Summary of Changes to PO October 2011

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Eliminating terms with Zea or Poaceae in the name

There were about 70 terms with Zea or Poaceae in the name. Most of these terms were identical to their superclass, except that they occurred in maize or other grasses. For example, a Zea anther is simply an anther in Zea mays. In keeping with the OBO Foundry best practice of not using taxon-specific term names, we have eliminated most of these terms by merging them into their superclass (e.g., Zea anther merged into Poaceae anther, and Poaceae anther merged into anther.

We felt that some of the terms should be kept, because they were structurally distinct, e.g., Zea ear, tassel, and the different types of florets. Many of these terms were renamed. For example. Zea ear is now called ear inflorescence and tassel is called tassel inflorescence.

Details of which terms were merged and other changes made to Zea/Poaceae related terms can be found on the wiki page: Eliminating_Zea/Poaceae_terms_from_PO.

Other changes to Poaceae terms:

Made floret part_of spikelet (instead of Poaceae floret part_of spikelet), because all florets are part of a spikelet, in both Poaceae and closely related species like Cyperaceae.

Renamed floret (PO:0009082) "spikelet floret" and added "ray flower", "disk flower", and "floret" as narrow synonyms of flower.

Made lemma and palea part of spikelet instead of part of spikelet floret (b/c a bract is defined as subtending a flower, not part of it). Added to comments of lemma, palea, and glume. Updated definitions of glume, glume of tassel spikelet, and glume of ear spikelet.

PO:0007047 (3 inflorescence visible) was renamed "3 inflorescence detectable stage" and redefined.

Definitions for PO:0007006 (IL.00 inflorescence just visible) and its sibling terms were modified.

Merged Poaceae inflorescence visible (PO:0007012) into 3 inflorescence detectable phase (PO:0007047) and made booting (PO:0007014) a subtype of IL.00 inflorescence just visible phase (PO:0007006)

PO:0007041 (inflorescence emergence phase from flag leaf sheath), was renamed inflorescence emergence phase to make it more general.

PO:0007032 (FF.00 fruit size 10%) was renamed FF.00 fruit size up to 10% and redefined to go from initiation of the fruit up to 10%. Sibling terms were renamed and redefined similarly.

Spanish synonyms

Added Spanish synonyms for all PAO terms.

New subset for plant cells

Added subset for plant cells for the Cell Ontology (CL). Includes plant cell (PO:0009002) and all subtypes (is_a descendants). CL can use this to extract all cell types from the PO to import into CL.

Removed all xrefs to obsolete CL terms (47 refs for 45 PO terms), plus xref to CL plant cell

Added xref for PO: meristematic cell to CL:0000034 stem cell.

Add header: treat-xrefs-as-genus-differntia: CL part_of NCBITaxon:3193 (Embryophyta)

More details available in the minutes from the PO/CL_Conference_call_08-30-11.

Miscellaneous

Added new term flower fascicle (PO:0025323)

Made embryo apical cell (PO:0025284) is_a sporophyte m.a.c., rather than is_a m.a.c., to fix redundancy.

Added OBSOLETE as prefix to the definitions of all recently obsoleted terms.

Anther and anther theca are both collective plant structures (see SF tracker for anther theca), but their definitions were not updated. Fixed them. Added comment to anther.

Added comments to juvenile, transition and adult leaf, to give more details of these types of leaves.

Changed lateral root primordium from derives_from pericycle to develops_from pericycle. Now derives_from is only used between an in vitro and an in vivo plant strucure.

Added stolon (PO:0003024) and subterranean tuber cortex (PO:0025057) to potato subset

New name and definition for 3 inflorescence visible New definition and comment for IL.00 inflorescence just visible. Also reworded definitions of siblings. Also added them to the subset for maize. merged Poaceae inflorescence visible (PO:0007012) into 3 inflorescence detectable phase (PO:0007047) Made booting (PO:0007014) a subtype of IL.00 inflorescence just visible phase (PO:0007006) new name and definition for PO:0007041 (inflorescence emergence phase, was inflorescence emergence phase from flag leaf sheath)

Megasporangium wall and microsporangium wall had no definitions -added simple genus-differentia defs. Added synonyms to inflorescence emergence stage (PO:0007041) and LP.18 eighteen leaves visible (PO:0007072). Updated comments for 3 inflorescence detectable stage, IL.00 inflorescence just visible stage, and all the booting stages. Changed all phase names to stage, except gametophyte, sporophyte and protonema.

Updated names and definitions of FF.00 fruit size 10% and its siblings.

Added new terms for: banner petal PO:0025324, wing petal PO:0025325, keel petal PO:0025326, keel PO:0025327, and fused perianth PO:0025328. Added relation fused collective tepal structure is_a fused perianth.

Added new terms for specific types of calyptras in Eucalyptus: calyptra calyx PO:0025329 and calyptra corolla PO:0025330.



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