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New Plant Ontology Release #20 Available

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/.

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: rice (Oryza sativa) Arabidopsis thaliana and cotton (Gossypium hirsutum).

Major revisions to the plant anatomical entity branch of the ontology include new and revised terms and definitions to describe:
- parts of fused perianth (PO:0025880), such as that found in [http://www.plantsystematics.org/imgs/kcn2/r/Musaceae_Musa_ornata_6516.html Musa flowers]
- different types of protoxylem (PO:0000272) tissue in the roots and shoots of vascular plants
- plant sap (PO:0025538) and sub-classes
- tapetum cell (PO:0025543) and sub-classes
- inflorescence branch (PO:0009081) and sub-classes; accessory paraclade (PO:0025546); cauline paraclade (PO:0025547); rosette paraclade (PO:0025548)
- infructescence branch (PO:0025243) and sub-classes
- sub-classes and parts of trichome (PO:0000282): trichome apex (PO:0025550) and trichome tip (PO:0025549) were added to describe the apical regions of different types of trichome (PO:0000282). Also, multicellular trichome apex (PO:0025551) and multicellular trichome tip (PO:0025535) and a unicellular trichome (PO:0025537) were also added.

Major revisions to the Plant Structure Development Stage branch include changes 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.
- flower meristem transition stage (PO:0025588) was added to describe the transition of the meristem from a vegetative to reproductive state.
- floral organ formation stage (PO:0025585), encompasses three sub-classes (formerly direct children of 'flower development stage') and ends with the onset of the flowering stage.
- flowering stage (PO:0007616) (formerly ''4 anthesis stage''). This term encompasses the former ''4 anthesis stage'' and "5 post anthesis stage" terms

- 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.
For full details of the changes, please see: the Release 20 page at: http://wiki.plantontology.org/index.php/Release_20

International Coordination Meeting for Ontology-Based Efforts for Plant Biology

A meeting to promote the coordination of the Gene, Protein, and Plant Ontologies and of other reference ontologies used in plant biology wa sheld on May 15 and 16, 2013 in Amherst (Buffalo) NY. Major goals of the meeting were:

  • To inform members of the Protein, Plant, Gene Ontology and related communities of developments in their respective ontologies in order to promote cross-ontology coordination. Specifically (1) to enhance the treatment of plant-related proteins in the Protein Ontology and (2) to address issues concerning reuse of GO terms to describe plant-related entities, for example in the treatment of plant life cycle and development stages.
  • To address general issues which arise when ontologies need to be extended to cover multiple species of organisms
  • To contribute to the cROP (Common Reference Ontologies for Plants) initiative
  • To contribute to the ontological understanding of phenotype and disease across organisms.
  • To identify potentially fruitful applications which enhanced ontology coordination might bring.

Meeting was attended by the participants representing the Protein Ontology, Plant Ontology, Gene Ontology, ChEBI, OBO Foundry, and the University of Buffalo.

For more information on the meeting and accessing the presentations, please visit the meeting website.

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