Manual

Accessing the OBIS database

pgAdmin

OBIS uses a PostgreSQL database, which can be accessed using a desktop tool such as pgAdmin.

Use the following configuration to access the OBIS stage database:

Tables

Schema geo

This schema is used for geographical features such as grid and area polygons.

Schema obis

This is the schema holding the main data tables.

Schema portal

Common queries

Obtaining taxon occurrence data

There are a few things to keep in mind when querying for occurrence data:

For example, to retrieve all occurrences of Phocoena, we will need to:

All this can be translated into the query below:

with taxon as (
	select id, storedpath
	from obis.tnames
	where tname = 'Phocoena'
)
select t.tname as accepted, p.*
from portal.points_ex p
left join obis.tnames t
on t.id = p.valid_id
inner join taxon
on t.id = taxon.id or t.storedpath like taxon.storedpath || taxon.id || 'x%'
order by p.tname;

The results of this query will include:

Obtaining taxon distribution data