Details of Changes to Release 20

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Includes all revisions from 1761 and on.

Merged or Obsoleted terms

• paraclade (PO:0004720) was merged into primary inflorescence branch (PO:0006321): No direct annotations, but one annotation on paraclade cortex: knat 1 from TAIR

Why doesn't paraclade (PO:0004720) show up as an exact synonym? The PO:0004720 should appear as a 2' id? See OBO-Edit User Guide

• post-anthesis (PO:0007617) was merged into flowering stage (PO:0007616; was anthesis stage) 8 annotations

post-anthesis (PO:0007617)shows up as a narrow: post anthesis stage with alt_id: PO:0007617. But neither term shows up on the obsoleted list.

New PAE terms:

Various:

• bundle sheath cell (PO:0025541): A ground tissue cell (PO:0000076) that is part of a bundle sheath (PO:0006023). part_of bundle sheath
• bundle sheath chlorenchyma cell (PO:0025542): A chlorenchyma cell (PO:0000076) that is part of a bundle sheath (PO:0006023).
• plant cuticle ridge (PO:0025536): A portion of plant cuticle (PO:000022) that forms a ridge, may be overlayed with epicuticular wax (PO:0025388). Comment: The plant cuticle ridges are mainly cutin (PO:0025385).
• adventitious shoot axis PO:0025534: A shoot axis (PO:00025029) that develops in an unusual place. develops from a bud (narrow synonym: adventitious bud)

parts of the perianth (PO:0009058):

• fused perianth (PO:0025880): A perianth (PO:0009058) in which one or more of the petals (PO:0009032), sepals (PO:0009031), and/or tepals (PO:0009033) are fused.

• fused corolla (PO:0025581): A corolla (PO:0009059) that is composed of fused petals (PO:0009032).

• fused calyx (PO:0025582): A calyx (PO:0009060) that is composed of fused sepals (PO:0025584).

• fused petal (PO:0025583): A petal (PO:0009032) that is part of a fused corolla (PO:0025581) or a fused perianth (PO:0025580).

• fused sepal (new PO:0025584): A sepal (PO:0009031) that is part of the fused calyx (PO:0025582) or a fused perianth (PO:0025580).

• free sepal (PO:0025587: A sepal (PO:0009031)that is part of a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).

• free petal (PO:0025569): A petal (PO:0009032) that is part of a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).

• epicalyx bract (PO:0025577): A flower bract (PO:0009034) that is part of the epicalyx (PO:0009063)

protoxylem terms

• centarch protoxylem (new PO:0025552): A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem of the shoot system progresses centrifugally with the oldest elements (protoxylem) in the center of the axis.

• mesarch protoxylem (new PO:0025553)- A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem (PO:0005849) of the shoot system (PO:0009006) progresses both centripetally and centrifugally from the center. comment: Mesarch protoxylem is found in ferns and cycads stems.

• exarch protoxylem (PO:0025554): A portion of protoxylem (PO:0000272) tissue in which the maturation of primary xylem (PO:0005849) progresses centripetally, the oldest elements (protoxylem) are farthest from the center of the axis. Comment: Typical of roots in seed plants.

• shoot system exarch protoxylem (PO:0025556): A portion of exarch protoxylem (PO:002554)tissue in which the maturation of primary xylem (PO:0005849) of the shoot system (PO:0009006) progresses centripetally, the oldest elements (protoxylem) are farthest from the center of the axis.

• root exarch protoxylem (PO:0025555): A portion of exarch protoxylem (PO:002554) tissue in which the maturation of primary xylem (PO:0005849) of the root system (PO:0025025) progresses centripetally, the oldest elements (protoxylem) are farthest from the center of the axis.

• monarch protoxylem (new PO:0025558)-A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has only one protoxylem strand or pole, and differentiation progresses centripedally, with the oldest element (protoxylem) farthest from the center of the axis.

• diarch protoxylem (new PO:0025559)- A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has two protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.

• triarch protoxylem (new PO:0025560)- A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has three protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.

• tertrach protoxylem (new PO:0025561)- A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has four protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.

• pentarch protoxylem (new PO:0025562)-A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has five protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.

• polyarch protoxylem (new PO:0025563)- A portion of root exarch protoxylem (PO:0025555) tissue in which the primary xylem (PO:0005849) of the root system (PO:0025025) has more than five protoxylem strands or poles, and differentiation progresses centripetally, with the oldest elements (protoxylem) farthest from the center of the axis.

• protoxylem tracheary element (PO:0025575): A primary xylem tracheary element (PO:0025444) with predominately annular or helical secondary wall thickening that are the first formed tracheary elements (PO:0000290) at a particular location.

• metaxylem tracheary element (PO:0025576):A primary xylem tracheary element (PO:0025444) that may have helical, scalariform, reticulate and/or pitted secondary wall thickenings.

plant sap (PO:0025538) terms

• plant sap (PO:00255380): A portion of plant substance (PO:0025161) that is an aqueous solution that can be transported through the apoplast (GO:0048046) or symplast (GO:0055044). Comment: plant sap should not be confused with latex or resins.

• xylem sap (PO:0025539): A plant sap (PO:0025538) that is an aqueous solution which may contain mineral elements, nutrients, and plant hormones, and is transported from the root system (PO:0025025) toward the leaves through the tracheary elements (PO:0000290) of the xylem. Comment: Transport of sap in xylem is characterized by movement from the roots toward the leaves.
  • root system xylem sap (PO:0025568): A xylem sap (PO:0025539) that is located in the root system (PO:0025025).
  • shoot system xylem sap PO:0025565 : A xylem sap (PO:0025539) that is located in the shoot system (PO:0009006).

• phloem sap (PO:0025540): A plant sap (new PO:0025538) that is an aqueous solution which may contain sugars, mineral elements, and plant hormones, and is transported through the phloem sieve elements (PO:0025406).
  • root system phloem sap (PO:0025567): A phloem sap (PO:0025540) that is located in the root system (PO:0025025).
  • shoot system phloem sap (PO:0025566): A phloem sap (PO:0025540) that is located in the shoot system (PO:0009006).

tapetum cell (PO:0025543) terms

• tapetum cell (PO:0025543): A plant cell (PO:0009002) that is part of the tapetum (PO:0025313). exact synonym: tapetal cell. comment: The tapetum is the inner-most layer of a sporangium wall (PO:0025306).
  • microsporangium tapetum cell (PO:0025544): A tapetum cell (PO:0025543) that is part of a microsporangium tapetum (PO:0025314). part_of a microsporangium tapetum; exact synonym: tapetal cell
    • anther wall tapetum cell (PO:0025545): A microsporangium tapetum cell (PO:0025544) that is part of the anther wall tapetum (PO:0009071). part_of the anther wall tapetum; exact synonym: anther wall tapetal cell

• megasporangium tapetum cell (PO:0025564): A tapetum cell (PO:0025543) that is part of a megasporangium tapetum (PO:0025315).

• revised name and definition: E 'anther wall' tapetum degeneration initiated stage (PO:0001032): An anther development stage during which degeneration of the anther wall tapetum (PO:0009071) is initiated, as the deposition on the surface of the microspore (PO:0020048) primexine proceeds.

inflorescence branch (PO:0009081)terms

• accessory paraclade (PO:0025546): A primary inflorescence branch (PO:0009081) borne in same axil as an existing primary inflorescence branch (PO:0009081).

• cauline paraclade (PO:0025547): An inflorescence branch (PO:0009081) borne on the elongated first order inflorescence axis (PO:0025104).

• rosette paraclade (PO:0025548): An inflorescence branch (PO:0009081) borne on the compacted first order inflorescence axis (PO:0025104), forming the rosette.

trichome (PO:0000282) terms

• unicellular trichome (new PO:0025537)- A trichome (PO:0000282) that is a single plant cell (PO:0009002). is_a trichome, is_a plant cell. comment: This should not be confused with a trichome cell, which is a plant cell (PO:0009002) that is part of a multicellular trichome (PO:0000282).

• trichome apex (new PO:0025550): A plant structure (PO:0009011) that is the apical most portion of a trichome (PO:0000282). comment: This term is the parent to the apex of a multicellular trichome (PO:0025162) or a unicellular trichome (PO:0025537), specifically, a multicellular trichome apex (PO:0025551) and an unicellular trichome apex (GO:0090552), which is a GO cellular component term. is_a plant structure, part_of trichome

• trichome tip (new PO:0025549): A plant structure (PO:0009011) that is the apical most portion of trichome apex (PO:0025550). is_a plant structure, part of trichome apex

• • multicellular trichome apex (new PO:0025551): A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome (PO:0025162). is_a trichome apex, part_of multicellular trichome (PO:0025551). comment: This term describes the apex region of a multicellular trichome (PO:0000282). The apex of a unicellular trichome is a GO cellular component: unicellular trichome apex (GO:0090552).

• • multicellular trichome tip (PO:0025535): A portion of plant tissue (PO:0009007) that is the apical most portion of a multicellular trichome apex (PO:0025551).comment: This term is the parent to the tip of a multicellular trichome (PO:0025162) or the tip of a unicellular trichome (PO:0025537), specifically, a multicellular trichome tip (PO:0025535) and a unicellular trichome tip (GO:0090553), which is a GO cellular component term.

New Plant Structure Development Stage terms:

• collective phyllome structure development stage (PO:0025578): A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).
• phyllome development stage (PO:0025579): A plant organ development stage (PO:0025339) that has a primary participant a phyllome (PO:0025023).
• flower meristem transition stage (PO:0025588): A flower development stage (PO:0007615) which begins with the transition from a portion of meristem tissue (PO:0009013) to a flower meristem (PO:0000229) and ends with the onset of the floral organ formation stage (PO:0025585).
• floral organ formation stage (PO:0025585): A flower development stage (PO:0007615) which begins with the floral organ meristem development stage (PO:0007601) and ends with the onset of the flowering stage (PO:0025586).

Renamed terms

No substantial change in the meaning of the definition

Format 'new_name'(PO:ID); was:'old_name'

PAE terms

• primary inflorescence branch (PO:0006321); was: second order inflorescence axis
• second order inflorescence branch (PO:0006322); was: third order inflorescence axis
• third order inflorescence branch (PO:0025105); was: forth order inflorescence axis
• fourth order inflorescence branch (PO:0025106); was: fifth order inflorescence axis
• fifth order inflorescence branch (PO:0025107); was: sixth order inflorescence axis
• sixth order inflorescence branch (PO:0025108); was: seventh order inflorescence axis
• seventh order inflorescence branch (PO:0025109); was: eighth order inflorescence axis
• eighth order inflorescence branch (PO:0025110); was: ninth order inflorescence axis
• ninth or higher order inflorescence branch (PO:0025111); was: tenth or higher order inflorescence axis

• primary infructescence branch (PO:0025112); was: second order infructescence axis
• second order infructescence branch (PO:0025113); was: third order infructescence axis
• third order infructescence branch (PO:0025114); was: forth order infructescence axis
• fourth order infructescence branch (PO:0025115); was: fifth order infructescence axis
• fifth order infructescence branch (PO:0025116); was: sixth order infructescence axis
• sixth order infructescence branch (PO:0025252); was: seventh order infructescence axis
• seventh order infructescence branch (PO:0025253); was: eighth order infructescence axis
• eighth order infructescence branch (PO:0025254); was: ninth order infructescence axis
• ninth or higher order infructescence branch (PO:0025255); was: tenth or higher order infructescence axis

• central spike of ear inflorescence (PO:0006505); was: central spike of ear
• central spike of tassel inflorescence (PO:0006324); was: central spike of tassel

• floral structure primordium (PO:0025477); was: floral organ primordium
• E anther wall tapetum degeneration initiated stage (PO:0001032) was: E tapetum degeneration initiated stage

whole plant fruit formation stage

PSDS terms

• E anther wall tapetum degeneration initiated stage (PO:0001032); was: E tapetum degeneration initiated stage
• floral organ meristem development stage (PO:0007601); was: 1 flower meristem visible stage
• floral organ primordium development stage (PO:0007602); was: 2 flower meristem notched stage
• floral organ differentiation stage (PO:0007600); was: 3 floral organ development stage
• flowering stage (PO:0007616); was: anthesis stage; was: 4 anthesis stage and also encompasses 5 post anthesis stage (PO:0007617)- merged into it

GO Requests

• list new terms or changes requested of the GO
• Link to GO Tracker

tapetum cell parts

GO terms:

tapetal cell differentiation, GO:0048657 tapetal cell fate specification, GO:0010234

Definitions refer to anther specific tapetum but there are non-anther tapetum terms in PO.

rename as anther wall tapetum cell differentiation, GO:0048657 and anther wall tapetum cell fate specification, GO:0010234.

In a similar way, the following terms need to be renamed, tapetal layer -> anther wall tapetum

tapetal layer formation, GO:0048656 tapetal layer development, GO:0048658 tapetal layer morphogenesis, GO:0048655

Revisit all definitions to make sure they are in line.

Relevant PO Sourceforge items: https://sourceforge.net/tracker/index.php?func=detail&aid=3298006&group_id=76834&atid=835555 https://sourceforge.net/tracker/index.php?func=detail&aid=3609728&group_id=76834&atid=835555

unicellular trichome branch (GO:0090405)

requested two terms to describe the apical most parts of a unicellular trichome.

New: unicellular trichome apex (GO:xxxxx): A cell projection part that is the apical most portion of a unicellular trichome (PO:0025537)

New: unicellular trichome tip (GO:xxxxx): A cell projection part that is the apical most portion of a unicellular trichome apex (GO:xxxxx)

[Term] +id: GO:0090552 +name: unicellular trichome apex +namespace: cellular_component +def: "A cell projection part that is the apical most portion of a unicellular trichome." [GOC:PO_curators, PO:0025537] +is_a: GO:0044463 ! cell projection part

+ +[Term] +id: GO:0090553 +name: unicellular trichome tip +namespace: cellular_component +def: "A cell projection part that is the apical most portion of a unicellular trichome apex." [GOC:PO_curators] +is_a: GO:0044463 ! cell projection part +relationship: part_of GO:0090552 ! unicellular trichome apex

Other Fixes

• Error in the header: in current version (r1916) and line 26, the tag is misspelled. You currently have a tag called treat-xrefs-as-genus-differntia in the header. The correct spelling is treat-xrefs-as-genus-differentia (Note the additional 'e' in differentia). Judging from the SVN logs, this error has been there for more than one year. inferences may be slightly incomplete or otherwise affected. Once fixed,should check your inferences, just to be sure.

Fixed- In revision 1964