Difference between revisions of "PO Annotation Extensions (column 16)"
| Line 1: | Line 1: | ||
| + | '''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 [http://wiki.geneontology.org/index.php/Annotation_Cross_Products GO wiki]. | 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 [http://wiki.geneontology.org/index.php/Annotation_Cross_Products GO wiki]. | ||
| − | Each PO annotation pairs a single gene product to a single term from the | + | 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 [http://obofoundry.org OBO ontologies], or they could be gene products. |
| + | |||
| + | This page describes column 16 in the gene annotation file (see [http://www.geneontology.org/GO.format.gaf-2_0.shtml GAF 2.0 format] and the PO wiki page on [[Annotation_Association_File_Format]]0, 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" [http://wiki.geneontology.org/index.php/Category:Cross_Products 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 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 (see example 1), for linking a structure to a specific growth or developmental stage, when that link does not already exist or cannot be inferred (example 2), for specifying spacial relations that may be present in the experiment being annotated, but that are not specified in the PO (example 3). | ||
| − | + | ==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 [http://www.geneontology.org/GO.format.gaf-2_0.shtml GAF 2.0 format] web page. | |
Revision as of 13:42, 13 June 2011
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 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 (see example 1), for linking a structure to a specific growth or developmental stage, when that link does not already exist or cannot be inferred (example 2), for specifying spacial relations that may be present in the experiment being annotated, but that are not specified in the PO (example 3).
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.
