Data Dictionary for Coral Reef Ecosystem Assessment and Monitoring
Database

This document will provide reference material specific to the Coral Reef
Ecosystem Assessment and Monitoring Database queries that are available
at www8.nos.noaa.gov/bpdm_web/reports.

Fish Queries:

I.  Reports available

    a.  Total Fish Data Download

    b.  Biomass

    c.  Abundance

    d.  Richness

    e.  Diversity

II. Query Parameters

    a.  Region

        i.  Regions include St. Croix & St. John US Virgin Islands, and
            Parguera, Puerto Rico.

        ii. Region is derived from the batch code data element

    b.  Year -- Year of survey drawn from Survey Data

    c.  Month

        i.  Drawn from batch code data element

        ii. Since some batch codes span two months, the month attribute
            refers to the first month of the mission.

    d.  Structure

        i.  Includes three possible structures: hard, soft or mangrove.

        ii. Hard structures: The following categories are delineated in
            NOAA's benthic habitat maps of PR & USVI.

            1.  COLONIZED BEDROCK

            2.  COLONIZED HARDBOTTOM

            3.  COLONIZED PAVEMENT

            4.  COLONIZED PAVEMENT WITH SAND CHANNELS

            5.  LINEAR REEF

            6.  PATCH REEF

            7.  PATCH REEF (AGGREGATED)

            8.  REEF RUBBLE

            9.  REEF UNKNOWN

            10. SPUR AND GROOVE

            11. UNCOLONIZED BEDROCK

            12. UNCOLONIZED HARDBOTTOM

            13. UNCOLONIZED PAVEMENT

            14. SCAT. CORAL AND ROCK IN SAND

        iii. Soft Structures: same as above

             1.  SUBMERGED AQUATIC VEGETATION

             2.  SEAGRASS

             3.  SAND

             4.  MACRO-ALGAE

             5.  MANGROVE

             6.  MUD

    e.  Family -- Grouping of fish genus (verify this)

    f.  Trophic Level -- Trophic group of fish derived from
        http://www.fishbase.org

    g.  Species

    h.  All query parameter lists allow for multiple selections except
        for region.

    i.  Query parameter lists are filtered according to selected values.
        Thus, selecting PUER-PARG in region will mean that only
        parameters specific to that region will be available in the
        Year, Month, Structure, Family, et al lists.

III. Report Methodology

     a.  General Data Elements

         i.  batch_code -- an alphanumeric code that identifies the
             region, month and year of each mission

         ii. survey_index -- a numerical index that uniquely identifies
             each specific station done within a mission

         iii. station_code -- an alphanumeric code describing each
              specific station done within a mission. Certain stations
              containing the prefixes MSR or CB. These stations have
              different types of habitat data associated with them.

         iv. Survey_Date -- the date in which a specific survey is done
             formatted as mm/dd/yyyy

         v.  survey_time -- the specific time of a dive formatted in
             military time

         vi. latitude -- the latitude of a station precise to 5 decimal
             places

         vii. longitude -- the longitude of a station precise to 5
              decimal places

         viii. habitat_structure- the structure of a specific station.
               Reference II.d

         ix. Species Code

             1.  Species codes uniquely identify fish species using a
                 lettering system that incorporates the first two
                 letters of the genus and the first two letters of the
                 species. Thus, the species code CHCY equates to
                 *Chromis cyanea.* In cases in which 2 species would
                 have the same letter code from the first two letters of
                 the genus and species, three or four letters from the
                 genus and species are used. In some cases, the full
                 genus name is used.

             2.  In cases in which the species is unknown but the family
                 or genus is known, the species code is delineated with
                 the full genus or family name and the letters UNK.
                 Hence, a fish belonging to genus Haemulon of
                 indeterminate species will have a code of Haemulon UNK.

         x.  Family -- same as II.e above.

         xi. Genus_name -- taxonomic genus of fish species

         xii. Scientific name -- taxonomic species name of fish created
              from the genus and species of fish.

         xiii. Trophic -- same as II.f above.

     b.  Query Specific Data Elements

         i.  Fish_data_download

             1.  All fish sizes are presented in cross-tabbed format.
                 Hence, each fish size is a separate column. The number
                 of fish size columns is limited by the parameters
                 selected for the query. The values for these columns
                 will be fish counts.

             2.  All fish sizes less than 35 cm are displayed as ranges.
                 Hence, a fish that is approximately 18 cm in length
                 will be counted as 15---20 cm. All ranges increase in
                 increments of 5 cm.

             3.  Prior to 2002, the actual length of fish that were
                 greater than 35 cm was not recorded. Hence, in this
                 query, these fish are given a size of 0. Any 0 size
                 fish are assumed to be of a size that is greater than
                 35 cm that were seen before 2002.

         ii. Biomass

             1.  Biomass is calculated using the following formula:
                 sum(a_lw \* average fish_size \* b_lw). The constants
                 a_lw and b_lw are taken from http://www.fishbase.org

             2.  The biomass values are grouped by site, species and
                 size and then summed. Thus, each individual fish size
                 column will have a separate biomass value for each
                 species seen, and sum column giving the total biomass
                 for that species at that site.

             3.  In the biomass query, the average size of animals with
                 a size range of 0---5 is 3. This is actually the
                 average size of animals with a size range of 1---5,
                 since there is no such thing as an animal with a size
                 of 0.

             4.  A size column of zero is in place to account for
                 surveys in which no fish were seen and therefore no
                 biomass value is given. This is different from the zero
                 size column in the fish_data_downolad cited in
                 III.b.i.1.

         iii. Abundance

              1.  Abundance is a sum of the total count of fish for a
                  given species at a given site regardless of size.

              2.  The abundance value is a single value grouped by
                  species, site and batch code.

         iv. Richness

             1.  Richness is a count of the total number of unique
                 species in a given site.

             2.  The richness value is a single value grouped by site
                 and batch code.

         v.  Diversity

             1.  Shannon Diversity is calculated using the following
                 formula: r = sum(pi \* log pi). pi is the total number
                 of fish of a given species in a site divided by the
                 total number of fish in that same site.

             2.  The diversity value is a single value grouped by site
                 and batch code.

IV. Technical Information

    a.  Coral Reef Ecosystem Assessment and Monitoring Database is a web
        enabled database that consists of a SQL Server 2000 database and
        a front end developed in ASP.Net using Visual Basic.Net as the
        coding language.

    b.  Coral Reef Ecosystem Assessment and Monitoring Database follows
        a strict security model established by the NOS technical team.