Summary of Changes to PO April 2012

This page is under construction.

More detailed descriptions of the changes made to the Plant Ontology file are available on the POC Meetings Minutes and the [SourceForge tracker].

New and Obsolete Terms

116 new terms for plant anatomical entities and 34 new terms for plant structure development stages were added in this release.

See separate page for a complete list of New_terms_and_obsolete_terms-March_2012_Release.

Changes to plant structure development stages

The release marks a major revision to the plant structure development stage branch of the PO. The bulk of the changes were in to whole plant development stage and its subtypes, but there were substantial changes made throughout this branch of the PO.

The decision was made to define stages as occurring during the interval between two landmarks (e.g., the sporophyte development stage occurs between fertilization and death). This means that any stage which occurs during that interval is a subtype of the longer stage, rather than a part of (e.g., sporophyte vegetative stage is_a sporophyte development stage, not part_of sporophyte development stage). The part_of and has_part relations can still be used for development stages, e.g., seed development stage has_part embryo development stage.

Change to root node

Plant structure development stage (PO:0007021) was merged into plant growth and development stage (PO:0009012) and plant structure development stage was made the primary name. The definition of this term was also updated.

The aspect (namespace in OboEdit) was changed from plant_growth_and_development_stage to plant_structure_development_stage.

Changes to whole plant growth stage and its subtypes

Made whole plant growth stage (PO:0007033) is_a plant structure development stage, renamed whole plant development stage and updated the definition.

Added a new term for life of whole plant (PO:0025337). The only instances of life of whole plant are a maximal gametophyte development stage and a maximal sporophyte development stage. Gametophyte development stage and sporophyte development stage are part_of life of whole plant but remain as subtypes of whole plant development stage, because not every gametophyte or sporophyte stage is a life of whole plant.

Made the following terms subtypes of sporophyte development stage (were subtypes of whole plant development stage), because they were already defined for sporophytes:

• sporophyte vegetative stage (PO:0007134)
• sporophyte reproductive stage (PO:0007130)
• sporophyte senscent stage (PO:0007017)
• sporophyte dormant stage (PO:0007132)

Added new terms for corresponding stages in gametophytes:

• gametophyte vegetative development stage (PO:0025340)
• gametophyte reproductive development stage (PO:0025341)
• gametophyte dormant stage (PO:0025342)
• gametophyte senescent stage (PO:0025343)

Made protonema whole plant development stage (PO:0030006) is_a gametophyte vegetative development stage (was a whole plant development stage) and updated definition.

Renamed "embryo development stages" (PO:0007631) to plant embryo stage, made it is_a sporophyte vegetative stage, and updated the definition.

Renamed "A zygotic stage" (PO:0001097) to plant zygote stage, made it is_a sporophyte development stage, and updated the definition.

Added relation seed dormant stage has_part plant embryo dormant stage.

Changes to other types of development stages

The subtypes of plant structure development stage were organized to reflect the structure of the plant anatomical entity branch of the PO. These subtypes include whole plant development stage (existing term, see details above), plus new terms for collective plant structure development stage, plant organ development stage, plant tissue development stage, and trichome development stage. Seed development stage was made a subtype of plant structure development stage, rather than a subtype of sporopyhyte vegetative development stage.

• Flower development stage, fruit development stage, and inflorescence development stage are now subtypes of collective plant structure development stage (PO:0025338).

• Leaf development stage and root development stage are now subtypes of plant organ development stage.

• Leaf trichome development stage is now a subtype of trichome development stage.

Added new terms for seed trichome development stage and its subtypes, at the request of annotators describing cotton development.

Added new terms for 'vascular tissue development stage, phloem development stage, and xylem development stage as subtypes of plant tissue development stage.

Added secondary xylem development stage and its subtypes, as part of an ongoing project to add terms to the PO for wood anatomy and development, in collaboration with a group of wood scientists (see Wood anatomy ontology meeting, 2012 at NYBG, agenda.

Updated definitions of radicle emergence stage, coleoptile emergence stage, epicotyl emergence stage, hypocotyl emergence stage so that they are now defined as emerging from the seed coat, rather than the soil.

See New_terms_and_obsolete_terms-March_2012_Release#New_plant_structure_development_stage_terms for a complete list of new and renamed terms. No plant structure development stage terms were made obsolete in this release.

General changes to plant structure development stage terms

A decision was made not to prefix new plant structure development stage terms with numbers or letters, and number/letter prefixes are being removed from existing terms as we update them. This means that terms may not be displayed in chronological order in the PO browser but makes the names clearer. Chronological order may be described by comments such as "stage X precedes stage Y", "stage Y is preceded by stage X", or "stage Y succeeds stage X". In future releases, this temporal relations may be specified in the PO.

"Stage" has been appended to the end of most plant structure development stage term names.

All term names are now singular.

Changes to plant anatomical entities

Major revisions to the overall structure of the plant anatomical entity branch of the PO were completed during previous revisions. Ongoing work on this branch is aimed at refining definitions (including converting text definitions to genus-differentia form and adding logical or cross-product definitions) and adding new terms to meet users needs.

Definition updates

Changed name of awn (PO:0006032) to lemma awn. Modified text definition to reflect that it is part of lemma. Existing annotations should stay with PO:0006032. Added new general term for awn (PO:0025349), plus new subtypes for palea awn (PO:0025350) and glume awn (PO:0025351)

-made flower meristem is_a reproductive shoot apical meristem, revised def'n

-made phyllome marginal meristem part_of phyllome

Modified def'n: seed trichome: (PO:0004511): A trichome that develops from seed coat epidermis.

Made seed is_a plant structure. Updated definition. Removed seed part_of fruit and added develops_from ovule, has_part embryo

As part of a general overhaul of the definitions of vascular tissue and cell types, updated definitions of: vascular tissue, vascular bundle, phloem, primary phloem, secondary phloem, protophloem, metaphloem, plant spore, xylem, primary xylem, protoxylem, metaxylem, secondary xylem, tracheid bar, leaf vein, midvein, primary vein, lateral meristem, cambium, vascular cambium, cork cambium, sieve tube member, tracheary element, xylem fiber cell, fiber tracheid, libriform fiber cell, axial system, ray system, wood parenchyma, axial wood parenchyma, ray wood parenchyma, wood parenchyma cell, ray wood parenchyma cell, upright wood parenchyma cell, procumbent wood parenchyma cell, axial wood parenchyma cell, tracheary element, tracheid, vessel member, schlerencyma cell, companion cell, sapwood, heartwood, early wood, late wood, growth ring, growth ring boundary.

Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it is defined.

Made growth ring boundary part_of growth ring, instead of is_a. This means it has no is_a parent for the moment.

Added comment to all leaf vein orders that they should only not be used with dichotomously branching vein patterns.

Updated definitions of second through higher order veins, renamed them leaf lamina veins

Updated definition of carpel anlagen (PO:0006005)

Set up shoot and root lateral meristems as XPs

Changed phellem and phelloderm to part_of periderm, from part_of shoot axis periderm.

Changed definition of fruit nucellus (PO:0008005).

Udated definitions of intercalary meristem (PO:0006073), leaf intercalary meristem (PO:0006346), stem intercalary meristem (PO:0006347), lateral meristem (PO:0020145), vascular cambium (PO:0005598), and secondary thickening meristem (PO:0025414). Renamed tassel branch meristem to tassel inflorescence branch meristem.

Updated definition of companion cell (PO:0000071), sclerenchyma cell (PO:0000077) and sclerid cell (PO:0025418), sapwood (PO:0004513), heartwood (PO:0004512), early wood (PO:0004515), late wood (PO:0004516), growth ring (PO:0004514), plus wood parenchyma types and wood parenchyma cell types, early wood, late wood, growth ring, growth ring boundary, plant fiber cell, gelatinous fiber cell, septate fiber cell.

Updated definition of root hair cell (PO:0000256). Renamed PO:0000263 from atrichoblast to non-hair root epidermal cell. Atrichoblast is exact synonym. Updated definition.

Synonyms

Added leaf venation as a related synonym of leaf vascular system (PO:0000036)

Added diaspore as broad synonym to seed (PO:0009010), fruit (PO:0009001), spore (PO:0025017), corm (PO:0025355), bulb (PO:0025356), tuber (PO:0004543)

-added exact synonym to leaf marginal meristem: leaf margin blastozone

Got rid of old GRO synonyms on sporophyte dormant stage.

Relation changes

Added new relation has_participant. Following BFO, the domain is occurent and range is "continuant", which correspond to plant structure development stage and plant anatomical entity, respectively, in the PO.

Added has_participant relations between a number of terms, such as:

-whole plant development stage (PO:0007033) has_participant whole plant (PO:0000003)

-trichome development stage (PO:0025368) has_participant trichome (PO:0000282)

-leaf trichome development stage (PO:0007039) has_participant leaf trichome (PO:0006504)

-xylem development stage (PO:0025425) has_participant xylem (PO:0005352)

plus other plant structure development stages, as appropriate

Added xrefs to BFO or RO for develops_from, has_part, part_of, and adjacent_to.

Changed id of derives_by_manipulation_from from derives_from to derives_by_manipulation_from, so it will not be confused with the more general relation derives_from.

Logical definitions

The PO currently has 64 terms with logical or "cross-product" definitions

New relations added for this release include:

More of these relations are being incorporated into the PO as we move forward.

Back to March_2012_Release_Page

Other

Links to images

We have added several test links to images on PlantSystematics.org:

Image_at_PlantSystematics:1597 to septum (PO:0000030) and fruit septum (PO:0025268)

Image_at_PlantSystematics:14891 and Image_at_PlantSystematics:8662 to pappus (PO:0025393) and pappus element (PO:0025394)

These show up as External References (near the bottom of the page, on AmiGO).

Glossary of PO terms

The definitions of all plant anatomical entities are now available in glossary from via (add link).