Creating a Workspace

How to Import a Workspace

  1. Click the Hamburger Button located at the top of the Synapse home screen.
  2. Users can drag and drop a table they have already created outside of Synapse – file types that can be used are listed at the bottom of the window
  3. Your file will automatically be added to your list of Workspaces. 

Creating a New Workspace 

  1. Click the Hamburger Button located at the top of the Synapse home screen. 
  2. From the drop down menu, click the blue Create Empty Workspace button at the bottom of the drop down. 
  3. Your New Workspace will now appear on your home screen for you to create and design. 

Load Table-Based Ontologies into Layar

A quick guide on how to upload your own ontologies into Vyasa Layar for implementation.

Table-Based Files (.csv, .xls, etc)

Step 1. Add your ontology file to Layar using one of your connectors (or local upload).

  • The ontology file can be any table-based file (for example, .csv, .tsv, .xls, etc are all compatible).
  • The system currently does not detect multiple sheets within your file. If you have multiple tabs of tables within your file, please save each sheet as a separate file before uploading to Layar.

Step 2. Once uploaded, click the file of interest within Layar.

Step 3. Click the vertical three-dot icon on any of the column headers within the table.

Step 4. Select “Create Ontology“.

Step 5. Give your ontology a name, and identify which column will populate the following properties:

  • Label (Required): The column you assign to this property will be considered the preferred label. These are the labels you will see when you view and navigate your ontology in the Ontologies section of Layar.
  • Synonyms: You can assign multiple columns to this property. All columns assigned to the synonyms property will be displayed as synonyms for a term. This synonym property is further used when running an explosive search in Layar. For example, the term “Tachycardia” has 48 synonyms for different uploaded ontologies uploaded to Layar, which you can expand your search to include.

Note: If any of your columns list out multiple synonyms as a list, identify what delimiter should be used to separate each term out as an independent synonym.For example: The list “Heart attack | Acute cardiac arrest | cardiac myopathy”, which are synonyms for “Heart Attack”, is pipe (|) delimited.

  • ID: If there is an ID or code associated with a label (such as the medical codes associated with a term in the ICD-10). These are specific to the ontology, and you can only select one.
  • Parents/Path/Superclass/SubClassOf: If your ontology is hierarchical, identify which column identifies the relation. You can only select one column. The column must refer to the “parent” term, also known as the class that term belongs to (e.g., “Cardiovascular Diseases” is the parent of “Heart Attack”).
  • Other Properties: Any other properties you wish to have connected to a term from the original table will be populated here. You can modify the list of other properties to your liking, and each property added into the “Other Properties” field will be treated as their own independent properties within the created ontology.
  • Delimiter: Finally, if any of the columns selected for the above properties uses delimiters to define a list in a cell, define that delimiter here. We typically suggest not using a comma (,) or hyphen (-) delimiter in your ontologies, as those are regularly used in nomenclature as part of your term (e.g., caffeine is also known as “1,3,7-Trimethylpurine-2,6-dione”. If you assigned a comma delimiter, you’d get synonyms “1”, “3”, 7-Trimethylpurine-2″, etc.
    Example delimiters:

Step 6. Once you are satisfied with the properties you’ve assigned, click “Create Ontology”.

Step 7. Your table will now be converted to into an ontology, which you can view by going to your “Ontologies” tab in the left-hand menu, and clicking on the name of your ontology.

Note: If your ontology is larger than 300 MB, or is hierarchical in nature, you may need to wait a few minutes before being able to view the classes in your ontology. You do not have to wait for this process- you can click out of the “Create Ontology from Table” popup and work on other things in Layar while the ontology is generated behind the scenes.

If you are creating an ontology from an .obo or .owl file, please read the following documentation.

To edit and modify ontologies further, see “How to Edit Ontologies“. This article will provide you with more information on the different capabilities available in Layar for you to edit your ontology.