October 2010 Release Page

New version of the PO released October 2010

The latest release of the Plant Ontology is now available on our Ontology Browser at http://www.plantontology.org. The main goal of this revision was to create an ontological framework that will encompass all plants, unlike previous versions that covered only flowering plants. The revisions include 83 new terms, revised definitions and modified child-parent relationships.

The upper-level parent terms of the Plant Structure Ontology (PSO) (version #0409) have been extensively re-organized, with ‘in vitro cultured cell, tissue and organ’, ‘organ’ and ‘tissue’ all being renamed. Two new upper-level parent terms have been added to the PSO, ‘collective plant structure’ and ‘cardinal organ part’ (version #1010). A major change that users will notice is the deletion of two top-level plant structure terms: ‘sporophyte’ and ‘gametophyte’, which are now narrow synonyms of whole plant. As an alternative, two new terms ‘sporophytic phase’ and ‘gametophytic phase’ were added to the Plant Growth and Development Stage Ontology (PGDSO). These terms describe the alternating phases of the life cycle of all plants, as well the associated plant structures. These terms will be used to describe structures that occur only during a specific growth phase.

The second and third level child terms in the PSO ontology also received extensive revision.

For example, we redefined the term ‘tuber’ (PO:0004543) and added many new children to it and its parts. This provided a test case for how to build relationships among the parts of a complex structure while at the same time providing terms that are needed to annotate potato genes.

Throughout the revision process, the curators worked to incorporate advances in ontology design and construction. These included the use of logical text and relational definitions and references to external ontologies where appropriate.

An effort was made to insure that widely studied plant structures such as flower, stem and gamete had working definitions and the correct parentage. Although this release contains only a few new terms that are specific to taxa outside angiosperms, we expect that the new structure will enable incorporation of terms originating from all plant species, including non-angiosperms in future releases.

For more information about the release and details on the changes made to the ontology, please visit http://wiki.plantontology.org:8080/index.php/Summary_of_changes_to_the_Plant_Ontology.

Your feedback on the release is welcome. Please use the Feedback Link: http://www.plantontology.org/db/feedback/send_feedback? or contact us at po-discuss@plantontology.org.

Beta version of the PO released August 2010

A beta version of the latest release of the Plant Ontology is available to user groups, interested parties and reviewers on our AmiGO Browser.

The primary structure of the PO, including one branch for Plant Structure Ontology (PSO) and one branch for Plant Growth and Developmental Stage Ontology (PGDSO), has not changed.

The main goal of this round of revisions was to create a framework that could accept new terms from all plants, with the focus on the re-organization of the PSO and minor changes (addition of only three new high-level terms) to the PGDSO.

In the PSO, new top-level terms were added, new definitions were written for many terms (including all top-level terms) and the second an third levels of the ontology were extensively re-organized. An effort was made to insure that widely studied plant structures such as flower, stem, and gamete had working definitions and correct parentage.

Detailed revisions, including the addition of many new terms, were made to the PSO term tuber (PO:0004543) and its is_a and part_of children. This provided a test case for how to build relationships among the parts of a complex structure while at the same time providing much needed terms for annotation of potato genes.

Throughout the revision process, the curators worked to incorporate new advances in ontology design and construction. These included the use of logical text and relational definitions and references to external ontologies where appropriate.

Although this release contains only a few new terms that are specific to taxa outside angiosperms, the new structure will enable us to incorporate these terms in future releases.

The POC is seeking feedback on the beta release. Please use the Feedback Link or contact us at po-discuss@plantontology.org.

Summary of Changes

For more information about the release, please visit our wikipage with a Summary of changes to the Plant Ontology.

How to Provide Feedback

You can send feedback via email from our Feedback link. This is available in the upper left corner of any page on the beta browser. If you have comments on a specific page or term, please include the url of the page/term you are referring to in the appropriate box of the feedback form. Be sure to include your email on the feedback form, so we can contact you with any questions.

You can also contact us at po-discuss@plantontology.org.

All comments from the feedback page go to the po-discuss mailing list. Archives of this list are available at the po-discuss archive.