Summary of changes to the Plant Ontology Oct2010 - Revision history

Cooperl: /* New or redefined second and third level terms */

2011-05-20T21:00:14Z

New or redefined second and third level terms

Cooperl: /* Changes to the top level */

2011-05-20T20:58:29Z

Changes to the top level

Rwalls: moved Summary of changes to the Plant Ontology to Summary of changes to the Plant Ontology Oct2010: conflicts with other summary of changes pages

2010-12-15T14:54:23Z

moved Summary of changes to the Plant Ontology to Summary of changes to the Plant Ontology Oct2010: conflicts with other summary of changes pages

Cooperl: /* Organization and summary of changes to the Plant Ontology (PO) */

2010-10-13T02:35:36Z

Organization and summary of changes to the Plant Ontology (PO)

Rwalls: changed summary of /* Plant Growth and Developmental Stage Ontology (PGDSO) */ so it reflects the current structure

2010-10-08T12:35:39Z

changed summary of Plant Growth and Developmental Stage Ontology (PGDSO): so it reflects the current structure

Rwalls at 12:28, 8 October 2010

2010-10-08T12:28:31Z

Rwalls: /* Changes to the top level */

2010-09-30T18:33:49Z

Changes to the top level

Rwalls: /* Changes to the top level */

2010-09-27T17:57:00Z

Changes to the top level

Rwalls: /* Structures that are specific to the gametophyte or sporophyte phase */

2010-09-27T17:56:24Z

Structures that are specific to the gametophyte or sporophyte phase

Rwalls: /* Structures that are specific to the gametophyte or sporophyte phase */

2010-09-27T16:43:42Z

Structures that are specific to the gametophyte or sporophyte phase

@@ Line 69: / Line 69: @@
 '''Descendants of whole plant:'''
-The only is_a children of whole plant are embryo, female gametophyte, male gametophyte and seed. The term seedling was made obsolete and annotation for seedling should use whole plant and the PGDSO term seedling growth (PO:0007131).
+The only is_a children of whole plant are embryo, female gametophyte, male gametophyte and seed. The term '''seedling PO:0008037''' was made obsolete and annotation for seedling should use whole plant (PO:0000003) and the PGDSO term seedling growth (PO:0007131).
 All structures (except in vitro structures) have a ''part_of'' relations rooted in whole plant.

@@ Line 34: / Line 34: @@
 In the previous version of the PSO, the top level was organized around the traditional characterization of plant anatomical structures (cell, tissue, organ, and whole plant), plus the classes gametophyte, sporophyte, and ''in vitro'' cultured cell, tissue and organ.
-After extensive discussion, the terms gametophyte (PO:0009004) and sporophyte (PO:0009003) were subsumed within whole plant. This was achieved by making gametophyte and sporophyte obsolete, with a suggestion to consider whole plant. For future releases, plant structures that are specific to the gametophytic or sporophytic phase will have a ''participates_in'' relation to the appropriate phase. Click this link for a more detailed discussion of the [[decision to obsolete sporophyte and gametophyte]] and how to annotate structures that are specific to one of those phases.
+After extensive discussion, the terms '''gametophyte (PO:0009004)''' and '''sporophyte (PO:0009003)''' were subsumed within whole plant. This was achieved by making gametophyte and sporophyte obsolete, with a suggestion to consider whole plant. For future releases, plant structures that are specific to the gametophytic or sporophytic phase will have a ''participates_in'' relation to the appropriate phase. Click this link for a more detailed discussion of the [[decision to obsolete sporophyte and gametophyte]] and how to annotate structures that are specific to one of those phases.
 The terms whole plant (PO:0000003) and plant cell (PO:0009002) were retained. Organ, tissue, and ''in vitro'' cultured cell, tissue and organ were also retained, but renamed plant organ (PO:0009008), portion of plant tissue (PO:0009007), and ''in vitro'' plant structure (PO: 0000004), respectively. Two new top-level terms were added: cardinal organ part (PO:0025001) and collective plant structure (PO:0025007). These new terms were necessary, because there are many commonly-referenced plant structures that are not a cell, organ, or tissue.

@@ Line 2: / Line 2: @@
 =Organization and summary of changes to the Plant Ontology (PO)=
-January through September 2010
+January through October 2010
 '''Curators''' (in alphabetical order): Cooper, Laurel D. (1); Elser, Justin (1); Gandolfo, Maria A. (2); Jaiswal, Pankaj (1), Mungall, Christopher (3); Smith, Barry (4); Stevenson, Dennis W. (5); Walls, Ramona L. (5)

@@ Line 26: / Line 26: @@
 The PGDSO had two main branches: plant structure developmental stages and whole plant growth stages. No changes were made to these branches.
-A new top-level term was added: plant life cycle phase (PO:0028001). This term has two new children: sporophytic phase (PO:0028002) and gametophytic phase (PO:0028003). Structures from the PSO that occur in only one of these phases will have a ''participates_in'' relation to the appropriate phase.
+Two new upper level terms were added: sporophytic phase (PO:0028002) and gametophytic phase (PO:0028003). Both are children of whole plant growth stage (PO:0007033). Structures from the PSO that occur in only one of these phases will have a ''participates_in'' relation to the appropriate phase.
 ==Plant Structure Ontology (PSO)==

← Older revision		Revision as of 12:28, 8 October 2010
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−	Back to [[2010 Release ~~Notes~~ Page]]	+	Back to [[2010 Release Page]]

	=Organization and summary of changes to the Plant Ontology (PO)=		=Organization and summary of changes to the Plant Ontology (PO)=

← Older revision	Revision as of 14:54, 15 December 2010
(No difference)

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 The terms whole plant (PO:0000003) and plant cell (PO:0009002) were retained. Organ, tissue, and ''in vitro'' cultured cell, tissue and organ were also retained, but renamed plant organ (PO:0009008), portion of plant tissue (PO:0009007), and ''in vitro'' plant structure (PO: 0000004), respectively. Two new top-level terms were added: cardinal organ part (PO:0025001) and collective plant structure (PO:0025007). These new terms were necessary, because there are many commonly-referenced plant structures that are not a cell, organ, or tissue.
-All top-level terms, including the root term plant structure (PO:0009011) were redefined, based on consultation of multiple plant anatomy books and consensus of the curators. All top-level terms except ''in vitro'' plant structure have a ''part_of'' relation to whole plant. It was decided that ''in vitro'' plant structures should remain separate from plant structures that occur ''in vivo'', thus ''in vitro'' structures may have a ''derives_from'' relation to other plant structures, but not an ''is_a'' or ''part_of'' relation.
+All top-level terms, including the root term plant structure (PO:0009011) were redefined, based on consultation of multiple plant anatomy books and consensus of the curators. The definitions were written so that the top level structure can accept new descendent terms from non-angiosperm plants. All top-level terms except ''in vitro'' plant structure have a ''part_of'' relation to whole plant. It was decided that ''in vitro'' plant structures should remain separate from plant structures that occur ''in vivo'', thus ''in vitro'' structures may have a ''derives_from'' relation to other plant structures, but not an ''is_a'' or ''part_of'' relation.
 Discussions are underway to have all plant cell terms mirrored in the cell ontology (CL) and all ''in vitro'' plant structure terms mirrored in the Ontology for Biomedical Investigation (OBI).

← Older revision		Revision as of 17:56, 27 September 2010
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	For a discussion of the options that were explored for how to order the child terms of bud, see the page [[Bud]]		For a discussion of the options that were explored for how to order the child terms of bud, see the page [[Bud]]
−
−	~~===Structures that are specific to the gametophyte or sporophyte phase===~~
−
−	~~Although this release of the PSO retains much of its angiosperm bias, the upper-level ontology structure is now ready to accommodate~~
−	~~terms from other plant groups. All of the top-level terms (plant cell,~~
−	~~plant organ, portion of plant tissue, etc.) were re-defined precisely so~~
−	~~that they could accept descendent terms from any group of plants, not just~~
−	~~angiosperms. Rather than grouping lower-level terms by the taxa in which~~
−	~~they occur, we chose to group them based on structural similarity. Although~~
−	~~we have not added many lower-level terms that are specific to plants outside~~
−	~~the angiosperms, we have included a few examples of how our schema would~~
−	~~work. For example, the term axial cell (PO:0000081) has descendents hydroid~~
−	~~(PO:0025032) and xylem element (PO:0000273). Hydroids, which occur in the~~
−	~~gametophytes of bryophytes, would have a participates_in relation to~~
−	~~gametophytic phase, while xylem elements, which occur in the sporophytes of~~
−	~~vascular plants, would have a participates_in relation to sporophytic phase.~~
−	~~Since we have not yet included the participates_in relation in this~~
−	~~revision, these relations are currently described in the comments. Another~~
−	~~example includes the children of leaf (PO:0025034): vascular leaf~~
−	~~(PO:0009025) participates_in sporophytic phase, and non-vascular leaf~~
−	~~(PO:0025075) participates_in gametophytic phase. Notice that by choosing to~~
−	~~group terms by structural similarity, we are not required to make hypotheses~~
−	~~about evolutionary homology (which usually is unknown). This allows~~
−	~~researchers to compare gene expression in similar structures, in order to~~
−	~~evaluate their own hypotheses.~~

	===General changes===		===General changes===

@@ Line 87: / Line 87: @@
 ===Structures that are specific to the gametophyte or sporophyte phase===
-Although this release of the PSO retains much of its angiosperm bias, we
+Although this release of the PSO retains much of its angiosperm bias, the upper-level ontology structure is now ready to accommodate
 terms from other plant groups.  All of the top-level terms (plant cell,
 plant organ, portion of plant tissue, etc.) were re-defined precisely so