Decision to obsolete sporophyte and gametophyte

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

Back to Summary_of_changes 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.