Document ID: EPA-HQ-OW-2008-0667-3588
Agency: epa
Document Type: Supporting & Related Material
Title: 
Posted Date: 2014-08-15T04:00Z

Using the SEAMAP Ichthyoplankton Databases

	The following document is intended to serve as a basic guideline for
working with SEAMAP ichthyoplankton data.  The goal of which is to
familiarize users with the primary data structures and variables, as
well as give users insight into how the data may be used for analysis. 
The document will assume that users of these database files are familiar
with basic database manipulations such as merges, sorts and the creation
and/or deletion or variables (fields).  Concepts for working to achieve
specific goals will be outlined in broad concepts.  This will allow
users to utilize their own preferred methods for database manipulation
and analysis.  The document is broken up into three sections.  Section
I, is a listing of database structures, variable definitions and
listings of codes specific to each variable.  Section II, describes the
relationships within and among the databases. Section III, addresses
concepts on how to utilize the databases to quantitatively summarize
data on fish eggs and larvae with comments on issues regarding specific
variables necessary for quantification.

SECTION I

Data Structures

	The 3 primary databases necessary to summarize data on fish eggs and
larvae are the STATCARD, ICHSTRWK and ICHSARWK.  The STATCARD contains
information on where and when sampling operations (stations) have taken
places.  The ICHSTRWK contains information on the plankton samples taken
at each station.  While the ICHSARWK contains information on the
individual taxa collected in each sample.  Each of the database
structures and its variables are outlined below:

STATCARD Database File Structure

	Field Name = database variable name

	Type = character, numeric or date variable

	Wid = width/format

	Dec = number of decimal places in field if applicable

	Range/Table = valid range of values or code table listing

	Req = Minimum required fields

	Units = Units recorded in

      Field Name  Type  Wid Dec  Range/Table     Req  Units

   1  CRUISE_NO   Char  
3                        *

   2  VESSEL      Char   2      
VESSELS          *

   3  P_STA_NO    Char  
5                        *

   4  TIME_ZN     Char   1       TIMEZONE        
*

   5  MIL_TIME    Char   4       0000 - 2359      * 
hrs, min

   6  S_LATD      Num    2       0 <= x <= 90    
*  degrees

   7  S_LATM      Num    5   2   0 <= x <
60         minutes

   8  S_LATH      Char   1       N or X

   9  S_LOND      Num    3       0 <= x <= 180   
*  degrees

  10  S_LONM      Num    5   2   0 <= x <
60         minutes

  11  S_LONH      Char   1       W or X

  12  ST_DEPTH    Num    6   1   x > 0           
*  fathoms

  13  S_STA_NO    Char   5

  14  MO_DAY_YR   Date  
8                        *  mm/dd/yy

  15  END_TIME    Char   4       0000 -
2359         hrs, min

  16  E_LATD      Num    2       0 <= x <=
90        degrees

  17  E_LATM      Num    5   2   0 <= x <
60         minutes

  18  E_LATH      Char   1       N or X

  19  E_LOND      Num    3       0 <= x <=
180       degrees

  20  E_LONM      Num    5   2   0 <= x <
60         minutes

  21  E_LONH      Char   1       W or X

  22  EDEPTH      Num    6   1   x >
0               fathoms

  23  GEARS       Char  14       GEARTYPE

  24  SURF_TEMP   Num    5   2   -1.1 <= x <= 34     deg
(C)

  25  BOT_TEMP    Num    5   2   -1.1 <= x <= 32     deg
(C)

  26  AIR_TEMP    Num    4   1   x >
-10             deg (C)

  27  B_PRSSR     Num    6   1   880 <= x <= 1032   
millibars

                                    
or x = 0

  28  WIND_SPD    Num    2       0 <= x <=
50        knots

  29  WIND_DIR    Num    3       0 <= x <= 360      
compass deg

  30  WAVE_HT     Num    4   1   0 <= x <= 10       
meters

  31  SEA_COND    Char   1       0 -
9               Beaufort Scale

  32  DATA_CODE   Char   2       DATACODE         *

  33  VESSEL_SPD  Num    4   1   0 < x <= 60        
knots

  34  STAT_ZONE   Num    5   1   x > 0

  35  TOW_NO      Char   1       1 - 9

  36  NET_NO      Char   1       1 - 3

  37  COMMENT     Char 111

Explanation Of STATCARD Variables

CRUISE_NO

	3-character cruise code.

VESSEL

	2-character vessel code.  Valid Values are:

	01     OREGON

	02     SILVER BAY

	03     GEORGE M. BOWERS

	04     OREGON II

	05     COMBAT

	06     PELICAN

	07     FRIGATA

	08     KINGFISHER

	09     HERNAN CORTEZ

	10     GERONIMO

	11     UNDAUNTED

	12     ANTILLAS

	13     CALAMAR

	14     ALCYON

	15     GULF RANGER

	16     WESTERN GULF

	17     TOMMY MUNRO

	18     TANYA & JOE

	19     ONJUKO

	20     JEFF & TINA

	21     DELAWARE II

	22     OSV ANTELOPE

	23     ALABAMA INSHORE VESSELS

	24     FLORENCE MAY

	25     LOUISIANA INSHORE VESSELS

	26     SUNCOASTER

	27     MISSISSIPPI INSHORE VESSE

	28     CHAPMAN

	29     NISSHING MARU #201

	30     R/V BELLOWS

	31     R.J.KEMP

	32     MATAGORDA BAY

	33     LAGUNA MADRE

	34     GALVESTON BAY

	35     LUMCON PELICAN

	36     HERNAN CORTEZ II

	37     OLD COLONY

	38     SEAWOLF

	39     ATLANTIC HARVESTER

	40     SABINE

	41     PERSISTANCE

	42     CAPTAIN GRUMPY

	43     GULF STREAM

	44     KELCY ANN

	45     MR.JUG

	46     CALANUS

	47     A.NEEDLER

	48     B.I.P.

	49     ALBATROSS IV

	50     MOLLY M.

	51     LADY LISA

	52     MISS CARRIE

	53     CSS HUDSON

	54     CORAL SEA

	55     CARETTA

	56     R/V ABREU

	57     R/V GUAYANILLA

	58     SEAHORSE

	59     LINDSAY

	60     TEDDY'S SCOW

	61     RELENTLESS

	62     RATFIELD VESSELS

	63     GORDON GUNTER

	64     FERREL

	65     TRINITY BAY

	66     ALABAMA 38ft BERTRAM

	67     NUECES BAY

	68     MCARTHUR

	69     SAN JACINTO

	70     R/V SARINNA

	71     HARVESTING SYSTEM TECH

	99     OTHER VESSELS

P_STA_NO

	5-character code designating the Pascagoula station number.

TIME_ZN

	1-character time zone code.  Valid values are:

               1    Eastern Standard
Time                   

               2    Eastern Daylight Savings
Time           

               3    Central Standard
Time                   

               4    Central Daylight Savings
Time           

               8    Greenwich Mean
Time                     

               9    Other - Explain in Comments
Section     

               5    Atlantic Standard
Time                  

               6    Atlantic Daylight Savings
Time   

MIL_TIME

	Starting time (HHMM) in 24 hour military time.

S_LATD

	Degree of latitude for the position occupied at the start time of 	a
station.

S_LATM

	

	Decimal minutes of latitude for the position occupied at the 	start
time of a station.	

S_LATH

	Hemi-sphere of latitude for the position occupied at the start 

	time of a station.

S_LOND

	Degree of longitude for the position occupied at the start time 	of a
station.

S_LONM

	

	Decimal minutes of longitude for the position occupied at the 	start
time of a station.

S_LONH

	Hemi-sphere of longitude for the position occupied at the start 

	time of a station.

ST_DEPTH

	Station depth in fathoms for the position occupied at the start

	time of a station.

MO_DAY_YR

	Date station was taken in MM/DD/YY format.

S_STA_NO

	5-character SEAMAP or alternate station number.

END_TIME

	Ending time (HHMM) in 24 hour military time.

E_LATD

	Degree of latitude for the position occupied at the end time of 	a
station.

E_LATM

	

	Decimal minutes of latitude for the position occupied at the 	end time
of a station.	

E_LATH

	Hemi-sphere of latitude for the position occupied at the end 

	time of a station.

E_LOND

	Degree of longitude for the position occupied at the end time 	of a
station.

E_LONM

	

	Decimal minutes of longitude for the position occupied at the 	end time
of a station.

E_LONH

	Hemi-sphere of longitude for the position occupied at the end 

	time of a station.

EDEPTH

	Station depth in fathoms for the position occupied at the end

	time of a station.

GEARS

	Up to seven 2-character gear codes.  Valid values are:

               A    ASSORTED

               C    BIOSONICS ACOUSTIC SYSTEM 

               BG   BATHYTHERMOGRAPH(CTD,STD) 

               BC   BOTTLE
CAST                   

               GR   BOTTOM GRAB OR CORE SAMPLER   

               MC  
CAMERA,MOVIE                  

               SC  
CAMERA,STILL                  

               VC  
CAMERA,VIDEO                  

               CS   CONTINUOUS FLOW SYSTEM       

               CM   CURRENT
DOPPLER               

               DL   DEEP
LINE                     

               DV  
DIVING                        

               CD  
DREDGE,CLAM                   

               QD  
DREDGE,QUAHOG                 

               SD  
DREDGE,SCALLOP                

               TD  
DREDGE,TUMBLER                

               XB   EXPENDABLE BATHYTHERMOGRAPH(XB

               FP   FISH
PUMP                     

               GN   GILLNET 

               BL  
LONGLINE,BOTTOM               

               KP   LONGLINE,KALI
POLE            

               OB  
LONGLINE,OFF-BOTTOM           

               LL  
LONGLINE,SURFACE              

               MQ  
MARQUESETTE                   

               MN  
MICROPEKTON                   

               ML  
MISCELLANEOUS                 

               NS  
NETSONDE                      

               LT   NIGHT
LIGHT                   

               OD  
ODOMETER                      

               OF  
OVERFLIGHT                    

               OX  
OXYGEN,SENSOR,CTD             

               OY  
OXYGEN,SENSOR,YSI             

               OH   OXYGEN,TITRATION,HACHKIT      

               OW   OXYGEN,TITRATION,WINKLER      

               OR   OYSTER
RAKE                   

               PN   PLANKTON,GENERAL(BONGO,ETC.)  

               MO  
PLANKTON,MOCNESS              

               NN   PLANKTON,SINGLE NEUSTON OR NEK

               DN   PLANKTON,DOUBLE NEUSTON OR NEK

               RG   PLANKTON,RING
NET             

               TU   PLANKTON,TUCKER
TRAWL         

               RF   RECORDING
FATHOMETER          

               RV   REMOTELY OPERATED VEHICLE(ROV)

               RT  
ROTENONE                      

               RN   ROUND
NET                     

               SA  
SALINITY,AUTOSAL              

               SB   SALINITY,BECKMAN
RS5          

               SF   SALINITY,CONTINUOUS FLOW SYSTE

               SX  
SALINITY,CTD                  

               RE   SALINITY,REFRACTOMETER       

               BS  
SEINE,BEACH                   

               LP  
SEINE,LAMPARA                 

               PS  
SEINE,PURSE                   

               TS   SEINE,PURSE,TURTLE 

               SO  
SONAR                         

               SJ   SQUID
JIG                     

               DR   SURFACE
DRIFTER               

               RL   TAG
RELEASE                   

               TA   TEMPERATURE,CONTINUOUS FLOW SY

               TC  
TEMPERATURE,CTD               

               TB   TEMPERATURE,BECKMAN RS5       

               TM  
TEMPERATURE,BUCKET            

               TF  
TEMPERATURE,FLUKE             

               TY  
TEMPERATURE,YSI               

               CT  
TRAP,CRAB                     

               TR  
TRAP,FISH                     

               LR  
TRAP,LOBSTER,REED             

               LW  
TRAP,LOBSTER,WIRE             

               WT  
TRAP,LOBSTER,WOOD             

               TV   TRAP
VIDEO                    

               BT  
TRAWL,BEAM                    

               BB  
TRAWL,BIB                     

               FT  
TRAWL,FISH                    

               EF   TRAWL,FISH,EXPERIMENTAL       

               FD   TRAWL,FISH
DEFLECTOR          

               FE   TRAWL,FISH
EXCLUDER           

               HO   TRAWL,HIGH OPENING BOTTOM     

               MT  
TRAWL,MIDWATER                

               PT  
TRAWL,SCALLOP                 

               SN  
TRAWL,SEPARATOR               

               SH  
TRAWL,SHUMAN                  

               ST  
TRAWL,SHRIMP                  

               ES   TRAWL,SHRIMP,EXPERIMENTAL     

               SM   TRAWL,STANDARD MONGOOSE       

               *T  
TRAWL,STAR                    

               TN  
TRAWL,TRYNET                  

               TE   TRAWL,TURTLE
EXCLUDER         

               TT  
TRAWL,TWIN                    

               KT  
TRAWL,WING                    

               TG   TROLLING
GEAR                 

               VD   VERTICAL
DRIFTLINE            

               CC   CAMERA,CLOSED CIRCUIT TELEVISI

               01  
COMBINATION--SS+CC            

               02  
COMBINATION--SS+PR            

               03  
COMBINATION--CC+PR            

               04  
COMBINATION--SS+CC+PR         

               05  
COMBINATION--FM+SS            

               06  
COMBINATION--FM+SS+PR         

               07  
COMBINATION--FM+PR            

               FM  
FATHOMETER                    

               FL   FLUORESCENCE,CONTINUOUS FLOW S

               FX  
FLUORESCENCE,CTD              

               PR   PROFILER,3.5 KHZ SUB-BOTTOM   

               SS   SONAR,SIDE
SCAN               

               IT   TRAP,ICHTHYOPLANKTON,ILLUMINAT

SURF_TEMP 

	Surface temperature in degrees (C).

BOT_TEMP

	

	Bottom temperature in degrees (C).

AIR_TEMP

	Air temperature in degrees (C).

B_PRSSR

	Barometric pressure in millibars.

WIND_SPD

	Wind speed in knots.

WIND_DIR

	Wind direction in compass degrees.

WAVE_HT

	Wave height in meters.

SEA_COND

	Sea surface condition according to Beaufort Scale.

DATA_CODE

	2-character data collection code designating collection agency.  	Valid
values are:

               AL   Alabama

               FL   Florida 

               GA  
Georgia                                 

               LA  
Louisiana                               

               MS  
Mississippi                             

               NC   North
Carolina                          

               SC   South
Carolina                          

               TX  
Texas                                 
  

               US   Federal
Vessel                          

               99  
Other                                 
  

               PR   Puerto
Rico                             

               VI   Virgin Islands

VESSEL_SPD

	Vessel speed in knots.

STAT_ZONE

	Code for SEAMAP shrimp statistical zone.  Valid values are 01 to 	22.

TOW_NO   

	Consecutive tow withing a SEAMAP (S_STA_NO). Valid values are 1 	to 9.

NET_NO

	Code designating tow position of trawl.  Valid values are

			1 = Port

			2 = Starboard

			3 = Stern Trawl

COMMENT     

	Short comment regarding station operations and any issues with 

	sampling.

ICHSTRWK Database File Structure

      Field Name  Type  Wid Dec  Range/Table     Req  Units

   1  CRUISE_NO   Char  
3                        *

   2  VESSEL      Char   2      
VESSELS          *

   3  P_STA_NO    Char  
5                        *

   4  SAMPLE_NO   Char  
5                        *

   5  SIPC_CODE   Char   1       SIPC

   6  DATA_CODE   Char   2       DATACODE         *

   7  CR_STDATE   Date  
8                            mm/dd/yy

   8  CRENDDATE   Date  
8                            mm/dd/yy

   9  AREA_PROJ   Char   2       AREA_PRO

  10  PI_CODE     Char   2       PI_CODE

  11  TIME_ZONE   Char   1       TIMEZONE         *

  12  TIME        Char   4       0000 - 2359     
*   hrs, min

  13  GEAR_CODE   Char   2       GEAR_ICH

  14  MESH_CODE   Char   2       MESH_ICH

  15  START_TIME  Char   6       000000 - 235959     
hrs,min,sec

  16  END_TIME    Char   6       000000 - 235959     
hrs,min,sec

  17  START_FLOW  Num    6       x >=
0               meter reading

  18  END_FLOW    Num    6       x >=
0               meter reading

  19  MIN_DEPTH   Num    4       x >=
0               meters

  20  MAX_DEPTH   Num    4       x >=
0               meters

  21  VOL_FILT    Num   
3                            cu. meters

  22  ROTOR       Num    5       x >= 0

  23  NO_EGGS     Num    6       x >= 0

  24  EGGS_ALIQU  Char   4       ALIQUOT

Explanation of ICHSTRWK Variables

CRUISE_NO

	3-character cruise code.

VESSEL

	2-character vessel code.  See explanantion of STATCARD variables

	for valid values.

P_STA_NO

	5-character code designating the Pascagoula station number.

SAMPLE_NO

	5-characer code designating the SEAMAP plankton sample number.  	This
is a unique identifier for each sample.

SIPC_CODE

	Sample initial preservative code.  Valid values are:

               0    Unknown             

               1    5% Formalin         

               2    10% Formalin        

               3    95% Ethanol         

               4    70% Ethanol         

               5    0T0FIX             

DATA_CODE

	Equivalent to DATA_CODE in the STATCARD database file.

CR_STDATE

	Date the cruise began in MM/DD/YY format.

CRENDDATE

	Date the cruise ended in MM/DD/YY format.

AREA_PROJ

	Code for area and project. Valid Values are:

               01   GOM/SEAMAP

               02   NOT SEAMAP

               03   CAN/RICHARDS

               04   W.J.RICHARDS

               05   SA/SEAMAP

PI_CODE

	Principle Investigator Code.  Valid Values are:

               01   NMFS           

               02   GCRL           

               03   TOPW           

               04   FL.DNR         

               05   LDWF           

               06   STATE OF AL    

               07   UNIV. MIA.     

               08   CANADA         

               09   MEXICO         

               10   FL. INST. OCEAN

               11   TEXAS          

               12   SOUTH CAROLINA	

TIME_ZONE

	Equivalent in structure and valid values to TIME_ZN in the

 	STATCARD structures.  May be different values and times than the

	STATCARD values.

TIME

	Approximate time (HHMM) plankton sampling operations began.

GEAR_CODE

	Plankton gear code.  Valid values are:

               01   60 cm Bongo         0.61

               02   1m Ring             1.00

               03   1X2m Neuston            

               04   1/2m Ring           0.50

               05   20 cm Bongo         0.20

               07   1m**2 Tucker Trawl      

               08   Double 1X2m Neuston     

               09   1m**2 Mocness           

               10   4m**2 Mocness           

               11   60 cm o/c Bongo     0.60

               12   20 cm o/c Bongo     0.20

               13   60 cm BNF1          0.61

               14   70 cm Bongo         0.70

               06   Other/Unknown

MESH_CODE

	Plankton net mesh size code.  Valid values are:

               01   .303m  

               02   .999m  

               03   .333m  

               04   .253m  

               05   .505m  

               06   UNKNOWN

               09   .946m  

               10   .363m  

               11   .153m  

               12   .202m  

               13   .760m  

               14   .064m  

               15   .100m 	 

 

START_TIME

	Time in hrs,min,sec (HHMMSS) that the plankton gear began fishing.

END_TIME

	Time in hrs,min,sec (HHMMSS) that the plankton gear stopped 	fishing.

START_FLOW

	Starting flow meter reading.

END_FLOW 

	Ending flow meter reading.

MIN_DEPTH

	Minimum tow depth in meters.

MAX_DEPTH

	Maximum tow depth in meters.

	

VOL_FILT

	Volume of water in cubic meters filtered through the plankton net.

ROTOR

	Constant valued from the flow meter manufacture used to convert

	flow meter counts to distance.

NO_EGGS 

	Number of fish eggs removed from the sample.

EGGS_ALIQU

	Size of sample aliquot eggs were removed from.  Valid Values are:

               1/1

               1/2

               1/4

               1/8

ICHSARWK Database File Structure

      Field Name  Type  Wid Dec  Range/Table     Req  Units

   1  CRUISE_NO   Char  
3                        *

   2  VESSEL      Char   2      
VESSELS          *

   3  P_STA_NO    Char  
5                        *

   4  SAMPLE_NO   Char  
5                        *

   5  SAMP_STAT   Char   1       SMPLSTAT

   6  DATA_CODE   Char   2       DATACODE         *

   7  CATALOG_NO  Char  13

   8  TAXONOMIC   Char  13       BIOCODE          *

   9  BIOCODE     Num    9      
BIOCODE          *

  10  LIFE_STAGE  Char   1       LIFESTA

  11  MEAS        Num    4       x >=
0           *

  12  NOT_MEAS    Num    4       x >= 0

  13  SAMP_DATE   Date  
8                        *  mm/dd/yy

  14  VOL_DISP    Num    3       x >=
0              milliliters

  15  ALIQUOT     Char   3       1/1,1/2,1/4,1/8

  16  STATUS      Char   2       STATUS

  17  COMMENT     Char  75

  18  SASBIOCODE  Char  12

  19  SASTAXON    Char  50

  20  TIMES       Char   2

  21  UP_YEAR     Char   4

  22  UP_DATE     Char  10

  23  UP_ACTION   Char   1

  24  UP_ID       Char   3

  25  UP_TYPE     Char  15

  26  UP_PREDATE  Char   1

Explanation of ICHSARWK Variables

CRUISE_NO

	3-character cruise code.

VESSEL

	2-character vessel code.  See explanantion of STATCARD variables

	for valid values.

P_STA_NO

	5-character code designating the Pascagoula station number.

SAMPLE_NO

	5-characer code designating the SEAMAP plankton sample number.  	This
is a unique identifier for each sample.

SAMP_STAT  

	

	Sample status sorting code.  Valid values are:

	0   
Unknown                                 

      1    Sorted with fish
caught                 

      2    Sorted with no fish caught              

      3    Sample lost or
broken                   

      4    Sample sorted for only selected taxa 

	5    Sample sent to Gulf Coast Research Lab

	6    Sample sent to Miami Laboratory

	7    Sample sent to Panama City Laboratory

	8    Sample used for student thesis

	9    Sample number assigned no sample taken

	A    Bongo/Neuston paired status	 

	*	Non-Quantitative

DATA_CODE

	Equivalent to DATA_CODE in the STATCARD database file.

CATALOG_NO

	13-character field containing the SEAMAP archive serial number.

TAXONOMIC                 

	13-character field containg the abbreviated SEAMAP taxonomic 

	code.  At the species level the 1st 7 character refer to the genus

	and the last 6 characters refer to the species.  At taxonomic 	levels
greater than species the whole field is used to identify a

	taxon.

BIOCODE

	9-digit numeric code for a taxon.

LIFE_STAGE

	Life stage of a taxon. Currently not used for fish larvae.  Valid

	values are:

			

			1    ZOEAE     

               	2    MEGALOPAE 

               	3    POSTLARVAE

               	4    JUVENILE    

MEAS

	Number of fish larvae measured for a specific CATALOG_NO. 

NOT_MEAS

	Number of fish larvae not measured for a specific CATALOG_NO.

              

SAMP_DATE

	Date sample (SAMPLE_NO) was taken in MM/DD/YY format.

VOL_DISP

	Wet displacement volume in milliliter/cubic centimeters of entire

	plankton sample.

ALIQUOT

	Size of sample aliquot from which fish larvae were sorted.  Valid

	values are:

               1/1

               1/2

               1/4

               1/8

STATUS

	Taxonomic identification status code.  Valid values are:

		   00   Normal condition.  No examination of or

                    changes in sample have been made.

               01   Specimen(s) lost.

               02   Specimen(s)
destroyed.                        

               03   Specimen(s) cleared and
stained.              

               04   Specimen(s) dessicated, but not
destroyed.    

               05   Specimen(s)
sectioned.                        

               06   ID change.  Orig ID incorrect; new
ID

                    positive to genus level. 

               07   ID change.  Orig ID incorrect; new
ID

                    positive to species
level.               

               08   ID change.  Orig ID incorrect; new
ID

                   
uncertain.                               
    

               09   ID change.  Orig ID incorrect; see
DCOMM(yr).

               10   ID change.  Orig ID incorrect;
disagreement

                    on correct ID among loan users;
see

                    DCOMM(yr).

               11   Orig ID
confirmed.                            

               12   ID change.  Orig ID incorrect; new
ID

                    positive to family
level.                     

               13   ID change.  Orig ID incorrect; new
ID

                    positive to order
level.                      

            14   Specimen(s) on permanent or long term
loan.

COMMENT

	Short comment documenting issues at the CATALOG_NO level.

SASBIOCODE, SASTAXON, TIMES, UP_YEAR, UP_DATE, UP_ACTION, UP_ID,
UP_TYPE, UP_PREDATE

	Variables added to the structure to allow for tracking updates to 	the
SEAMAP ichthyoplankton databases by the data management team.  	They are
not documented for the original SEAMAP system.

SECTION II

Within Table Relationships

STATCARD

	The STATCARD database contains individual records for each station at
which sampling occurred, including stations at which gear other than
plankton gears were used.  Each unique record in the database is defined
by the combination of the VESSEL + CRUISE_NO + P_STA_NO variables.  Only
the combination of all three variables will define a unique station.

ICHSTRWK

	The ICHSTRWK database contains individual records for each plankton
sample number (SAMPLE_NO) taken at a station.  The database therefore
contains 1 record for each sample number.  However, there may be
multiple samples (SAMPLE_NO) for each combination of VESSEL + CRUISE_NO
+ P_STA_NO. 

ICHSARWK

	The ICHSARWK database contains at least one record for each sample
number (SAMPLE_NO) in the ICHSTRWK.  Within the ICHSARWK database the
combination of the VESSEL + CRUISE_NO + P_STA_NO + SAMPEL_NO +
CATALOG_NO define a unique record.  Samples with a sample status
(SAMP_STAT) equal to 0, 2, 3, 5, 6, 7, 8, and 9 contain a single record.
 These records are place holders that indicate the disposition of
samples taken under the SEAMAP umbrella.  Samples with a sample status
equal to 1, 4 or * may have multiple records associated with a sample
number.  Only, records with a sample status of 1, 4, and * will have
information pertaining to specific taxon.  Records with a sample status
of 1 or 2 are the only samples that should be used for quantitative
analysis and summaries.  A sample status of 1 indicates the sample was
shorted for all fish larvae, and a status of 2 indicates a valid sample
with no fish larvae.  The taxonomic (TAXONOMIC) and/or biocode (BIOCODE)
variables do not define a unique record, and multiple entries for a
specific taxon may be valid for multiple catalog numbers under a single
sample number.

Among Table Relationships

	

	The STATCARD, ICHSTRWK and ICHSARWK databases are relational, and
information in them follows a hierarchical progression.   In regards to
ichthyoplankton data, the statcard with its location information is at
the station level, the ICHSTRWK is at the level individual samples
collected at a station, while the ICHSTRWK contains information on the
individual fish larvae taken in the samples.  In order to link to
information contain in each of the separate databases the following
relationships can be used.

	Information between the STATCARD and ICHSTRWK can be linked (merged) by
setting a relationship between the unique combination of the VESSEL +
CRUISE_NO + P_STA_NO variables.

	Information between the ICHSTRWK and ICHSARWK can be linked (merged) by
setting a relationship between the unique combination of VESSEL +
CRUISE_NO + P_STA_NO + SAMPLE_NO variables.

	Information may also be linked by setting relationships between any of
the variables common among the 3 databases.  Suggestions for how to link
(merge) the databases for quantitative analysis can be found in the next
section.

SECTION III

Suggestions for Quantitative Analysis

	This section is written for user wishing to use the SEAMAP
ichthyoplankton databases to develop quantitative analyses and
summaries.  The focus will be on utilizing the standard SEAMAP bongo and
neuston collections to determine abundance estimates for eggs,
displacement volume, total fish larvae and larvae of specific taxon.  It
assumes that users will wish to select data from specific geographic
areas. 

	Ichthyoplankton samples have been collected during fishery-independent,
resource surveys in the Gulf of Mexico (GOM) since 1982 under the
Southeast Area Monitoring and Assessment Program (SEAMAP).  Surveys are
conducted by the National Marine Fisheries Service in cooperation with
the states of Florida, Alabama, Mississippi, and Louisiana.  The SEAMAP
samples compose a majority of the data in the ICHSTRWK and ICHSARWK
databases.

Most but not all SEAMAP, standard plankton stations (bnumbers) are
located at 30 mile or ½ degree (~56 km) intervals in a fixed,
systematic grid across the GOM (Figure 1), although, only every other
N-S transect of stations is sampled during spring surveys and during
fall plankton surveys in 1988-1991. Summer and Fall SEAMAP sampling is
conducted at bnumbers over the continental shelf, and Spring sampling in
the open waters of the Gulf of Mexico.  Occasionally during surveys,
samples are taken at nonstandard locations or stations are moved to
avoid navigational hazards. Samples are taken upon arrival on station
regardless of time of day. At each station either a bongo and/or neuston
tow are made depending on the specific survey.

Standard SEAMAP survey plankton sampling is conducted with 61 cm bongo
nets and/or single or double 1x2 meter neuston net.  The 61 cm bongo net
is fitted with 0.333 (0.335) micron mesh nets.  Bongo nets are fished in
an oblique tow path from the surface to a maximum

depth of 200 m or to 2-5 m off the bottom at depths less than 200 m.  A
mechanical flowmeter is mounted off-center in the mouth of each bongo
net to record the volume of water filtered. Volume filtered ranges from
~20 to 600 m3 but is typically 30 to 40 m3 at the shallowest stations
and 300 to 400 m3 at the deepest stations.  Typically, abundance for
eggs, displacement volume and fish larvae are expresses as the number or
volume under 10 m2 of sea surface.  Alternately, abundance may be
expresses as the number or volume per volume of seawater filtered
through the net.  However, per volume of seawater estimates are
integrated over the entire depth range.  Neuston nets are fitted with
0.947 (0.950) 1 mm mesh net.  The neuston gear is towed at the

surface with its frame half-submerged for 10 minutes.  Data are only
available for fish larvae.  Abundance estimates of fish larvae are
expressed as the number per 10 minute tow.  Non-standard gear and mesh
sizes have been used to collect plankton samples and are coded as such
in the database.

In order arrive at these abundance estimates it will be necessary to
utilize data from all of the STATCARD, ICHSTRWK and ICHSARWK databases. 
This is necessary since the databases are optimized for efficient
storage not data analysis and summary.  For instance, examining the
basic database structures outlined above we can see position information
is located in the STATCARD; information of the gear used and effort are
located in the ICHSTRWK; and variables necessary to enumerate larvae of
individual taxon and sample status are located in the ICHSARWK. 
Therefore, in order to determine abundance estimates of fish larvae for
a specific gear and mesh combination within a given geographic area
requires the building of a dataset that contains all the necessary
variables from all three databases.  The rest of this document will deal
with the specifics of arriving at these estimates for the standard
SEAMAP samples.  Each section covers a different topic. 

Putting all the variables needed to do quantitative analysis into a
singe dataset.

Since most personal computers have the storage and memory requirement to
handle large amounts of data, start by merging the three separate
databases into a single database/dataset that can be further
manipulated.  The following steps outline suggested concepts necessary
to do this:

Add a new numeric variable to the STATCARD database called STAREC
(statcard record) and set it equal to 1 for all records.

Add a new numeric variable to the ICHSTRWK database called ISTREC
(ichstrwk record) and set it equal to 1 for all records.

Add a new numeric variable to the ICHSARWK file called ISAREC (ichsarwk
record) and set it equal to 1 for all records.

Sort/index the STATCARD file on VESSEL + CRUISE_NO + P_STA_NO

Sort/index the ICHSTRWK file on VESSEL + CRUISE_NO + P_STA_NO

6.  Sort/index the ICHSARWK file on VESSEL + CRUISE_NO + P_STA_NO       

    + SAMPLE_NO.

Merge/combine the STATCARD and ICHSTRWK files by setting a    
relationship/link between the STATCARD and ICHSTRWK databases on VESSEL
+ CRUISE_NO + P_STA_NO.

Sort/index the combined STATCARD/ICHSTRWK file on VESSEL + CRUISE_NO +
P_STA_NO + SAMPLE_NO.

9. Next, merge/combine the newly combined STATCARD/ICHSTRWK

   database/dataset with the ICHSARWK database by setting a

   relationship/link between the combined STATCARD/ICHSTRWK and

   the ICHSARWK database on VESSEL + CRUISE_NO + P_STA_NO +

   SAMPLE_NO.

Keep only the records in the final database/dataset where

The variables STAREC = 1 and ISTREC = 1 and ISAREC = 1.  The final
database/dataset should have as many records as were found in the
original ICHSARWK database.  The final dataset should now contain the
STATCARD and ICHSTRWK information for each record in the ICHSARWK
database.  

Filtering data by geographic area.

The SEAMAP BNumbers (Figure 1) represent the systematic sampling grid
design of the SEAMAP surveys.  The bnumbers when recorded are found in
the SEAMAP Station Number Field (S_STA_NO).  Unfortunately, the bnumbers
are not consistently recorded for all cruises, nor are they recorded in
a consistent manner in the S_STA_NO variable.  For example, bnumber B001
may appear in the database as B1, B01, B001, B-001 etc..  Therefore,
filtering data by geographic area is best done by longitude and
latitude.  Figure 1 can be used to find the approximate area a bnumber
represents.  It is easiest to work in decimals degree.  Using the
combined database created earlier or with the STATCARD database, decimal
longitude and latitude can be calculated as follows (make sure to
include parentheses in the formula):

Decimal Longitude:

( ( S_LOND + ( S_LONM / 60 ) ) * -1 )

Decimal Lattitude:

( S_LATD + ( S_LATM /60 ) )

Filtering Data by Gear and Sampling Status

The beginning of this section outlines the SEAMAP sampling design and
the standard bongo and neuston net sampling gears.  The primary
difference between the two gears is that the bongo gear can give
estimates of abundance for eggs, displacement volume, total fish larvae
and individual taxonomic categories, while the neuston gear only
provides data on fish larvae and individual taxonomic categories. 
However, egg and displacement volume may not be available for all bongo
samples.  Bongo net samples as noted above are towed in an oblique
pattern from the surface to near bottom and then back to the surface. 
Therefore abundance estimates based on volume or surface area, for a
sample are intergraded over the water column.  Nueston net samples are
only collected from the surface half meter of the water column and are
effort bases on time.

Valid quantitative SEAMAP samples can be filter out of the combined
STATCARD/ICHSTRWK/ICHSARWK data set by selecting only records where:

For Standard SEAMAP Bongo Net Tows:

(GEAR_CODE = “01” and MESH_CODE = “03”) and 

(SAMP_STAT = “1” or SAMP_STAT = “2”)

I.E, give me only samples where gear = 61 cm bongo with a mesh size of
.333 with a sorting status of sorted with fish larvae found or sorted
with no larvae.

For Standard SEAMAP Neuston Net Tows:

( ( (GEAR_CODE = “03” or GEAR_CODE = “08”) and MESH_CODE =
‘09’ ) and (SAMP_STAT = ‘1’ or SAMP_STAT = ‘2’)

I.E, give me only samples collected where gear = a single or double
neuston net sample with a mesh size of .947 with a sorting status of
sorted with fish larvae found or sorted with no larvae.

Figure 1.  Gulfwide distribution of SEAMAP BNumbers.

A merged dataset is necessary since the GEAR_CODE and MESH_CODE
variables are taken from the ICHSTRWK database and the SAMP_STAT
variable from the ICHSARWK database.

The majority of the database has only a data for only a single bongo or
neuston sample taken at each station.  In some cases both samples from a
paired gear (bongo or double neuston) may have data from both samples
taken at a station.  These samples can be considered as replicates.  In
addition, some stations may have multiple bongo or nueston tows at the
same station.  Currently, the database does not code for paired samples
or multiple samples taken at a station.

Estimating Abundance of Fish Larvae from Bongo Net Samples. 

	As noted above, abundance estimates of fish larvae can be volume or
surface area based.  Additionally, estimates of fish larvae can be based
on all fish larvae in a sample (total fish larvae), or based on
individual taxonomic categories.  This section will outline the
necessary calculation and concepts necessary to properly enumerate total
fish larvae and fish larvae by taxonomic category.  

	At this point, we will assume that our combined dataset created at the
beginning of this section has been pre-filtered by geographic area and
contains only records for valid (SAMP_STAT = 1 or 2) bongo (GEAR_CODE =
‘01’ and MESH_CODE = ‘03’) samples.  The dataset should contain
a single record for each unique combination of VESSEL + CRUISE_NO +
P_STA_NO + SAMPLE_NO + CATALOG_NO.  Unique combinations of VESSEL +
CRUISE_NO + P_STA_NO + SAMPLE_NO + CATALOG_NO for samples with a
SAMP_STAT = 2 in the dataset will have a empty CATALOG_NO variable, and
will have only a single record in the dataset.  As the only record, the
blank CATALOG_NO field is unique for that SAMPLE_NO.  Unique
combinations of VESSEL + CRUISE_NO + P_STA_NO + SAMPLE_NO + CATALOG_NO
with a SAMP_STAT = 1 will have a unique CATALOG_NO for each record, and
will have one record for each unique CATALOG_NO for a unique SAMPLE_NO. 
Therefore, there are 1 or more records for SAMPLE_NOs with a SAMP_STAT =
1.  However, there may be several unique CATALOG_NOs in a sample with
the same TAXONOMIC category.  Figure 2 shows a hypothetical minimum
dataset for 3 unique SAMPLE_NOs for 2 samples with a SAMP_STAT = 2 and
single SAMPLE_NO with a SAMP_STAT = 1.

	The minimum variable set necessary to calculate the number of larvae
under 10 m2 for each unique combination of VESSEL + CRUISE_NO + P_STA_NO
+ SAMPLE_NO + CATALOG_NO is MEAS, NOT_MEAS, ALIQUOT, VOL_FILT and
MAX_DEPTH.  The minimum variable set necessary to calculate the number
of larvae per m3 is MEAS, NOT_MEAS, ALIQUOT, VOL_FILT.  However, several
changes to the dataset are needed prior to calculating these values due
to the way the data is stored in the original databases:

	1.  In some instances the numeric MEAS and NOT_MEAS fields are blank
(null) or may contain -9 (also considered a null value). In these cases,
the blanks and -9 must be set to a value of 0 (zero).  For example, if
MEAS = -9 then MEAS = 0 or if MEAS = NULL (database dependent) then MEAS
= 0, and likewise for NOT_MEAS.

	2.  ALIQUOT in the database is a character variable with valid values
of ALIQUOT = “1/1”, “1/2”, “1/4” or “1/8”.  SAMPLE_NOs
with a SAMP_STAT = ‘1’ will have one of the valid values. 
SAMPLE_NOs with a SAMP_STAT = ‘2’ may have a valid value or be left
blank.  In order to properly calculate the larvae/10 m2 or larvae/10 m3
values, a numeric variable to be used as an ALIQUOT multiplier will be
necessary.  The multiplier is the reciprocal of the fraction represented
in the ALIQUOT variable, i.e. “1/2” = 2.  This step is necessary in
order to account for sub-sampling by aliquoting.  For SAMPLE_NOs with a
SAMP_STAT = ‘2’  the aliquot multiplier is 1.  The new variable can
be created with the following logic:

	If ALIQUOT = “1/1” then MULTIPLIER = 1

	If ALIQUOT = “1/2” then MULTIPLIER = 2

	If ALIQUOT = “1/4” then MULTIPLIER = 4

	If ALIQUOT = “1/8” then MULTIPLIER = 8

	If SAMP_STAT = ‘2’ then MULTIPLIER = 1

Figure 3 shows the modifications to the pertinent variables for the
sample numbers in our hypothetical dataset from Figure 2.

	Once these modifications have taken place it is possible to calculate
larvae/10 m2 or larvae/10 m3 for each unique combination of VESSEL +
CRUISE_NO + P_STA_NO + SAMPLE_NO + CATALOG_NO (Figure 4).  The formula
for larvae/10 m2 is:

((MEAS + NOT_MEAS) * MULTIPLIER) * ((MAX_DEPTH/VOL_FILT) * 10)

where:

	((MEAS + NOT_MEAS) * MULTIPLIER) = Extrapolated total number of 							
    fish larvae for unique    							     combination of VESSEL + 						
	     CRUISE_NO + P_STA_NO + 								     SAMPLE_NO + CATALOG_NO

	((MAX_DEPTH/VOL_FILT) * 10)      = The standard haul factor for a

						     unique combination of VESSEL +

                                         CRUISE_NO + P_STA_NO +

                                         SAMPLE_NO

      Note:  The 10 in the standard haul factor can be changed to any

             multiplier.  For example, 100 which will result in

     	       larvae/100 m2.

The formula for larvae/ m3 is:

((MEAS + NOT_MEAS) * MULTIPLIER) / (VOL_FILT)

where:

	((MEAS + NOT_MEAS) * MULTIPLIER) = Extrapolated total number of 							
    fish larvae for a unique    							     combination of VESSEL + 				
			     CRUISE_NO + P_STA_NO + 								     SAMPLE_NO + CATALOG_NO

		

Figure 2.  Hypothetical minimum dataset showing data for three unique
sample numbers from a cruise.

VESSEL	CRUISE_NO	P_STA_NO	SAMPLE_NO	SAMP_STAT	VOL_FILT	MAX_DEPTH
CATALOG_NO	TAXONOMIC	MEAS	NOT_MEAS	ALIQUOT

	4	145	41077	3115	2	100	100

4	145	41078	3116	2	200	200

	-9	-9	1/1

	4	145	41079	3117	1	100	50	SML20218-000	BOTHIDAE	2	-9	1/2

4	145	41079	3117	1	100	50	SML20603-001	DECAPTEPUNCTA	2	-9	1/2

4	145	41079	3117	1	100	50	SML21163-000	GOBIIDAE	2	13	1/2

4	145	41079	3117	1	100	50	SML21892-001	SCOMBERCAVALL	1	-9	1/2

4	145	41079	3117	1	100	50	SML20329-000	SYACIUM	2	7	1/2

4	145	41079	3117	1	100	50	SML20867-000	LUTJANUCAMPEC	10	0	1/2

4	145	41079	3117	1	100	50	SML22236-000	LUTJANUCAMPEC	5	0	1/2

  

Figure 3.  Modifications to the pertinent variables for the sample
numbers in our hypothetical dataset from Figure 2.  VESSEL CRUISE and
P_STA_NO not shown.

SAMPLE_NO	SAMP_STAT	VOL_FILT	MAX_DEPTH	CATALOG_NO	TAXONOMIC	MEAS
NOT_MEAS	ALIQUOT	MULTIPLIER

	3115	2	100	100

	0	0

1

	3116	2	200	200

	0	0	1/1	1

	3117	1	100	50	SML20218-000	BOTHIDAE	2	0	1/2	2

3117	1	100	50	SML20603-001	DECAPTEPUNCTA	2	0	1/2	2

3117	1	100	50	SML21163-000	GOBIIDAE	2	13	1/2	2

3117	1	100	50	SML21892-001	SCOMBERCAVALL	1	0	1/2	2

3117	1	100	50	SML20329-000	SYACIUM	2	7	1/2	2

3117	1	100	50	SML20867-000	LUTJANUCAMPEC	10	0	1/2	2

3117	1	100	50	SML22236-000	LUTJANUCAMPEC	5	0	1/2	2

Figure 4.  Calculated larvae/10 m2 and larvae / m3 for each unique
VESSEL + CRUISE_NO + P_STA_NO + SAMPLE_NO + CATALOG_NO for our
hypothetical dataset from Figure 3.

SAMPLE_NO	SAMP_STAT	VOL_FILT	MAX_DEPTH	CATALOG_NO	TAXONOMIC	MEAS
NOT_MEAS	ALIQUOT	MULTIPLIER	TOTAL FISH	SHF	LARVAE	LARVAE

LARVAE

10 SQR METER	CUBIC METER

	3115	2	100	100

	0	0

1	0	10	0	0

	3116	2	200	200

	0	0	1/1	1	0	10	0	0

	3117	1	100	50	SML20218-000	BOTHIDAE	2	0	1/2	2	4	5	20	0.04

3117	1	100	50	SML20603-001	DECAPTEPUNCTA	2	0	1/2	2	4	5	20	0.04

3117	1	100	50	SML21163-000	GOBIIDAE	2	13	1/2	2	30	5	150	0.3

3117	1	100	50	SML21892-001	SCOMBERCAVALL	1	0	1/2	2	2	5	10	0.02

3117	1	100	50	SML20329-000	SYACIUM	2	7	1/2	2	18	5	90	0.18

3117	1	100	50	SML20867-000	LUTJANUCAMPEC	10	0	1/2	2	20	5	100	0.2

3117	1	100	50	SML22236-000	LUTJANUCAMPEC	5	0	1/2	2	10	5	50	0.1

 VOL_FILT                         = Volume of water filtered for a 

                                         unique combination of VESSEL +

                                         CRUISE_NO + P_STA_NO +

                                         SAMPLE_NO in cubic meters

Sorry this is an ongoing process and I have been redirected to another
project.  Please contact me as below for further details.

David S. Hanisko

Research Fisheries Biologist

National Marine Fisheries Service

Pascagoula Laboratory

3209 Frederic St.

Pascagoula MS, 39568

 

Voice: 228-762-4591 x204

Fax: 228-769-9200

  HYPERLINK "mailto:David.S.Hanisko@noaa.gov"  David.S.Hanisko@noaa.gov 

or

  HYPERLINK "mailto:David.S.Hanisko.atsea@noaa.gov" 
David.S.Hanisko.atsea@noaa.gov