Difference between revisions of "Release 20"
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| − | + | Back to [[Main_Page#PO_Releases_and_Database_Updates]] | |
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=Summary and Announcements= | =Summary and Announcements= | ||
The latest release of the Plant Ontology, version #20, is available on our [http://www.plantontology.org/amigo/go.cgi Plant Ontology Browser]. | The latest release of the Plant Ontology, version #20, is available on our [http://www.plantontology.org/amigo/go.cgi Plant Ontology Browser]. | ||
| − | This full release features the addition of 48 new terms, for both the ''Plant Anatomical Entity'' (44) and ''Plant Structure Development Stage'' (4) branches. | + | This full release features the addition of 48 new terms, for both the ''Plant Anatomical Entity'' (44) and ''Plant Structure Development Stage'' (4) branches. |
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| + | * This Release also includes new and updated annotation data for: | ||
| + | ** <i>Oryza sativa</i>: Added about 300 annotations to about 80 genes associated with characterized mutant phenotypes. This work was part of the [http://www.phenotypercn.org/?p=1099 Plant Phenotype Pilot Project]. You can find more information about the annotated genes at: [[Rice_IMP,_Gramene_Genes]]. | ||
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| + | ** Additional annotation data was contributed by our collaborators for cotton (<i>Gossypium hirsutum</i>); (AgBase) and <i>Arabidopsis thaliana</i>. (TAIR). | ||
| − | + | * Includes all revisions of the Plant Ontology from Revision #1761 to 2199- available on the [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=log SVN Site] | |
-For more information, please see also: [[Details_of_Changes_to_Release_20]] | -For more information, please see also: [[Details_of_Changes_to_Release_20]] | ||
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The release features revision to the following sections: | The release features revision to the following sections: | ||
| − | =Revisions to the ''plant anatomical entity'' branch:= | + | ==Major Revisions to the ''plant anatomical entity'' branch:== |
| − | + | * New terms were added to describe the parts of the perianth (PO:0009058), specifically to describe the different forms of a fused perianth (PO:0025880), such as that found in [http://www.plantsystematics.org/imgs/kcn2/r/Musaceae_Musa_ornata_6516.html Musa flowers]. | |
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| − | + | * Thirteen new terms were added to describe the different types of protoxylem (PO:0000272) tissue in the roots and shoots of vascular plants. | |
| + | * A term was created for plant sap (PO:0025538) and six sub-classes were added to specify from which part of the plant the sap was collected. | ||
| − | + | * We revised the existing tapetum cell (PO:0025543) (was 'tapetal cell') and added three child terms to specify the different types. In collaboration with the Gene Ontology, the corresponding GO biological process terms (anther wall tapetum cell differentiation; GO:0048657 and anther wall tapetum cell fate specification; GO:0010234) were also revised to match. | |
| − | + | * Inflorescence branch (PO:0009081) and its child terms were extensively revised. The existing term paraclade (PO:0004720) was merged into primary inflorescence branch (PO:0006321) and three new child terms were created the describe different types of paraclades: accessory paraclade (PO:0025546); cauline paraclade (PO:0025547); rosette paraclade (PO:0025548). | |
| + | **All the children of inflorescence branch (PO:0009081) designating the different branching orders (primary, secondary etc) were renamed from xxx inflorescence axis to xxx inflorescence branch. | ||
| − | + | * All the children of infructescence branch (PO:0025243) designating the different branching orders (primary, secondary etc) were renamed from xxx infructescence axis to xxx infructescence branch. | |
| − | + | * trichome PO:0000282 terms: | |
| + | ** Two new direct children of plant structure (PO:0009011) were added to describe the apical regions of different types of trichome (PO:0000282): trichome apex (new PO:0025550) and trichome tip (new PO:0025549). These have this unusual parentage since they can be part of a multicellular trichome (PO:0000282) (making them a 'portion of plant tissue (PO:0009007)', or part of a unicellular trichome (new PO:0025537), in which case they are a GO cellular component: unicellular trichome apex (GO:0090552) or unicellular trichome tip (GO:0090553). | ||
| + | We also added the subclasses: multicellular trichome apex (new PO:0025551) and multicellular trichome tip (PO:0025535) and a new term was added to describe a unicellular trichome (new PO:0025537). | ||
| − | + | * For additional minor revisions, please see: [[Details_of_Changes_to_Release_20]] | |
| − | + | ==Revisions to the ''plant structure development stage branch''== | |
| − | + | * Major revisions were made to ''flower development stage (PO:0007615)'' and its sub-classes. The five existing sub-classes which were revised into a new set of three classes and sub-classes which better describe flower development across flowering plants. | |
| + | **A new term ''flower meristem transition stage (PO:0025588)'' was added to describe the transition of the meristem from a vegetative to reproductive state. | ||
| + | * The second stage is the ''floral organ formation stage (PO:0025585)'' which encompasses three sub-classes (formerly direct children of ''flower development stage (PO:0007615)'') and ends with the onset of the ''flowering stage (PO:0025586)''. | ||
| + | **Sub-classes- Renamed terms: | ||
| + | *** floral organ meristem development stage (PO:0007601); was: 1 flower meristem visible stage | ||
| + | *** floral organ primordium development stage (PO:0007602); was: 2 flower meristem notched stage | ||
| + | *** floral organ differentiation stage (PO:0007600); was: 3 floral organ development stage | ||
| − | '''PO: | + | * The new third stage is the ''flowering stage (PO:0007616)'' which was formerly called ''4 anthesis stage''. The flowering stage begins when pollen is released by anther dehiscence (GO:0009901) and/or the stigma (PO:0009073) is receptive and ends with the process of pollination (GO:0009856), and/or floral organ senescence (GO:0080187). |
| − | + | *The new ''flowering stage (PO:0007616)'' also encompasses ''5 post anthesis stage (PO:0007617)'' which was merged into it. Although the term 'post-anthesis' is widely used in the plant science literature, we felt it was not clearly defined as to what processes were occurring. Annotations on 5 post anthesis stage (PO:0007617) were moved to the new flowering stage (PO:0007616) term. | |
| − | + | ===New relation added to order the stages=== | |
| + | A new relation "preceded_by" was added to the Plant Ontology in order to order the plant structure development stages. | ||
| + | This was used in the revision of the flower development stages, as shown below: | ||
| − | + | [[File:Preceded_by.png]] | |
| − | + | You can find more details about the new 'preceded_by' relation on the [[Relations_in_the_Plant_Ontology]] wiki page. | |
| − | =Other= | + | ==Other new PSDS terms== |
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| − | + | * collective phyllome structure development stage (PO:0025578): A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023). | |
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| + | * phyllome development stage (PO:0025579): A plant organ development stage (PO:0025339) that has a primary participant a phyllome (PO:0025023). | ||
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| − | + | ==List of species with annotation data in release #20== | |
| − | + | Arabidopsis thaliana | |
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| − | + | Oryza sativa (Rice) | |
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| − | + | Zea mays (maize, corn) | |
| − | + | Lycopersicon esculentum (tomato) | |
| − | + | Solanum insanum/Solanum melongena (eggplant) | |
| − | + | Fragaria vesca (strawberry) | |
| − | + | Physcomitrella patens | |
| − | + | Vitis vinifera (grape) | |
| + | Gossypium hirsutum (cotton) | ||
| − | + | Other Solanum species: | |
| + | * Anisodus acutangulus | ||
| + | * Atropa baetica | ||
| + | * Capsicum annuum (pepper) | ||
| + | * Coffea arabica (coffee) | ||
| + | * Datura strumonium (jimson weed) | ||
| + | * Hyoscyamus niger (black henbane) | ||
| + | * Nicotiana tabacum (tobacco) | ||
| + | * Petunia hybrida (hybrid petunia) | ||
| + | * Physalis spp | ||
| + | * Solanum chmielewskii | ||
| + | * Solanum pennellii | ||
| + | * Solanum tuberosum (potato) | ||
Latest revision as of 18:30, 29 December 2014
Back to Main_Page#PO_Releases_and_Database_Updates
Summary and Announcements
The latest release of the Plant Ontology, version #20, is available on our Plant Ontology Browser.
This full release features the addition of 48 new terms, for both the Plant Anatomical Entity (44) and Plant Structure Development Stage (4) branches.
- This Release also includes new and updated annotation data for:
- Oryza sativa: Added about 300 annotations to about 80 genes associated with characterized mutant phenotypes. This work was part of the Plant Phenotype Pilot Project. You can find more information about the annotated genes at: Rice_IMP,_Gramene_Genes.
- Additional annotation data was contributed by our collaborators for cotton (Gossypium hirsutum); (AgBase) and Arabidopsis thaliana. (TAIR).
- Includes all revisions of the Plant Ontology from Revision #1761 to 2199- available on the SVN Site
-For more information, please see also: Details_of_Changes_to_Release_20
The release features revision to the following sections:
Major Revisions to the plant anatomical entity branch:
- New terms were added to describe the parts of the perianth (PO:0009058), specifically to describe the different forms of a fused perianth (PO:0025880), such as that found in Musa flowers.
- Thirteen new terms were added to describe the different types of protoxylem (PO:0000272) tissue in the roots and shoots of vascular plants.
- A term was created for plant sap (PO:0025538) and six sub-classes were added to specify from which part of the plant the sap was collected.
- We revised the existing tapetum cell (PO:0025543) (was 'tapetal cell') and added three child terms to specify the different types. In collaboration with the Gene Ontology, the corresponding GO biological process terms (anther wall tapetum cell differentiation; GO:0048657 and anther wall tapetum cell fate specification; GO:0010234) were also revised to match.
- Inflorescence branch (PO:0009081) and its child terms were extensively revised. The existing term paraclade (PO:0004720) was merged into primary inflorescence branch (PO:0006321) and three new child terms were created the describe different types of paraclades: accessory paraclade (PO:0025546); cauline paraclade (PO:0025547); rosette paraclade (PO:0025548).
- All the children of inflorescence branch (PO:0009081) designating the different branching orders (primary, secondary etc) were renamed from xxx inflorescence axis to xxx inflorescence branch.
- All the children of infructescence branch (PO:0025243) designating the different branching orders (primary, secondary etc) were renamed from xxx infructescence axis to xxx infructescence branch.
- trichome PO:0000282 terms:
- Two new direct children of plant structure (PO:0009011) were added to describe the apical regions of different types of trichome (PO:0000282): trichome apex (new PO:0025550) and trichome tip (new PO:0025549). These have this unusual parentage since they can be part of a multicellular trichome (PO:0000282) (making them a 'portion of plant tissue (PO:0009007)', or part of a unicellular trichome (new PO:0025537), in which case they are a GO cellular component: unicellular trichome apex (GO:0090552) or unicellular trichome tip (GO:0090553).
We also added the subclasses: multicellular trichome apex (new PO:0025551) and multicellular trichome tip (PO:0025535) and a new term was added to describe a unicellular trichome (new PO:0025537).
- For additional minor revisions, please see: Details_of_Changes_to_Release_20
Revisions to the plant structure development stage branch
- Major revisions were made to flower development stage (PO:0007615) and its sub-classes. The five existing sub-classes which were revised into a new set of three classes and sub-classes which better describe flower development across flowering plants.
- A new term flower meristem transition stage (PO:0025588) was added to describe the transition of the meristem from a vegetative to reproductive state.
- The second stage is the floral organ formation stage (PO:0025585) which encompasses three sub-classes (formerly direct children of flower development stage (PO:0007615)) and ends with the onset of the flowering stage (PO:0025586).
- Sub-classes- Renamed terms:
- floral organ meristem development stage (PO:0007601); was: 1 flower meristem visible stage
- floral organ primordium development stage (PO:0007602); was: 2 flower meristem notched stage
- floral organ differentiation stage (PO:0007600); was: 3 floral organ development stage
- Sub-classes- Renamed terms:
- The new third stage is the flowering stage (PO:0007616) which was formerly called 4 anthesis stage. The flowering stage begins when pollen is released by anther dehiscence (GO:0009901) and/or the stigma (PO:0009073) is receptive and ends with the process of pollination (GO:0009856), and/or floral organ senescence (GO:0080187).
- The new flowering stage (PO:0007616) also encompasses 5 post anthesis stage (PO:0007617) which was merged into it. Although the term 'post-anthesis' is widely used in the plant science literature, we felt it was not clearly defined as to what processes were occurring. Annotations on 5 post anthesis stage (PO:0007617) were moved to the new flowering stage (PO:0007616) term.
New relation added to order the stages
A new relation "preceded_by" was added to the Plant Ontology in order to order the plant structure development stages.
This was used in the revision of the flower development stages, as shown below:
You can find more details about the new 'preceded_by' relation on the Relations_in_the_Plant_Ontology wiki page.
Other new PSDS terms
- collective phyllome structure development stage (PO:0025578): A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).
- phyllome development stage (PO:0025579): A plant organ development stage (PO:0025339) that has a primary participant a phyllome (PO:0025023).
List of species with annotation data in release #20
Arabidopsis thaliana
Oryza sativa (Rice)
Zea mays (maize, corn)
Lycopersicon esculentum (tomato)
Solanum insanum/Solanum melongena (eggplant)
Fragaria vesca (strawberry)
Physcomitrella patens
Vitis vinifera (grape)
Gossypium hirsutum (cotton)
Other Solanum species:
- Anisodus acutangulus
- Atropa baetica
- Capsicum annuum (pepper)
- Coffea arabica (coffee)
- Datura strumonium (jimson weed)
- Hyoscyamus niger (black henbane)
- Nicotiana tabacum (tobacco)
- Petunia hybrida (hybrid petunia)
- Physalis spp
- Solanum chmielewskii
- Solanum pennellii
- Solanum tuberosum (potato)
