Biodiversity image datasets in the Mediterranean Sea (1980 – 2005)

Dataset summary:
The dataset contains underwater images taken in the Mediterranean Sea, between 1980 and 2005.
These images provide essential qualitative and quantitative data for assessing and monitoring the coastal marine environment by documenting organisms and their natural habitats. Image inventory assembles pictures illustrating the most representative aspects of benthic domain.
Each underwater image is temporally and spatially associated. However, despite the availability of detailed coordinates, the location name is designated as the principal reference and primary identifier for the survey site.
The dataset includes underwater images that help describe and analyse three distinct aspects of marine ecosystem studies, collected in a GeoPackage (GPKG), a standard, open, and portable format for storing geospatial data.
The GeoPackage file is organised into three layers, reflecting and classifying the content of the three main types of images:
Species: It refers to the distinct groups of living organisms within the biological/taxonomic classification system. Environment: It refers to the habitat in which an organism lives or the context where an image has been taken. The environment section describes the type of biocenosis, the zone and the type of substrate. Method: It refers to the mode of execution of the survey, defining its primary functional objective and scope. The information specifies the actual scientific action being performed and often determines the nature of the data collected. A full inventory of the instruments, sensors, and equipment utilised, detailing their model numbers and technical specifications, is presented to ensure the reproducibility of the procedure and to validate the technical context of the recorded data.
Dataset structure:
The current dataset, structured as a GeoPackage, represents an upgrade of an earlier version based on unstructured data. This upgrade reflects comprehensive enhancements spanning both the IT implementation and the precision of the taxonomic classification. Concerning the IT aspect, a dedicated re-engineering initiative was undertaken to restructure the existing data entities and implement them within a relational database, ensuring standardized data representation and greatly simplifying future updates and management. Furthermore, the relational database was used to build the GeoPackage file constituted by three layers that are linked to the three main image typologies of the dataset.
Concurrently, the taxonomic completeness has been substantially improved. Initially, the completeness of the taxonomic data at the time of the catalogue's publication was limited. This gap has been addressed by updating the fields related to species classification. As a result of this revision, the classification accuracy has been significantly improved. The catalogue now reflects the most recent and authoritative taxonomy, fully aligning with the scientific standard provided by the World Register of Marine Species (WoRMS).
The “Images” directory contains all pictures. In each table of the GeoPackage, the field named “Img_code” serves as the unique identifier (or key) referencing the respective image.
The GeoPackage tables include the following further information:
- img_code (image identifier code)
- date
- photographer_name
- context (the activity during which the image was taken)
- mode (the gear used to take the image)
- location_name (toponym)
- position (specifies if the survey point is identified by coordinates or toponym)
- lat
- lon
- depth
- notes (operator’s comment)
- caption (additional description)
Further information is provided according to the three main image typologies:
1 Species: Flora and fauna species are inventoried according to the usual hierarchical order of the systematic categories. As a result of the dataset upgrade, two fields related to species names are provided: the first refers to the species name of the older version of the dataset, and the second one refers to the updated species name. Therefore, the GeoPackage table for the Species layer includes the following fields:
- previous_species_name: It refers to the specific nomenclature according to the earlier classification
- updated_species_name: It refers to the specific name according to the updated classification
- species_name_author
- phylum/division
- superclass
- class
- order
- family
- species
2 Environment: It provides a description of the operational environment, the type of substrate and the zone. The latter is defined according to the Benthos Committee of the International Commission for the Scientific Exploration of the Mediterranean (CIESM). Consequently, the provided fields are the following:
- description
- substrate: It refers to the kind of substratum (Hard or Soft)
- zone: The catalogue details four zones that are accessible to scientific diving operators (Supralittoral, Mid-littoral, Infralittoral, Circumlittoral)
3 Method: It refers to the methodology adopted to acquire the observation. The attribute table provides the following information:
- method_description
- surface/underwater: It describes the operational environment, distinguishing between techniques that require diving (by human operators and through instruments) and those performed from the sea surface
- method_typology: It refers to the specific technique and qualifies the method used (e.g. sampling, direct measurement, visual, etc.).