Summary of Changes to PO May 2011

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General and top-level changes

Translations

-Added new subset for Spanish language synonyms. Scope is exact synonyms.

Changes in 'in vitro plant structure' (PO:0000004), and its children

We agreed (4-12-11 POC) to make the in vitro structures children of their respective plant structure parents (cell, tissue and embryo) and keep "in vitro plant structure" and use a textual definition and assert dual parentage to it. This was after consultation with PATO, OBI, and GO; CM. Both of the parentage relations had to be asserted in this case because (fill in reason).

This is how it looked before:

This is how it looks now: Make better image with the rest of the terms

Changes in the part_of relationships to whole plant:

Removed the part_of relationships to whole plant from: All the children of plant structure that are defined as " A plant structure...." and also plant cell.

As they are already part of a plant and can also include entities that were derived from a plant (such as the in vitro structures) or plant material such as wood, which is no longer part of a whole plant.

New relations

adjacent_to

Used when one plant structure (the child) is in permanent contact with another plant structure (the parent).

intersection_of (cross-product definitions)

portions of phyllome epidermis

Added stamen epidermis intersection_of is_a epidermis, intersection_of part_of stamen. Did the same thing for other phyllome epidermises (except the various leaf abaxial and leaf adaxial stomatal epidermises). This allows stomatal complexes and prickles to be inferred is_a children of their respective portions of epidermal tissue, without creating dual parentage.

Other

Renamed terms

• cultured somatic plant embryo (PO:0000011)

• nucellar plant embryo (formerly adventitious embryo)(PO:0004537)

Renamed parts of the anther wall:

(also added pollen sac… as synonyms for all of these)

-Endothecium (PO:0020002) > anther wall endothecium (needs new definition – not a hypodermis)

-Exothecium (PO:0020004) > anther wall exothecium

-Middle layer (PO:0004700) > anther wall middle layer (definition needs work)

-primary parietal cell layer (PO:0006006) > anther wall primary parietal cell layer (definition needs work)

-secondary parietal cell layer (PO:0006007) > anther wall primary parietal cell layer (definition needs work)

-inner secondary parietal cell layer (PO:0006008) > anther wall inner secondary parietal cell layer (definition needs work)

-outer secondary parietal cell layer (PO:0006009) > anther wall outer secondary parietal cell layer (definition needs work)

-tapetum (PO:0009071) > anther wall tapetum

Changed primary name of bud scale (PO:0020054) to bud scale leaf.

Added "leaf, vascular" and "scale-like leaf" as synonyms of vascular leaf.

Added a bunch of adjective/noun synonyms. For example, archegonium egg cell as synonym for archegonial egg cell, antheridial jacket layer as synonym of antheridium jacket layer. At some point, the names should be normalized.

Miscellaneous Changes

Made pollen sac part_of microsporophyll, instead of part_of anther, and added anther has_part pollen sac.

Made anther wall is_a microsporangium wall

Made nucellar epidermis (PO:0008006) is_a megasporangium exothecium

Removed anther wall tapetum develops-from anther wall inner secondary parietal cell layer. Made is_a microsporangium tapetum.

Removed modified aleurone part_of aleurone layer, because it was already is_a aleurone layer.

Added Spanish synonyms for plant cell and plant embryo, but accented characters don't display properly in Amigo.

Added "portion of … tissue" as synonyms to several tissue types of tissue that had single word names (like epidermis, collenchyma).

• Changed names of child terms of sporangium/spore capsule:

PO:0025093 Moss capsule annulus > spore capsule annulus

PO:0025231 Moss capsule columella > spore capsule columella

PO:0025229 Moss capsule valve>spore capsule valve

Added anther lobe as narrow synonym of pollen sac. Was there on the old term, but didn’t get transferred when it was obsoleted and replaced.

Made theca is_a collective organ part structure, part of anther, has_part pollen sac.

Made microsporocyte part of microsporangium, instead of part of microsporocyte. Made sporocyte part of sporangium.

Added synonyms to vascular leaf (frond, needle-like leaf) and non-vascular leaf (phyllid, gametophyll, gametophytic leaf).

Moved juvenile, transition and adult leaf from vascular leaf to leaf. Also simple leaf and compound leaf.

Moved leaf aerenchyma, leaf mesophyll, leaf lamina, leaf margin, leaf intercalary meristem and leaf sheath from part_of vascular leaf to part_of leaf.

Moved leaf endodermis from part_of leaf to part_of vascular leaf.\

Add subsets for bryophytes, pteridophytes and gymnosperms (in addition to angiosperms)

Add new relation participates_in

Removed has_part relations from all pairs of terms that has reciprocal has_part/part_of relations

Updated definition of radicle. Removed radicle part_of embryo axis, added embryo axis has_part radicle.

Updated definition of hypocotyl and made it is_a stem internode, instead of is_a cardinal organ part.

Updated definition of epicotyl and made it is_a stem internode, instead of is_a embryonic plant structure.

Made hypocotyl-root junction is_a cardinal organ part. Already part of embryo axis.

Made mesocotyl is_a stem internode. Did not change definition, need to wait for discussion.

Made embryonic leaf is_a leaf, part_of embryo.

Made plumule is_a terminal bud, part_of embryo.

Made scutellar node is_a stem node, part_of embryo axis.

Added formal relations for: sporophyte replaced_by saprophytic phase and gametophyte replaced by gametophytic phase. Couldn't do this for the previous release because of separate files. Did not add replaced by relation for seedling, b/c there is not seedling phase yet.

Updated definition of embryo sac.

Updated definitions of archegonium egg cell, embryo sac egg cell, antheridium sperm cell, and pollen sperm cell

Added vascular leaf and non-vascular leaf part_of vascular and non-vascular shoot system, respectively.

Changed embryo to plant embryo.

Removed embryonic axis has_part radicle, has_part hypocotyl, has_part epicotyl, hypocotyl-root junction, has_part root meristem (b/c not true in all plants)

Added prothallium as narrow synonym of whole plant.

Added appropriate subsets for apical cell terms and other terms.

Changed theca (PO:0009069) to anther theca

Made sporangium (PO:0025094) is_a plant organ instead of is_a cardinal organ part.

Made female archesporial cell (PO:0006015) and male archesporial cell (PO:0006014) children of archesporial cell (PO:0030056)