environment

Sample Environment (To be updated for OBIS-SEAMAP 2.5)

See sampled values online

To see the sampled environmental data online (on Dataset page or Species Profile page),

1. Switch to [points] layer.
2. Click (identify) the observation point you are interested in.
3. In the popup that came up, click "Show" under [Env. Data] column.
   

The sampled values show up. See the table below for the abbreviation and units.

Download sampled values and utilize them

The environmental data sampled are included in the downloaded shapefile and CSV file for both species and datasets. The data are written in a compact form and you will need to parse them to utilize them.

Shapefile

1. Add an attribute field to the shapefile whose precision and scale should be large enough to store the data at a desired accuracy. See notes below.
   
2. In ArcToolBox, go to [Data Management Tools]-[Fields]-[Calculate Field].
3. In [Expression], enter the following expression.
   

   parse_oceano('!OCEANO!', "SST_Y", -9999)

   
   Replace SST_Y to the appropriate layer type and averaging period (e.g. CHL_M).
   Also replace -9999 to a numeric value you want to use as a null value.
   Do not change '!OCEANO!'.
4. Choose Python for [Expression Type].
5. Enter the following Python script into [Code Block].
   

   def parse_oceano(oceano, env_type, null_value):
     dist_oceano = eval("{" + oceano[1: len(oceano) - 1] + "}")
     if dist_oceano.has_key(env_type):
       value = dist_oceano[env_type]
     else:
       value = null_value
     return value

6. Run the tool.

When calculation is done, you will see the newly added field (e.g. [SST_M]) in the attribute table filled with the environmental data (in this case, monthly sea surface temperature) parsed out from [oceano] field.

• Carefully consider the attribute field's precision and scale. They should be at least 8 and 3, respectively but usually you will want to define precision 12 and scale 4.
  
• The null value for the third parameter in parse_oceano() must be a numeric value. You can't use "null" or "None" or any other words.
  
• Be careful not to use a null value that is possible for the environment you have chosen. For example, do not use -9999 for bathymetry as it easily reaches 9999m below the sea surface.
• Do not forget to eliminate the rows with the null value you specified from your analysis.
  

CSV

1. Open the CSV file with Excel.
2. Make sure "oceano" column is placed in Column N. If not, please add or delete columns so that "oceano" comes to Column N.
3. In the cell O1 (the first cell in Column O), enter the data type name (e.g. SST_Y).
4. In the second cell (O2), enter the following formula. The link below opens a new window/tab that contains the fomula, so you can easily copy and paste it into the cell.
   Link to Formula
   
5. If you want to get more data types, enter the names in P1 cell, Q1 cell and so on and copy the formula entered in O2 to P2, Q2 etc.
6. Copy the formula all the way down to the last row.

Get simple statistics

You can see a graph of the monthly average of the sampled environmental data online.

1. Switch to [Environment] tab.
2. If you are looking at the Dataset page, choose your species of interest from the list at upper left. If you are looking at the Species Profile page, no need to choose a species/dataset.
   
3. Select a type of environment (Bathymetry , SST, SSH or Chlorophyll).
4. Click [Update] button.

A graph is inserted below. The average is calculated by a simple arithmetic average per month over all observations for the chosen species using environmental data sampled on monthly averaged satellite images (e.g. SST_M, SSH_M).

For more advanced analysis, download the shapefile or CSV. The download file includes the complete environmental data sampled. See "Download sampled values and utilize them" above to know how to get a certain environmental data from the download file.

Notes: The chart does not reflect the region of interest drawn on the map or the time range set with the temporal chart. It always takes in all the observations for the chosen species.

FAQ

Q. Did the sampled environmental data come from in-situ measurements?

No. The environmental data were sampled from satellite images. 

Q. What data/layers did you use to sample the environment values?

 The data/layer description is found in [Environment] tab.

 Q. Why do some points have SST, SSH and chlorophyll while others have SST only?

 What data are sampled is determined by the date of the observation. Due to the varying availability of the data, older observations will have fewer data sampled. For example, an observation made in 1990 will have SST sampled but no chlorophyll because chlorophyll data are available since 1997.