Marine Data Literacy 2.0

Providing instruction for managing, converting, analyzing and displaying oceanographic station data, marine meteorological data, GIS-compatible marine and coastal data or model simulations, and mapped remote sensing imagery





Home > 3. Principal Archives > 3.6 OBIS Taxon

3.6 Managing Global Biological Records for One Taxon in OBIS

  • Exercise Title:  Managing Global Biological Records for One Taxon in the Ocean Biogeographic Information System (OBIS)

  • Abstract:  In this exercise you learn how to navigate around in the OBIS and to download data of interest.  In this exercise we're emphasizing what you can do with a single species that is widely found.  You'd use slightly modified methods for a few species and/or a local region.  We need to take control of these data, so although OBIS can produce very good graphical analyses, we capture the original data and completely re-analyze them in Saga.  In a companion exercise, 3.7, you'll learn how to work with many species in a small "area of interest", which is the other side of the coin from this exercise.

  • Preliminary Reading (in OceanTeacher, unless otherwise indicated):

    • N/A

  • Required Software:

    • Saga

    • Excel (or any equivalent spreadsheet)

  • Other Resources: 

  • Authors:  Lica Krug (first half), Murray Brown (second half; not completely updated)

  • Version:  11-19-2014

1.  Open the OBIS website, and take some time to get acquainted with the materials.
2.  Click on the MAPS tab to see graphics that give a general overview of the collections.

The total number of records is over 40 million.

3.  This graphic shows the number of species, per 5-degree block.
4.  And this graphic shows the results of a specific "diversity" calculation, named ES50.  Because it is a derived quantity, it only partially parallels the above figures.

For example, the northeast atlantic, which is heavily emphasized in the records and species counts, appears here to have a distinctly low diversity

5.  In this exercise, we'll investigate how to manage the data for a large area (e.g. the globe) for only one species.  If the species you select is not global, then an appropriate reduction to hemispheric- or ocean-scale would be appropriate.

6.  Click on SEARCH DATA to see this interface.  [You may see an temporary HELP SCREEN over the map; ignore it and it will go away automatically.] 

7.  This is the author's summary of the the 5 selection tools on the left margin:
  • TAXA - Huge hierarchical index to the species records.  You can burrow down to any one (or multiple) species here.  If you do not select any specific taxon, it is a good idea to specify BIOTA to make sure that everything is searched.  It is not certain that the default setting is to search everything.
  • DATASETS - Master list of the datasets that cover the map area.  There is a control to SELECT ALL, and there is an OTHERS category, but it is not clear that they work as you would expect.  The author suggests that unless you have a good reason to select specific collections to search, don't choose anything here, not even SELECT ALL.
  • REGION - Several ways to pick the area of interest.  Includes selecting one of a few specially named areas (would benefit by contacting the MARINE REGIONS website), a drawing tool, and a coordinate entry form (Top, Bottom, Left and Right).  To actually use the drawing tool method you must select REGION > UPDATE MAP
  • DATE & SEASON - Not explored yet; would range in utility from hugely helpful (for well-represented species), to tantalizing (for poorly sampled areas or species).
  • OCEANOGRAPHY - Selection criteria based on the few "oceanographic" variables that have been gleaned from the species accounts, such as temperature, salinity, depths, nutrients, etc.

And above these selectors are:

  • UPDATE MAP - Click this to see the map, or to make sure that it has been synchronized with your REGION settings.
  • SHOW RESULTS - Click this to see all the results of a search, by tabs.  Includes the important DOWNLOAD tab for the actual data records, and the data map.

Learn to navigate the interface mainly using these 2 controls to move from selection criteria to results.  Be a good data citizen and do not specify huge searches (many species/large areas), unless you have a real analysis plan in place.  The server is fast, but you do not want to overload it and cause problems for other users.  In general, the author finds that TAXA and REGION are the most important tools for ordinary use, but you will probably have a need for all of them after you become an avid OBIS user.

8.  Select TAXA to begin a search for a randomly selected taxon.  In this case the author is looking for TUNA, and -- not being a biologist -- has only the vaguest idea of where it would be.
9.  Select BIOTA > ANIMALIA > CHORDATA > VERTEBRATA and then you will run into an enormous list of orders (?).  If you're a really smart biologist, then be my guest and try to find the tunas.
10.  But if you're a poor old chemical oceanographer, then change the search type to COMMON NAME and enter the beginning of the common name ALBACOR.  The search engine will jump ahead of you and suggest a list of valid and invalid records. 

Just click on the first valid entry ALBACORA (SPECIES, 110,743) to repeat the search, then delete the A in ALBACORA and you'll get a list of choices again.

11.  This page appears to show you what that selection covers.  You can see immediately how much work has been put into getting the names gathered and organized.  The items along the bottom indicate that this same fish is represented in certain major collections.

12.  Click UPDATE MAP to see this great 5-degree map of abundance.  We're going to download these data and learn how to make this same sort of map in Saga.  It is nice to be able to get these results online and automatically, but real marine science requires that you be able to make the same analyses with OBIS data or your own local records.

13.  Strangely, the map legend does not appear automatically, but you can select the LAYERS control in the upper right corner to see it.  [You can also make a few changes here.]

If you examine the real scale of abundances (below in Saga section), you'll how grotesquely the OBIS scale masks the actual conditions.

14.  You can click SHOW RESULTS to see all the other information and products available for this fish.  Take the time to explore these tabs, with a view to what you might be able to do.

15.  To get the actual data, click on DOWNLOAD to see this settings window.

You can explore the WFS, WMS and KML options on your own.  These are graphics-oriented products.

For our own purposes, we'll get the CSV file, because it contains the actual data.  So select POINTS and click on CSV.

16.  Navigate to the folder DATA > OCEAN > OBIS and save the file as
17.  Unzip the file and open it in Excel to see the internal structure.
18.  Here is a summary of the fields in the database records.  There is a record for each individual specimen encountered, and no aggregation is indicated.
  • ID






















19.  A good data manager always looks closely at the horse's mouth.  If you do so, you'll find commas in the TAUTHOR column, which is is an unforgiveable formatting error in a CSV file;  it will cause extra work before the data can be used. ``
20.  Use Excel's FIND/REPLACE ALL function to replace all the commas with nulls.(i.e. nothing), as you see here  You need to do this in these fields:

If you find any problems with the CSV file, you can always come back here to clean them up.

Need a little help with the Portuguese?


Now save the cleaned data back into the same file location and filename.  We make these changes, because the final target software cannot handle all these extra commas.

  • If you will use OBIS again immediately, take the time to remove THUNNUS from the selector by clicking the RED X you see here.
  • You might also select BIOTA at the top level to make certain that you will see other records after searching.
22.  To work with these cleaned up CSV data, run Saga.
23.  Select IMPORT/EXPORT-TABLES > IMPORT TEXT TABLE.  Make these choices and click OK.

OPTION:  In Saga select the imported table and use SHOW to see that everything looks ok in the fields.  If any problems, then go back to the Excel step.  You'll be surprised to note that there are almost 110,000 records for this taxon in the table.-

24.  Convert the table to a point shape with the module SHAPES-POINTS > CONVERT TABLE TO POINTS, as you have done in 5.1 Converting a Data Table to a Point Shape in Saga
24.  And here is the map of the point shape.  There are fascinating stories about the distribution and natural history of these valuable fish.
25.  Just for an example, here is the distribution of records offshore Louisiana, in the USA.  Individual large tuna caught here are overnight freighted to Asian markets, through the local airport in New Orlans, due to their enormous value!
26.  To analyze these data exactly as shown in the 5-degree OBIS distribution maps, we first need a 5-degree graticule.
27.  Select MODULES > SHAPES TOOLS > CREATE GRATICULE.  Make these choices, then click OK.

The choice of RECTANGLES for type is extremely important, because we need to work with a polygon shape.

28.  Here is the new graticule.  The coloring of each cell indicates it is a polygon.
29.  For future use with OBIS, save the graticule shape in the folder PRODUCTS > SAGA > VECTORS with the name graticule_global_5deg.shp
30.  Now we need to see how many tuna records there are in each cell.  Select MODULES > SHAPES-POINTS > COUNT POINTS IN POLYGONS.

Make these choices, then click OK.





31.  Nothing new appears in the DATA list.  But select the graticule polygon and ATTRIBUTES > SHOW
32.  A fields has been added to the original graticule shape, named POINTS.  In it you can find some surprisingly large values along with many zero values.
33.  To make sure you know which file is which, you can change the name of the graticule shape, as you see here.

NOTE:  The object name is set at the top line of the PROPERTIES panel, then use SETTING > APPLY.

34.  Now we need to get X and Y locations for each cell in the graticule.  Select MODULES > SHAPES-POLYGONS > POLYGON CENTROIDS.

Make these settings, then click OK.

35.  Now you have a new point shape, containing the results of the centroid additions. natuiral

36.  If you want, for quality control purposes, you can actually view the new point shape, using the settings you see below.  You can immediately see that the data are beginning to resemble the original OBIS map.

37.  But we really need to grid the data to see the final product.  Select MODULES > GRID-GRIDDING > INVERSE DISTANCE WEIGHTED.

Make these selections, then click OK.

NOTE:  You may not like the visual results, so return here on your own time to play with these settings.

38.  Here are the values to insert for a "USER DEFINED" target grid.  You enter these values:
  • LEFT = -180
  • RIGHT = 180
  • BOTTOM = -90
  • TOP = 90

But as soon as you enter the CELLSIZE, Saga will make appropriate changes to match up exactly with the globe.   Then click OK.

39.  This new grid will appear.
40.  Make these settings in the PROPERTIES panel on the right.  Then click SETTINGS > APPLY at the bottom.
41.  Here is the grid, mapped with the WORLD BORDERS shapefile.  The log value range mode is very important here, due to the huge range of values.

The values here are species records per 5-degree cell per period of record. 

NOTE:  If used in any report or publication, this figure must be accompanied by an appropriate note attributing the data to OBIS.  Check the OBIS website for a recommended citation format.

42.  Be sure to save the final grid in the folder PRODUCTS > SAGA > GRIDS with the filename albacore_spp_per5degcells_obis.sgrd