Decision to obsolete sporophyte and gametophyte - Revision history

Cooperl at 20:25, 2 November 2010

2010-11-02T20:25:34Z

Rwalls at 17:55, 27 September 2010

2010-09-27T17:55:53Z

Rwalls: /* Structures that are specific to the gametophyte or sporophyte phase and structures from non-angiosperm taxa, */

2010-09-27T17:55:21Z

Structures that are specific to the gametophyte or sporophyte phase and structures from non-angiosperm taxa,

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

2010-09-27T17:54:11Z

Structures that are specific to the gametophyte or sporophyte phase

Rwalls at 17:32, 27 September 2010

2010-09-27T17:32:39Z

Rwalls at 16:40, 27 September 2010

2010-09-27T16:40:06Z

Rwalls at 16:39, 27 September 2010

2010-09-27T16:39:41Z

Rwalls at 16:38, 27 September 2010

2010-09-27T16:38:39Z

Rwalls: Created page with 'Although this release of the PSO retains much of its angiosperm bias, we feel that the upper-level ontology structure is now ready to accommodate terms from other plant groups. …'

2010-09-27T16:38:00Z

Created page with 'Although this release of the PSO retains much of its angiosperm bias, we feel that the upper-level ontology structure is now ready to accommodate terms from other plant groups. …'

New page

Although this release of the PSO retains much of its angiosperm bias, we
feel that 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.

As part of the upper level re-structuring, we made the decision to obsolete
the terms gametophyte and sporophyte and subsume them within whole plant.
This decision was made for several reasons. First, it allows for a cleaner
ontology structure. If there is a structure that can occur in either
gametophytes or sporophytes (such as stem or leaf), then in order to have
the correct part_of relations, we would have to have two new terms (e.g.,
gametophyte stem and sporophyte stem). This would quickly lead to
unnecessary term inflation. Unlike the previous release of the PO, in which
most structures had part_of relations that were ultimately rooted in
sporophyte, all plant structures now have their part_of relations (their
partonomy, as it were) rooted in whole plant. Second, we felt that it was
biologically appropriate to subsume gametophyte and sporophyte within whole
plant, since all gametophytes and all sporophytes are whole plants, in the
sense that they are genetically distinct individuals, even if they may be
dependent upon or even contained within the other generation in some
instances. We retained the terms male gametophyte and female gametophyte (as
is_a children of whole plant), because we felt that these were structurally
distinct instances of whole plant that could not be described solely by the
temporal distinction of the life cycle phase in which they occur.

With the new PO structure, if someone searches for the term sporophyte or
gametophyte, they will come up as narrow synonyms of whole plant. Although
the web-based browser does not currently have the capacity to display
obsolete terms, users who access the PO flat file (via OboEdit, or a text
editor) can see that the obsolete terms sporophyte or gametophyte both have
a suggestion to consider whole plant and consider sporophytic phase or
gametophytic phase. As an example of how we would expect users to create
annotations with these terms, take the paper 'A Novel Plant Major Intrinsic
Protein in ''Physcomitrella patens'' Most Similar to Bacterial Glycerol
Channels' from Plant Physiology
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1203378/). In this study, DNA
was isolated from gametophytes of ''P. patens'', and a gene encoding GlpF-like
intrinsic protein (GIP1;1) was expressed. Thus, GIP1;1 would have an
annotation to both PO:0000003, whole plant, and PO:0028003, gametophytic
phase, for P. patens. Annotations to more specific structures that occur
only in bryophyte gametophytes (such as hydroids) would be associated with
both the specific structure in the PSO and gametophytic phase in the PGDSO.
Thus, it is not necessary to have more specific developmental stages for
mosses or other plants, in order to annotate their specific structures.
Although the participates_in relation will allow genes associated with the
structure to automatically be associated with gametophytic phase once the
two ontologies are integrated, it is best to attach annotations to both
terms, in case a user is viewing one of the ontologies separately.

← Older revision		Revision as of 20:25, 2 November 2010
Line 1:		Line 1:
−	(for 9/2010 release)	+	(for October 2010 release)

	As part of the upper level re-structuring, we made the decision to obsolete		As part of the upper level re-structuring, we made the decision to obsolete

← Older revision		Revision as of 17:55, 27 September 2010
Line 1:		Line 1:
		+	(for 9/2010 release)
		+
	As part of the upper level re-structuring, we made the decision to obsolete		As part of the upper level re-structuring, we made the decision to obsolete
	the terms gametophyte and sporophyte and subsume them within whole plant.		the terms gametophyte and sporophyte and subsume them within whole plant.

@@ Line 45: / Line 45: @@
-===Structures that are specific to the gametophyte or sporophyte phase and structures from non-angiosperm taxa, ===
+===Structures that are specific to the gametophyte or sporophyte phase and structures from non-angiosperm taxa===
 The upper-level structure of the PO is now ready to accommodate
-terms from other plant groups.  All of the top-level terms (plant cell,
+terms from all 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

← Older revision		Revision as of 16:40, 27 September 2010
Line 1:		Line 1:
−	~~Although this release of the PSO retains much of its angiosperm bias, we~~
−	~~feel that 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.~~
−
	As part of the upper level re-structuring, we made the decision to obsolete		As part of the upper level re-structuring, we made the decision to obsolete
	the terms gametophyte and sporophyte and subsume them within whole plant.		the terms gametophyte and sporophyte and subsume them within whole plant.

@@ Line 45: / Line 45: @@
-===Structures that are specific to the gametophyte or sporophyte phase===
+===Structures that are specific to the gametophyte or sporophyte phase and structures from non-angiosperm taxa, ===
-Although this release of the PSO retains much of its angiosperm bias, the upper-level ontology structure is now ready to accommodate
+The upper-level structure of the PO 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
+they occur, they are grouped based on structural similarity. Although
-we have not added many lower-level terms that are specific to plants outside
+this release contains few lower-level terms that are specific to plants outside
-the angiosperms, we have included a few examples of how our schema would
+the angiosperms, there are a few examples of how the schema would
-work. For example, the term axial cell (PO:0000081) has descendents hydroid
+work.
 (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
+Since the PO does 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
+group terms by structural similarity, POC curators make hypotheses
 about evolutionary homology (which usually is unknown). This allows
 researchers to compare gene expression in similar structures, in order to

← Older revision		Revision as of 17:32, 27 September 2010
Line 43:		Line 43:
	terms, in case a user is viewing one of the ontologies separately.		terms, in case a user is viewing one of the ontologies separately.

		+
		+
		+	===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.

@@ Line 24: / Line 24: @@
 As part of the upper level re-structuring, we made the decision to obsolete
 the terms gametophyte and sporophyte and subsume them within whole plant.
 This decision was made for several reasons. First, it allows for a cleaner
@@ Line 71: / Line 66: @@
 two ontologies are integrated, it is best to attach annotations to both
 terms, in case a user is viewing one of the ontologies separately.