be branched in gymnosperms. See GO for pollen tube and pollen tube tip. (need to add GO term ids)
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| − | * '''papilla cell''' (PO:0025166): An epidermal pavement cell with a short protuberance. [source: POC:curators] Comment: See GO for the subcellular component papilla.(need to add GO term ids)
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| − | * '''stigma papilla cell''' (PO:0025168):
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| − | * '''leaf papilla cell''' (PO:0025167):
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| − | * '''archegonium egg cell'''
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| − | * '''embryo sac egg cell'''
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| − | * '''antheridium sperm cell'''
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| − | * '''pollen sperm cell'''
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| − | | |
| − | ==List of new terms: trichome==
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| − | * '''trichome''' (PO:0000282) not new?
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| − | * '''multicellular trichome'''
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| − | * '''trichome cell'''
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| − | * '''multicellular trichome branch'''
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| − | * '''multicellular trichome branch cell''' (replaces trichome branch)
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| − | * '''bract trichome'''
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| − | * '''carpel trichome'''
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| − | * '''stem trichome'''
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| − | * '''branch trichome'''
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| − | * '''phyllome trichome (PO:0025186)''' (parent to leaf trichome; existing?)
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| − | * '''sepal trichome (PO:0025182)'''
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| − | * '''petal trichome (PO:0025187)'''
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| − | * '''tepal trichome (PO:0025188)'''
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| − | | |
| − | * '''phyllome epidermis'''
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| − | * '''stem epidermis'''
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| − | * '''branch epidermis'''
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| − | .
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| − | | |
| − | * '''thorn'''
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| − | * '''prickle''' (PO:0025169)
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| − | * leaf prickle (PO:0025175)
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| − | * root prickle (PO:0025170)
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| − | * shoot axis prickle (PO:0025171)
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| − | | |
| − | * '''spine'''
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| − | ==new terms- elongation and differentiation zones:==
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| − | * plant axis differentiation zone (PO:0025119)
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| − | * plant axis differentiation zone (PO:0025119)
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| − | * root differentiation zone (PO:0020135); renamed (obsoleted?) old term differentiation zone (PO:0020135)
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| − | | |
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| − | '''On dev browser 1-4-11:'''
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| − | new:
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| − | * '''branch internode differentiation zone''' (PO:0025103): A shoot internode differentiation zone that is part of a branch internode.
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| − | * '''plant axis differentiation zone''' (PO:0025119): A cardinal organ part that is part of a plant axis and is located behind the
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| − | * '''shoot internode differentiation zone''' (PO:0025102): A plant axis differentiation zone that is part of a shoot axis.
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| − | * '''root differentiation zone''' (PO:0020135): A plant axis differentiation zone that is the part of a root and is located behind a root elongation zone.(renamed)
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| − | | |
| − | Old:
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| − | * '''lateral root differentiation zone''' (PO:0003016): A root differentiation zone that is part of a lateral root elongation zone and contains cells that are differentiating into their final form and function.
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| − | * '''primary root differentiation zone''' (PO:0003015): A root differentiation zone that is part of a primary root.
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| − | | |
| − | * '''stem internode differentiation zone''' ; PO:0008042 [show def][view annotations]
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| − | * '''root elongation zone''' (PO:0025181): (because definition of elongation zone was incorrect and added new term, new id)
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| − | * '''elongation zone'''
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| − | * '''plant axis elongation zone'''(PO:0025180)
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| − | | |
| − | Questions about:
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| − | * '''differentiation zone''' not new??? (see PO:0020135)
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| − | | |
| − | ==List of Terms stomatal complex:==
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| − | * stomatal complex
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| − | * phyllome stomatal complex
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| − | * leaf stomatal complex
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| − | * petiole stomatal complex
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| − | | |
| − | * leaf lamina stomatal complex
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| − | * leaf lamina abaxial stomatal complex
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| − | * leaf lamina adaxial stomatal complex
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| − | | |
| − | * petiole abaxial stomatal complex
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| − | * petiole adaxial stomatal complex
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| − | | |
| − | * root nodule meristem (PO:0025194): A root meristem that gives rise to a root nodule.
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| − | * basal endosperm transfer layer (PO:0025196) (replaces PO:0009019, with same name): A portion of plant tissue that is part of an endosperm and is composed of basal endosperm transfer cells. [source:POC:rw]
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| − | | |
| − | ==List of Renamed Terms==
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| − | * Secretory trichome was renamed glandular trichome
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| − | * seed trichome was made the primary name for PO:0004511, (changed seed hair to exact synonym, added pubescence as related synonym)
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| − | * root differentiation zone (PO:0020135; renaming of old term differentiation zone)
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| − | Changed valve to fruit valve, and updated definition and parent.
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| − | Updated name, definition and parent of Poaceae hull.
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Release announcements
January 21, 2011
The latest release (Version #14) of the Plant Ontology is now available on our Ontology Browser.
This release is aimed at restructuring the Plant Structure Ontology to accommodate all plants.
For more information about the release and details on the changes made to the ontology, please visit: Summary of Changes to PO Jan2011
January 7, 2011
A beta version of the new Plant Ontology file is available for internal review. For this release, the former plant_anatomy.obo and plant_structure.obo files have been merged into one file (plant_ontology.obo).
About 10 terms have been obsoleted or renamed/redefined. This may impact annotations from TAIR, MaizeGBD, Gramene and SGN . See New_terms_and_obsolete_terms_for_Jan2011_release, where it is possible to review the changes, with links to the annotation pages and suggestions as to where the annotations should be moved to.
Summary of Changes
For more information about the release, please visit our wikipage with a Summary of Changes to PO Jan2011.
You can also view a list of new terms and obsolete terms for Jan2011 release
How to Provide Feedback
You can send feedback via email from our Feedback link. This is available in the upper left corner of any page on the beta browser. If you have comments on a specific page or term, please include the url of the page/term you are referring to in the appropriate box of the feedback form. Be sure to include your email on the feedback form, so we can contact you with any questions.
You can also contact us at po-discuss@plantontology.org.
All comments from the feedback page go to the po-discuss mailing list. Archives of this list are available at the po-discuss archive.
