ABOUT TOFF
TOFF (Traits OF Fish) focuses on the functional traits of fishes, including hagfishes, lampreys, chimaeras, sharks and rays, lobe-finned fishes, and ray-finned fishes. Its objective is to bring together behavioral, morphological, phenological, and physiological (BMPP) traits, coupled with environmental measurement contexts, into a single open-access repository. The database can host diverse types of data derived from multiple literature sources, including peer-reviewed articles, theses, monographs, and books.
TOFF has been designed to store records, defined as information on BMPP traits for a given fish species at a specified developmental stage (i.e., larva, juvenile, or adult), sex, and ploidy level, measured in a characterized environment and derived from a scientific source. TOFF is a flexible SQL relational database that uses an entity–attribute–value model coupled with controlled vocabularies. These vocabularies are semantic tools consisting of standardized terms, their definitions, and associated properties such as units, value ranges (e.g., 0–14 for pH), predefined spellings for drop-down menus (e.g., categorical variables), and data formats. Access to the TOFF thesaurus is available here or at https://doi.org/10.6084/m9.figshare.10253219.v6
The relational database schema comprises five core modules :
Reference module– stores bibliographic metadata, including authorship, publication type, and year of publication.
Trait module – integrates the functional traits included in the database, grouped into four classes: behavioral, morphological, phenological, and physiological traits.
Measure module – contains individual measurements (i.e., attributes of traits) and is linked to the Trait module. It also stores information on sample size (i.e., the number of individuals on which a measurement is based), ploidy level (e.g., diploid or triploid), developmental stage (i.e., larva, juvenile, adult, or unknown), sex (i.e., male, female, hermaphrodite, or unknown), type of measurement (i.e., direct measurement, computed value, or model-derived estimate), and the identity of the data contributor.
Environment module – documents the environmental context in which measurements were recorded. Environmental features are classified into three categories: abiotic environment (e.g., geographic occurrence, water parameters), biotic environment (e.g., population density, species diversity), and feeding conditions (e.g., ad libitum).
Species module – provides a table of valid fish species names based on the FishBase species database (www.fishbase.org).
Further details on the TOFF database structure are available in the associated data descriptor at https://www.nature.com/articles/s41597-019-0307-z
Thomas Lecocq is an associate professor (senior lecturer). He works on functional ecology, ecological niche modelling, systematics, and phylogeography. His research projects focus on the development of conceptual approaches to support diversification of animal production. He explores how intraspecific diversity and interspecific interactions can facilitate domestication process and increase animal production sustainability.
Marielle Thomas is an associate professor (senior lecturer) in University of Lorraine. Her scientific expertise is in the field of animal biology, fish quality, functional ecology, and agroecology. She studies processes that structure fish communities in the farming environment (interspecific relationships, practices, and farming systems) for the development of more efficient and sustainable aquaculture systems.
Alain Pasquet is a senior scientist of the CNRS (National Centre for Scientific Research). His skills are in the field of animal behavior (interindividual relationships, personality, predatory behavior), behavioral ecology (variability of behavioral patterns relatively to environmental constraints, performances, fitness), and evolution. He developed researches on Invertebrates (Spiders) and Vertebrates (fish) species.
Alain Benard is an engineer at the institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE). He works on information systems and systems administrator as well as analysis, modeling, and development of database.
Jérémy Weber is a research technician. He works on databases, as well as software and web development.
Florent Petronin is a bioinformatician. He works on data extraction, cleaning, and analysis.
TOFF is used in the following projects:
DIVERSIFY4Future – Diversifying aquaculture for the future:
DIVERSIFY4Future (2026-2030) aims to include low-trophic species for sustainable, innovative, healthy and circular food system. His goal is to improve aquaculture diversification through organic aquaculture, integrated multitrophic aquaculture (IMTA), aquaponic–
polyculture systems, and cultivation of low trophic (LT) species. It targets six key regions (the Mediterranean, Black Sea, Delta del Ebro
lagoon, Nile Delta, inland waters of Central/Western Europe, and the northeast Atlantic), with 10 small and 5 commercial scale studies.
(Logos to be determined)
ValoSEPURE – New strategies for building and managing pond production systems for sustainable fish farming
CEDRE – ????
OPTICED – Optimization of freshwater shrimp farming
The main objective of OPTICED (2024-2026) is to support the development in France of the freshwater shrimp, Macrobrachium rosenbergii, industry. More precisely, OPTICED must make it possible to support the transition/diversification of the pond fish farming sector through research actions aimed at optimizing yields and controlling the potential animal health and environmental risks of this breeding.
POLYRAS – Optimization of aquaculture production in RAS
POLYRAS (2024-2028) is a research and development project with 13 partners that aims to optimize local aquaculture production in Grande Région (Belgium, Germany, Lorraine) by using polyculture. This approach, usually applied to open extensive systems with low productivity, is applied here in an innovative intensive way, while respecting fish welfare.
SEPURE – New strategies for building and managing pond production systems for sustainable fish farming
SEPURE (2020-2023) is a research and development project with 6 partners that aims at defining sustainable pond production strategies to meet productivity and environmental objectives, based on biodiversity. It provides references and operational tools, based on trials carried out in experimental stations and directly by professionals.
PERCIPONIE – Development of perciculture in aquaponics
PERCIPONIE (2020-2022; 11 partners) is a technology transfer program that aims at disseminating a new technology for the coupled production of autotrophic (aromatic plants) and heterotrophic organisms (fish), with an optimal management of nutrient flows and the consideration of plant metabolites and fish welfare.
ICHTYOSERV – ICHTYOdiversity, driving force behind the operation of re-circulating water rearing systems? Evaluation of Ecosystem SERVICES as a decision criterion
The objective of ICHTYOSERV project (2018-2020; 6 partners) aims at developing, using functional ecology approaches, a methodology for integrating ichthyodiversity into fish farming systems in order to increase their efficiency and sustainability.
Aquaspecies – Fish farming in multispecies aquaculture: anopportunity to develop a more efficient aquaculture?
The Aquaspecies
project (2016-2017; 3 partners) studies theorical and functional bases
of fish assemblages in rearing systems by considering biodiversity both
as an objective to be achieved and as a resource to be used. For this,
the work has consisted to develop TOFF database.