Mediterranean
Targeted
Project
II,
MAss Transfer
and Ecosystem
Response
A project of the European
Commission's
MArine Sciences & Technology (MAST)
programme
The MEDATLAS format will be used for vertical profiles and also for time series with minor modifications (date and time instead of pressure in the first columns). This format has been designed, in conformity with the international the ICES/IOC GETADE recommendations (see references), to fulfil the following requirements :
1) To facilitate the reading of the data, (and not to optimise the data archiving on the magnetic medium, neither to speed up the data processings).
2) To be independent of the computer.
The consequence of these two points is that an auto-descriptive ASCII format will be preferred.
3) To keep track of the history of the data including the data collection and the processing. Then each cruise must be documented.
4) To allow the processing of profile independently. Therefore the date, time and geographical co-ordinate must be reported on each profile header.
5) To be flexible and accept (almost) any number of different parameters.
6) The real numbers (floating numbers must remain in the same way as they have been transmitted, not transcoded into integer numbers). The number of decimals must implicitly indicate the accuracy of the measurements.
These requirements have been taken into account in the MEDATLAS exchange format which has been designed by the MEDATLAS and MODB consortia, in the frame of the European MAST II programme. The profiles measured with the same instrument (eg. bottles, CTD, XBT..) during the same cruise, are grouped within the same file which includes :
The sequence 'profile header + data records ' is repeated
for each profile. The main fields are
described further on.
BP = Beginning Position, SL = string length, NDT= Number of data types (ROSCOP)
NCO = Number of comment lines (textual information on the cruise)
LINE FIELD DESCRIPTION BP SL TYPE
1 1st character * 1 1 char
cruise MEDATLAS reference 2 13 char
name originator cruise name/ref. 16 32 char
ship code standardised WDCA/ICES/IOC code 49 4 char
ship name full ship name 54 25 char
2 start date DD/MM/YYYY 1 10 char
end date DD/MM/YYYY 12 10 char
region GF3 table 23 35 char
3 country Source laboratory country code 1 2 char
address Laboratory, institution, town 4 75 char
4 name chief scientist full name 1 40 char
key word 'Project=' 42 8 char
project name of the project 50 28 char
5 key 'Regional Archiving=' 1 19 char
data centre regional archiving centre code 21 2 char
key word 'Availability=' 42 13 char
availability Data Availability code (P/L/C) 55 1 char
5+1 key word 'Data Type=' 1 10 char
data type ROSCOP code 11 3 char
TO key word 'n=' 15 2 char
number number of profiles for the type 17 4 num
5+NDT key word 'QC=' 22 3 char
QC Y/N (Yes or No) 25 1 char
6+NDT key word 'COMMENT' 1 7 char
...... ...... ..................................
5+NDT+NCO key word any other cruise information 1 80 char
EXAMPLE *GN36199102701 POEM-I-91(P191) 36AE AEGAEO (AEGAIO PRE-10/94) 02/10/1991 13/11/1991 MED., EASTERN BASIN 36 NCMR, ATHENS, GREECE THEOCHARIS A. Project=POEMBCO91 Regional Archiving= GN Availability=P Data Type=H10 n= 109 QC=Y COMMENT DM=P T S DENS controlled with Levitus 83
NP = number of observed parameters incl. the reference (pressure); BP =Beginning Position
NCO = number of comment lines in the header; SL = string length
The information behind the comment lines (end of the station, secchi disk, meteorological observations) are optional.
The first observed parameter is the reference :
Columns of observations must be separated by a blank
character.
LINE FIELD DESCRIPTION BP SL TYPE
1 start character * 1 1 char
reference MEDATLAS ref. (cruise+station+cast) 2 18 char
key word 'Data Type=' 21 10 char
data type ROSCOP code 31 3 char
2 date '*DATE=', DDMMYYYY 1 14 char
time 'TIME=',HHMN 16 9 char
latitude N/S 'LAT=', N or S 26 5 char
lat. degrees latitude degrees (0 to 90) 31 2 char
lat. minutes latitude minutes.hundredth 34 5 char
longitude E/W 'LON=', E or W 40 5 char
long. degrees longitude degrees (0 to 180) 45 3 char
long. minutes minutes.hundredth 49 5 char
key word 'DEPTH=' 55 6 char
bottom depth bottom depth in metres 61 6 num
key word 'QC=' 68 3 char
time flag QC flag on date and time 71 1 num
lat. flag QC flag on latitude 72 1 num
long. flag QC flag on longitude 73 1 num
depth flag QC flag on bottom depth 74 1 num
3 key word *NB PARAMETERS= ' 1 15 char
nb. of columns number of measured parameters (NP) 16 2 num
key word 'RECORD LINES=' 19 13 char
number of lines number of observations records (NL) 32 5 num
4 1st character * 1 1 char
title column p GF3 code for parameter p 2 4 char
TO parameter p parameter full name (IOC def.) 7 30 char
unit p ( 'IS/IOC unit' ) 37 30 char
3+NP key word 'def.=' 68 5 char
default val. string of '9'.string of '9' 73 nlen(np) num
same format as the parameter p
4+NP key word '*GLOBAL PROFILE QUALITY FLAG=' 1 29 char
profile QC global quality flag for the profile 30 1 num
key word 'GLOBAL PARAMETERS QC FLAGS=' 32 27 char
profile QC global quality flags for the 50 NP num
NP parameters
5+NP collect hist.1 '*DC HISTORY='method, instrum. etc 1 80 char
6+NP collect hist.2 '*', continuation 1 80 char
7+NP archv. hist.1 '*DM HISTORY', data mangt. history 1 80 char
8+NP archv. hist.2 '*', end of data management 1 80 char
9+NP comment 1 '*COMMENT ', (optionnal) record END 1 80 char
10+NP date '*DATE=', DDMMYYYY 1 14 char
time 'TIME=',HHMN 16 9 char
latitude N/S 'LAT=', N or S 26 5 char
lat. degrees latitude degrees (0 to 90) 31 2 char
lat. minutes latitude minutes.hundredth 34 5 char
longitude E/W 'LON=', E or W 40 5 char
long. degrees longitude degrees (0 to 180) 45 3 char
long. minutes minutes.hundredth 49 5 char
key word 'DEPTH=' 55 6 char
bottom depth bottom depth in metres 61 6 num
key word 'QC=' 68 3 char
time flag QC flag on date and time 71 1 num
lat. flag QC flag on latitude 72 1 num
long. flag QC flag on longitude 73 1 num
depth flag QC flag on bottom depth 74 1 num
TO comments '*SECCHI DISK' 1 80 char
8+NP+NCO comment '*', end of comments 1 80 char
9+NP+NCO surface obs. 1 '*SURFACE SAMPLES=', samples 1 80 char
10+NP+NCO surface obs. 2 '*', end of surface samples 1 80 char
EXAMPLE
*GN3619910270140470 Data Type=H10 *DATE=27101991 TIME=0415 LAT=N34 30.00 LON=E022 30.00 DEPTH=2760 QC=1111 *NB PARAMETERS=03 RECORD LINES=01999 *PRES SEA PRESSURE sea surface=0 (DECIBAR=10000 PASCALS) def.= -999.9 *TEMP SEA TEMPERATURE (CELSIUS DEGREE) def.= 99.999 *PSAL PRACTICAL SALINITY (P.S.U.) def.= 99.999 *GLOBAL PROFILE QUALITY FLAG=1 GLOBAL PARAMETERS QC FLAGS=111 *DC HISTORY= SBE 9/11 CTD System, Sea-Bird. *Sensor calibration: 09/01/1989 by Sea-Bird. *DM HISTORY * *COMMENT *Raw data interpolated every meter with Lagrance third degree polynomial *formula. Salinity correction by Autosal Salinometer (NCMR). Temperature *and salinity intercalibrated with Italian,Turkish,Israel POEM stations. *SURFACE SAMPLES= *
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Each parameter p can have any length nlen(p), but this length must be constant in the profile, and the decimal points at a constant position. The separators are blanks of one character (or more), after each parameter value. The quality flags are grouped after the last separator, with no blank between them.
The position of the first character of parameter p in the record line is then :
bp(p)=nlen(1)+ ..+ nlen(p-1) + p
and the position of the first quality flag :
bp(q1)= bp(NP) + nlen(NP) + 1
nlen(p)=number of digits of parameter p; NP = number of measured parameters (columns)
NL=number of observations records (lines)
hheader = NP+NCO +11 = total number of header lines; NCO = number of comment lines
BP =Beginning Position, SL = string length
LINE FIELD DESCRIPTION BP SL TYPE
nheader start character * 1 1 char
title 1 'PRES' or ref. parameter 2 4 char
separator blank 6 nlen(1)-4 blank
title 2 GF3 code parameter 2 bp(2) 4 char
separator blank bp(p-1)+4 nlen(p-1)-3
title par. P GF3 code parameter p bp(p) 4 char
title NP GF3 code parameter NP bp(np) 4 char
nheader parameter 1 parameter 1 in IS units 1 nlen(1) num
+1 separator blank bp(2)-1 1
to parameter 2 parameter 2 in IS units bp(2) nlen(2) num
+NL separator blank bp(np)-1 1
...................................................................
parameter NP parameter NP in IS units bp(np) nlen(np) num
separator blank bp(q1)-1 1
QC Flag 1 Quality Flag parameter 1 bp(q1) 1 num
...................................................................
QC Flag NP Quality Flag parameter NP bp(q1)+np 1 num
nheader def. val. par.1 '-999.9' or string of '9' 1 nlen(1) num
+NL+1 separator blank bp(2)-1 1
(Last def. val. par.2 string of '9'as in header bp(2) nlen(2) num
line .............................................
of the def. val. par.NP string of '9'as in header bp(NP) nlen(NP) num
profile) separator blank bp(q1)-1 1
QC Flag 1 '9' (Def. val.Quality Flag) bp(q1) 1 num
......................................
QC Flag NP '9' (Def. val.Quality Flag) bp(q1)+np 1 num
EXAMPLE *PRES TEMP PSAL 2.0 22.527 38.864 111 3.0 22.535 38.864 111 4.0 22.536 38.865 111 5.0 22.535 38.865 111 6.0 22.535 38.865 111 7.0 22.534 38.866 111 8.0 22.530 38.867 111 9.0 22.525 38.869 111 10.0 22.523 38.869 111 ........................ ........................ 1999.0 13.701 38.705 111 2000.0 13.700 38.705 111 -999.9 99.999 99.999 999
All the profiles measured with the same instrument (eg. bottles, CTD, XBT..) are grouped within the same file. The data file begins with a short cruise descriptor based on the ROSCOP information forms. The profiles are attached behind an each of them begins with a profile header giving all the necessary environmental information on the observations. Each observed parameter represent a separate column. There is no limitation to the number of parameters (columns) but the number of parameters within the same cruise must be constant. If a parameter is missing in one station, the corresponding column must be fulfilled by default values.
The records consist in data collected at the same level. The record (line) length is not limited for observed data but reasonable (<120) number of characters in the lines is recommended.
For missing data, the default characters are :
- in character strings : 'X' as many times as the missing string length or 'UNKNOWN'
- in numbers : 9 or -9 at the same format as the expected numbers.
In order to avoid ambiguity, N/S and E/W will be specified for latitude and longitude instead of signs.
- Pressure is the reference co-ordinate (first column) for the vertical profiles.
- When the pressure is not explicitly defined (mainly the oldest historical data sets which have the depth measurements instead), the vertical co-ordinate is supposed to be pressure in decibars (which makes no significant differences on historical data).
- The first colum parameter which is the reference (the pressure for vertical profiles) must be recorded in increasing order.
- Temperature, salinity and any archived parameters are observed parameters. The calculated parameters like density or potential temperature are not archived.
- Other measured parameters like nutrients are archived with the GF3 parameter code as the column title. The parameter code is related to the same unit, normaly the International Systm (IS). A different unit corresponds to a different parameter code.
In order to maintain some flexibility with the format and not to loose existing complementary information on the data processing, meteorological observations etc. not taken into account in the format, three specific fields terminate each header profile :
*DC HISTORY for the information linked to the data collection at sea (like instrument, calibration)
*DM HISTORY for the information linked to the data management and archiving (like the source latitude if the sign or th evalue has been changed)
*COMMENT for all optional data and meta data like time and location
at the end of the profile, meteorological observations. Avoid to repeat
character strings already used (ex use LATEND= and not LAT=) to specify
the end latitude of a station. The number of *COMMENT lines is not limited.
Codes are used in the database when the information (meta-data) is frequently exchange. The codes may be internal to the MEDATLAS format, or international (IOC/GF3, ICES) :
Cruise and profile references
Oceanographic data centres
Countries (GF3)
Oceanographic regions
Observed parameters
ROSCOP code for data sets
Ship (ICES)
Quality flags
Availability
total 13 characters BP=Beginning Position, SL=
string length
field description BP SL type
Data Centre regional data centre in charge of the 1 2 char
Code data set from MEDATLAS table
Country Code of the institution who performed the 3 2 char
measurements from the GF3 table
year of the beginning of the cruise 5 4 char
(numbers in characters to avoid the
blanks)
serial number originator reference or given by the 9 5 char
regional data centre
5 characters
Each profile is referenced unambiguously in the following way :
cruise reference code + the original station number from the field
experiment + the cast number.(total 18 characters)
field description BP SL type cruise given by the regional data centre 1 13 char reference station number given by the originator 14 4 char cast number from the experimentator (0 to 9) 18 1 char
FI France IFREMER/SISMER
GN Greece HNODC
IO Italy OGS
72 Albania
AL Algeria
11 Belgium
CY Cyprus
26 Denmark
27 Egypt, Arab Republic of
35 France
96 German Democratic Rep.
06 Germany, Federal Rep.
36 Greece
47 Israel
48 Italy
52 Lebanon
53 Lybian Arab Jamaihiriya
ML Malta
MO Monaco
56 Morocco
64 Netherlands
58 Norway
68 Portugal
73 Romania
RU Russia
29 Spain
77 Sweden
78 Switzerland
80 Syrian Arab Republic
88 Tunisia
89 Turkey
32 U.S.A.
UR Ukrainian Soviet Socialist Rep
90 FSU
74 United Kingdom
31 United States of America
95 Yougoslavia
IN Intergovernmental /International
NAME
MEDITERRANEAN SEA
MED. WESTERN BASIN
GIBRALTAR STRAIT
ALBORAN SEA
BALEARIC SEA
LIGURIAN SEA
TYRRHENIAN SEA
MED., EASTERN BASIN
IONIAN SEA
ADRIATIC SEA
AEGEAN SEA
BLACK SEA
SEA OF MARMARA
SEA OF AZOV
To each measured parameter and each compartment :
A GF3 like parameter code is attributed, uniquely linked with parameter name and unit. These codes are used as comumn titles of the MEDATLAS format. The more common (GF3) are :
PRES pressure in decibars
TEMP temperature
PSAL Practical salinity.
The extended list of the parameter code is given in
MTP II-MATER Data Manual Vol. II.
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These general codes are related to an instrument and are used in
the cruise header where several types of observations can be listed. A
profile is related to only one.
ROSCOP TYPE OF OVBSERVATIONS CODE B01 Primary productivity B02 Phytoplankton pigments (eg chloroph B06 Dissolved organic matter (inc DOC) H09 Water bottle stations H10 CTD stations H11 Subsurface meas. underway (T,S) H13 Bathythermograph H16 Transparency (eg transmissometer) H17 Optics (eg underwater light levels) H21 Oxygen H22 Phosphate H23 Total - P H24 Nitrate H25 Nitrite H26 Silicate H27 Alkalinity H28 pH H30 Trace elements H31 Radioactivity H32 Isotopes H33 Other dissolved gases H71 Surface measurements underway (T,S) H72 Thermistor chain H73 Geochemical tracers (eg freons) H74 Carbon dioxide H75 Total - N H76 Ammonia H80 Hydrographic atlas data H90 Other chemical oceanographic meas.
Ships identified on the MTP II/MATER Cruise Plannning. Other ships
can be added if necessary.
France ATALANTE 35A3
EUROPE 35EU
GEORGES PETIT 35GP
KOROTNEFF 35KR
SUROIT 35LU
TETHYS II 35TE
Germany, Federal Republic of POSEIDON 06PO
Greece AEGAEO 36AE
Italy URANIA 48UR
Spain HESPERIDES 29HE
GARCIA DEL CID 29GD
ODON DE BUEN 29DB
CODE MEANINIG
0 NOT CONTROLLED VALUE
1 CORRECT VALUE
2 VALUE INCONSISTENT WITH STATISTICS Out of narrow range limits)
3 UBIOUS VALUE (SPIKE)
4 FALSE VALUE (Out of broad range regional limits, or corresponding to a
vertical unstability ..)
5 VALUE MODIFIED DURING QC (only for obvious location or time errors)
6-8 Not used
9 NO OBSERVED VALUE
CODE SIGNIFICATION
P PUBLIC DOMAIN DATA
L LIMITED ACCESS TO DATA (PROJECT ONLY)
C CONFIDENTIAL DATA (SUBMITTED TO CHIEF SCIENTIST PERMISSION)
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