Release 21

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Summary and Announcements

• The latest release of the Plant Ontology, version #21, is available on our Plant Ontology Browser.
• Link to Release Notes on PO home page: [1]

• This full release features the addition of 37 new PO terms, for both the Plant Anatomical Entity (PAE) (31) and Plant Structure Development Stage (PSDS) (6) branches of the ontology.

• This Release also includes new and updated annotation data for:

• • Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato

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: Plant_Pheontype_Pilot_Project_2015.

• • Additional annotation data was contributed by our collaborators for cotton (Gossypium hirsutum); (AgBase) and Arabidopsis thaliana. (TAIR).

• Names have been revised for 23 PAE terms and 21 PSDS terms, and definitions of many more terms have also been revised and updated.

• Includes all revisions of the plant_ontology.obo file from Aug 2013 (#2228) to July 24th 2015 (#3502) on the PO SVN site.

• After August 1, 2015, all the ontology files were moved to Planteome GitHub Repository

• This Release includes all the changes from Aug. 6th, 2015 #33ae100 to Sep 25, 2015 #01901fa

• Term trackers Xrefs have have been converted from the old SourceForge ids to link out to the new GitHub Issue Tracker (https://github.com/Planteome/plant-ontology/issues)

• For more details of the new and revised terms, please see: Details_of_Changes_to_Release_21

Major revisions to the plant anatomical entity branch:

• After consultation with the GO Consortium, a new child term of plant cell was added. Native plant cell describes plant cells that are either part of a multicellular whole plant (PO:0000003) in vivo, or a unicellular organism in natura (i.e. part of a natural environment). This term is a sibling to cultured plant cell which covers all the cells grown in vitro.
  • All the children of plant cell are now descendants of either native plant cell or cultured plant cell.

• New terms were added to special types of flowers, inflorescences, strobili and infructesences

• Special terms added to accommodate data curation of specific plants for our collaborators e.g strawberry (Fragaria vesca; receptacle cortex and receptacle pith), hops (Humulus lupulus; lupulin gland, megasporangiate strobilus); maize (Zea mays; ear infructescence, stem tegument layer ), Poplar (pistillate flower, pistillate inflorescence, staminate flower, staminate inflorescence), Arabidopsis (rosette); non-vascular plants (gemma)

• New and Revised terms describing special roots (proteoid root) and shoot-borne (adventitious) roots and their parts (e.g. shoot-borne internode root, shoot-borne nodal root, shoot-borne root meristem, shoot-borne root apical meristem, shoot-borne root epidermis, etc).

Many more revisions....

Revisions to the plant structure development stage branch:

• leaf development stages
  • Revisions to vascular leaf differentiation stage and child terms new child term of leaf development:

non-vascular leaf development stage (new PO:0025573); New term: vascular leaf primordium polarity determination stage (PO:0025572):

• • Added preceded_by relations to the vascular leaf expansion stages: vascular leaf senescence stage, mature vascular leaf stage, vascular leaf initiation stage.

flower development

• Changed floral organ formation stage (PO:0025585) to be part_of flower development stage (PO:0007615), rather than is_a.

plant embryo development stages

• revised names and def'ns

• • Moved plant embryo dormant stage (PO:0025377) to be is a mature plant embryo stage (PO:0001081) .

• • Added new relation- 'precedes' to link the plant embryo coleoptilar stage (PO:0001094) plant embryo cotyledonary stage (PO:0001078) and the plant embryo true leaf formation stage (PO:0001095) to the mature plant embryo stage (PO:0001081).

Other changes:

• Added new term: multi-tissue plant structure development stage (PO:0025571). Moved seed development, fruit development, and plant organ development to be child terms and updated their definitions.

• seed development stages: preceded_by to order, Updated def'n of seed dormant stage (PO:0025374);

New relations added to order the stages

A new relation "precedes" was added to the Plant Ontology in order to order the plant structure development stages.

This was used in the revision of the plant embryo development stages, as shown below:

• Also used in seed development stages and on vascular leaf primordium polarity determination stage (PO:0025572).

You can find more details about the new 'precedes' relation on the Relations_in_the_Plant_Ontology wiki page.

New Translations

Added missing Spanish synonyms on: PO:0025511 petal spur estribo del pétalo (Spanish) PO:0025513 organ lamina lámina órgano (Spanish) PO:0025517 leaf lamina lobe lóbulo de la lámina de la hoja (Spanish) PO:0025518 leaf lamina tooth diente de la lámina de la hoja (Spanish) PO:0025519 leaf lamina crena crena de la lámina de la hoja (Spanish) PO:0025520 leaf lamina intramarginal vein vena intramarginal de la lámina de la hoja (Spanish) PO:0025523 tuberous root raiz tuberosa (Spanish) PO:0025545 anther wall tapetum cell célula de la pared del tapete de la antera (Spanish)

Added missing Japanese translation synonyms on: PO:0025511 petal spur 花弁距 (Japanese) PO:0025513 organ lamina 器官 葉身 (Japanese) PO:0025517 leaf lamina lobe 葉身裂片 (Japanese) PO:0025518 leaf lamina tooth 葉身歯 ((Japanese)) PO:0025519 leaf lamina crena 葉身鈍鋸歯 (Japanese) PO:0025520 leaf lamina intramarginal vein 葉身辺縁葉脈 (Japanese) PO:0025523 tuberous root 塊茎根 PO:0025545 anther wall tapetum cell 葯壁絨毯細胞 (Japanese) PO:0025557 endarch protoxylem 内原型原生木部 (Japanese) and protoxilema endarch (Spanish)