Video Annotation and Reference System (VARS)

VARS Knowledgebase User Guide

This guide gives basic instructions for starting and using the VARS knowledgebase interface. Useful definitions and descriptions can be found in the glossary. If you need extra help or information, see Contacts section here.

Getting Started

Start the program by double-clicking on the VARS knowledgebase icon. This logo will appear while the knowledgebase loads. After the knowledgebase finishes loading, the knowledgebase interface opens.



  1. To annotate in VARS and to enter and edit data in the VARS knowledgebase, you will need a VARS user account.If you already have a user account, you can simply log into the knowledgebase. Click on the padlock icon at top right of the screen. Select or type your user name in the login dialog and click OK.
    knowledgebase_login 2
  2. Create a new account with the appropriate permissions level for the knowledgebase.
    • ReadOnly (no editing)
    • Maint (editing without final approval)
    • Admin (editing and final approval)
  3. Click on the padlock icon at top right of the screen. In the dialog that appears, enter Login name, Password, First and Last Names, Email Affiliation, and Permissions level. Click OK.

Do not use your network password as the VARS administrators can view the password you choose.


Search and browse

  1. Type all or part of the search term in the box at the top left of the interface. Hit enter or the magnifier icon to scroll through the results in the browse panel.Knowledgebase data are arranged in hierarchical form. Each entry represents an object or a Concept. The root concept, or parent, is normally called simply, an “object”; from there, nested hierarchy suited for the particular field of study or data analysis needs (e.g. behaviors, regions, chemistry, geology, biology, other data types) can be created.Red font indicates that the concept name or its properties have been edited and require administrator approval.A small grey rectangle indicates that an image can be found associated with that concept.
  2. knowledgebase_search_browseSelect desired concept and right click to access the browsing and editing features.knowledgebasae_create_new_or_edit_concept

Browse features include:

  • Show Image
  • Expand
  • Collapse

Alternately, use the triangle icons to Expand and Collapse the selected node.

Edit features for the primary concept name include:

  • Add Concept
  • Remove Concept
  • Edit Concept

Add new concept name, or edit values including Parent, Author, ID Code, Rank Name, Rank Level, Reference. A concept name can also be selected for editing via the Edit Menu > Edit Selected Concepts.

Refresh – Reloads the latest data from the database.

Notes on editing concept names:

  • Capitalization will be displayed throughout VARS as entered in the knowledgebase. e.g., the first letter of each proper taxonomic name (except species).
  • Italics, bold, and other formatting options are not available in the knowledgebase.
  • Primary concept names cannot be changed in this field; use Name tab to update names (below).
  • To move a concept to a different node in the hierarchy, choose the new Parent from the drop down list of existing names.
  • Dialog windows confirming the concept(s) being marked for deletion (e.g., may be more than one, if removing an entire node) provide additional level of protection against accidental deletion.
  • Plan ahead when renaming a concept. If a concept name is going to be deleted entirely as opposed to a name update, any remaining annotations created with that concept will need to be appropriately renamed. The best method for moving existing annotations to a new concept name is to a) change its Parent to the new name (thereby placing it under the name) and b) right click and select Delete. Note: this deletion must be approved by a user with administrator permission. See History below which explains the options for handling name deletions.


For internal users, please view our MBARI conventions for Search and Browse here.


Access the Names tab for the selected concept to add or edit the primary concept name and any alternate names.

Primary concept name and author can be updated by changing the appropriate fields and clicking the Update button.

Click New to add alternate names, types (e.g., common, synonym, former), and authors.


Notes about Names:

  • If a concept’s identity is unknown, consider creating a “placeholder” name according to the MBARI VARS conventions. For example, Henricia sp. 1or lava formation A.
  • It is not uncommon for a primary name to undergo a taxonomic name change. In the knowledgebase GUI, update the Concept to the new name using the Edit feature.

For internal users, please view our MBARI conventions for Names here.


Templates are a series of related fields that can be used to describe a Concept or object.

They are created once in the knowledgebase and can then be used repeatedly to: a) attach as a “static” property (also known as an attribute or link realization) to any concept name in the Knowledgebase, and b), attach an “instance” property to any real observation made during the creation of annotations.

Templates include the following fields:

  • From = the selected concept name
  • Link Name = the type or description of the attribute
  • To Concept = to which concept is it referring; this is often “self”
  • Link Value = the value of the attribute; can be nil (blank) if the Link Name is a self-contained descriptor


Click New to open the dialog window for adding a new Template (Note: Search feature is disabled here as user expected to create a new, unique Template). To change an existing Template, select and edit the field and click Update.


Notes about Templates:

  • Care should be taken to not duplicate descriptors.
  • If a property could be relevant to multiple, related concepts within a larger group, it should be added at a higher level in the hierarchy. If a property would only be applicable to a specific concept, it can be added at that specific level.
  • The Link Value field character limit when making a new Template is 2048.

For internal users, please view our MBARI conventions for Templates here.


Properties are created from preexisting Templates.

As described above, Properties are added as a) “static” properties attached to, and always known to be true for, a specific concept in the Knowledgebase or b) as “instance” properties to unique observations made during the annotation process.

There are three types of Properties that can be created:

  • Stand-alone fixed
    • marine organism | schooling | nil |nil
      • nil’s in both the To and Value fields indicate the descriptor stands alone and is not related to another object, nor does it require the Value be filled in
    • physical object | shape-geometry | self | irregular form
      • this is a stand-alone property that describes the selected physical object and contains a predetermined value
    • Stand-alone variable
      • marine organism | length-centimeters | self | 0
        • where 0 varies according to individual concept type or unique observation
    • Linked (i.e., related to another object)
      • physical object | attaching-to | physical object | nil


Click New to open the dialog window for adding a new Property. To change an existing Property, select and edit the field and click Update.

Notes about Properties:

  • Pre-populate the knowledgebase with common properties expected to be needed for describing the concepts and procedures for the particular area of study (e.g. geology, chemistry, ecology, equipment, sample identity schemes, etc.).
  • Avoid potential for misspellings and variable entries by limiting the number of properties that allow for free form Value entries.
  • The Link Value field character limit when creating a new Property is 2048.

For internal users, please view our MBARI conventions for Properties here.


Any type of media file can be linked to individual concepts in the Knowledgebase. Typically they would be the best representative imagery, e.g., for identification or illustration of particular features.knowledgebase_media_tab

In the dialog window that appears, enter URL (location of image), Media Type (icon, image, video), Caption, Credit, and check box if it is the Primary image (e.g. best representative for identification).


Notes about Media:

  • Devise a consistent location, directory structure, and media naming scheme for image recall and reconciliation purposes

For internal users, please view our MBARI conventions for Media here.


All Knowledgebase changes by all users are tracked in the History.  As noted above, concepts with new edits appear red in the hierarchy until they are approved.

For each entry, the following parameters are viewable by all users: Created by and on which date, Approved (Rejected) by and on which date, Action, Field, and New and Old values.


Users with Administrator permission can approve additions, deletions, and edits to the Knowledgebase. To do so, select Reject or Accept each change using the buttons on the bottom right of the screen.

If a concept name(s) or properties are being deleted, additional dialog boxes will appear for the user to make a final confirmation.

If annotations that have been made using the Concept name(s) marked for removal still exist in the database, a final dialog will appear indicating the number of annotations that will be effected by the deletion. The options are to:

  • Cancel the operation
  • Ignore the name deletion and leave them as is, thereby orphaning those names in the observations database
  • Update them with the Concept name of its parent


Notes about History:

  • Grayed out entries have been rejected

Additional Features

Edit menu

  • Edit User Account
    • Edit User Account
      • Administrator can edit user account information [Brian not working now]

Error Reports

  • Details can be viewed by expanding the arrow >
  • Details can be reported to and administrator
  • Select Don’t Send to close the error dialog window



Data repository
Data policy
What is happening in Monterey Bay today?
Central and Northern California Ocean Observing System
Chemical data
Ocean float data
Slough data
Mooring ISUS measurements
M1 ISUS CTD Data Display
Southern Ocean Data
Mooring data
M1 Mooring Summary Data
M1 Asimet
M1 Download Info
M1 EMeter
M1 Flourometer (CeNCOOS)
M1 GPS Location
Molecular and genomics data
ESP Web Portal
Seafloor mapping
Upper ocean data
Spatial Temporal Oceanographic Query System (STOQS) Data
Tide prediction
Image gallery
Video library
Previous seminars
David Packard Distinguished Lecturers
Research software
Video Annotation and Reference System
System Overview
Annotation Interface
Video Tape User Guide
Video File User Guide
Still Images User Guide
Annotation Glossary
Query Interface
Basic User Guide
Advanced User Guide
Query Glossary
VARS Publications
Oceanographic Decision Support System
MB-System seafloor mapping software
MB-System Documentation
MB-System Announcements
MB-System Announcements (Archive)
How to Download and Install MB-System
MB-System Discussion Lists
MB-System FAQ
Matlab scripts: Linear regressions
Introduction to Model I and Model II linear regressions
A brief history of Model II regression analysis
Index of downloadable files
Summary of modifications
Regression rules of thumb
Results for Model I and Model II regressions
Graphs of the Model I and Model II regressions
Which regression: Model I or Model II?
Matlab scripts: Oceanographic calculations
Matlab scripts: Sound velocity
Visual Basic for Excel: Oceanographic calculations
Educational resources
MBARI Summer Internship Program
Education and Research: Testing Hypotheses (EARTH)
EARTH workshops
2016—New Brunswick, NJ
2015—Newport, Oregon
2016 Satellite workshop—Pensacola, FL
2016 Satellite workshop—Beaufort, NC
EARTH resources
EARTH lesson plans
Lesson plans—published
Lesson plans—development
Lesson drafts—2015
Lesson drafts—2016 Pensacola
Center for Microbial Oceanography: Research and Education (C-MORE) Science Kits
Sample archive