General description
The station header includes, in the first lines, mandatory information like the station identifier, date, time, location, list of observed parameters and units. The environmental information on the observations archived either behind " *DC= " (for Data collection), other relevant information behind "*DM=" (for Data Management) or "COMMENT" is optional.
- The first observed parameter is the reference :
- pressure in decibars or depth in metres for the observations in the water
- depth (in meters) below the bottom for sediment observations
- BP =Beginning Position
- SL = string length
- MAND = Mandatory if X in the column
- NP = number of observed parameters incl. the reference (pressure or depth)
- NCO = number of comment lines in the header
LINE |
FIELD |
DESCRIPTION |
BP |
SL |
TYPE |
MAND |
1 |
start character |
'*' |
1 |
1 |
char |
X |
reference |
MEDATLAS ref.(cruise+station+cast) |
2 |
18 |
char |
X |
|
key word |
'Data Type=' |
21 |
10 |
char |
X |
|
data type |
31 |
3 |
char |
X |
||
2 |
date |
'*DATE='DDMMYYYY |
1 |
14 |
char |
X |
time |
'TIME='HHMN |
16 |
9 |
char |
X |
|
latitude N/S |
'LAT='N or S |
26 |
5 |
char |
X |
|
lat. degrees |
latitude degrees (0 to 90) |
31 |
2 |
char |
X |
|
lat. minutes |
latitude minutes.hundredth |
34 |
5 |
char |
X |
|
longitude E/W |
'LON=', E or W |
40 |
5 |
char |
X |
|
long. degrees |
longitude degrees (0 to 180) |
45 |
3 |
char |
X |
|
long. minutes |
minutes.hundredth |
49 |
5 |
char |
X |
|
key word |
'DEPTH=' |
55 |
6 |
char |
X |
|
bottom depth |
bottom depth in metres (nothing if unknown) |
61 |
6 |
num |
||
key word |
'QC=' |
68 |
3 |
char |
X |
|
time flag |
QC flag on date and time |
71 |
1 |
num |
X |
|
lat. flag |
QC flag on latitude |
72 |
1 |
num |
X |
|
long. flag |
QC flag on longitude |
73 |
1 |
num |
X |
|
depth flag |
QC flag on bottom depth |
74 |
1 |
num |
X |
|
3 |
key word |
'*NB PARAMETERS= ' |
1 |
15 |
char |
X |
nb. of columns |
number of measured parameters (NP) |
16 |
2 |
num |
X |
|
key word |
'RECORD LINES=' |
19 |
13 |
char |
X |
|
number of lines |
number of observation records (NL) |
32 |
5 |
num |
X |
|
3+1to 3+NP |
1st character |
* |
1 |
1 |
char |
X |
code param. p |
Code for parameter p |
2 |
4 |
char |
X |
|
parameter p |
parameter full name (IOC def.) |
7 |
30 |
char |
X |
|
unit param. p |
('IS/IOC unit') |
37 |
30 |
char |
X |
|
key word |
'def.=' |
68 |
5 |
char |
X |
|
default val. |
string of '9'.string of '9' same format as the parameter p |
73 |
nlen(np) |
num |
X |
|
4+NP |
key word |
'*GLOBAL PROFILE QUALITY FLAG=' |
1 |
29 |
char |
X |
profile QC |
global quality flag for the profile |
30 |
1 |
num |
X |
|
key word |
'GLOBAL PARAMETERS QC FLAGS=' |
32 |
27 |
char |
X |
|
profile QC |
global quality flags for the NP parameter |
59 |
NP |
num |
X |
|
5+NP |
key word + collect hist.1 |
'*DC HISTORY=' method, instrument used for data collection |
1 |
80 |
char |
X |
6+NP |
collect hist.2 |
'*'continuation |
1 |
80 |
char |
X |
7+NP |
key word + data manag. hist.1 |
'*DM HISTORY=' data management history |
1 |
80 |
char |
X |
8+NP |
arch. hist.2 |
'*'continuation |
1 |
80 |
char |
X |
9+NPto 8+NP+NCO |
key word |
'*COMMENT' |
1 |
8 |
char |
X |
comment |
'*'comment line 1 |
1 |
80 |
char |
X |
|
comment |
'*'comment line n |
1 |
80 |
char |
||
9+NP+NCO |
key word + surface obs. 1 |
'*SURFACE SAMPLES=', samples |
1 |
80 |
char |
X |
10+NP+NCO |
surface obs. 2 |
'*'continuation |
1 |
80 |
char |
X |
Specific information for SeaDataNet
A set of ‘special’ mandatory comment lines that must appear at the end of the station header comments. Their function is to map the text strings used to label the data columns to standardized SeaDataNet concepts, which is necessary if data files from different sources are to be combined in a meaningful way.
The comment must contains the following consecutive lines: *SDN_parameter_mapping
This is followed by a line for each parameter column, including the primary variable, made up from three parts, each tagged to look like an XML element:
- subject element: This contains the MEDATLAS parameter code prefixed by the text ‘SDN:LOCAL:’ to encode it as a SeaDataNet URN.
- object element This contains the URN to a concept from the SeaDataNet P01 vocabulary List, which contains over 37,000 terms)
- units element This contains a URN for the storage units used IN THE MEDATLAS FILE for the data column in the SeaDataNet P06 vocabulary list
Examples of valid data column semantic descriptions:
*<subject>SDN:LOCAL:PRES</subject><object>SDN:P01::PRESPS02</object><units>SDN:P06::UPDB</units>
*<subject>SDN:LOCAL:TEMP</subject><object>SDN:P01::TEMPPR01</object><units>SDN:P06::UPAA</units>
*<subject>SDN:LOCAL:PSAL</subject><object>SDN:P01::PSLTZZ01</object><units>SDN:P06::UUUU</units>
*<subject>SDN:LOCAL:DOX1</subject><object>SDN:P01::DOXYZZXX</object><units>SDN:P06::UMLL</units>
*<subject>SDN:LOCAL:PHOS</subject><object>SDN:P01::PHOSZZXX</object><units>SDN:P06::UPOX</units>
*EDMO_CODE = EDMO identifier of the data centre managing the CDI
*LOCAL_CDI_ID = local identifier of the station
To guarantee the iniquity of the LOCAL_CDI_ID, the local identifier of the station must be a concatenation of the MEDATLAS cruise reference, the last 5 characters of the station reference and station data type.
Examples of a valid LOCAL_CDI_ID lines:
*LOCAL_CDI_ID = FI35200200121_00001_H10
*LOCAL_CDI_ID = FI35200500301_00042_H09
Optional linkage to external resources may also be added that provide links to web resources related to the data in the file.
Examples of linkage to external resources:
Linkage to the CDI web description:
*<sdn_reference xlink:href="http://seadatanet.maris2.nl/v_cdi_v3/print_xml.asp?edmo=486&identifier=FI35200748001_0000A_H10" xlink:role="isDescribedBy" xlink:type="SDN:L23::CDI"/>
Linkage to the corresponding Cruise Summary Report (CSR) web description:
*<sdn_reference xlink:href="http://seadata.bsh.de/cgi-csr/XML/xmlDownload_V2.pl?edmo=486&identifier=7480010" xlink:role="isObservedBy" xlink:type="SDN:L23::CSR"/>
Linkage to the Ship of the cruise:
*<sdn_reference xlink:href="http://vocab.nerc.ac.uk/collection/C17/current/35C4" xlink:role="isObservedBy" xlink:type="SDN:L23::NVS2CON"/>
Station reference
String of 18 characters (no blank character allowed)
- BP=Beginning Position
- SL= String Length
FIELD |
DESCRIPTION |
BP |
SL |
TYPE |
MAND. |
cruise reference |
Cruise reference to which the station belongs |
1 |
13 |
char |
X |
station number |
Station reference |
4 |
4 |
char |
X |
cast |
This can be used as a fifth character for the station number or as a character to describe the cast of one station if several casts are performed as the same location |
1 |
1 |
char |
X |
Detailed explanation
First character of the header lines
All the lines begin with the character " * ".
Latitude and Longitude
In order to avoid ambiguity, N/S and E/W are specified for latitude and longitude instead of signs.
Missing information
Missing time should be assigned to '9999' and "TIME IS UNKNOWN" added in comment line.
Other missing information (when optional) in character strings: 'X' as many times as the missing string length or 'UNKNOWN' or ‘9’ for numerical values (like bottom depth). Example: DEPTH=-99999
Detailed parameters list
The first observed parameter is the reference, which for vertical profiles must be the pressure in decibars or the depth in metres.
The list of each observed parameter (pressure, temperature, salinity, nutrients...) include the parameter code (SeaDataNet P09 vocabulary list) , name (SeaDataNet P09 vocabulary list), unit (MedAtlas unit) and default value. A different unit corresponds to a different parameter code.
History and information on the data processing
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 the value has been changed)
*COMMENT for all optional data and meta data like time and location at the end of the profile, meteorological observations. The number of comment lines is not limited.
Do not repeat keywords (ex use EDATE=, ETIME= ELAT=, ELON=, EDEPTH and not DATE, TIME, LAT, LON, DEPTH) to specify the end date, time, latitude, longitude and bottom depth of a station. The number of *COMMENT lines is not limited. All the meteorological information and the information behind the comment lines (end of the station, secchi disk, meteorological observations) is optional, but to access them easely, it is better to use P09 codes as keywords (3.6)
Last line
The last line begins with the character " * " and the parameter P09 codes as titles of the columns of observations. They should be the same as the list given in the detailed parameter list.
Identifiers description
Cruise/Mooring/Experiment identifiers
String of 13 characters
Example : GN36199704901
- GN = data centre code that gives the cruise code
- 36 = IOC country code of the source of the data
- 1997 = year of the beginning of the cruise (number)
- 04901 = free number/characters assigned to the cruise by the data centre
Station/Time series identifiers
String of 18 characters
Example : FI0619975100100010
- FI06199751001 = cruise identifier
- 00010 = station number given by the originator