Tutorial: SPARC Portal Map Annotation Tool

Flatmap Provenance

SCKAN version:
https://github.com/SciCrunch/NIF-Ontology/tree/sckan-2024-03-26

Published on:
September 10, 2024

View publication:
https://github.com/AnatomicMaps/human-flatmap/blob/f4baf0395ece6b1b2606c55b292124ad6620a5f4/male.manifest.json

Table of Contents

• Quick start tutorials
• Get authorized and log in
• Adding evidence
  • Support an existing connection
  • Support an existing feature
  • Add a new connection
  • A new anatomical feature
• Add a new connection
  • Connection between a new and an existing feature on the human female flatmap
  • Connection when I only know the origin and destination but not the route on the male flatmap
• Suggest Corrections for Incorrectly Routed Connections
• Suggest an Incorrectly Located Anatomical Feature
• Review the actions taken based on my annotations
• Compare Suggested New Connections to Existing Connections
• Review Annotations as a map curator

Quick start tutorials

The following tutorials give quick start guides to achieving specific tasks using the map annotation tool. Full details on the map annotation tooling is available at SPARC Portal Annotation Tool .

Get authorized and log in

Before making any updates, ensure you have the necessary permissions to access and edit annotations. Follow the authorization instructions to gain access.
Once authorized, log in to the SPARC Portal using your credentials.

Adding evidence

Support an existing connection

1. Locate the Map and Connection:
   Navigate to the map containing the connection you wish to support. Once on the correct map, identify and select the desired connection.
2. Open the Annotation Sidebar:
   Click on the connection to open the Annotation Sidebar. For example, the figure below shows the Rat Flatmap with an annotation sidebar for a selected connection.

3. Enter Edit Mode:
   Click on the pencil icon to open the Suggest changes Dialog. This dialog provides fields for updating the feature's annotations.

4. Provide Additional Evidence:
   In the Evidence section, you can select the appropriate evidence type to support your update. Options include:
   • DOI (Digital Object Identifier)
   • PMID (PubMed Identifier)
   • "No Evidence" (if applicable)
     Enter the evidence reference in the provided input box.

5. Add Comments:
   Use the Comment box to include any relevant notes, clarifications, or justifications for the update. Comments are optional but highly encouraged for transparency and collaboration.
6. Submit Your Changes:
   Once all necessary updates are made, click the Submit button to save your changes. Be sure to review all entered information for accuracy before submitting your changes.

Support an existing feature

To update or provide additional details for an existing feature, follow these steps:

1. Locate the Feature:
   Navigate to the map interface and locate the feature you wish to support.
2. Open the Annotation Sidebar:
   Click on the feature to open the Annotation Sidebar. For example, the figure below shows the Rat Flatmap with an annotation sidebar for a selected anatomical feature. In this sidebar, verify the Feature Annotations to ensure that it matches the feature you intend to support.

3. Add and submit annotation:
   Upload your supporting evidence, leave comments and submit your changes. For detailed instructions, please refer to "Adding Evidence - Support an Existing Connection, Steps 3-6."

Add a new connection

To establish evidence for a new connection on the map, follow these detailed steps:

1. Define the Connection Path:
   Using the draw tool to create a new connection by choosing the LineString and defining its path on the map. Ensure that the line begins and ends at specific map features to establish connectivity.
2. Finalize the Drawing:
   After setting the points, a Finalize Drawing dialog will appear, as shown in the figure below. The dialog displays the details of the drawn LineString, showing the connected parts, such as "Pterygopalatine ganglion to nasal cavity mucosa via nasopalatine nerve" and the "olfactory bulb." Review the connection path and make adjustments if necessary. Once you are satisfied with the route, confirm the drawing to finalize the line.

3. Annotate the New Connection:
   Upload your supporting evidence, leave comments and submit your changes.
   For detailed instructions, please refer to "Adding Evidence - Support an Existing Connection, Steps 3-6."

A new anatomical feature

To create evidence for a new anatomical feature, follow the steps below:

1. Outline the Feature's Area:
   In the drawing tools interface, choose the Polygon Tool. This tool allows you to outline and highlight the area of the new anatomical feature on the map.
   ![null][image6]

2. Open the Annotation sidebar:
   Once the shape is complete, an Annotation sidebar will appear. This sidebar allows you to add supporting evidence and provide details about the new anatomical feature.
3. Provide Supporting Evidence:
   Upload your supporting evidence, leave comments and submit your changes.
   For detailed instructions, please refer to "Adding Evidence - Support an Existing Connection, Steps 3-6."

Add a new connection

Connection between a new and an existing feature on the human female flatmap

1. Navigate to the human female flatmap:

Choose "Human Female" from the Species dropdown menu located in the top-left corner of the AC flatmap.

2. Draw a new feature:

Use the Polygon Tool to draw a new feature. For detailed instructions, please refer to "Adding Evidence-A new anatomical feature".

3. Add a new connection:

Use the LineString Tool to draw a new connection. For detailed instructions, please refer to "Adding Evidence-A new connection".

4. Provide Supporting Evidence:
   On each step, upload your supporting evidence, leave comments and submit your changes.
   For detailed instructions, please refer to "Adding Evidence - Support an Existing Connection, Steps 3-6."

   Connection when I only know the origin and destination but not the route on the male flatmap

5. Navigate to the human male flatmap:

Choose "Human Male" from the Species dropdown menu located in the top-left corner of the AC flatmap.

2. Mark the Origin and Destination:

In the drawing tools interface, choose the Point Tool, which allows you to place points on the flatmap. Click on the map to mark the Origin location of the connection, and in the annotation sidebar that appears, add any relevant details, such as the anatomical structures or regions it represents. Next, mark the Destination by placing a second point at the destination location.

3. Draw an Approximate Route:

Add a placeholder connection using the LineString Tool with approximate routing. For detailed instructions, please refer to "Adding Evidence-A new connection."

4. Provide Supporting Evidence:

When uploading evidence, use the comment field to note that the drawn route is approximate or unclear, and explain the reasoning behind it. Include relevant references or expert input for context, then submit your changes. For detailed instructions, see "Adding Evidence - Support an Existing Connection, Steps 3-6."

Suggest Corrections for Incorrectly Routed Connections

1. Identify the Incorrect Connection:

Locate the connection on the flatmap that you believe is incorrectly routed.

2. Highlight the Issue:

Click on the connection to open the Annotation Sidebar and add a comment describing the issue. For detailed instructions, please refer to "Adding Evidence-Support an existing connection."

3. Edit the Incorrect Route (Optional):

If the incorrect connection is a new annotation drawn using the annotation tool and has not yet been published, it can be edited. Use the Edit mode to edit and update the incorrect route.

4. Propose a New Route (Optional):

If the incorrect connection is published or you prefer to retain the incorrect route but also suggest the correct one, use the LineString Tool to draw the corrected route and annotate it. For detailed instructions, please refer to "Adding Evidence-A new connection."

Suggest an Incorrectly Located Anatomical Feature

1. Identify the Incorrect Feature:

Locate the feature on the flatmap that you believe is incorrectly placed.

2. Highlight the Issue:

Click on the feature to open the Annotation Sidebar and add a comment describing the issue. For detailed instructions, please refer to "Adding Evidence-Support an existing feature."

3. Propose a Corrected Location:

Use the Polygon Tool to draw the corrected route and annotate it. For detailed instructions, please refer to "Adding Evidence-A new anatomical feature."

Review the actions taken based on my annotations

1. Filter your annotations:

Use the Annotated By to switch the display of the drawn annotation features, which are annotated by either Anyone, Me, or Others.

2. Review your annotations:

Review each of your annotations and make adjustments if necessary.

Compare Suggested New Connections to Existing Connections

1. Locate the New and Existing Connections:

Use the search or filter tools to find both the newly suggested connection and similar existing connections.

2. Open the Connections:

Click on each connection to open their respective Annotation Sidebars.

3. Compare Details:

Review the annotations, routing, and evidence provided for each connection.

4. Annotate Differences:

If discrepancies are found, add notes or comments highlighting the differences and potential impacts. For detailed instructions, please refer to "Adding Evidence-Support an existing feature."

Review Annotations as a map curator

1. Filter annotations:

Use the Annotated By to switch the display of the drawn annotation features, which are annotated by either Anyone, Me, or Others.

2. Review annotations:

Review each annotation and make adjustments if necessary.

3. Provide Feedback (Optional):

Add comments or annotations for further clarification, if necessary.