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20 Annotations

An Annotation is a reference with additional information, which you can add to a Pathway Element to provide additional information.

Required information for an Annotation are:

  1. Value - the term
  2. Type - the Annotation type

Optional information for an Annotation are:

  1. Identifier - the identifier for a database for this Annotation.
  2. Database - the database for this Annotation.
  3. Url link - the url link for this Annotation.

20.1 Annotation Types

  • Ontology (e.g.subcellular location)
  • Taxonomy (e.g.organism)
  • Undefined (other)

20.2 Databases/DataSources

There are a number of possible DataSources for Annotations. To learn more, please see BridgeDb.

20.3 Adding an Annotation

20.3.1 From Properties Dialog

You can navigate to the window to add an Annotation by:

  1. Double clicking on the Pathway Element.
  2. Selecting the Annotations Tab.
  3. Clicking on “New annotation” button.
  4. Enter required Annotation information.

20.3.2 From Right-Click > Add Reference > Add Annotation

You can navigate to the window to add an Annotation by:

Right-click on the Pathway Element > Add Reference > Add Annotation. Then enter required Annotation information.

## Editing an Annotation

You can navigate to the Annotations Tab Window in two ways:

  1. Double clicking on the Pathway Element and selecting the Annotations tab.
  2. Right-click on the Pathway Element > Edit Reference > Edit Annotations.

To Edit an Annotation, mouse over that Annotation and click on the Blue Edit button. Enter information as normal.

20.4 Deleting an Annotation

To Delete an Annotation, mouse over that Annotation and click on the Red Delete button.

20.5 Nested Citations and Evidences (Advanced)

An Annotation can contain nested Citations and/or Evidences which are related to or support the current Annotation. As of now, PathVisio4 does not have a user interface to support nested References. Advanced users may added nested Citations and Evidences manually by editing the GPML2021 file in a text editor.

To add a nested Citations and/or Evidences to the Annotation of a Pathway Element, you must do the following:

  1. Add a nested CitationRef with elementRef pointing to the elementId of the Citation. Add a nested EvidenceRef with elementRef pointing to the elementId of the Evidence
<AnnotationRef elementRef="a0001">
  <CitationRef elementRef="c0002" />
  <EvidenceRef elementRef="e0003" />
</AnnotationRef>
  1. The Citation and/or Evidence and all their information should be at the end of the GPML, this may also need to be added manually if this Citation and/org Evidence is not already referenced elsewhere in your pathway.
<Annotations>
  <Annotation elementId="a0001" name="thyroid cancer" type="Disease">
      <Xref identifier="1781" dataSource="DOID"/>
        <Url link="https://identifiers.org/DOID:1781"/>
  </Annotation>
</Annotations>
<Citations>
    <Citation elementId="c0002">
        <Xref identifier="7730304" dataSource="pubmed"/>
        <Url link="https://identifiers.org/pubmed:7730304"/>
    </Citation>
</Citations>
<Evidences>
    <Evidence elementId="e0003" value="experimental evidence">
        <Xref identifier="0000006" dataSource="ECO"/>
        <Url link="https://identifiers.org/ECO:0000006"/>
    </Evidence>
</Evidences>