Summary of Changes to PO October 2011

Go here for the list of New terms and obsolete terms for September2011 release

New and Obsolete Terms

See separate page for a list of New terms and obsolete terms for October 2011 release.

Note: There were no terms made obsolete in this round of revisions.

Eliminating terms with Zea or Poaceae in the name

Complete details can be found on the wiki page: Eliminating_Zea/Poaceae_terms_from_PO.

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. Complete details 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"

Added to comments of lemma, palea, and glume. Updated definitions of glume, glume of tassel spikelet, and glume of ear spikelet and lemma and palea.

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.

Renamed booting (PO:0007014) "booting stage" and made it a subtype of IL.00 inflorescence just visible phase (PO:0007006).

Added synonyms to inflorescence emergence stage (PO:0007041) and LP.18 eighteen leaves visible (PO:0007072).

Term with name changes:

in PAO:

PO:0009082 floret to spikelet floret

PO:0020126 tassel to tassel inflorescence

PO:0020136 Zea ear to ear inflorescence

PO:0025173 leaf spine to spine leaf

PO:0025174 stipule spine to spine stipule

PO:0006340 adult leaf to adult vascular leaf (now is_a vascular leaf)

PO:0008018 transition leaf to transition vascular leaf (now is_a vascular leaf)

PO:0006339 juvenile leaf to juvenile vascular leaf (now is_a vascular leaf)

in PGDSO:

PO:0007032 FF.00 fruit size 10% to FF.00 fruit size up to 10% stage

PO:0007009 FF.01 fruit size 30% to FF.01 fruit size 11 to 30% stage

PO:0007029 FF.02 fruit size 50% to FF.02 fruit size 31 to 50% stage

PO:0007007 FF.03 fruit size 70% to FF.03 fruit size 51 to 70% stage

PO:0007027 FF.04 fruit final size to FF.04 fruit size 71% to final size stage

PO:0007014 booting to booting stage

PO:0007047 3 inflorescence visible to 3 inflorescence detectable stage

PO:0007041 inflorescence emergence from flag leaf to inflorescence emergence stage

PO:0007022 imbibition to seed imbibition stage

PO:0007030 shoot emergence to seedling shoot emergence stage

PO:0007057 0 germination to 0 seed germination stage

Spanish and Japanese synonyms

Added Spanish and Japanese 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.

is_a completeness

The following relations were added:

• seed imbibition stage (PO:0007022) is_a seed germination stage
• seedling development stage (PO:0007131) is_a vegetative growth stage
• seedling shoot emergence stage (PO:0007130) is_a seedling development stage

All PAO and PGDSO terms now have an is_a parent.

Changes to the list of Dbxrefs:

• Updated the links to MaizeGDB, SGN and Gramene ( for full details see: POC_Conf._Call_9-27-11 and POC_Conf._Call_10-4-11).

• Added new links for Strawberry annotations

Links for non-standard reference

Some definitions and synonyms have references from books without ISBN numbers or journals that are not in PubMed. This prevents us from using the standard reference abbreviations (PMID:id or ISBN:id).

We have created a PO Reference Database for these terms (see PO_references). Each reference can now be identified using the abbreviation "PO_REF:xxxxx", and this abbreviation will create a link to the wiki page for that reference.

Miscellaneous

• Made embryo apical cell (PO:0025284) is_a sporophyte meristematic apical cell, rather than is_a meristematic apical cell, to fix redundancy.

• 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.

• 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

• Megasporangium wall and microsporangium wall had no definitions -added simple genus-differentia defs.

• Added cone, ovulate cone and pollen cone as synonyms of strobilus (PO:0025083)

• Changed the following terms from part_of leaf to part_of vascular leaf (some of them changed automatically by transitivity):

spongy mesophyll cell (PO:0006205), palisade mesophyll cell (PO:0006206), buliform cell (PO:0004001), long cell (PO:0004717), short cell (PO:0004718), leaf sheath (PO:0020104), leaf sheath pulvinus (PO:0008017), leaf sheath epidermis (PO:0025249) leaf sheath abaxial epidermis (PO:0025250), leaf sheath adaxial epidermis (PO:0025251), epidermal cork cell (PO:0000041), silica cell (PO:0004009), spongy mesophyll (PO:0005647) palisade mesophyll (PO:0005648)

• Renamed adult leaf (PO:0006340) to adult vascular leaf, transition leaf (PO:0008018) to transition vascular leaf and juvenile leaf (PO:0006339) to juvenile vascular leaf. All three are now is_a vascular leaf, instead of is_a leaf. Added comments to all three to give more details of these types of leaves.

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