D2.1 Specification for species occurrence cubes and their production

This document presents the specification for “species occurrence cubes”, a format to summarize species occurrence data. It also outlines the requirements for software to produce such cubes and how it can be integrated in services provided by the Global Biodiversity Information Facility (GBIF). Producing a species occurrence cube will broadly involve the following steps:

1. Search and filter data: a user will be able to restrict a cube to occurrence data of their interest.
2. Define cube dimensions: a user will be able to select from a number of dimensions and categories that determine how occurrence data will be grouped into a cube. For
example, taxonomic information can be grouped by family, temporal information by year, and spatial information by a chosen grid reference system, taking into account the spatial uncertainty associated with occurrences.
3. Generate cube: based on the parameter selection by the user, software will process the occurrences into a species occurrence cube, providing measures for each combination of dimensions (e.g. 5 occurrences for species x at year y in grid cell z). The software can also provide reference measures to assess sampling bias.
4. Deposit cube: the user can define in what format and where (cloud storage location) a cube should be deposited. Deposited cubes will be automatically documented with metadata and assigned a Digital Object Identifier (DOI) so they can be reproduced and referenced.

The software developed for this service must be open source and documented, so that users can understand, use, install and contribute to it. It must also be demonstrated to operate on one or more public cloud providers.