Biol Cube

BiolCube is a gCube application bundle offering facilities to practitioners working with species occurrence data and taxonomic profiles. It included the following applications.

Occurrence and Taxonomic Data Discovery This application offers facilities for discovering and accessing species occurrence and taxonomic data from major repositories and information systems, e.g., OBIS, GBIF, Catalogue of Life, WoRMS. The discovery mechanism is simple (based on species common names or scientific names) yet powerful since it supports query expansion and additional filters. The identified datasets are enriched with links to other species, can be displayed on a map as well as saved in standard formats (e.g., DarwinCore, DarwinCore-Archive, CSV) for future uses.

Occurrence Data Processing This application offers facilities for species occurrence datasets processing. These facilities include algebraic operations (union, intersection, subtraction, and duplicates deletion) based on spatial and syntactic similarity measurements, clustering (e.g., density based algorithms such as DBScan, distance based algorithms such as K-means), outliers detection (e.g., Local Outlier Factor approach), occurrence points representativeness (e.g., Habitat Representativeness Score technique), and occurrence points enrichment with chemical and physical environmental parameters.

Species Distribution Modeling This application offers facilities for building a rich array of species distribution models by relying on algorithms and approaches including AquaMaps. AquaMaps is actually a family of approaches (e.g., suitable, native) producing species distribution probabilities on half-degree cells by relying on (i) a table containing species envelops (HSPEN), (ii) a table containing environmental parameters (HCAF) and (iii) a table containing species occurrences points (half-degree cells). Moreover, if offers methods for producing new versions of HSPEN and HCAF.

Species Distribution Maps Discovery This application offers facilities for retrieving species distribution maps. It offers (i) simple search by species name, (ii) advanced search by supporting criteria on species name, code, taxonomy, and/or characteristic, and (iii) support for visualisation of products by image, by detailed record, and by scientific record.

Taxonomic Data Comparison This application offers facilities for comparing two taxonomic checklists in DarwinCore-Archive format. In particular, the application provides the user with a flexible environment for detecting, analysing and reporting relationships among taxa of the compared checklists (e.g., corresponds, includes, overlaps, not found in).

Taxonomic Data Matching This application offers facilities for taxonomic data matching, i.e., the identification of most suitable scientific names given a list of species names. In particular it offers a workflow base approach that enable users to combine a number of matchers (e.g., GSay, FuzzyMatcher, Levensthein, Trigram) and tune their contribution while identifying the proper scientific names recognised by a number of authoritative sources.

See Also


Applications realising a framework conceived to support practitioners willing to develop applications interfacing and benefitting from gCube facilities.


Applications offering a comprehensive suite of tools for standard oriented data publication environment, including semantic technologies.


Applications to help practitioners dealing with geospatial information to properly access, consume, and produce data.


Applications offering core facilities for the deployment, operation and management of an Hybrid Data Infrastructure.


Applications comprising support for tabular data validation, data enrichment and efficient analytical tools.