PO Annotation Extensions (column 16)

This page is under development, and the policies herein have not yet been approved by the Plant Ontology Consortium or curators.

The use of annotation extensions in the PO is based on the usage developed by the GO. A discussion of GO's annotation extension column can be found on the GO wiki.

Each PO annotation pairs a single gene product or other object to a single term from the PO. This restricts annotators in what they can say - there must be a pre-existing term in the ontology, or one must be requested. It would be far less restrictive if the annotator could combine additional terms in a single annotation. These terms could even come from other OBO ontologies, or they could be gene products.

This page describes column 16 in the gene annotation file (see GAF 2.0 format and the PO wiki page on Annotation_Association_File_Format0, which allows additional terms to be specified to extend the meaning of an annotation. If and when an annotator chooses to do this, they are effectively creating an "on-the-fly" cross product term. We say "on-the-fly" because the combinatorial term is not added to the ontology (although it could be at a later stage, if the ontology editors choose to do do).

Uses

There are many possible cases where one might with to create annotation extensions. For now, the PO limits the use of annotation extensions to links to other PO terms and to a limited set of relation. Annotators wishing to create other types of extensions in column 16 should contact the POC curators.

Annotation extensions to other PO terms

Column 16 should be used when the appropriated part_of or participates_in relation is not specified or cannot be inferred within the PO, for example, for creating specific part_of relations when only a general part_of relation exists or for linking a structure to a specific growth or developmental stage.

Plant structures that are part_of another plant structure

The anatomical structure branch of the PO is structured with general categories of structures that are parents to more specific children. For example, vascular leaf and non-vascular leaf are children of leaf, and aerial tuber and subterranean tuber are children of tuber. Any plant structure that can only be a part of one of the specific children will have a part_of relation only to that specific child (for example, costa part_of non-vascular leaf and leaf vascular system part_of vascular leaf), while plant structures that can be part of more than one type of the specific children will have a part_of relation to the more general term (for example, leaf tip part_of leaf).

In order to prevent massive term inflation, PO curators prefer not to pre-compose all of the possible combinations of specific is_a and part_of children of more general term. For example, leaf has 15 is_a descendents (juvenile leaf, transition leaf, adult leaf, transition leaf, non-vascular leaf, vascular leaf, simple leaf, compound leaf, rosette leaf, cauline leaf, cigar leaf, embyro leaf, leaf spine, cotyledon, and flag leaf). To completely populate this branch of the ontology with leaf tip types would require the creation of 15 new terms (juvenile leaf tip, transition leaf tip, etc.), not to mention the terms for all of the other leaf parts, such as leaf lamina, leaf base, leaf epidermis, etc. Instead, column 16 can be used to post-compose any combination of is_a and part_of leaf that is needed. If it becomes clear that certain post-composed terms are being used extensively in annotations, pre-composed classes can be created.

Examples:

1. If a gene product is localized to the leaf tip of a vascular leaf, the annotator would enter "PO:0025142" (leaf tip) in column 5 for POid, and "part_of(PO:0009025)" (vascular leaf) in column 16 for the annotation extension.

2. If a gene product is localized in a callus parenchyma cell that is part of a wound response on a branch, the annotator would enter "PO:0025285" (callus parencyma cell) in column 5 for POid, and "part_of(PO:0025073)" (branch) in column 16 for the annotation extension. It might be possible to add an additional annotation extension to, e.g., participates_in(GO:0009611) (response to wounding).

Plant structures that occur during a particular growth stage

Example 2: If a gene product is localized in a leaf during senesence, the PO ID (column 5) would be leaf (PO:0009025), and the annotation extension column would contain a cross-reference to participates_in leaf senescence stage (PO:0001054).

Other types of relations to PO terms

The use of relations other than part_of and participates_in for column 16 has not yet been approved. However, there may be times when annotators wish to use other relations to post-compose PO terms using column 16.

The other relations used in the PO are:

• has_part
• develops_from
• derives_from
• adjacent_to

The PO can only specify a relation between two classes when that relation is true for every instance in every taxon in which the two classes occur (the all-some rule). That is, A has_part Bis is only specified when every A has some B as part, and A develop_from B is only specified when every A develops from some B. Because of the diversity among different plant taxa, there are many cases where a relation is valid for some taxa but not others. Although the PO cannot specify these relations, they could be added as annotation extensions.

Examples:

1. Specifying a part_of relationships that is present in the experiment being annotated, but is only present as the reciprocal has_part relation in the PO.

For example, the PO specifies inflorescence has_part flower, because every inflorescence has at least one flower as a part. However, it does not specify flower part_of inflorescence, because there are many flowers in many species that are not part of an inflorescence. If a user wanted to create an annotation for an experiment where a gene was expressed in a flower that was part of an inflorescence, s/he would enter "PO:0009046" (flower) in column 5 for the POid, and enter "part_of(PO:0009049)" (inflorescence) in column 16 for the annotation extension.

2. Specifying spacial relations that may be present in the experiment being annotated, but that are not specified in the PO.

For example, the PO specifies sporangium wall endothecium adjacent_to exothecium, because in every plant that has a sporangium wall endothecium, the endothecium is adjacent to (in permanent contact with) the exothecium. However, the PO does not specify exothecium adjacent_to sporangium wall endothecium, because there are plants that have an exothecium but no sporangium wall endothecium, and therefor the exothecium is not adjacent to the endothecium in those cases. If a user wanted to create an annotation for an experiment for a species that did have both an exothecium and a sporangium wall endothecium, and wanted to specify that a gene was expressed in an exothecium that was adjacent to a sporangium wall endothecium, s/he would enter "PO:0030073" (exothecium) in column 5 for the POid, and enter "adjacent_to(PO:0030049)" (sporangium wall endothecium) in column 16 for the annotation extension.

This type of annotaion extension is still under development, and users should contact the PO curators if they wish to use column 16 in this way.

Annotation extensions to terms from other ontologies or databases

Please contact the PO to discuss the type of cross product you wish to create, so that we can work out formatting specifications.

Usage specifications

See the Annotation_Association_File_Format PO wiki page and the GAF 2.0 format web page.