Difference between revisions of "Release 19"
From Plant Ontology Wiki
Jump to navigationJump to search| (99 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
| − | + | =Summary and Announcements= | |
| − | + | The latest release of the Plant Ontology, version #19, is available on our [http://www.plantontology.org/amigo/go.cgi Plant Ontology Browser]. | |
| − | + | This full release features the addition of 35 new terms, for both the ''Plant Anatomical Entity'' (20) and ''Plant Structure Development Stage'' (15) branches. It also includes new and updated annotation data for <i>Oryza sativa</i>, <i>Vitis vinifera</i>, <i>Gossypium hirsutum</i> and <i>Arabidopsis thaliana</i>. | |
| + | This release also includes a new feature: Japanese translations displayed on the browser for the ''Plant Anatomical Entity'' terms. | ||
| − | + | The release features revision to the following sections: | |
| − | |||
| − | = | + | =Revisions to the ''plant anatomical entity'' branch:= |
| − | + | * A new parent term for all types of ''tuber'' (PO:0025522) has been created. This encompasses those tubers derived from branches; ''shoot axis tuber'' (PO:0004543), and those that arise from roots; ''tuberous root tuber'' (new term; PO:0025476). Data associated with tubers from plants such Cassava (''Manihot esculenta'') or sweet potato (''Ipomoea batatas''), should be annotated to the new term ''tuberous root tuber'' (PO:0025476), while that associated with tubers derived from a ''branch'' (PO:0025073), as found in potatoes (Solanum spp.) and yams (Dioscorea spp.), should use the one of the two subclasses of the term ''shoot axis tuber'' (PO:0004543); either ''aerial tuber'' (PO:0004548), or ''subterranean tuber'' (PO:0004547). | |
| − | + | * A new general term for all types of ''spermatogenous cell'' (PO:0025525) has been added to the Plant Ontology. For data annotations in liverworts, hornworts and mosses, please use the term ''spermatogenous cell''. For angiosperm species, please use the more specific term ''generative cell'' (PO:0020097), and for gymnosperms, the new term ''body cell'' (PO:0025526). | |
| − | + | * New terms to describe shape of the ''phyllome lamina'' (PO:0025396) and ''leaf lamina'' (PO:0020039) were added: | |
| + | ** ''phyllome lamina lobe'' (PO:0025514) | ||
| + | ** ''phyllome lamina tooth'' (PO:0025515) | ||
| + | ** ''phyllome lamina crena'' (PO:0025516) | ||
| + | ** ''leaf lamina lobe'' (PO:0025517) | ||
| + | ** ''leaf lamina tooth'' (PO:0025518) | ||
| + | ** ''leaf lamina crena'' (PO:0025519) | ||
| − | + | If you are annotating to the latter three terms (describing ''leaf lamina''), please add an additional annotation to ''vascular leaf'' (PO:0009025) or ''non-vascular leaf'' (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes (ferns) should go to ''vascular leaf'' (PO:0009025) and all annotations for bryophytes should go to ''non-vascular leaf'' (PO:0025075). | |
| − | + | * The term ''plant gametangium'' has been renamed ''multicellular plant gametangium'' (PO:0025124) and a new child term created: ''unicellular plant gametangium'' (PO:0025521). This allows users to differentiate between the gametangia that are plant organs and the ones which are a single cell, such as those that occur in some green alga, such as Ulva. | |
| − | |||
| − | '''PO: | + | * Major revisions were done to the sections describing the ''multicellular plant gametangia'' (PO:0025124): ''archegonium'' (PO:0025126) and ''antheridium'' (PO:0025125) and their parts. |
| − | |||
| − | |||
| − | + | These revisions included the addition of four new cell types: | |
| + | ** archegonium central cell (PO:0025509) | ||
| + | ** archegonium initial cell (PO:0025510) | ||
| + | ** prothallial cell (PO:0025533) | ||
| + | ** ventral canal cell (PO:0025524) | ||
| − | + | ==Revisions to the ''Plant Structure Development Stage branch== | |
| − | + | * A new parent term was created: '''whole plant fruit development stage (PO:0025500)''' to encompass the classes: '''whole plant fruit formation stage (PO:0007042)''' and '''whole plant fruit ripening stage (PO:0007010)'''. This branch describes the stages of a fruiting cycle for a whole plant that begins when the plant starts to produce fruit and ends when all of the fruit on the plant are ripe, or the plant enters a senescent or dormant stage before all the fruit is ripe. Note this is not to describe the development of individual fruits, but the whole plant. | |
| − | + | * '''whole plant fruit formation stage (PO:0007042)''': renamed from '5 fruit formation stage' and child terms were renamed and the definitions were revised: | |
| + | ** whole plant fruit formation stage up to 10% (PO:0007032) | ||
| + | ** whole plant fruit formation stage 10 to 30% (PO:0007009) | ||
| + | ** whole plant fruit formation stage 30 to 50% (PO:0007029) | ||
| + | ** whole plant fruit formation stage 50 to 70% (PO:0007007) | ||
| + | ** whole plant fruit formation stage 70% to final size (PO:0007027) | ||
| + | * '''whole plant fruit ripening stage (PO:0007010)''': renamed from '6 ripening stage' and child terms were renamed and the definitions were revised: | ||
| + | ** beginning of whole plant fruit ripening stage (PO:0007036) | ||
| + | ** early whole plant fruit ripening stage (PO:0007001) | ||
| + | ** mid whole plant fruit ripening stage (PO:0007031) | ||
| + | ** late whole plant fruit ripening stage (PO:0007050) | ||
| + | ** whole plant fruit ripening complete stage (PO:0007038) | ||
| − | ''' | + | * A new parent term was created '''shoot system development stage (PO:0025527)'''to encompass the stages of development of various child terms of the shoot system: |
| + | ** '''bud development stage (PO:0025528)''' | ||
| + | *** bud dormancy stage (PO:0025529) | ||
| + | *** bud swell stage (PO:0025531) | ||
| + | *** bud burst stage PO:0025532 | ||
| − | + | * Added new term: '''reproductive shoot system development stage (PO:0025530) '''and revised the two existing child terms: | |
| + | ** flower development stage (PO:0007615) | ||
| + | ** inflorescence development stage (PO:0001083) | ||
| − | + | * The parent term '''fruit development stage (PO:0001002)''' was revised and 2 new child terms were added to describe the stages of ripening of individual fruits: '''fruit formation stage (PO:0025501)''' and '''fruit ripening stage (PO:0025502)'''. | |
| + | * New children of fruit formation stage (PO:0025501: | ||
| + | ** fruit size up to 10% stage (PO:0025504) | ||
| + | ** fruit size 10 to 30% stage (PO:0025505) | ||
| + | ** fruit size 30 to 50% stage (PO:0025506) | ||
| + | ** fruit size 50 to 70% stage (PO:0025507) | ||
| + | ** fruit size 70% to final size stage (PO:0025508) | ||
| − | + | * Children of '''fruit ripening stage (PO:0025502)''': will be added in the next round of revisions | |
| + | =New or expanded Annotation Files= | ||
| + | * <i>Oryza sativa</i> rice: [[Rice_LCM_Aya_et_al,_2011]] | ||
| + | * <i>Vitis vinifera</i> grape: [[Vitis_vinifera;_grape]] | ||
| − | + | * <i>Gossypium hirsutum</i> cotton- [http://www.agbase.msstate.edu/ AgBase] | |
| − | |||
| − | > | ||
| − | |||
| − | > | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| + | =Other Changes= | ||
| + | * Many terms have updated definitions which include the PO:ids- for full details please see the [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=log SVN site] and the [[Details_of_Changes_in_PO_Release_19]] | ||
| + | |||
| + | * [[New_terms_and_obsolete_terms_Release_19]] | ||
| − | * | + | * For more information and to view a summary of the release statistics, please visit: [http://archive.plantontology.org/docs/release_notes/releasenotes19.html Plant Ontology Release #19 Jan 2013]. |
Latest revision as of 01:00, 18 April 2014
Summary and Announcements
The latest release of the Plant Ontology, version #19, is available on our Plant Ontology Browser.
This full release features the addition of 35 new terms, for both the Plant Anatomical Entity (20) and Plant Structure Development Stage (15) branches. It also includes new and updated annotation data for Oryza sativa, Vitis vinifera, Gossypium hirsutum and Arabidopsis thaliana.
This release also includes a new feature: Japanese translations displayed on the browser for the Plant Anatomical Entity terms.
The release features revision to the following sections:
Revisions to the plant anatomical entity branch:
- A new parent term for all types of tuber (PO:0025522) has been created. This encompasses those tubers derived from branches; shoot axis tuber (PO:0004543), and those that arise from roots; tuberous root tuber (new term; PO:0025476). Data associated with tubers from plants such Cassava (Manihot esculenta) or sweet potato (Ipomoea batatas), should be annotated to the new term tuberous root tuber (PO:0025476), while that associated with tubers derived from a branch (PO:0025073), as found in potatoes (Solanum spp.) and yams (Dioscorea spp.), should use the one of the two subclasses of the term shoot axis tuber (PO:0004543); either aerial tuber (PO:0004548), or subterranean tuber (PO:0004547).
- A new general term for all types of spermatogenous cell (PO:0025525) has been added to the Plant Ontology. For data annotations in liverworts, hornworts and mosses, please use the term spermatogenous cell. For angiosperm species, please use the more specific term generative cell (PO:0020097), and for gymnosperms, the new term body cell (PO:0025526).
- New terms to describe shape of the phyllome lamina (PO:0025396) and leaf lamina (PO:0020039) were added:
- phyllome lamina lobe (PO:0025514)
- phyllome lamina tooth (PO:0025515)
- phyllome lamina crena (PO:0025516)
- leaf lamina lobe (PO:0025517)
- leaf lamina tooth (PO:0025518)
- leaf lamina crena (PO:0025519)
If you are annotating to the latter three terms (describing leaf lamina), please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes (ferns) should go to vascular leaf (PO:0009025) and all annotations for bryophytes should go to non-vascular leaf (PO:0025075).
- The term plant gametangium has been renamed multicellular plant gametangium (PO:0025124) and a new child term created: unicellular plant gametangium (PO:0025521). This allows users to differentiate between the gametangia that are plant organs and the ones which are a single cell, such as those that occur in some green alga, such as Ulva.
- Major revisions were done to the sections describing the multicellular plant gametangia (PO:0025124): archegonium (PO:0025126) and antheridium (PO:0025125) and their parts.
These revisions included the addition of four new cell types:
- archegonium central cell (PO:0025509)
- archegonium initial cell (PO:0025510)
- prothallial cell (PO:0025533)
- ventral canal cell (PO:0025524)
Revisions to the Plant Structure Development Stage branch
- A new parent term was created: whole plant fruit development stage (PO:0025500) to encompass the classes: whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010). This branch describes the stages of a fruiting cycle for a whole plant that begins when the plant starts to produce fruit and ends when all of the fruit on the plant are ripe, or the plant enters a senescent or dormant stage before all the fruit is ripe. Note this is not to describe the development of individual fruits, but the whole plant.
- whole plant fruit formation stage (PO:0007042): renamed from '5 fruit formation stage' and child terms were renamed and the definitions were revised:
- whole plant fruit formation stage up to 10% (PO:0007032)
- whole plant fruit formation stage 10 to 30% (PO:0007009)
- whole plant fruit formation stage 30 to 50% (PO:0007029)
- whole plant fruit formation stage 50 to 70% (PO:0007007)
- whole plant fruit formation stage 70% to final size (PO:0007027)
- whole plant fruit ripening stage (PO:0007010): renamed from '6 ripening stage' and child terms were renamed and the definitions were revised:
- beginning of whole plant fruit ripening stage (PO:0007036)
- early whole plant fruit ripening stage (PO:0007001)
- mid whole plant fruit ripening stage (PO:0007031)
- late whole plant fruit ripening stage (PO:0007050)
- whole plant fruit ripening complete stage (PO:0007038)
- A new parent term was created shoot system development stage (PO:0025527)to encompass the stages of development of various child terms of the shoot system:
- bud development stage (PO:0025528)
- bud dormancy stage (PO:0025529)
- bud swell stage (PO:0025531)
- bud burst stage PO:0025532
- bud development stage (PO:0025528)
- Added new term: reproductive shoot system development stage (PO:0025530) and revised the two existing child terms:
- flower development stage (PO:0007615)
- inflorescence development stage (PO:0001083)
- The parent term fruit development stage (PO:0001002) was revised and 2 new child terms were added to describe the stages of ripening of individual fruits: fruit formation stage (PO:0025501) and fruit ripening stage (PO:0025502).
- New children of fruit formation stage (PO:0025501:
- fruit size up to 10% stage (PO:0025504)
- fruit size 10 to 30% stage (PO:0025505)
- fruit size 30 to 50% stage (PO:0025506)
- fruit size 50 to 70% stage (PO:0025507)
- fruit size 70% to final size stage (PO:0025508)
- Children of fruit ripening stage (PO:0025502): will be added in the next round of revisions
New or expanded Annotation Files
- Oryza sativa rice: Rice_LCM_Aya_et_al,_2011
- Vitis vinifera grape: Vitis_vinifera;_grape
- Gossypium hirsutum cotton- AgBase
Other Changes
- Many terms have updated definitions which include the PO:ids- for full details please see the SVN site and the Details_of_Changes_in_PO_Release_19
- For more information and to view a summary of the release statistics, please visit: Plant Ontology Release #19 Jan 2013.
