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Water Quality of San Francisco Bay
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JULIAN DATE: The date as expressed in the format YYYYDDD, that is, the full four digits of the year, followed by the three digit number of days since the start of the year. For Example- 1994001=January 1, 1994, 1994365=December 31, 1994
DAYS SINCE 01/01/??: The integer number of days that have passed since a certain date. Negative numbers refer to days prior to the selected date.
DECIMAL DATE: The date, expressed as YYYY.ddd where YYYY is the full four-digit year, and ddd is the fraction calculated by dividing the day of the year (DDD in Julian Date) by the number of days in the year. For example: 1996.50546 = Julian Date 96185 (July 3, 1996) [185/366]
STATION NUMBER: Data are usually collected at the same series of stations in the bay. Sampling stations are located along a transect from Rio Vista on the Sacramento River south to the entrance to Coyote Creek in South Bay near San Jose. See map page for further details
DISTANCE FROM 36: This location information, expressed in kilometers, is very useful for producing longitudinal profiles and graphs from the data. Station 36 is located in the far South Bay, and values increase as you move along the ship transect towards the north.See map page for further details
DEPTH: depth of measurements/sampling, as meters below the water surface.
CTD AND DISCRETE DATA CTD (multi-sensor instrument) data are collected approximately 20 times per year on a series of cruises along a consistent transect stopping at stations through the entirety of San Francisco Bay. The CTD-instrument package makes continuous measurements about every 3-4 cm as it is lowered into the water. Values reported here are the average values of all the measurements made within 1-meter increments, or bins. For example, values reported for 1 meter depth are the mean of all measurements made between the depth range 0.5 to 1.5 meters. Relative data such as fluorescence and optical backscatter are calibrated with discrete measurements to achieve the calculated cholorphyll and SPM results.
DISCRETE CHLOPHYLL: discrete measurement of chlorophyll a concentration, in units of micrograms per liter (equivalent to milligrams per cubic meter). This discrete measurement is made by laboratory analysis of the chlorophyll content of a water sample collected onto a filter.
CHLOROPHYLL a/a+PHA RATIO: the ratio of chlorophyll a to the sum of (chlorophyll a + phaeopigments). The phaeopigments are degradation products of chlorophyll, produced as the chlorophyll molecules within algal cells are degraded.. When this ratio is high (near 1), most of the pigments are active chlorophyll a; this is often the case when the phytoplankton population is growing quickly. When the ratio is low (< 0.5), the pigments are highly degraded. Low ratios are often seen when blooms terminate, or during episodes of strong resuspension because the bottom sediments are rich in phaeopigments. So, this ratio indicates whether the pigments are predominantly those of active cells or those of degraded algal material from the bottom sediments.
FLUORESCENCE: raw voltage-based output of the chlorophyll fluorometer, a relative measure of the concentration of chlorophyll a in the water. Over the years and between cruises, different sensors and different sensor ranges are used, thus these values may not be comperable between cruises. On some occasions, the sensor range is switched within the cruise, and fluoresence is not comparable within cruises. Fluorometer voltage output from the low range (10x) fluorometer not reported.
CALCULATED CHLOROPHYLL a: estimated concentration of chlorophyll a, calculated from the fluorometer voltage output FLUOR and linear regression (calibration) between the discrete measures of chlorophyll a and the corresponding fluorometer voltages. The standard error of the calculated value for each cruise is listed at the top of the data table. Units of measurement are micrograms per liter (equivalent to milligrams per cubic meter).
DISCRETE OXYGEN: discrete measurement of the concentration of oxygen dissolved in bay water at the corresponding station and depth. These discrete measurements are made by laboratory analysis (Winkler titration) of water samples that are collected and stored in BOD bottles. Units of measurement are milligrams per liter.
OXYGEN ELECTRODE OUTPUT: voltage output of the oxygen electrode, a relative measure of the concentration of oxygen dissolved in the water. Over the years this sensor has changed, these values may not be comperable between cruises.
OXYGEN SATURATION %: the value CALCULATED OXYGEN expressed as a percentage of the dissolved oxygen concentration that would be present if there was perfect equilibrium between the oxygen content of water and that in the atmosphere. This saturation value varies with salinity and temperature, so we present the oxygen data this way to eliminate the effects of salinity and temperature on oxygen solubility in water. Values less than 100% indicate that the total rate of oxygen consumption by all biological/chemical processes is occurring faster than the rate of oxygen production by photosynthesis. Values greater than 100% occur when the rate of algal photosynthesis exceeds the rate of oxygen consumption by other biota (e.g., during phytoplankton blooms).
CALCULATED OXYGEN: estimated concentration of dissolved oxygen, calculated from the oxygen electrode voltage output OXYG which is (calibrated) using linear regression with the discrete measures of the dissolved oxygen. The standard error of the calculated value for each cruise is listed at the top of the data table. Units of measurement are milligrams of oxygen per liter.
DISCRETE SPM: discrete measurement of the concentration of suspended sediments (or suspended solids) in Bay water at the corresponding station and depth. These discrete measurements are made by weighing the mass of solids collected onto filters after drying. Units of measurement are milligrams per liter.
OBS: voltage output of the optical backscatter sensor, a relative measure of the concentration of suspended sediments or solids in the water. Due to sensor changes and gain differences, this value is only comperable within cruises and may not be comperable between cruises.
CALCULATED SPM: estimated concentration of suspended sediments, calculated from the OBS voltage output and linear regression (calibration) between the discrete measures of suspended solids and the OBS voltage. The standard error of the calculated value for each cruise is listed at the top of the data table. Units of measurement are milligrams per liter.
CALCULATED EXTINCTION COEFFICIENT: The light extinction coefficient defines the rate of attenuation of photosynthetically active radiation (PAR) in the water column. The calculated version of Extinction Coefficient parameter was collected 1977-1987. The calculated light extinction coefficient was computed from Secchi depth or nephelometer measurements using an empirical relationship derived for San Francisco Bay. This parameter is not calculated using PAR measurements and is sometimes measured concurrently with the Extinction Coefficient. Units are per meter.
(Measured) EXTINCTION COEFFICIENT: The light extinction coefficient defines the rate of attenuation of photosynthetically active radiation (PAR) in the water column. This value is calculated from vertical profiles of PAR, and units are per meter. Even though this value is reported for the depth of 1 meter, it is assumed to be valid for the entire region of the water column that has detectable light.
SALINITY: measured in practical salinity units (virtually identical to "parts per thousand").
TEMPERATURE: measured in degrees Centigrade.
SIGMA-t: a measure of the density of the water, which is calculated as a function of salinity and temperature. Density increases with increasing salinity and decreasing temperature. The density difference from the surface to the bottom is a good indicator of the potential rate of mixing, because large density gradients act to impede mixing. Uniform density, from surface to bottom, indicates rapid vertical mixing. Units are kilograms per cubic meter (mass per unit volume).
NUTRIENTS: The concentration of various nutrients important for phytoplankton growth and for characterizing water quality. Water samples are collected near the water's surface or at depth. The concentration of the various nutrients are measured by colorimetric analysis after the samples are returned to the laboratory. Units are micromoles per liter.
CONJUNCTIONS: The "AND" and "OR" conjunctions are used to connect two different parts of the refinements clause. They are used just as they are in English. For AND to be true, both conditions have to be satisfied; for OR to be true, only one of the conditions has to be fulfilled.
PARENTHESES: These are used to group a set of conditions together, such that they are evaluated first. For example: X AND (Y OR Z ) -- "Y OR Z" gets evaluated for truth first, and its result is evaluated against X using AND
PARAMETER NAMES: Here, you choose which parameter you want to test against a specified criteria. It does not neccesarily need to be a column that you are displaying for output.
COMPARISON OPERATORS: Most of these are self-explanatory (> >= < <= =). The two you may not be familiar with are "> <" which means "BETWEEN". With between, you can put two numbers (separated by "and") in the value field to the right, and the database will only retrieve rows for which the parameter's value is between (or equal to one of) the two numbers. For example: "Depth > < 1 and 5" returns date with depth values in the range 1-5.
Another option is "IN". Here, you can specify a list of numbers to match with, separated by commas For example -- "Station Number IN 36,27,21" will only return data whose "station number" parameter is 36, 27, or 21.
VALUES: Numerical input that specifies which numbers are allowable. This must always be strictly a number, except in the cases of using the between or IN operator (see COMPARISON OPERATORS).
SORTING THE DATA: It is possible to sort the data by up to 3 fields. The default options are to sort by Julian Date, Station Number, and Depth. This means that all the output rows will be sorted by Date first, then all rows with the same date will be sorted by station number, and all rows with the same Julian Date and Station Number will be sorted by Depth. In addition, you can choose whether any of these fields should be sorted in ascending or descending order using the checkboxes at right.
OUTPUT FORMATS: Data can be output in one of two formats; 1) as an HTML table which is easily viewable in browsers, or 2) as a comma-delimited text file, which can be saved or copied and pasted into other programs such as spreadsheet or text.
SHOW TABLE OF PARAMETERS: displays a small 2 row table at the top of the query output page, describing exactly what it is that is being displayed.
SHOW STATISTICS: tacks an added three lines onto the bottom of the table, which calculated the average, minimum, and maximum values in each column. On multi-page requests, these will only be shown on the last page. Not yet available with comma-delimited output.
OUTPUT LINES PER PAGE: Organizes the output into the specified number of pages for easier viewing and faster downloading.

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