Download OBIS-SEAMAP data

General

OBIS-SEAMAP provides flexible and powerful data download features. The observation records and effort / telemetry tracks can be downloaded as a CSV or an ESRI shapefile. You can download all the observation records of a dataset or a species. Moreover, you can set criteria and download the data that meet the criteria (e.g. multiple species from parrticular datasets in your study area).

Data follow the standardized OBIS-SEAMAP schema and not from the data originally provided by data providers. They include publicly available or minimum fields: locations (latitude and longitude in decimal degrees), date/time of the observations, the species identification and group size. For a telemetry or photo-id dataset, animal or device id is included. See below for more details about the fields.

Also see "FAQ" at the bottom of the page.

Data sharing policy

Please observe the data sharing policy and follow the Terms of Use. The data sharing policy is set per dataset. You are not allowed to download the dataset under "permission required" option unless you have gotten permission from the data provider. Please note that records from datasets under "permission required" policy will show up on the maps on the OBIS-SEAMAP mapping tools but not be included in the download file. The data sharing policy per dataset is summarized in the datasets_and_citations.csv file included in the zipped file.

OBIS-SEAMAP adopts Creative Commons licenses and adds the "permission required" option.


Permission Attribution Commercial use
Attributes
CC0
Not required
No but strongly suggested Yes All
CC BY
Not required Yes Yes
Minimum unless "With all attributes" is selected
CC BY-NC
Not required Yes No Minimum unless "With all attributes" is selected
Permission required
Required Yes - -

The data sharing policy of the dataset is found in the "Sharing policy" in the metadata section of the Dataset Page.

On the Species Page or Advanced Search, the quickest way to see the data sharing policy is to open up the Datasets on Map window. The gridded table that lists the contributing datasets has a column "Share Policy".

How to download

  1. Find the dataset or species you are interested in and visit the Species Profile Page or Dataset Page. If you are interested in multiple species or datasets, visit the Advanced Search.
  2. Set up criteria and make sure the map shows the data you are interested in or move to the next step without setting up criteria if you want to download the whole data for a species or a dataset, .
  3. Click [Download] botton in the toolbar below the map.
    Note: [Download] botton is disabled for the dataset under "permission required" policy.
  4. Read 'OBIS-SEAMAP Terms of Use' and agree to it by clicking [Agreed on the Terms]. Otherwise, click [Cancel] to close the download wizard window. If you don't agree on the Terms of Use, you can't download the data.
  5. In the second wizard panel, fill in the 'Full name', 'Affiliation', 'E-Mail', 'Prospectus' boxes. All fields are required.

    The information provided here helps us trace the usage of the OBIS-SEAMAP database and recognize your research goals. The OBIS-SEAMAP team members may contact you to better understand your porpose of the data download.

    The information will be stored in our database but not be used to other porposes than the management of OBIS-SEAMAP.
  6. Once all the boxes are filled, click [Filled the Form].
  7. In the third wizard panel, choose 'Data Selection' option.

    In the Advanced Search, "Data on map under current criteria" is the only option available. This option extracts data you see currently on the map reflecting the criteria you set up though those from datasets under "permission required" are excluded.

    In the Dataset Page, "Dataset on Dataset Page" is also available. This option downloads a prepared set of data including observation records and tracks if available. This option does not take in any criteria currently set.

    In the Species Profile Page, "Species on Species Profile Page" is also available. This option downloads a prepared set of observation records of the species. This option does not take in any criteria currently set. Note that a set of observation records will grow as new datasets are added that observed the species of interest. Therefore, writing down the date you downloaded the data is useful. Also note that records from datasets under "permission required" are excluded.
  8. Select one of the download formats. What are included in the download zip file are slightly different among the formats. See the table below.
  9. Note that
  10. Click [Start download]. It may take several minutes to prepare the download data. You see the progress in 'Download Status' column.
  11. When the browser's save dialog appears, select the folder you want to save it in. Data in any format except WMS are zipped. A WMS image will open up in a new browser tab/window.
  12. Unzip the downloaded file.

What included

The zipped download file includes the following files depending on the type (platform) of the dataset, "Data Selection" option and the page you downloaded the data on (i.e. Dataset Page, Species Page or Advannced Search).

Page / Data Selection Dataset on Dataset Page Species on Species Page Data on map
Data type  Observation
(boat, plane)
Telemetry
(tag)
Mix
Mix
Point observations Yes No Yes Yes, if the Points layer is on.
Point telemetry location No Yes Yes, if exists Yes, if exists
Ship/plane effort lines Yes, if available No No No
Animal track lines No Yes, if available No No
Gridded summary No No No Yes, if the Summary layer is on.
datasets and citations info
Yes
Yes
Yes
FGDC metadata
Yes
Yes (including all datasets contributing observations) Yes (including all datasets contributing observations)
Style sheet (FGDC_SEAMAP.xsl)
Yes for shapefile; No for CSV
Yes for shapefile; No for CSV Yes for shapefile; No for CSV
Terms of Use (termsofuse.html)
Yes
Yes Yes
File name dataset_[dataset_id]_points_[format]
species_[tsn]_points_[format]
custom_[request_id]_[layer_type]_[format]

All file names have a prefix "obis_seamap_".

[format] indicates the format you chose: "csv", "shapefile" or "wfs".

[dataset_id] indicates the Dataset ID, which you can see 'OBIS-SEAMAP ID' row in the Dataset Page (effort or telemetry track lines has a different ID) as well as [dataset_id] field in the CSV / shapefile.

[tsn] indicates the taxonomic serial number (TSN) of the species.

[request_id] indicates an unique ID assigned by the system per download request.

[layer_type] indicates the layer selection option you chose: "points", "dist_sp_xxxdeg" or "dist_taxa_xxxdeg" where xxx is the resolution (1, 01 or 001).

 

datasets and citations info

The information on datasets that provided the data you downloaded is listed in the CSV file. The actual file name follows the rule :

obis_seamap_[download type]_[id]_datasets_and_citations.csv

where [download type] is "dataset", "species", or "custom" according to the Data Selection options "Dataset on Dataset Page", "Species on Species Profile Page" and "Data on map", respectively.

The informatoin includes dataset name, provider's contact information, data sharing policy and citation to the dataset as well as the link to the online metadata (XML format) for the dataset. The CSV file should include only one record when you downloaded the data with "Dataset on Dataset Page" option.

When you use the downloaded data for your research that leads to publicly available product or publication, you are required to give credit to all datasets/providers that provided data you downloaded. We suggest you use the citation in the CSV file.

 

FGDC metadata

The FGDC-compliant metadata in XML format for all the datasets that provided the data you downloaded are placed in the "fgdc_metadata" folder in the zipped download file. It is very helpful to take a look at the metadata for proper use of the data for your analyses. The datasets and citations info file (CSV) includes the links to the local or online metadata so that you can quickly find the metadata for the dataset you are interested in. Note that there should be only one metadata in the fgdc_metadata folder when you downloaded the data with "Dataset on Dataset Page" option.

 

CSV/ Shapefile field definition

Observation and telemetry point data

The CSV and shapefile have the same field definition. Ignore [Type] for CSV.

Field Type Description
dataset_id Long integer Dataset ID.
row_id Text Row id unique among the OBIS-SEAMAP database.
latitude Double Latitude of the point in decimal degrees.
longitude Double Longitude of the point in decimal degrees.
sp_code Text Species code that the data provider used to identify the species.
scientific Text Species scientific name.
common Text Species English common name, if any.
tsn Long integer Taxonomic Serial Number for the species organized by Integrated Taxonomic Information System.
count Long integer Number of animals observed at the sighting. May have different definition, count methods. Contact the data provider for more detail. This is always 1 (one) for telemetry data.
series_id Text Identification of the animal. For telemetry or PhotoID data only.
obs_date Date Date of the observation. Time is not included.
date_time Text Date and time of the observation in "yyyy-mm-dd hh:mm:ss" format.
Note: An ESRI shapefile can not contain both date and time in a Date type field.
last_mod Text Date and time the data was last modified. Note that the data may be updated due to error correction or other reasons.
provider Text The institution name of the data provider.
owner Text The data provider expressed as an OBIS-SEAMAP user account.
oceano Text Remote sensed oceanographic data sampled againt the observation location and date.
depth Double The depth of the observation, if available.
ds_type Text Data type.

 

Effort and animal track lines

Ship/plane effort line and animal track line data have the same field definition.

Field Type Description
dataset_id Long integer Dataset ID seen in 'Effort'/'Trackline' row in Dataset page. This is different from that for the related observation/telemetry dataset.
row_id Text Row id unique in the OBIS-SEAMAP database.
series_id Text Identification of the animal for telemetry data.
lon_s Double Longitude of the beginning point of the line segment in decimal degrees.
lat_s Double Latitude of the beginning point of the line segment in decimal degrees.
lon_e Double Longitude of the end point of the line segment in decimal degrees.
lat_e Double Latitude of the end point of the line segment in decimal degrees.
date_s Date Date of the beginning point of the line segment.
date_e Date Date of the end point of the line segment.
datetime_s Text Date and time of the beginning point of the line segment.
datetime_e Text Date and time of the end point of the line segment.
length_km Double The length of the segment in km.
speed_kph Double Averaged speed in km/h at which the ship/plane/animal travels along the line segment.
eff_status Text Effort status (on or off) for ship/aerial surveys, if available.
ds_type Text Data type.

 Summary data

The CSV and shapefile have the same field definition.

Field Type Description
CSV
Shapefile
oid / FID Integer Unique ID for row
Y (oid)
Y (FID)
longitude Double Longitude of the centroid of the cell in decimal degrees.
Y
Y
latitude Double Latitude of the centroid of the cell in decimal degrees
Y
Y
providers Text Provider names, separated with ";"
Y
N
species Text Species scientific name, separated with ";"
Y
Y
datasets Text Dataset IDs, separated with ";"
Y
Y (dataset)
date_min Text Minimum date of the records in the cell.
Y
Y
date_max Text Maximum date of the records in the cell.
Y
Y
num_records Integer The number of records that fall in the cell.
Y
Y (num_record)
num_animals Integer The sum of the group size in the cell.
Y
Y (num_animal)
num_species Integer The number of species in the cell.
Y
Y (num_sp)
csquare Text String expression of the cell.
Y
Y
geom_wkt Text Well known text representation of the cell.
Y
Y
shannon Double Shannon diversity index (included on dist_taxa mode)
Y
Y
simpson Double Simpson diversity index (included on dist_taxa mode)
Y
Y
hurlberts Double Hurlbert's diversity index (included on dist_taxa mode)
Y
Y

*dist_taxa mode: dist_taxa mode is visualized when no dataset or species is set as a criterion.

 

OBIS-SEAMAP Stylesheet for ArcGIS

OBIS-SEAMAP Stylesheet for ArcGIS is a stylesheet for metadata that nicely visualizes taxonomic information added to FGDC-compliant metadata in ArcCatalog. Taxonomic part of the metadata is compliant with Biological Data Profile organized by National Biological Information Infrastructure (Content Standard for Digital Geospatial Metadata; Part 1: Biological Data Profile. FGDC-STD-001.1-1999. Defined by National Biological Information Infrastructure) and all the datasets in OBIS-SEAMAP has taxonomic information put in the metadata.

The stylesheet extends the original stylesheet named FGDC ESRI, which is pre-defined in ArcCatalog, adding a column titled Taxonomy to show taxonomy elements.

 

stylesheet

 

CSV/ Shapefile FAQ

Why is [date_time] field of text type?
The database that ESRI shapefiles are based on (DBF) does not support Time type and a Date type field cannot hold time part due to the field size limit. Thus, we decided to hold date and time values in a text field. The date part is also available in [obs_date] field that is date type.
I want to sort the attribute table by date/time. How can I do it?
Since [date_time] field is written in a format appropriate for sorting, the sorting on date/time will work fine even though it's a text type field.

1. Open the attribute table (in ArcMap or ArcCatalog).
2. Select the [date_time] field.
3. Keeping it highlighted, right-click and select 'Sort Ascending/Descending'.
sort by date
 
I don't see the effort shapefile in the zipped file?
Not all the datasets have effort data. You can make sure if the dataset has effort data in Datasets page ('yes' in 'effort' column) or Dataset Detail page ('Effort' or 'Trackline' row).
How do I use oceanographic sample data in [oceano] field?
See "Download sampled values and utilize them" in the Oceanographic variables in details page.