The <ontology> tag enables the autocompletion feature on an input field based on the ontology file specified. There can be zero or more ontologies per field.
Name | Description | Legal Values | Required | Default |
name |
This is the name that is displayed in the drop-down chooser box for ontology selection during autocompletion in the Data Entry section. |
any text value | yes | |
file | This is the name of the file containing the ontology. You can specify the filename by itself or a URL of a repository to check for updates. | any text value | yes | |
repos-subdir |
The location (such as a subdirectory) of the file in the specified repository. If not included, then no checks against the obo-repository will be performed. [RETIRED. Incorporated into file.] |
any text value |
no | |
slim | [not sure yet how this works...] |
any text value |
no | |
is-postcomp-rel | The ontology file specified here will be used to populate the relationships for postcomposition. Typically this will the the relationship.obo file. Specifying the is-postcomp-rel triggers Phenote to allow the post-compostion feature along with a button to display. |
|
no | false |
Each <ontology> element specifies one ontology to be used with the autocompletion feature in a single <field> element. To include the same ontology in a separate <field> element, it must be listed in both. The order in which the <ontology> elements are listed within the <field> is the order they are displayed in the drop-down chooser box. A URL specified in the filename can be different for each ontology, so that each ontology can be checked against different repositories, if desired.
<ns:field name="Entity" syntax-abbrev="E" enable="true">
<ns:ontology name="Relationship" file="relationship.obo" repos-subdir="OBO_REL" is-postcomp-rel="true"/>
<ns:ontology name="GO" file= "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/genomic-proteomic/gene_ontology.obo"/>
<ns:ontology name="CHEBI" file= "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
</ns:field>
In this example there are two ontologies specified: GO and CHEBI. The resulting input item would display a drop-down chooser box with the names GO and CHEBI. The autocompletion on that field would query the gene_ontology.obo and chebi.obo ontologies. Additionally, because is-postcomp-rel is specified, this field would allow for post composition, and those terms would draw their relationships from the relationship.obo ontology.
The resulting element would look like this in the Data Entry panel: