National Oceanographic Data Center Internal Report 14 WORLD OCEAN DATABASE 1998 CD-ROM Data Set Documentation Version 1.0 M.E. Conkright, S. Levitus, T.P. Boyer, T. O'Brien, C. Stephens, D. Johnson, L. Stathoplos, O. Baranova, J. Antonov, R. Gelfeld, J. Burney, J. Rochester, C. Forgy Ocean Climate Laboratory National Oceanographic Data Center Silver Spring, MD February, 1998 U.S. DEPARTMENT OF COMMERCE William M. Daley, Secretary National Oceanic and Atmospheric Administration D. James Baker, Administrator National Environmental Satellite Data and Information Service ------------------------------------------------------------------------------- Table of Contents iii List of Tables vi I. Introduction 1 About this Product 2 Acknowledgments 2 II. CD-ROM Disc Contents 4 A. Data Sources 4 1. Bottle and Low Resolution CTD data 4 2. High Resolution CTD Data (Conductivity, Temperature, Depth probe) 6 3. MBT Data (Mechanical Bathythermograph) 6 4. XBT Data (Expendable Bathythermograph) 6 B. Station Description 7 1. Primary Header 8 2. Character Data 8 3. Secondary Header 8 4. Biological Header 11 5. Taxa-specific and Biomass Data 11 6. Depth Dependent Measured Variables 15 III. Quality Control Procedures 16 Explanation of error flags 17 IV. CD-ROM Disc Structure 20 V. File Structure/Format 21 A. Description of the CD-ROM Documentation 25 B. UTIL Directory 28 GZIP Directory 28 C. System Requirements 29 VI. List of Acronyms Used in the CD-ROM Documentation 30 VII. References 31 Appendix 1. NODC Country Codes 32 Appendix 2. NODC Secondary Header Code Tables 34 2A. Ocean Weather Station - Secondary Header Code 9 34 2B. Cast Direction - Secondary Header Code 11 35 2C. Water Color (Forel-Ule Scale) - Secondary Header Code 14 35 2D. Wind-wave Direction (WMO 0877) - Secondary Header Code 16/21 36 2E. Wave Height (WMO 1555) - Secondary Header Code 17 37 2F. Sea State (WMO 3700) - Secondary Header Code 18 37 2G. Wind Force (Beaufort Scale) - Secondary Header Code 19 38 2H. Wave Period (WMO 3155) - Secondary Header Code 20 38 2Ia. Weather (WMO 4501 ) - Secondary Header Code 26 39 2Ib. Weather (WMO 4677 ) - Secondary Header Code 26 40 2J. Cloud Type (WMO 500) - Secondary Header Code 27 42 2K. Cloud Cover (WMO 2700) - Secondary Header Code 28 43 2L. Recorder Type (BT - WMO 4770) - Secondary Header Code 32 44 2M. Digitization Method (NODC 0612) - Secondary Header Code 35 45 2N. Digitization Interval (NODC 0613) 36 - Secondary Header Code 45 2O. Data Treatment And Storage (NODC 0614) - Secondary Header Code 37 46 2P. Instrument For Reference Temperature (NODC 0615) - Secondary Header Code 40 46 2Q. Horizontal Visibility (WMO 4300 - Secondary Header Code 41) 47 2R. Filter Type - Secondary Header Code 59 48 Appendix 3. Code Tables for Temperature-Salinity Probes 49 Appendix 4. Codes For Methods 51 Appendix 5. Codes For Originator's Variable Units 52 Appendix 6. List of Code Tables Associated With The Biological Headers 53 6A. Type of Tow - Biological Header 4 53 6B. Gear And Flowmeter Codes - Biological Header 7 53 6C. Preservative Codes - Biological Header 10 54 6D. Weight Method - Biological Header Code 11 54 6E. Count Method - Biological Header Code 13 55 6F. Flowmeter Calibration - Biological Header Code 19 55 6G. Depth Determination - Biological Header Code 24 55 6H. Volume Method - Biological Header Code 25 55 Appendix 7. Code Tables Used to Describe The Taxonomic Data 56 7A. Taxonomic Lifestages - Taxa Variable 5 56 7B. Taxonomic Sex Code - Taxa Variable 6 57 7C. Taxonomic Presence/Abundance Codes - Taxa Variable 7 57 7D. Taxonomic Trophic Level - Taxa Variable 8 58 7E. Taxonomic Realm - Taxa Variable 9 58 7F. Taxonomic Features - Taxa Variable 16 58 7G. Taxonomic Modifiers - Taxa Variable 17 59 Appendix 8. Biological Group Codes 59 Appendix 9. Definition of Quality Control Flags 60 Appendix 10A. WMO Squares for the Atlantic and Indian Oceans 61 Appendix 10B. WMO Squares for the Pacific Ocean 62 Appendix 11A. Inventory of Secondary Headers 63 Appendix 11B. Inventory of Biological Headers 65 Appendix 11C. Inventory of Taxonomic Headers 66 Appendix 12A. Total Number of Kbytes per Probe Type 67 Appendix 12B. Total Number of Kbytes by Region 68 Appendix 13. Sample Output for Observed Level Data from WOD98-03\DATA\NPAC20 -90\BDO7617 STATION 67064 69 ------------------------------------------------------------------------------- LIST OF TABLES Table 1. Comparison of the Number of Stations in WOD98 with Previous World Ocean Databases 1 Table 2. File Types in the WOD98 4 Table 3. Variables in the NODC Bottle Data File (NBD) 5 Table 4. Variables in the Project Bottle Data File (BD) 5 Table 5. Inventory of Data for Each Probe 7 Table 6. List of Secondary Header Variables in WOD98. 9 Table 7. List of Biological Header Variables. 12 Table 8. List of Biomass and Taxa-specific Variables. 13 Table 9. List of Biomass Variable Codes 14 Table 10. Standard Levels and Depths (meters) 16 Table 11. Contents of the WOD98-01 through WOD98-05 20 Table 12. Description of the OCL ASCII Format. 22 ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- I. INTRODUCTION The World Ocean Database 1998 (WOD98) CD-ROMs, containing observed and standard level profile data, represent the first part of an extension of earlier work (World Ocean Atlas 1994 - WOA94). The second part will be the World Ocean Atlas 1998 (WOA98) which will present objectively analyzed fields of many of the variables in WOD98. WOD98 expands on WOA94 by including the additional variables nitrite, pH, alkalinity,chlorophyll, and plankton, as well as all available metadata and meteorology. During the past three years, the number of data sets received at NODC/WDC-A (National Oceanographic Data Center/World Data Center-A for Oceanography) has increased (see Table 1) as a result of the Intergovernmental Oceanographic Commission (IOC)/NODC Global Oceanographic Data Archaeology and Rescue project (GODAR), (Levitus et al., 1998, Levitus et al., 1994). The figures in Table 1 show the increase in data from 1982 to 1998. The reason the WOD98 total for MBT, XBT, and ABottle and low resolution CTD@ do not show even larger increases from WOD94, is that large numbers of duplicates were identified in these databases and removed since its publication. Whereas exact duplicate profiles are easy to identify and remove, Anear@ duplicates are more difficult. These can result from receiving the same data from different sources, where key variables such as latitude, longitude, or date/time were treated differently. As the procedures for identifying duplicate stations improved, more of these Anear@ duplicate stations were identified. NOAA atlases describing the distribution of the WOD98 data will be prepared as part of WOD98. Table 1. Comparison of the number of stations in WOD98 with previous world ocean databases. =============================================================================== DATA TYPE CLIMATOLOGICAL ATLAS OF WORLD OCEAN WORLD OCEAN THE WORLD OCEAN 1982 ATLAS 1994 DATABASE 1998 =============================================================================== Bottle and 425,000 1,337,862 1,373,440 low resolution CTD stations High resolution N.A. N.A. 189,555 CTD stations MBT and DBT profiles 775,000 1,947,185 2,077,200 XBT profiles 285,000 1,281,942 1,644,911 TOTAL STATIONS 1,485,000 4,566,989 5,285,106 Plankton only N.A. N.A. 42,885 stations (1) Surface only data (2) N.A. N.A. 131,823 =============================================================================== (1) stations with only plankton and biomass data and no physical/chemical measurements (2) includes ship-of-opportunity data The format used in WOD98 is different from the format in WOA94, and is more space efficient. This change is necessary due to the increased amount of information contained in WOD98. The Ocean Climate Laboratory (OCL) invites comments on this format so improvements can be made toward achieving the goal of producing a general format that is useful to as wide a group as possible. The CD-ROMs are formatted according to the ISO 9660 standard. Data are stored in ASCII format and are sorted geographically by World Meteorological Organization (WMO) squares. The data on the CD-ROMs are compressed using theuniversal "gzip" UNIX compression utility. This utility is provided on each CD-ROM under the directory "UTILS/GZIP" for both Unix and DOS operating systems. ABOUT THIS PRODUCT The OCL has been expanding the World Ocean Atlas 1994 database since its release. As can be seen from Table 1, the database has increased greatly. The OCL has attempted to ensure that the conversion from originator to OCL format was accurate, that duplicates were removed, and that "suspect" data were flagged. This last task is an ongoing effort. Every effort was made to identify and correct errors in the database. As scientists and data managers utilize the WOD98, and errors are identified, they will be corrected. Some data flagged as being in error or "suspicious" may not deserve this designation. The OCL requires the help of users of this product in identifying cruises which need to be flagged as having "suspicious" data, and cruises which were flagged and should not have been. In working toward the release of WOA98, the OCL will continue to examine data quality. Included as part of this release is software contributed by various individuals which can be used as examples of how to read the data into different formats. These programs are preliminary and continue to be developed and improved. Any comments and suggestions for additional programs, which will increase the number of users who can benefit from this product, would be appreciated. Updates will be posted in the OCL World Wide Web site at: http://www.nodc.noaa.gov/ ACKNOWLEDGMENTS The OCL is supported by the NOAA Climate and Global Change program and the NOAA Environmental Science Data and Information Management program (ESDIM) to produce scientifically quality controlled oceanographic databases, produce objectively analyzed global fields of oceanographic variables, and to perform diagnostic studies based on these databases. The Intergovernmental Oceanographic Commission (IOC) supported the GODAR project which has resulted in the rescue of much historical ocean data. In particular, Dr. Iouri Oliounine has shared the enthusiasm for this project and has been critical to its success. The OCL expresses its thanks to all those who provided comments and helped develop an improved product. Special thanks to Steve Worley (National Center for Atmospheric Research, NCAR), Dr. Harry Dooley (International Council for the Exploration of the Sea, ICES) and Norm Hall (NODC) for testing the CD-ROMs prior to distribution. John E. O'Reilly (National Marine Fisheries Service, NMFS) contributed the conversion programs from the OCL ASCII format to IDL; Dr. Harry Dooley contributed the conversion program from OCL to ICES/OceanPC format. Thanks also to Josh Malasheskie for formatting files to enter names into the ITIS database. The OCL would also like to acknowledge the help received over the years from our colleagues in the other divisions here at NODC, particularly Francis Mitchell (helped with all the code lists and accessions), Andrew Allegra (prepared the CD-ROMs), Robert VanWie (provided information on the archived NODC files), Melanie Hamilton (provided GTSPP data), J. D. Hardy (researched and documented the correct status of many plankton names), Sheri Phillips (helped O. Baranova design the CD-ROM background), Mike Simmons and Maggie Dunklee (wrote the P3 format description), Ervin Trammell, Charlotte Sazama and Ron Moffatt (helped in locating data for rescue in the WDC-A archives), and Mary Hollinger, James Berger, Patricia Kirk, and Don Collins who distribute this product. ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- II. CD-ROM DlSC CONTENTS A. DATA SOURCES The data used in this project are all the data found in the NODC archives as of the first quarter of 1994 as well as some of the data submitted to NODC since 1994.In addition, data gathered as a result of the IOC/IODE GODAR project, the Global Ocean Database project and Global Temperature Salinity Profile Project (GTSPP) project, were included in this study. There are nine different files associated with each WMO square. These files represent the different instruments (probes) used to sample profile data (XBT, MBT, High Resolution CTD, Bottle and Low Resolution CTD). In addition, for each probe type, the data are separated into the NODC archived data and the data received through projects such as the GODAR project. Table 2 presents the different file types which are further described in the following section. Table 2. File types in the WOD98 =========================================================================== FILE NAME SOURCE =========================================================================== NBD NODC archived bottle data and low resolution CTD BD Bottle data and low resolution CTD received from projects BIO Plankton data received from projects NCT NODC archived high resolution CTD data CTD High resolution CTD data received from projects NMB NODC archived MBT data MBT MBT data received from projects NXB NODC archived XBT data XBT XBT data received from projects =========================================================================== Flagged data types on the CD-ROM series include: 1. Bottle and low resolution CTD data a. NODC Bottle Data (NBD) Variables: This file also includes STD (Salinity/Temperature with Depth), low resolution CTD data, and surface only data. Bottle data may have one or more of the following variables: Table 3. Variables in the NODC Bottle Data File (NBD) ====================================================== CODE VARIABLE UNIT/SCALE ====================================================== 1 Temperature (in situ) degrees C 2 Salinity PSS and p.p.t. 3 Oxygen ml/l 4 Phosphate micromolar 6 Silicate micromolar 7 Nitrite micromolar 8 Nitrate micromolar 9 pH unitless ====================================================== b. Project Bottle Data (BD) Variables: This file includes low resolution CTD data, surface only data (mainly from ship-of-opportunity) and plankton/biomass data. Bottle data may have one or more of the following variables: Table 4. Variables in the Project Bottle File (BD) =================================================== CODE VARIABLE UNIT/SCALE =================================================== 1 Temperature (in situ) degrees C 2 Salinity PSS and p.p.t. 3 Oxygen ml/l 4 Phosphate micromolar 6 Silicate micromolar 7 Nitrite micromolar 8 Nitrate micromolar 9 pH unitless 11 Chlorophyll ug/l none Plankton/Biomass various 17 Alkalinity meq/l 25 Pressure decibars =================================================== c. Project Plankton/Biomass variables (BIO) Variables: Plankton taxa-specific and biomass measurements 2. High Resolution CTD Data (Conductivity, Temperature, Depth probe) a. NODC High Resolution CTD/STD (NCT) Source: NODC high resolution CTD data in the F022 format. Variables: Temperature, salinity, oxygen, pressure b. Project High Resolution CTD data (CTD) Variables: Temperature, salinity, oxygen, chlorophyll, pressure 3. MBT Data (Mechanical Bathythermograph) a. NODC MBT data (NMB) Source: NODC MBT file (Includes MBT data from the NODC Selected Bathythermograph (SBT) file which contains data at selected depths) Variable: Temperature b. Project MBT (MBT) Variable: Temperature. This file also includes Digital Bathythermograph (DBT) data. 4. XBT Data (Expendable Bathythermograph) a. NODC XBT data (NXB) Source: NODC XBT file. (Includes XBT data from the NODC SBT file) Variable: Temperature b. Project XBT data (XBT) Variable: Temperature (includes GTSPP data which contains TAO buoy data) Table 5 is an inventory of the data found in each of the files described. The WOD98 contains a total of 5,459,814 stations, of which 131,823 are surface only data (primarily in the project Bottle Data file - BD), and 83,650 are plankton observations in both the project Bottle data file (BD) and the Bio file (BIO). Table 5. Inventory of Data for Each Probe ================================================================================ VARIABLES BD NBD CTD NCT MBT NMB XBT NXB BIO ================================================================================ Temperature 717450 724759 88906 99717 945845 1131355 733708 911203 Salinity 661134 682446 85891 98044 Oxygen 215428 265290 16482 10672 Phosphate 152675 126336 Silicate 109198 77028 Nitrite 75558 44779 Nitrate 94626 49897 pH 38879 64459 Chlorophyll 131690 3852 Biochem 62229 21421 (Plankton) Alkalinity 6759 Pressure 52393 32640 54350 TOTAL 799502 727225 89830 99725 945845 1131355 733708 911203 21421 PER PROBE TOTAL BY 1526727 189555 2077200 1644911 21421 PROBE TYPE ================================================================================ B. STATION DESCRIPTION In WOD98, a station is comprised of as many as six parts: (1) Primary Header: contains all information vital to the identification of an individual profile, such as date, time, location, NODC country code, cruise code, and a unique station number; (2) Character Data (originator's cruise codes and originator's station codes) and Principal Investigator; (3) Secondary Header: contains information such as meteorological data, water column characteristics (such as depth to bottom), information about the probe used, ship, institute, project, originator's units, and methods; (4) Biological Header: contains information necessary to understand how biological data were sampled. "Biological" data are arbitrarily defined as plankton biomass (weights or volumes) and taxa-specific observations. It does not include chlorophyll data. (5) Taxa-specific and Biomass Data: contains plankton weights, volumes, and/or concentrations, for an entire sample (biomass) or for individual groups of organisms (taxa-specific). (6) Depth Dependent Measured Variables: temperature, salinity, oxygen,phosphate, silicate, nitrite, nitrate, pH, chlorophyll, alkalinity, and pressure data vs. depth. 1. Primary Header The primary header contains information about the number of bytes in the station, a unique number which identifies each station, the country code (see code list in Appendix 1), a cruise number, date, time, position, and the number and type of variables in the station. Time and location are all written in the same format: a) number of significant digits b) total digits c) precision of measurement d) data value Total digits will be one more than significant digits if the value is a negative number. Total digits will also be different than significant digits if a value has been converted or identified as a trace value (TR = 0.005). The station type identifies whether the data are at observed depth levels (0) or standard levels (1). The number and type of variables identifies the depth dependent variables in a station. Depth-dependent variables are listed with the number which identifies them in Table 4. 2. Character Data Character data are used to report the originator's cruise identification and the originator's station identification, if provided. Under this heading, the Principal Investigators (PI) are also identified by numeric code and by variable code. The Principal Investigator is the person responsible for collecting the data and is included whenever available. A list of the numeric codes associated with each PI can be found in the CODES directory of each CD-ROM (file name: PINAMES.TXT). 3. Secondary Header The secondary header contains metadata (information about the data) and meteorological information associated with each station. Table 6 lists the different types of secondary header data we include for each station, when the information is available. Many of the meteorological variables have WMO code tables associated with them. These code tables are grouped together in Appendix 2 and are also individually listed in the CODES directory. The OCL secondary header information is always in numeric form, whereas some of the NODC codes are alphanumeric. Therefore, some of the code tables will have an OCL code and the equivalent NODC code. Table 6. List of secondary header variables in WOD98. The "App. #" column indicates the Appendix where the code list is found, or if it is included in a separate file in the CODES directory (listed in file = SECONDH.TXT). ================================================================================ ID # DESCRIPTION App.# ID # DESCRIPTION App.# ================================================================================ 1. NODC Accession Number file 31 Calibration Temperature none 2. NODC Project Code file 32 BT recorder (WMO 4770) 2L 3. OCL Platform Code file 33 Depth fix none 4. NODC Institution Code file 34 Bottom Hit none 6. WOD98 Unique none 35 XBT Digitization Method 2M Station Number (NODC 0612) 7. Originator's none 36 XBT Digit. Interval 2N station number (NODC 0613) 8. Depth precision none 37 XBT Data Treatment 2O (NODC 0614) and Storage Method 9. Ocean Weather Station 2A 38 MBT Depth Correction none Code 10. Bottom Depth (meters) none 39 MBT Temperature none Correction 11. Cast Duration (hours) none 40 Instrument for reference 2P temperature (NODC 0615) 12. Cast Direction 2B 41 Horizontal visibility 2Q (down assumed) (WMO Code 4300) 13. High resolution pairs none 45 Absolute Humidity (g/m3) none 14. Water Color 2C 46 Reference/Sea none Surface Temperature 15. Water Transparency none 47 Sea Surface Salinity none (Secchi disk) 16. Wave Direction 2D 48 Chlorophyll method 4A (WMO 0877 or NODC 0110) 17. Wave Height 2E 49 Nutrient method 4B (WMO 1555 or NODC 0104) 18. Sea State 2F 54 O2 originator's unit 5A (WMO 3700 or NODC 0109) 19. Wind Force 2G 55 Nutrient 5B (Beaufort scale or NODC 0052) originator's unit 20. Wave Period 2H 56 Chlorophyll 5C (WMO 3155 or NODC 0378) originator's unit 21. Wind Direction 2D 58 Alkalinity 5D (WMO 0877 or NODC 0110) originator's unit 22. Wind Speed (knots) none 59 Filter type size 2R 23. Barometric Pressure none 60 Alkalinity method 4C (millibars) 24. Dry Bulb Temperature none 65 Conductivity standard (degrees C) (milliohms/cm) none 25. Wet Bulb Temperature none 67 O2 method method 4D (degrees C) 26. Weather Conditions 2I 68 Salinity method 4E (WMO 4501 or 4677) 27. Cloud Type 2J 69 Temperature method 4F (WMO 0500 or NODC 0053) 28. Cloud Amount 2K 71 Radio signal none (WMO 2700 or NODC 0105) 29. T-S Probe 3 72 XBT Wait none (Temperature/Salinity probe) 30. Calibration Depth none 73 XBT Frequency none ============================================================================== The following is an explanation of the secondary header codes which do not have code tables associated with them: Code 1 NODC accession number: number assigned by NODC to each batch of data received; Code 3 Platform: code list identifies the platforms associated with the data. It should be noted that the database contains negative platforms which were assigned to unidentified ships from Russian and Ukrainian institutes for which we expect to receive the information in the near future. Negative platforms are unique only to the accession number where found (filename: SHIPNAME.TXT); Code 6 OCL Unique Station Number: OCL assigned unique station numbers. This number will not change in future releases; Code 7 Originator's station number: station number assigned by the data submittor or data originator, if numeric; Code 8 Depth precision: precision of the depth field (number of digits to the right of the decimal); Code 10 Bottom depth: depth from water surface to sediment-water interface, in meters; Code 11 Cast duration: duration of the cast, in hours; Code 13 High resolution pairs: unique station number identifying where HCTD and Bottle data were sampled at the same station; Code 15 Water transparency: Secchi depth, in meters; Code 20 Wave Period: Note that NODC code 0378 is not equivalent to WMO 3155, therefore these data need to be used with caution unless the users can identify which code is being reported; Code 22 Wind speed: surface or near-surface wind speed, in knots; Code 23 Barometric pressure: the atmospheric pressure at sea level due to the gravitational force on the column of air above it (millibar); Code 24 Dry bulb temperature: identical to air temperature, indegrees Celsius; Code 25 Wet bulb temperature: the temperature a parcel of air would have if it were cooled adiabatically with no heat transfer, in degrees Celsius; Code 30 Calibration depth: deviation on an XBT from the zero depth. This difference between points was used to adjust the profile when it was digitized; Code 31 Calibration temperature: deviation on an XBT from a 16.7EC reference point. This difference between points was used to adjust the profile when it was digitized; Code 33 Depth fix: a one (1) is assigned if a depth correction was applied to XBT using recalculated drop rate; Code 34 Bottom hit: a one (1) is assigned if the probe hits the bottom; Code 38 Depth correction: average difference between the surface trace and the surface depth line of the grid for an MBT; Code 39 Temperature correction: correction for difference between reference temperature and MBT reading or correction to the original data by the submittor - in some cases the correction has already been applied; Code 45 Absolute Humidity (g/m3): sometimes referred to as the vapor density because it is the ratio of the mass of water vapor present to the volume occupied by the moist air mixture present in the atmosphere; Code 46 Reference/Sea Surface Temperature: temperature used to check the probe or a separate measure of sea surface temperature; Code 47 Sea Surface Salinity: the salinity of the layer of sea water nearest to the atmosphere; Code 65 Conductivity standard: conductivity value of seawater, at salinity 35 PSS and temperature 15C, used to calculate the conductivity ratio. The conductivity ratio is then used to calculate salinity. Code is included when only conductivity is submitted. Units are milliohms/cm; Code 71 Radio signal (code 71): identifies whether data is received from radio signal (real time data), identified with a one (1); Code 72 XBT Wait: Wait is the time difference between the launch of the probe and the time it begins recording data; Code 73 XBT Frequency: Frequency is the sampling rate of the recorder. Appendix 3 lists the different codes associated with the T-S probe type (temperature-salinity). Also listed in CODES/TSPROBE.TXT in the CD-ROMs. Appendix 4 lists the methods associated with each variable measured. This list represents the methods reported with the data submitted and is not a comprehensive list of variable methods. Also listed in CODES/METHODS.TXT in the CD-ROMs. Appendix 5 lists the units codes which identify the submittor's original units. Also listed in CODES/UNITS.TXT in the CD-ROMs. 4. Biological Header The biological header section contains any metadata (information about the data) for the taxonomic and biomass measurements at a station. Table 7 lists the different types of biological header data we include for each station, if the information is available. Similar to the secondary header information, much of the information is represented by code lists. Appendix 6 includes these lists. 5. Taxa-specific And Biomass Data Two types of data are represented in this portion of the station: biomass measurements and taxa-specific variables (see Table 8 for a list of these variables). Biomass are data for the entire sample or net haul (e.g. displacement volume of total haul),whereas taxa-specific data refers to a group or species (e.g. number of Calanus per sample). Table 7. List of biological header variables. All code tables are listed in Appendix 6 (the biological headers are listed in file = BIOHEADR.TXT). ================================================================================ ID# DESCRIPTION App.# ID# DESCRIPTION App.# ================================================================================ 1. Water volume filtered (m3) none 14. Tow distance (meters) none 2. Sampling duration (minutes) none 15. Average tow speed (knots) none 3. Mesh size (ug) none 16. Sampling start time (GMT) none 4. Type of tow 6A 17. NOT USED 5. Large removed volume (ml) none 18. Flowmeter type 6B 6. Large plankters removed? none 19. Flowmeter calibration 6F 7. Gear code 6B 20. Counting institution file 8. Sampler volume (liters) none 21. Voucher institution file 9. Net mouth area (m2) none 22. Wire angle start (degrees) none 10. Preservation 6C 23. Wire angle end (degrees) none 11. Weight method 6D 24. Depth determined 6G 12. Large removed length (cm) none 25. Volume method 6H 13. Count method 6E ================================================================================ The following is a description of the biological header codes. [Note that values were stored as provided and were only calculated for net mouth area]: Code 1 Water volume filtered: total volume of water filtered by the sampling gear, in m3; Code 2 Sampling duration: time over which the sampling gear was towed, in minutes; Code 3 Mesh size: pore size of the sampling device, in micrometers; Code 5 Large removed volume: the minimum volume criteria for removing large plankters, in ml, see also code 12; Code 6 Large plankters removed: if large plankters were specified as being removed (1) or not removed (2), this code is marked. See also code 5 and code 12; Code 8 Sampler volume: internal volume of the sampling gear (e.g. volume of Niskin bottle), in liters; Code 9 Net mouth area: mouth or opening area of the sampling gear, in m2. If mouth diameter was provided, area was calculated (area = pi times (diameter/2)raised to the second power); Code 12 Large removed length: the minimum size/length criteria for removing large plankters, in cm, see also code 5; Code 14 Tow distance: distance over which sampling gear was used, in meters; Code 15 Average tow speed: average speed used to tow the sampling gear, in knots; Code 16 Sampling start time: in GMT; Code 22 Wire angle start: wire angle of the towing apparatus at sampling start, in degrees; Code 23 Wire angle end: wire angle of the towing apparatus at sampling end, in degrees. Table 8. List of biomass and taxa-specific variables. Code tables for these variables are listed in Appendix 7 (biomass and taxa variables are listed in file = TAXVAR.TXT). ================================================================================ ID# DESCRIPTION App# ID# DESCRIPTION App# ================================================================================ 1. Parameter number file 13. Taxon wet weight none (>0 ITIS tsn tax code, (ug/UNIT) -200 biomass code, -5000 group code) 2. Upper depth none 14. Taxon dry weight none (meters) (ug/UNIT) 3. Lower depth none 15. Taxon ash-free weight none (meters) (ug/UNIT) 4. Biomass value none 16. Taxon feature 7F (code table) 5. Taxon lifestage 7A 17. Taxon modifier 7G (code table) (code table) 6. Taxon sex code 7B 18. Size min (mm) none (code table) 7. Taxon present 7C 19. Size max (mm) none (code table) 8. Taxon troph 7D 20. Unit 5 (code table) 9. Taxon realm 7E 21. Taxon radius (um) none (code table) 10. Taxon count none 22. Taxon length (um) none (count of taxon / UNIT) 11. NOT USED 23. Taxon width (um) none 12. Taxon volume (ml/UNIT) none ================================================================================ The following is a description of biomass and taxa-specific variables: Code 1 Parameter number: type of taxon or biomass sampled, represented with an ITIS taxonomic serial number (> 0), a group code (<5000) , or a biomass parameter code (< -201 and > -210) (Table 9); Code 2 Upper depth: the upper depth sampled, in meters; Code 3 Lower depth: the lower depth sampled, in meters; Code 4 Biomass value: contains biomass value measured, units are specified by the biomass parameter code (code 1, Table 9); Code 10 Taxon count: the number of an individual taxa counted, in count per unit (as specified by code 20); Code 12 Taxon volume: the volume of an individual taxa counted, in ml per unit (as specified by code 20); Code 13 Taxon wet weight: the wet weight of an individual taxa counted, in :g per unit (as specified by code 20); Code 14 Taxon dry weight: the dry weight of an individual taxa counted, in :g per unit (as specified by code 20); Code 15 Taxon ash-free dry weight: the ash-free dry weight of an individual taxa counted, in :g per unit (as specified by code 20); Code 18 Minimum size range description: the smaller size range used in a taxonomic description, in mm; Code 19 Maximum size range description: the larger size range used in a taxonomic description, in mm; Code 20 Unit: additional unit identifier for biomass and taxa- specific measurements (listed in Appendix 5); Code 21 Taxon radius description: the radius (diameter ) 2) size used in a taxonomic description, in um; Code 22 Taxon length description: the length or height used in a taxonomic description , in um; Code 23 Taxon width description: the width or shortest-dimension used in a taxonomic description, in um. Taxa-specific data is information about a specific group of plankton. The group can be described by a scientific taxon name (e.g. Calanus finmarchicus), or by a descriptive phrase (e.g. heterotrophic nanoflagellates). The data for taxa- specific measurements are the relative abundance, the concentration, the volume, or the weight of the group observed. The total set of plankton descriptors are included in a small number of categories: name, lifestage, sex, trophic mode, realm, features, minimum size, maximum size, length, width, radius, and special modifier. The special modifier category retains qualifying terms like `other', `sp.' or `spp.'. Appendix 7 includes more details about these categories. Measurement identifiers (i.e. what group, species or type of biomass was measured) are stored as a code number in the Parameter number field (code 1). Biomass measurements are represented with code values of -201 though -210 (see Table 9). Scientific taxa names were translated using ITIS (Integrated Taxonomic Information System, http://www.itis.usda.gov/itis) as an authority list, and are represented in the WOD98 under the proper ITIS taxonomic serial number (see code-file "ITISTSN.TXT"). When a vague, or broad, taxonomic group or general description was used (e.g. "fish", "plankton", "crabs"), a non- taxonomic `group code' was assigned for the group, starting at a value of -5000 (see code-file "NONTAXSN.TXT" and Appendix 8). Codes -206 to -210 were assigned to biomass values which exceeded 1xE9 ml or mg. Table 9. List of biomass parameter codes (file = BIOMASS.TXT) ================================================= Parameter DESCRIPTION Number ================================================= -201 Total displacement volume, ml -202 Total settled volume, ml -203 Total wet weight, mg -204 Total dry weight, mg -205 Total ashfree dry weight, mg -206 Total displacement vol, m3 -207 Total settled volume, m3 -208 Total wet weight, kg -209 Total dry weight, kg -210 Total ashfree dry weight, kg ================================================= Unlike depth-dependent variable data (e.g. temperature, oxygen, nitrate, etc.), taxa-specific and biomass data are stored in sets of unique observations, called `taxa-sets', with each set containing upper and lower depths and all of its associated taxa-specific or biomass variables. For biomass measurements, this usually includes a Parameter number, a Biomass value, a Unit, an Upper depth, and a Lower depth. For taxa-specific measurements, this usually includes a Parameter number, a taxon measurement (e.g. Taxon count, Taxon wet weight), a Unit, an Upper depth, a Lower depth, and an associated special taxonomic descriptors (e.g. Life stage, Sex code, special Modifier, etc.). Examples of taxa-sets: Biomass (displacement volume) measured from 0-100m, and 200-500m, will have two taxa-sets, one for each depth range. Biomass (displacement volume and wet weight) measured from 0-250m will have two taxa-sets, one for each type of biomass measurement. A taxa-specific measurement of a single species, counted at five bottle depths, will have five taxa-sets, one for each depth. A taxa-specific measurement of ten species, counted at five bottle depths, will have 50 taxa-sets, five depths x ten species. Note that taxa with different taxonomic descriptors (e.g. Life stage, Sex code, etc.) are treated as different taxa, and therefore are stored in different taxa- sets. For example: Calanus eggs, Calanus juveniles, Calanus adults (male), and Calanus adults (female) would be stored as four separate observations, each with the same Parameter number, but differing in their life stage and sex code values. 6. Depth Dependent Measured Variables The number of variables and the type of variable are identified in the primary header,as well as with an error code for each variable if all values of that variable in the station have been flagged. Table 4 lists the variables and their identifying codes. Appendix 9 lists the flags assigned to each variable. Stations with data on pressure surfaces have their depths computed, so depth is always present and the pressure value is stored. Some data were reported with both depth and pressure in which case both are stored. Similarly, stations which come in with conductivity readings have salinity computed. Some stations may be reported on standard depth levels (see Table 10) such as most of the Japanese and Former Soviet Union (F.S.U.) data. It is uncertain whether these data were originally measured at standard levels or interpolated to standard depth levels. Included under this category, are surface only data which are also mostly from ships-of-opportunity. ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- III. QUALITY CONTROL PROCEDURES The quality control procedures will be fully documented in separate NOAA technical reports. This section is a brief summary of the procedures used. These procedures were used to identify possible problems with the data by examining the entire database. The OCL continues to quality control the data and requests input from the users as to possible problems identified when using the data. This is particularly the case when examining the nutrient data where many cruises from the F.S.U. were flagged. Differences in the definition of units and the conversion of units exist possibly and will be resolved in collaboration with colleagues from the F.S.U. Observed level data were checked for quality prior to interpolation to standard levels. For many analysis purposes, it is necessary to interpolate from observed levels to standard depth levels. The standard depth analysis levels selected for this study are listed in Table 10 and include the 30 NODC standard depths and additional levels at 3500, 4500, 5500, 6000, 6500, 7000, 7500, 8000, 8500, and 9000 meters. Table 10. Standard levels and depths (meters) ====================================================================== Depth Level Depth Level Depth Level Depth Level ====================================================================== 0 1 250 11 1200 21 4500 31 10 2 300 12 1300 22 5000 32 20 3 400 13 1400 23 5500 33 30 4 500 14 1500 24 6000 34 50 5 600 15 1750 25 6500 35 75 6 700 16 2000 26 7000 36 100 7 800 17 2500 27 7500 37 125 8 900 18 3000 28 8000 38 150 9 1000 19 3500 29 8500 39 200 10 1100 20 4000 30 9000 40 ====================================================================== The quality of the observed and standard level data were checked using the following procedures: 1. Various checks to ensure the conversion from originator to OCL format was correct (e.g. comparison between converted stations and original data); 2. Preliminary checks - checks for duplicate stations, depth inversions, range checks of primary- and secondary-header variables, cruise integrity checks (i.e., ship speed, cruise duration, duplication or overlap with existing cruises within the database); 3. Range check of the observed level data for each major basin as a function of depth; 4. Large inversion and gradient checks for all variables; [Note: An additional gradient check, called a "zero anomaly check", was used to locate large gradients due to an anomalous value of " 0.00 " within a station. These instances were often due to the use of " 0.00 " as a missing value indicator, and had to be carefully distinguished from " 0.00 " as a data value]; 5. Density inversion check on the standard level data; 6. XBT drop rate correction before interpolation of observed level to standard level data for T4, T6, and T7 probes (Hanawa et al., 1994); 7. Standard deviation check; 8. Check for unrealistic features after an initial computation of the objective analysis. Explanation of error flags -------------------------- Data observations and profiles determined to be "non-representative", "suspect", or "erroneous" by the quality control were flagged using the criteria summarized below. In most cases, only the specific observations are flagged (e.g., a single range outlier or a depth level inversion). In cases where a systematic problem is found to exist throughout the entire profile (e.g., multiple depth problems or standard deviation outliers), then the entire profile may be flagged. A description of the flags can be found in Appendix 9. 1. Check for depth inversions and duplicate depths Depth error flags are assigned if: (A) the second of two successive depths is shallower than the first (a depth inversion), the second depth will be marked with a flag value = 1. (B) three successive depths are shallower than the first depth, every depth reading in the profile following the first will be marked with a flag value = 1. (C) two successive depth readings are equal, the second reading will be marked with a flag value = 1. All correct depths are marked with a flag value = 0. 2. Standard deviation check on standard level data This check calculates the mean and standard deviation of data by five-degree square latitude-longitude boxes for annual (all variables), seasonal (temperature, salinity, oxygen, chlorophyll, nitrate, phosphate, silicate), and monthly (temperature and salinity) periods at each standard level. Data are flagged if: (A) a value is five standard deviations away from the mean in coastal waters (defined as any one-degree grid box adjacent to a land grid point or any one-degree grid box with a bottom depth of less than 200 m). (B) a value is four standard deviations away from the mean in near coastal waters or near the ocean floor (defined as any one-degree grid point where the depth is equal to or less than the depth in an adjacent one-degree box) or any adjacent five-degree grid box is designated coastal. (C) a value is three standard deviations away from the mean in the open ocean. (D) if a station contains two or more standard deviation failures, the whole station is flagged. 3. Density and stability checks for temperature and salinity stations The criteria for an instability is described by Levitus (1982). Flags are assigned: (A) for density inversions at the depths where they occur in the observed and standard level stations. (B) when two or more density inversions (or instabilities) occur in a standard level station. The entire station is then flagged. [Note: Stability checks were performed on observed as well as standard level data. Observed level flags are included for information only, since they were not used to exclude any data from the station data sets. Whole-station flags for stability and standard deviation checks are for standard level data only. For informational purposes, if a standard level station includes a whole station density flag (or standard deviation flag), the observed level data will also include a whole station flag.] 4. Range outlier, gradient, inversion, and zero anomaly flags Observed level data that fell above or below variable-specific ranges were flagged (flag = 1) as range outliers, per Boyer et al. (1994) and Conkright et al. (1994). Suspiciously large decreases (gradients, flag = 3) and increases (inversions, flag = 2) of observed level data over depth were flagged if they were larger or smaller than maximums set for the entire world ocean. Large gradients followed by a large inversion due to a value of "0.00" were marked as a "zero anomaly" (flag = 4). Combinations of range outliers and gradient/inversion/"zero anomaly" are flagged as in Appendix 9. 5. Cruise flags Indicates all stations from a cruise have anomalous data. If an entire accession number is found to have anomalous data, all cruises for that accession will be assigned a cruise flag. This flag also was used to identify data submitted as MBT with dates prior to 1941 and XBT data with dates prior to 1966. 6. Bullseye flags Flags individual values which cause unrealistic features such as Abullseyes@ in the contoured objectively analyzed data. This flag is assigned to the observed and standard level data if any value is identified as "incorrect". ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- IV. CD-ROM DISC STRUCTURE The WOD98 is comprised of five CD-ROMs containing profile and plankton/biomass data in compressed format. WOD98-01 through WOD98-04 contain observed level data, WOD98-05 contains all the standard level data. The data are organized by ten-degree latitude-longitude squares numbered using the WMO ten-degree square numbering scheme (illustrated in Appendices 10A-10B). Within each of the WMO subdirectories are four files containing the NODC archived data NBD, NCT, NXB, and NMB and five PROJECT data files named BD, CTD, MBT, XBT and BIO (these are in separate files since they have not yet been archived at the NODC). Stations in each file are sorted by date. Appendix 11 shows an inventory of the contents in each probe type. Table 11 shows the contents of WOD98-01 - WOD98-05. WOD98-01 contains observed level data for the North Atlantic from 30-90N and includes the Mediterranean Sea, Baltic Sea, North Sea, and the Arctic Ocean from 100W to 100E. WOD98-02 includes observed level data for the North Atlantic 0- 30N and the South Atlantic. WOD98-03 contains observed level data for the North Pacific from 20N-90N including the Arctic Ocean from 100E-100W. WOD98-04 contains observed level data for the North Pacific 0-20N, the South Pacific Ocean, the Indian Ocean, Red Sea, and Persian Gulf. WMOs 7007, 7008, 7108 and 7109 are duplicated in WOD98-02 and WOD98-04 since the North Atlantic and North Pacific Oceans overlap in these areas. All the standard level data are on WOD98-05. As with the observed level data, the data are organized by WMO square. Within each WMO square are eight files containing the data associated with each probe or instrument type (the data in BIO do not have standard levels). [Note: Some of the WMO files listed in the CD-ROMs contain no data since they correspond to land areas.] A positive longitude in the data denotes the Eastern Hemisphere, a negative longitude denotes the Western Hemisphere, a positive latitude denotes North and a negative latitude denotes South. Table 11. Contents of the WOD98-01 through WOD98-05 ====================================================== CD-ROM CONTENT ====================================================== WOD98-01 North Atlantic 30N-90N WOD98-02 North Atlantic 0-30N South Atlantic WOD98-03 North Pacific 20N-90N WOD98-04 North Pacific 0-20N South Pacific North Indian South Indian WOD98-05 Standard level data for all ocean basins ======================================================= ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- V. FILE STRUCTURE/FORMAT All observed and standard level data files are written as a series of 80 character length ASCII records. For UNIX users, note that the ASCII records contain a DOS CR-LF (Carriage Return-Line Feed) end-of-record marker which may need to be stripped (see section V.B.2 - Special Note for UNIX Users). A detailed record layout for the data can be found in Table 12. There is a carriage return after each 80 bytes (CR-LF). Each station begins on a new line. Each section of a station (e.g. character data, secondary header, biological header) begins with a total byte count for that section. If there are no data for that section, the byte count is zero. If there are data for that section, the byte count can be used to skip over sections which are of no interest to the user. The header includes the country code (see Appendix 1 for a listing of these codes), NODC cruise number, position, date-time, OCL unique station number, the number of observed or standard depth levels, an identifier for observed or standard level data, number of variables, variable codes, and a flag if all of a variable's data in that station fails a quality control check (see Appendix 9 for a description of the flags). Appendix 12 shows the byte count for each probe type. Appendix 13 shows sample data output from Station 67064 (using the program ocldemo.f), found on the WOD98-03 CD-ROM in file WOD98-03\DATA\NPAC2090\7617\BD07617. This file contains temperature, salinity, oxygen, phosphate, silicate, nitrite, and taxonomic/biomass data ("f" denotes the flag assigned to the variable; numbers in parenthesis represent the number of significant digits in the value; "ERR" identifies whole profile flags for each variable). For compactness, each variable (other than most in the first header), is written in this fashion: STPVVVVVV[E] where: S = Number of significant digits in a value; T = Total number of digits in a value. This is usually the same as [S], but can vary in cases of negative numbers, converted values, and data in which the values are reported with more precision than a probe is capable of recording; P = Precision of a variable (number of places to the right of the decimal point); V = The actual value. This is read in using [T] and [P]; E = Error code. This is not used for all variables. For example: A salinity value, written as [553338910] means that S = 5, T = 5, P = 3. Using this information, there are five bytes in the salinity reading, with a precision of three, so V(sal) = 33.891, and E = 0. A missing value in this data format is always represented with an S = '-' (the minus character). That is, when the number of significant digits in read in,the character encountered will be a negative sign. This tells the user that no value was recorded and to skip to the next value. The file naming convention is redundant so that files downloaded from the CD-ROM to DOS or UNIX storage devices can be completely identified from their names. For example, an NBD (NODC Bottle data) file from the North Atlantic will have a fully qualified name such as \NATL3090\5008\5008NBDO.gz (if observed level data) and \NATL3090\5008\5008NBDS.gz (if standard level data). TABLE 12. DESCRIPTION OF THE OCL ASCII FORMAT. OCL ASCII FORMAT FOR PRIMARY HEADER ============================================================================== FIELD LENGTH FORMAT DESCRIPTION ============================================================================== 1. Bytes in field (2) 1 I1 2. Bytes in station from (1) Integer 3. Bytes in field (4) 1 I1 4. OCL station number from (3) Integer OCL station id. 5. Country code 2 A2 NODC country codes (Appendix 1) 6. Bytes in field (7) 1 I1 7. Cruise number from (6) Integer NODC/OCL number 8. Year 4 I4 9. Month 2 I2 10. Day 2 I2 11. Time - if time is missing its denoted as (-) in the Sig.Digits. field; if so, skip to (12) a. Sig. digits 1 I1 (-)if time missing b. Total digits 1 I1 not present if a is (-) c. Precision 1 I1 not present if a is (-) d. Value from (b) from (a-c) not present if a is ( -) 12. Latitude - if latitude is missing its denoted as (-) in the Sig.Digits . field; if missing, skip to (13) a. Sig.digits 1 I1 (-)if missing b. Total digits 1 I1 not present if a is (-) c. Precision 1 I1 not present if a is (-) d. Value from (b) from (a-c) not present if a is (-) 13. Longitude - if longitude is missing its denoted as (-) in the Sig.digits field; if missing, skip to (14) a. Sig. digits 1 I1 (-)if missing b. Total digits 1 I1 not present if a is (-) c. Precision 1 I1 not present if a is (-) d. Value from (b) from (a-c) not present if a is (-) 14. Bytes in field (15) 1 I1 15. Number of Levels from (14) Integer Number of depths 16. Station type 1 I1 (0) Obs, (1) Std 17. Number of Variables 2 I2 read (18-20) in station (N) N times 18. Bytes in field (19) 1 I1 19. Variable codes from (18) Integer OCL parameter codes (Table 4) 20. Error code per 1 I1 see Appendix 9 variable ================================================================================ "^" denotes blank space OCL ASCII FORMAT FOR CHARACTER DATA, SECONDARY AND BIOLOGICAL HEADER ============================================================================== FIELD LENGTH FORMAT DESCRIPTION ============================================================================== ------------------------------------------ CHARACTER DATA AND PRINCIPAL INVESTIGATOR ------------------------------------------ 1. Bytes in field (2) 1 I1 if "0" go to secnd. header 2. Total bytes for char. data from (1) Variable 3. Number of types 1 I1 orig. cruise of data (N) and/or orig.sta. and/or PI IF FIELD (4) IS 1=Originators Cruise, OR 2=Originators station code (read fields 4-6 N times) 4. Type of data 1 I1 (1)orig. cruise (2)orig. station 5. Bytes in field (6) 2 I2 6. Character data from (5) A IF FIELD (4) IS 3=Principal investigator 4. Type of data 1 I1 always 3 5. Number of P.I. names 2 I2 read fields 6-9 N times 6. Bytes field (7) 1 I1 7. Variable code from (6) Integer OCL code (Table 4) 8. Bytes in field (9) 1 I1 9. P.I. code from (8) Integer OCL code file=PINAMES.TXT) ----------------- SECONDARY HEADER ----------------- 1. Bytes in field (2) 1 I1 if "0" go to biological header 2. Total bytes for secnd. hdrs from (1) Variable 3. Bytes in field (4) 1 I1 4. Number of entries (N) from (3) Integer read fields 5-10 N times 5. Bytes in field (6) 1 I1 6. Secondary header code from (5) Integer OCL code (Table 6) 7. Significant digits 1 I1 8. Total digits 1 I1 9. Precision of value 1 I1 10. Value from (9) from (7-9) ----------------- BIOLOGICAL HEADER - entries (5-10) repeated based on number read in (4) ----------------- 1. Bytes in field (2) 1 I1 if "0" go to station data 2. Total bytes for biology from (1) Integer 3. Bytes in field (4) 1 I1 4. Number of entries (N) from (3) Integer read 5-10 N times 5. Bytes in field (6) 1 I1 6. Biological header code from (5) Integer OCL code (Table 7) 7. Significant digits 1 I1 8. Total digits 1 I1 9. Precision of value 1 I1 10. Value from (5) from (7-9) ================================================================================ OCL ASCII FORMAT FOR BIOMASS AND TAXONOMIC DATA ================================================================================ FIELD LENGTH FORMAT DESCRIPTION ================================================================================ ------------------------------- TAXONOMIC AND BIOMASS DATA SETS ------------------------------- 1. Bytes in next field 2 I1 if "0" go to next section 2. Number of taxa sets from (1) Integer 3. Bytes in next field 1 I1 4. Number of entries from (3) Integer steps 3-11 per taxa set repeated based on step 2 5. Bytes in next field 1 I1 6. Taxa or biomass from (5) Integer steps 5-11 variable code repeated based on step 4 (Table 8 and Table 9) 7. Significant digits 1 I1 8. Total digits 1 I1 9. Precision 1 I1 10. Value from (5) from (4-6) 11. Error code for value 1 I1 always "0" ------------- PROFILE DATA - all steps repeated based on number of levels listed in the primary header ------------- 1. Number depth sig. digits 1 I1 2. Total digits in depth 1 I1 3. Precision of depth value 1 I1 4. Depth value from (2) from (1-3) 5. Depth error code 1 I1 6. Number variable sig. digits 1 I1 7. Total digits in variable 1 I1 8. Precision of variable 1 I1 9. Variable value from (7) from (6-8) 10. Variable error code 1 I1 Appendix 9 =============================================================================== A. DESCRIPTION OF THE CD-ROM DOCUMENTATION Each CD-ROM contains two files (a README.TXT file, which describes the contents of the CD, and a WMOTOT.TXT file, with tallies of the amount of Kbytes/instrument for each WMO) and five directories named: > CODES - contains codes associated with the secondary header, biological header, and taxa data; > DATA - contains the data; > DOC - contains the documentation; > PROGRAMS - contains sample programs for reading the data and programs which allow the user to convert the data so it can be read into IDL (prepared by John E. O'Reilly, NMFS), OceanPC (prepared by Harry Dooley, ICES), Matlab (prepared by Cathy Stephens, NODC), and the NODC station database format P3 (prepared by Tim Boyer, NODC). > UTILS - contains the utilities necessary to convert from DOS to Unix and to decompress the data. The following is a description of the files contained in DOC, CODES, PROGRAMS and UTILS. Files in the directory DOC of every CD-ROM: DOC.TXT - description of the files in this directory FORMAT.TXT - ASCII table describing the format of the data FORMAT.HTM - HTML table describing the format of the data FORMAT.WPD - Word Perfect 6.0 table describing the format of the data FORMAT.DOC - Microsoft Word for Windows 2.0 table describing the format of the data READMEV1.TXT - ASCII version of this document READMEV1.HTM - HTML version of this document READMEV1.WPD - Word Perfect 6.0 version of this document READMEV1.DOC - Microsoft Word for Windows 2.0 version of this document The following gif images are also contained in this directory as they are needed when viewing the HTML version of the documentation. ATLWMO.GIF - WMO squares of the Atlantic and Indian Oceans PACWMO.GIF - WMO squares of the Pacific Ocean DOCLOGO.GIF - Department of Commerce logo NOAABW.GIF - NOAA logo in black/white SERVICES.GIF - information about NODC Files in the directory PROGRAMS of every CD-ROM: PROGRAMS.txt - description of the files in this directory The following subdirectories containing sample converters from the OCL format to other formats, are included in this directory: COLUMN Written by C. Stephens and J. Antonov, NODC README.MAT - describes the use of MATLAB.F MATLAB.F - prints output in columns which can be read by MATLAB. README.GR - file describing how to display the output from MATLAB.F SAMPLE.GRF - GRAPHER template SAMPLE.MAT - sample output data from MATLAB.F COMMA Written by T. Boyer , NODC FORMATP3.WPD - Word Perfect for Windows description of the NODC P3 format FORMATP3.HTM - HTML description of the NODC P3 format OCLTOP3.C - C program reads OCL data and prints output in the NODC P3 format OCLREAD.DIR - contains all the functions for reading in OCL formatted data OCLTOP3.DIR - contains all the functions for writing data in P3 format README.COM - describes the programs in this directory ICES Written by Dr. Harry Dooley, ICES README.IC - description of files in this directory CDW98-IC.EXE - BASIC executable which reads the OCL data and converts it to ICES format - NOTE - THIS PROGRAM ONLY RUNS IN DOS ICES_SRC.TXT - source code in BASIC for CDW98-IC.EXE OCLNODCC.TXT - OCL and NODC ship codes used by CDW98-IC.EXE IDL Written by John E. O'Reilly, NMFS README.IDL - describes IDL programs and shows examples OCL2IDL.PRO - contains subroutines which extract the data OCLBROW.PRO - opens and reads a WOD98 ASCII file, plots profile and metadata OCLOPEN.PRO - opens a WOD98 ASCII file OCLPLOT.PRO - plots station data OCLREAD.PRO - reads a station from a WOD98 ASCII file OCLSTR.PRO - creates an IDL structure for the data OCLWRITE.PRO - produces comma separated output file of a profile SAMPLE.CSV - an example of a comma separated output file SAMPLE.GIF - a gif image of the sample output file OCL Written by T. Boyer and T. O'Brien, NODC OCLDEMO.F - sample FORTRAN program for reading the data OCLDEMOC.C - sample C program for reading the data README.OCL - readme file describing the ocldemo program.s SAMPLE.OCL - sample of run output for ocldemo.f Files in the directory CODES of every CD-ROM: NOTE: all files in this directory are in ASCII format CODES.TXT - description of the files in this directory ACCESION.TXT - list of accession numbers, submitting institutes, submitting investigator, and date of receipt of data BIOHEADR.TXT - code table identifying the biological headers BIOMASS.TXT - code table identifying the plankton biomass parameter codes CASTDIR.TXT - code table identifying cast direction CLOUDAMT.TXT - code table identifying the cloud amount (WMO-2700 or NODC- 0052) CLOUDTYP.TXT - code table identifying the cloud type (WMO-0500 or NODC-0053) CNTMETH.TXT - code table identifying the counting methods COUNTRY.TXT - code table identifying countries (NODC codes) DATATR.TXT - code table identifying data treatment (NODC-0614) DEPTHDET.TXT - how the upper and lower depths were determined for biological observations DIGITINT.TXT - code table identifying digitization interval (NODC-0613) DIGITMET.TXT - code table identifying digitization method (NODC-0612) FILTER.TXT - code table identifying filter codes FLAGS.TXT - code table identifying flags assigned to the data FLOWCAL.TXT - code table identifying flowmeter calibration methods GEAR.TXT - biological sampling gear and flowmeter types INST.TXT - code table identifying institutes (OCL codes) ITISTSN.TXT - Taxonomic serial numbers and associated names based on the ITIS taxonomic code list METHODS.TXT - code table identifying methods for the station data NONTAXSN.TXT - biological group codes assigned by OCL OWSCODES.TXT - code table identifying the ocean weather stations PINAMES.TXT - code table for identifying the Principal Investigator PRESERV.TXT - code table identifying sample preservatives used PROJECTS.TXT - code table identifying projects RECORDER.TXT - code table identifying the recorder type (WMO-4770) REFTYPE.TXT - code table identifying the reference type (WMO-0615) SEASTATE.TXT - code table identifying the sea state (WMO-3700 or NODC-0109) SECONDH.TXT - code table identifying the secondary header variables SHIPNAME.TXT - code table identifying the ships TAXABUND.TXT - taxon presence, absence, and relative abundance terms TAXFEATR.TXT - code table identifying taxon shape or other features TAXLIFE.TXT - table identifying taxon life stages TAXMODIF.TXT - code table identifying the taxon modifying terms (e.g., "sp.") TAXREALM.TXT - code table identifying the taxon realm (e.g., "benthic") TAXSEX.TXT - code table identifying the taxon sex TAXSIZE.TXT - code table identifying the taxon size delimiters TAXTROPH.TXT - code table identifying the taxon trophic mode TAXVAR.TXT - code table listing the biomass/taxa-specific variable codes TOWTYPE.TXT - code table identifying the gear towing method TSPROBE.TXT - code table identifying the Temperature/Salinity instrument type UNITS.TXT - code table identifying originator's variable units VARMEAS.TXT - code table for measured variables VISIBIL.TXT - code table identifying visibility (WMO-4300) VOLUMETH.TXT - code table identifying volume determination methods WATERCOL.TXT - code table identifying water color (Forel-Ule scale 00-21) WAVEHGT.TXT - code table identifying wave height (WMO-1555 or NODC-0104) WAVEPER.TXT - code table identifying wave period (WMO-3155 or NODC-0378) WEATHER1.TXT - code table identifying weather (WMO-4501) WEATHER2.TXT - code table identifying weather (WMO-04677) WINDFOR.TXT - code table identifying wind force (Beaufort scale or NODC- 0052) WINWAVED.TXT - code table identifying wind/wave direction (WMO-0877 or NODC- 0110) WTMETH.TXT - code table identifying weight determination methods B. UTIL DIRECTORY GZIP Directory Within the UTIL directory of each CD-ROM there is a GZIP directory which contains two files used for decompressing the data on the WOD98. The first (GZIP124.EXE) is a self-extracting DOS executable and the second (gzip- 1.2.4.tar.Z) is a compressed and tar'd file containing source code for UNIX users. a. Installing gzip For the First Time DOS Users: The file GZIP124.EXE is a self-extracting DOS executable. Copy GZIP124.EXE to your hard disk; preferably into a directory listed in your path. Run GZIP124.EXE and use the file gzip.exe to uncompress data from the WOD98 CD-ROMS as described below. UNIX Users: Copy gzip-1.2.4.tar.Z to your UNIX system. Run the following commands: uncompress gzip-1.2.4.tar.Z tar xvf gzip-1.2.4.tar These commands will create a directory named gzip-1.2.4 which include the gzip source code and documentation on copyrights, compression methods and how to compile and install the gzip code. Read through the README file and when ready to build the gzip executable, follow the instructions in the INSTALL file. b. Decompressing Data From WOD98 To uncompress the WOD98 files, it is easier to copy the files to the hard disk. Use gzip to uncompress selected files or a directory and all of it's subdirectories with one command. gzip has a limited help menu accessible with the -h option (i.e., gzip -h) To uncompress a single file: gzip -d To uncompress the contents of a directory and all of it's subdirectories: gzip -dr Special Note for UNIX Users The DOS CR-LF (Carriage Return-Line Feed) indicates the end of a record and may cause problems when working in a UNIX environment. Many systems have a "dos2unix" program which removes these characters from an ASCII file. Files can also be converted by transferring from DOS/WINDOWS using FTP (File Transfer Protocol). The UNIX "tr" or "perl" utilities will also remove the CR-LF. (a) To use the UNIX translate utility, "tr": tr -d '\r' < original_filename > new_filename (Note that the "<" and ">" must be typed for this command to work). (b) To use the UNIX perl utility: perl -pi -e 's/\r\n/\n/g' filename C. SYSTEM REQUIREMENTS The minimum hardware requirements for accessing data and information from the CD-ROMs are: CD-ROM reader capable of accessing a disc formatted with the ISO 9660 standard;Microsoft MS-DOS Extensions for CD-ROM, Version 2.0 or higher for DOS machines. ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- VI. LIST OF ACRONYMS USED IN THE CD-ROM DOCUMENTATION BD Bottle Data CTD Conductivity, Temperature, Depth probe DBT Digital Bathythermograph ESDIM Environmental Science Data and Information Management FSU Former Soviet Union GODAR Global Oceanographic Data Archaeology and Rescue project GTSPP Global Temperature Salinity Profile Project ICES International Council for the Exploration of the Seas IOC Intergovernmental Oceanographic Commission IODE International Ocean Data Exchange ITIS Integrated Taxonomic Information System MBT Mechanical Bathythermograph meq Milli-equivalents NMFS National Marine Fisheries Service NOAA National Oceanic and Atmospheric Administration NODC National Oceanographic Data Center OCL Ocean Climate Laboratory PSS Practical Salinity Scale TSN Taxonomic Serial Number SBT Selected Bathythermograph STD Salinity/Temperature with Depth TAO Tropical Atmosphere-Ocean uM Micromolar UCAR University Corporation for Atmospheric Research WOA94 World Ocean Atlas, 1994 WOD98 World Ocean Database 1998 WDC-A World Data Center A for Oceanography WMO World Meteorological Organization XBT Expendable Bathythermograph ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- VII. REFERENCES Boyer, T. P. and S. Levitus, Quality control and processing of historical temperature, salinity and oxygen data. NOAA Technical Report NESDIS 81:65, 1994. Conkright, M. E. T. P. Boyer and S. Levitus, Quality control and processing of historical nutrient data. NOAA Technical Report NESDIS 79:75, 1994. Hanawa, K.P., P. Rual, R. Bailey, A. Sy, and M. Szabados, Calculation of New Depth Equations for Expendable Bathythermographs Using a Temperature-Error- Free Methods (Application to Sippican/TSK T-7, T-6 and T-4 XBTs). Intergovernmental Oceanographic Commission Technical Series, 42:1-46, 1994. *Jeffrey, S.W. and G.F. Humphrey, New spectrophotometric equations for determining chlorophylls a, b, c1 and c2 in higher plants, algae and natural phytoplankton. Biochem. Physi-l. Pflancen.167: 191-194, 1975. *Knudsen, M., C. Forch, and S.P.L. S`rensen, Bericht hber die chemische und physikalische Untersuchung des Seewassers und die Aufstellung der neuen Hydrographischen Tabellen, Band N F 6, pp. 125-184, Wiss. Meeresunters., Komm. Unter. Deutsch. Meere, Kiel, 1902. Levitus, S., R. Gelfeld, T. Boyer, and D. Johnson, Results of the NODC Oceanographic Data and Archaeology and Rescue Project. Key to Oceanographic Records Documentation; 19:73, 1994. Levitus, S., Climatological Atlas of the World Ocean. Rockville, Md.: NOAA Professional Paper 13, 1982. *Murphy, J. and J. P. Riley, A modified single solution method for the determination of phosphate in natural waters. Analytica Chim. Acta 27:31- 36,1962. *Strickland, J.D.H. and Parsons, T.R., A practical handbook of sea water analysis. Bull. Fish. Res. Bd. Can.: 167, 1972. *Wickstead, J.H., An introduction to the study of tropical plankton. Hutchinson Trop. Manogr.: 160pp., 1965. *Zubov, N., Purpose and substance of the hydrological observations of the Second International Polar Year. Moscow-Leningrad, 1937. * These references are listed in Appendix 4 - Codes for Methods