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The VARS Public Query database is currently undergoing a major redevelopment. Updated information will be posted as soon as this project is completed. Meanwhile, for questions or assistance with acquiring VARS data, please contact us.
This guide is in three sections:
Following are detailed instructions for using the new VARS Query, including descriptions of the screens and examples. The VARS Query interface should already be installed on your computer – see the VARS Query Application page for installation information.
You can view an animated demonstration of the VARS Query.
Start the VARS Query by double-clicking the JNLP file.
The first steps in defining a search begin on the Basic screen (right, click to enlarge) that appears when the VARS Query is opened.
Concepts are selected from an alphabetical list of all formal and common taxonomic, geologic, and technical names. There are two ways to enter a concept:
1. Begin typing a name in the Search for box. The selection updates alphabetically until you press Enter.
2. Open the drop-down list, and scroll through the alphabetical list of concepts available in the knowledge base. Click on a name to enter it.
In the example below (click to enlarge), the concept Nephtheidae has been entered.
Beyond selection of the primary concept name, the constraints can be extended to any level that exists in the MBARI knowledge base by checking one of the associated boxes.
Parent extends the search up one level in the hierarchy of the knowledge base.
Siblings extends the database search to all genera found in the same family.
Children extends the query to species level of the genus. In the example of Nephtheidae all observations would be included in the returns.
Descendants extends the query to levels below.
If the concept is a geologic or technical term, the same logic follows. For example, selection of concept manipulator extended to Children broadens the search to all types of manipulators–such as kraft-raptor, mongo, schilling-arm, etc.
An alphabetized association list allows constraint of a query by a specific descriptive term. After typing a descriptive term in the Search box, you must click Enter.
An association will appear in the box under the Search.
WARNING! You must clear or re-enter the association entries whenever you enter a new concept in the Search for box.
The example illustrates a search for the association close, which restricts the loligo query to observations annotated as close-up images. Use the drop-down menu scroll through the list of associations and select one.
When all search criteria are entered for a concept, click the big green + Add button. The Searchbutton at the bottom of the screen becomes active when the first criteria are added.
For related associations and/or concurrent observations included in the query returns, check the appropriate boxes near the bottom of the Basic screen.
To select multiple items for a simultaneous search, choose and enter each of the target concepts and associations as described above, and add them to the list.
To remove a query from the list, select it and click Remove. To clear all queries from the list, click Clear. To clear multiple queries, use the Shift key (for consecutive selections) or the Control Key (for non-consecutive selections.
At this point you can click the Search button (green arrow) at the bottom of the screen, and the query will be processed. A box will appear to show that the query is running. When the query is finished, the box will close and the Query Results screen will appear.
See the Query Results page for instructions on viewing, interpreting, and saving the results.
Instructions for the Advanced query screen.
Select the Advanced tab to view all possible searchable parameters grouped by type of data. The top two groups are shown in the screen grab at right. Details on all the types are described below.
At the left of the screen are two columns of checkboxes, labeled above in small type. In the return column check boxes to select information to be returned with the search. In the constrain column, check boxes to restrict the query by the desired parameters. By default, some return columns are already selected.
To get a unique value, enter the same information in both Min and Max.
The items that can be constrained or returned in an advanced query are listed below with format, units, and examples when appropriate.
Association values are infrequently used. Contact the Video lab staff for more information.This parameter provides descriptive information about a concept specified with three fields—Link Name, To Concept, and Link ValueLink Name | To Concept | Link Value.
A camera value set by the annotator to indicate whether the ROV is descending, ascending, transecting, or stationary. Check the return box to get direction information returned with query results. Check the constrain box and enter values to limit the information returned. The available MBARI values for direction are: ascend, cruise, descent, endtransect, launch, starttransect, stationary, and transect.
Camera Name specifies the camera used to record the selected video observation. To constrain the query to a particular camera, enter the name. Almost all annotations are associated with main camera. However, the available MBARI names are aux-camera, bioluminescent-camera, color-bars, main camera, sit-camera, and still-photo-camera.
This is a calculated camera value that provides an estimated size of the current field of view in centimeters. Field width varies with the Zoom value.
Focus (focal length) indicates the distance in millimeters (mm) from the center of the lens to the focal point. The general range is from -511 to 1000 mm.
The iris value is the setting for the aperture, which controls the light and depth of field. This setting indicates the amount of light allowed to enter the camera lens for recording. Settings range from 0 to 4095.
For this purpose, Zoom indicates the relative distance from an object. The units are in millimeters (mm) and values generally range from -200 to 1000.
To query for dives by a particular chief scientist, type the last name. (Example: Robison)
Dates and times are in UTC. Choose the range of end dates (Min, Max), from the drop-down calendars. To constrain the search to one day, choose the same date for Min and Max.
The dive number must be a 4-digit number (such as 0989). A specified dive number requires a specified ROV Name (see below).
Dates and times are in UTC. Choose the range of start dates (Min, Max), from the drop-down calendars. To constrain the search to one day, choose the same date for Min and Max.
equired if you are searching by dive number. Type in the ROV name, Ventana or Tiburon (the only MBARI ROVs as of 2005). If this is left blank, you will get all ROV dives.
Type the ship name, Point Lobos or Western Flyer (MBARI ships equipped with ROVs and video cameras as of 2005).
To constrain to a particular concept, type in the term. If the same real concept is entered on the Basic search page, this will further constrain the query according to the specified term. If only the ‘nil’ concept is entered on the Basic search page, the entire database will be searched for the specified term.
Used infrequently. Contact Video Lab staff. An observation is part of a sequence if there is more than one annotation about the same object. To further constrain the query by the presence of a sequence, type either true or false.
Notes are free-form text about an annotation that the science party may have entered. To constrain the query by searching for terms in the notes column, type the search term.Example: mystery mollusc.
This is the date that the annotation was made. It is not necessarily the same as the Recorded Date. Dates and times are in UTC. Choose the range of observation dates (Min and Max), from the drop-down calendars. To constrain the search to one day, choose the same date for Min and Max.
To search for observations by a particular person, type that person’s username. Example: schlin.
Dates and times are in UTC. Choose the range of recorded dates (Min, Max), from the drop-down calendars. To constrain the search to one day, choose the same date for Min and Max. This might be helpful in locating daily migrations or night-time versus day-time recordings of animals.
Tape time code starts at the beginning of a dive and is continuously incremented throughout the dive. The code registers hours, minutes, seconds, and frames. For example: The beginning code is 00:00:00:00. The timecode at 2 hours, 40 minutes, 30 seconds, and 10 frames into the dive is 02:40:30:10.To constrain the query by the time code at which an annotation was made, type the time code in the format hh:mm:ss:ff (hours, minutes, seconds, frames), as in the examples.
Enter a minimum and maximum depth value in meters. For a single depth, enter the same value in Min and Max.
Enter a minimum and maximum latitude, in decimal degrees. For one latitude, enter the same value in Min and Max
Enter a minimum and/or maximum light transmission value (percent transmission).
Enter a minimum and maximum longitude in decimal degrees. For one longitude, enter the same value in Min and Max.
To constrain a search by recorded oxygen, enter minimum and maximum oxygen values. Oxygen concentration is measured in milliliters per liter (ml/l) of seawater. For example, enter Min: 0.81 and Max: 0.83 oxygen values to find all noted oxygen concentrations within that range. The database currently includes annotations from January 1, 1988 to the present, for both ROV Ventana and ROV Tiburon.
Salinity is a value calculated from the conductivity and pressure measurements. To constrain the search by salinity, select the checkbox, and enter minimum and maximum salinity values.For example, enter Min: 31 and Max: 35 to search for an organism in that range of salinity.
Temperature is recorded in degrees Celsius by the ROV CTD instrument.To limit temperature values, check constrain and enter minimum and maximum temperature values. For a single temperature, enter the same value in Min andMax.
The choices for annotation format are detail and outline.
If a framegrab was taken with the annotation, the framegrab link will be returned with each annotation. To view the framegrab, double-click on the link (Image field) in the Results table. The image links are returned by default. If you don’t want image links, uncheck the return box under Image.
To return the number used to track observations in the VARS database, click the return box. If you know a tracking number and want to see its associated entry, check the constrain box
To constrain the query by archive number, type the Archive Name such as T9999-01. The name consists of T for Tiburon, or V for Ventana, followed by a four-digit dive number, hyphen, and a two-digit tape number. A search that specifies a dive number without a tape number will return all observations for that entire dive.
See Query Results below for instructions on viewing and saving the results.
Please see the MBARI Data Use Policy for information regarding data quality and use of data for research and publication.
Search results will automatically be entered into a table and displayed in a separate window on the desktop. The Data tab displays a table of the return information. Because the table is very wide, it is shown below in two sections.
Items in a column can be sorted by clicking on the column title. First click sorts in ascending order (upward pointing arrow), second click sorts in descending order (downward arrow), and third click restores the original results order.
To rearrange columns horizontally, click and hold at the top of a column, then drag it to the desired position.
Query results can be saved in a text file. To save the results, select the Save button on the Query Results window and a Save As dialog box appears. The data table is formatted as tab-delimited text. Save the file to your desired location, being certain to name the file with the .txt extension. You can then import the .txt file into common spreadsheet and statistics applications for further data analysis.
Query results can be saved as a Google KML file for use in Google Earth and other geospatial visualization or mapping applications. Save the file to your desired location, being certain to name the file with the .kml extension.
Images are listed in the table as web URLs. Double-click an entry to preview the image in a new window. Save the image from the window, using File > Save.
To save all the images from a query, click the Save Images button. In the dialog box, enter the path to the directory where the images will be stored. Images will automatically be saved in a folder hierarchy as follows: ROV name/Stills/Year/Year-day.
The Query tab shows the database against which the Query was run and the SQL code used to execute the Query.
This is a list of the various entry items and buttons on the VARS query interface. The specific window or tab where the item appears is noted in parentheses. Details on how to use these features are in the VARS Query User Guide.+ ADD button (Basic)Use to add a concept and any associations to the query.
Advanced tabPresents a form for entering detailed requests and constraints for query returns. Check the return boxes to get detailed information returned with query results. Check the constrain boxes and enter appropriate values to specify and/or limit the information returned. Instructions for entries are on the User Guide page for Advanced Queries.
Association (Advanced)A section of the Advanced tab, with the following entry items:
Also see Association in the User Guide.
Associations (Advanced)A sub-section of Association, on the Advanced tab. Also see Associations in the User Guide.
association (Basic)Allows specifying of annotations that describe the concept name in more detail (behavior, color, posture, sample information, etc.).
Camera Data (Advanced)A section where details of camera settings—minimum and maximum—can be entered for the following items:
See Camera Data in the User Guide for more information.
Camera Direction (Advanced) A sub-section of Camera Data, on the Advanced tab. See Camera Direction in the User Guide for more information.Camera Name (Advanced) A sub-section of Camera Data, on the Advanced tab. See Camera Name in the User Guide for more information.Chief Scientist (Advanced) The scientist in charge of the dive. A sub-section of Dive, on the Advanced tab. See Chief Scientist in the User Guide for more information.Children (Basic) A checkbox that extends a search from the name selected to the concept name one level below this name. For example, when searching for a genus name, selecting Children will extend the search to all species names within that genus.Clear (Basic) A button on the Basic tab that will clear all query entries that have been added.constrain (Advanced) Checkboxes for the selections on the Advanced query page. Check to limit results by narrowing the search down to specific terms or other parameters such as depth, time, chief scientist, etc.CTD The common name for a set of core data—conductivity, temperature, depth—measured by instruments on the ROV. These measurements generate the Physical Data values of Salinity, Temperature, and Depth. (Salinity is calculated from conductivity and temperature values.)Date See Observation Date or Recorded Date.Data tab (Results) The tab on the Results window that displays the information returned by a query.Depth (Advanced) A sub-section of Physical Data, on the Advanced tab. See Depth in the User Guide for more information.Descendants (Basic) Extends search from the name selected to all names that exist in the knowledge base beneath this name. If you are searching for a family name, select Descendants to extend the search to all genus and species names that exist in the knowledge base under the family name.Dive (Advanced). A section where details of a dive can be entered for the following items:
See Dive in the User Guide for more information.
Dive Number (Advanced) A sub-section of Dive, on the Advanced tab. See Dive Number in the User Guide for more information.Dive End Date (Advanced) A sub-section of Dive, on the Advanced tab. See Dive End Date in the User Guide for more information.Dive Start Date(Advanced) A sub-section of Dive, on the Advanced tab. See Dive Start Date in the User Guide for more information.fields The columns that are presented in the Results table. The columns can be rearranged by selecting with the mouse and dragging to the left or right, then releasing.Field Width (Advanced) A sub-section of Camera Data, on the Advanced tab. See Field Width in the User Guide for more information.File name (Results>Save) Enter a filename (with extension *.txt) to save search results.Files of type (Results>Save) On Save window, this information is currently “All Files *.*”. Users are encouraged to save their files as *.txt files.Focus (Advanced) A sub-section of Camera Data, on the Advanced tab. See Focus in the User Guide for more information.Help See the User Guide.Image (Results) A sub-section of Miscellaneous, on the Advanced tab. See Image in the User Guide for more information.In Sequence (Advanced) A sub-section of Observation, on the Advanced tab. See In Sequence in the User Guide for more information.Iris (Advanced) A sub-section of Camera Data, on the Advanced tab. See Iris in the User Guide for more information.Knowledge base A dictionary of names created by MBARI and referenced by the video annotation interface and the VARS query to ensure consistent annotations. The names consist of marine organisms and geological features commonly seen in Monterey Bay and other regions where MBARI ROVs (remotely operated vehicles) have recorded video. The knowledge base contains terms for equipment attached to the ROVs or deployed by the ROVs for deep-sea experiments. In addition, it contains a number of associations or formats that annotators can use to describe the behavior, color, position, or appearance of an organism, geological feature, or piece of equipment.Sample knowledge base entryLatitude (Advanced) A sub-section of Physical Data, on the Advanced tab. See Latitude in the User Guide for more information.Link Name (Advanced-Association) Used infrequently. Contact Video Lab staff.Link Value (Advanced-Association) Used infrequently. Contact Video Lab staff.Longitude (Advanced) A sub-section of Physical Data, on the Advanced tab. See Longitude in the User Guide for more information.NIL Entering NIL as a concept will return records of all concepts in the database except for what is filtered out by specified constraints. To avoid getting tied up by an overwhelming number of returns, NIL concept searches should only be done on a very limited time range, such as a few days.Notes (Advanced) A sub-section of Observation, on the Advanced tab. See Notes in the User Guide for more information.Observation Date (Advanced) A sub-section of Observation, on the Advanced tab. See Observation Date in the User Guide for more information. This is the date that the video was annotated. It may, or may not, be the same as the recorded date.Observer (Advanced-Observation) A sub-section of Observation, on the Advanced tab. See Observer in the User Guide for more information. This is the name of the person who did the annotation.Oxygen (Advanced-Physical Data) A sub-section of Physical Data, on the Advanced tab. See Oxygen in the User Guide for more information.Parent (Basic) A checkbox that extends the search from the name selected to the concept name that is one level above this name. When searching on a genus name, selecting this box will extend the search to the family name.Query tab (Results) Displays a summary of the query, depending on what items are checked for return on the Advanced tab.Recorded Date (Advanced) A sub-section of Observation, on the Advanced tab. See Recorded Date in the User Guide for more information. This is the date that the video was recorded. It may, or may not, have been annotated at that time. See Observation Date.Remove (Basic) A button on the Basic tab that will remove selected items from a query. Click one item to select it. To select a series of items, click the first one, and Shift-click the last one. To select several separated items, Control-click each one.Results (Results) Results are displayed in table format. Columns can be rearranged by selecting and dragging to new location. Multiple Results windows may be opened at one time. So when you return to the main VARS Query interface (Constraints) and initiate a new Search, a new Results window will be displayed.return Checkboxes for the selections on the Advanced query page. Check for each item desired on the query results listing.ROV Name A sub-section of Dive, on the Advanced tab. See ROV Name in the User Guide for more information.Salinity (Advanced) A sub-section of Physical Data, on the Advanced tab. See Salinity in the User Guide for more information. Salinity is calculated from conductivity and pressure values.Save (Results) Select to save search results and parameters in a text file. Results will be saved as a tab-delimited text file which can be opened in a word processing program or spreadsheet program for printing or further analysis. See Saving query results in the VARS Query User Guide for more information.Search (big green arrow) Click on this button to begin the search.Search for (Basic) In the Basic tab, a place to type in, or select with the drop-down list, a name from the knowledge base. The name can be an organism, geological feature, or piece of equipment.Ship Name (Advanced) A sub-section of Dive, on the Advanced tab. See Ship Name in the User Guide for more information.Siblings (Basic) A checkbox which extends search from the name selected to the concept name that is at the same level as the selected name. When searching for a genus name, select this box to extend the search to other genus names within the same family.Tape Time Code (Advanced) A sub-section of Observation, on the Advanced tab. See Tape Time Code in the User Guide for more information.Temperature (Advanced) A sub-section of Physical Data, on the Advanced tab. See Temperature in the User Guide for more information.To Concept (Advanced) Used infrequently. Contact Video Lab staff.VARS Video Annotation and Reference System, an annotation software system developed in-house at MBARI.VIMS Video Information Management System. Encompasses all programs relating to MBARI’s video archive management.Zoom (Advanced) A sub-section of Camera Data, on the Advanced tab. See Zoom in the User Guide for more information.