How to Edit Ontologies

Getting Started

Step 1. Click the “Ontologies” subsection under your “Data Catalog” menu, located on the left-hand side of your Layar home page.

Step 2. Click the ontology name to see the Ontology View for that ontology, with the terms, synonyms, and related metadata.

Step 3. Search andclick on a term to see its references, synonyms, and other metadata. Here I have searched for “Antineoplastic chemotherapy regimen“.

Now you are ready to modify this ontology term.

Add a Parent Node

  1. On the “+” Icon, to the right of the Ontology Search Bar.
  2. Complete the information on the modal pop up for the new parent node, including the term, synonyms, and any database that references this entity with its own unique ID.
  3. Click “Save
  4. You will now see the parent node within the ontology, with an Ontology Card with the information you provided in step 2.

Add a Child Node

  1. On the Ontology Card, click the icon with three vertical dots and select “Add Child Node“.2. Complete the information on the modal pop up for the child node, including the term, synonyms, and any database that references this entity with its own unique ID. 3. Click “Save” 4. You will now see the child node underneath the parent term, with an Ontology Card with the information you provided in step 2. Edit an Ontology TermTo Edit, click the icon with three vertical dots on the Ontology Card and select “Edit“.For any of the properties of that term, you can add additional values (one per line). For example, I added in three new references for my “Xrefs” property below. Click Save. The new values will be populated in the property they were added to. Delete an Ontology TermTo Delete, click the icon with three vertical dots on the Ontology Card and select “Delete”. Confirm you want to permanently remove this ontology term. Any child nodes underneath that ontology term will also be permanently deleted.

Identifying Document ID & Data Source in Vyasa Layar

Identifying a document ID or data source is useful for both search and API calls. Below is a step-by-step guide for identifying both via the Layar interface.

Identifying a Document ID

1. Select a document from the Layar data catalog.

2. Click the three-dot menu on the right-hand side of the Layar document view.

3. Select “Access with Layar ID” from the drop-down menu.

4. Copy/paste Layar ID from pop-up window.

Identifying a Document Data Source

1. View document URL in the web browser.

2. Identify document data source directly after Document ID in URL.

For more information, please visit the Vyasa Developer Hub.

Table Extraction Tutorial

How to use Vyasa Layar’s automated table extraction feature.

Step 1: Click the “View Original” menu item from the Three Dot menu in the upper left hand corner of the Document view.

Step 2: Navigate to the page with the table you are interested in extracting. Click and Drag a box to fit around the table.

Step 3: Click “Extract Table”

Step 4: Click out of the PDF Preview and refresh your webpage.

Step 5: Click the “Related Documents” link beneath the title of the document.

Step 6: Use the filters on the right-hand side and select “Tables”. If you’ve extracted multiple tables, you’ll need to search through the thumbnails to identify which one you are interested in. Click the thumbnail of the table you are interested in.

Step 7: Click “View Detail” to view the extracted table in a Document View in Layar.

Step 8: Compare to the original PDF table by clicking “Compare to Original Image” on the right-hand side of the table.

Step 9: Make any touch-ups or edits necessary for the table. All edits are saved automatically.

Boolean Operators in Layar Search

While Layar can handle keyword and boolean search, we find it helpful to provide an overview of boolean operators to enhance your Layar search experience. 

What are Boolean Operators? 

If you have ever Googled something, you have already created Boolean search strings. If you use it without realizing it, you can learn a few Boolean operators that will drastically improve your current sourcing efforts.

NOTE: Be sure to include single or double quotes to trigger the Boolean search.

Boolean Operators

  1. AND
    Narrows your search results to include only relevant results that contain your required keywords (e.g. “Alzheimer’s” AND “target” will only yield documents that have both of those keywords).
  2. OR
    Expands your search results so all results must contain at least one, if not more, of your defined keywords or phrases. OR is useful for two scenarios: (1) you need to include all synonyms for a given title, phrase or word (e.g. interleukin-1 OR IL-1 OR IL1), or (2) creating a list of all possibilities where you only need at least one of the keywords to be returned (e.g. Merck OR Pfizer OR Novartis).
  3. NOT
    Limits your search by excluding defined keywords and/or phrases from your results (e.g. drug NOT vitamin reveals all results that discuss drugs, excluding those that also mention “vitamin”).
  4. “Quotation Marks”
    Use quotes around a phrase that needs to be returned in that exact order. For example, “United States of America” will yield results with that exact term, but without quotes, each word in the phrase will be treated separately, as if you used OR between each word (United OR States OR of OR America).
  5. (Parenthesis)
    Parentheses are used to give priority to the keywords contained within over the other elements around it. As a rule of thumb, parentheses should be used around OR statements, ensuring the search engine properly resolves the OR statement before moving on to other operators. For example, (Tumor OR Carcinoma OR Cancer) AND treatment will yield results that mention treatment and any one or several of the key terms in parenthesis.
  6. Asterisks*
    * on a term matches multiple characters preceding a stem. For example, hydroxych* yields results for hydroxychloroquine, hydroxycholesterol, etc.
  7. Question Mark?
    ? on a term matches a single character preceding a stem. For example, a?duction can yield results for abduction and adduction. Another example can be anemi? to find results for anemia and anemic.

Adding Expanded Terms to a Column

  1. Highlight a cell or multiple cells you would like to find related terms for. 
  2. Right click the cell(s) and click the Radar – Expand Terms button from the drop down menu or click the radar tab from the right menu bar represented by a radar symbol. 

3. Determine what related terms from the index you would like to add to your table (column) and click the “+” next to the term. Please Note: You must choose what column you would like to add the related term to from the drop down menu located at the top of the related terms list. 

4. Your related term will now be added to the table at the bottom of the column that was indicated from the Add terms to column drop down list.

Sorting in the Radar Tab

Users have different options and combinations of options when sorting the Radar Tab

  1. Proximity – Users can filter proximity by most closely related (down arrow) and least likely related (up arrow) to represent related terms and their relation to the cell that was selected.
  2. Trending – This filter will show the relation between related terms and the selected cell term and how often that appears within the Layar Data Fabric
  3. Show Trend Lines – This represents the trending filter in a line graph form next to each individual related term
  4. Group Terms – Group terms will group related terms that appear in sources together. It is An NLP task thatmerges like-terms (“Vyasa Analytics”, “Vyasa Analytics, LLC” ) into a single term to mitigate redundancy.

Filtering in the Radar Tab

Below are the different filter options for Radar Tab

  1. Click the filter button at the top of the radar tab represented by a funnel icon 
  2. The Search Bar allows users to search for specifics in the related terms list 
  3. Source Filter enables users to select what sources within Synapse they would like to filter the expanded terms to 

4. Types Filter will filter expanded terms based on preset types such as – DNA, Cell Type, Organ, Location and RNA

What is the Radar tab?

The Radar tab assists users in finding contextually similar terms to highlighted terms in their table based on current sources in the system. From this section, users can also search the web and view evidence for expanded terms in the list.

For example, add the term ‘headache’ to a cell in your table and find expanded terms such as ‘dizziness,’ ‘general pain,’ or ‘dysphagia.’

How to Upload a File to Sources

  1. Click the Data Sources tab on the right menu bar on the home screen.
  2. Scroll down to the User Upload Section.
  3. Drag and Drop an accepted file type (.pdf, .doc, .docx) anywhere into Synapse to add the file to sources.