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New Plant Ontology Release #20 Available

Greetings from the Plant Ontology!

We are pleased to announce that the latest release of the Plant Ontology, version #20, is available on our browser at http://www.plantontology.org. For full details of the changes, please see: the Release 20 page at: http://wiki.plantontology.org/index.php/Release_20

Release features:

  • Addition of 48 new terms, for both the Plant Anatomical Entity (44) and Plant Structure Development Stage (4) branches.
  • Major revisions to the plant anatomical entity branch of the ontology include:
    • 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].
    • 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) and infructescence branch (PO:0025243) designating the different branching orders (primary, secondary etc) were renamed from xxx axis to xxx 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 (PO:0025550) and trichome tip (PO:0025549). They 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 (PO:0025551) and multicellular trichome tip (PO:0025535) and a new term was added to describe a unicellular trichome (PO:0025537).
  • Major revisions to the Plant Structure Development Stage branch include:
    • 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 floral organ formation stage (PO:0025585), encompasses three sub-classes (formerly direct children of 'flower development stage (PO:0007615)') and ends with the onset of the flowering stage (PO:0025586).
    • The new third stage is the flowering stage (PO:0007616) (formerly ''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). This term also encompasses 5 post anthesis stage (PO:0007617) which was merged into it.
    • A new relation "preceded_by" was added to the Plant Ontology in order to order the plant structure development stages. You can find more details about the new 'preceded_by' relation here: http://wiki.plantontology.org/index.php/Relations_in_the_Plant_Ontology.
  • In addition to these changes, the names and definitions of many other terms have been revised.
  • New and updated annotation data for:

Plant Ontology defined stages of plant lifecycle can provide clues for defining aging stages in humans.

Prof. Barry Smith from the University of Buffalo, NY, delivered a Keynote address at the 2013 Rostock Symposium on Systems Biology and Bioinformatics in Ageing Research. He examined definitions of terms central to ageing research in the Gene Ontology (GO), the Foundational Model of Anatomy Ontology (FMA) and the Plant Ontology (PO). His talk shows how the Plant Ontology definition of stages in the plant lifecycle can be used as a starting point for an understanding of the aging stage in humans.

References/Acknowledgements:
Talk source: YouTube.
Gene Ontology (GO): http://geneontology.org
FMA Ontology: http://sig.biostr.washington.edu/proj...
Plant Ontology (PO): http://www.plantontology.org/
Selaginella apoda lifecycle video: Original version
Selaginella apoda lifecycle video*: Version with Plant Ontology annotations

*This video was edited and annotated using Plant Ontology terms by the PO curator Laurel Cooper.

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