Downloading species observations from the Ocean Biogeographic Information System (OBIS) with the DiGIR protocol

THIS EXAMPLE IS UNDER CONSTRUCTION

This example shows how invoke MGET tools from ArcGIS to download species observation records from OBIS and save them as a point feature class. This example assumes you have basic familiarity with ArcGIS.

What are OBIS and DiGIR?

The  Ocean Biogeographic Information System (OBIS) is a strategic alliance of people and organizations sharing a vision to make marine biogeographic data, from all over the world, freely available over the World Wide Web. OBIS maintains a database of species observations contributed by member organizations and individuals. At the time of this writing, the database contained over 16 million records. Most records include a latitude, longitude, and date, making them suitable for geospatial analysis.

Records may extracted from the OBIS database with the  Distributed Generic Information Retrieval (DiGIR) protocol. This protocol is in widespread use throughout the bioinformatics community. OBIS uses it to collect records from contributing organizations such as  OBIS-SEAMAP, a database of marine mammal, seabird, and sea turtle records maintained here at Duke University. The  Global Biodiversity Information Facility (GBIF) uses it to collect records from OBIS into a larger biogeographic database for all taxa. At the time of this writing, there were dozens of servers that implemented the DiGIR protocol. The  Big Dig website maintained a list of DiGIR servers. Big Dig stopped operating in February 2008 but many of the servers listed there are still operational and can be queried with DiGIR.

Although DiGIR is widely used, it is no longer under development. A new protocol,  TAPIR, may eventually replace it. And although GBIF uses DiGIR to collect data from its many contributors, it exposes data through several  GBIF-specific web services. As far as we know, you cannot query GBIF with DiGIR.

Like many "web service" protocols, DiGIR is an XML-based stateless request/response protocol. For technical details, please see the documents and XML schemas on the  DiGIR home page.

Finding MGET's DiGIR tools

You must have MGET 0.7a10 or a later release to use the tools. They appear in the Marine Geospatial Ecology Tools node in the ArcToolbox window. If you do not see the ArcToolbox window, click the Show/Hide ArcToolbox Window button on the toolbar.

DiGIR server URLs

Before you can use the MGET tools, you must obtain the URL for the server you wish to query. The best way to obtain the URL is to contact the server operator. The  Big Dig website contains a list of several hundred URLs for servers that were active as of February 2008. (That website uses the formal DiGIR term provider rather than server. The terms are synonymous.) At the time of this writing, the URL for the OBIS server was  http://iobis.marine.rutgers.edu/digir2/DiGIR.php. The URL for the OBIS-SEAMAP server maintained by Duke was  http://seamap.env.duke.edu/digir/DiGIR.php.

Before you attempt to use the MGET tools, it is a good idea to enter the server URL into a web browser to make sure the server is responding. Some servers may take several minutes to respond if they have not been accessed by anyone for a while. Eventually you should receive some XML or be prompted to save a document that contains XML. For example, the OBIS server returns a response that looks like this in Internet Explorer:

If you get a response similar to this, it is likely that the server is functional and the MGET tools will work. If you don't, something is wrong and the MGET tools will probably fail. You should follow up with the server operator to resolve any problems.

Discovering the resources available from a DiGIR server

Each DiGIR server hosts a set of resouces. A resource is a collection of related species observation records. Once you obtain a URL to a server, it is possible to immediately start downloading these records, but it is usually worthwhile to first understand what resources are available from the server and review some metadata about them. MGET's Get DiGIR Resources as Table tool assists with this process.

The input parameters to the tool are the URL to the server and the paths and names of five tables of metadata:

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