Salmonid management around the Channel (SAMARCH). Estimating salmonid growth and survival at sea: a database to manage samples, data, and results of analyses.

[Lien vers la fiche source] In order for the data on salmon and sea trout that were produced by SAMARCH to be FAIR (Findable, Accessible, Interoperable, Reusable), all data were put together in file formats that could be read by anyone without computer skills and in international standards. Internally, the data was stored in a Postgresql database or in Excel files. We made interfaces or extractions in .csv format in order to make the data available to the scientific community. The data concerns the samples used and the analyses performed in the SAMARCH project. In total, 17133 biological samples were used to obtain 3 types of results (growth, sex and genetic characteristics). 14756 growth analyses, 12633 sex analyses, 1182 genetic analyses and 13682 photos were produced using 5 different protocols (scale reading and growth measurement, genetic sexing, genotyping, tracking and acoustic). ## Samples As part of the SAMARCH project, 14756 scales of salmon and sea trout were used for age determination, growth measurement and sexing. In addition, 1099 fin clips were preserved in alcohol and used for genetic analysis (Figure 1). The samples are stored and managed by the organisations that collected them. Some of them are managed by the Colisa Biological Resource Centre (Marchand et al., 2018), which makes them visible and available through an online catalogue. This online catalogue has been improved with the SAMARCH funding and display all the samples collected in France (Figure 2). A first home page gives access to the description of Colisa and a summary of the number of samples per species and per type of tissue. Access to more detailed information on the samples and to the request form is possible after registering on the website. Finally, thanks to the interoperability of the data and in order to widen access to the samples, data are also integrated into the international databases of the Global Biodiversity Information Facility (GBIF) and the Global Genome Biodiversity Network (GGBN). ## Images and analysis From the samples, different variables could be measured and the value of a variable is defined as the result of an analysis. Some results (age and sex) are made available immediately in an Excel file. This file is built from scripts that were used in the SAMARCH project, and can be reused in future research programmes. Depending on the type of variable, the results can be compiled directly into a "master" file or from links to other files stored in a directory linked to the file. The raw data files are very large (71 GB) and are therefore not stored online. Therefore, the name of a contact person is provided for each sample. Also, some results are only accessible (e.g. genetics) upon request to the contact person. ## File description The file is composed of two tabs, one for the different fields describing the samples and a second one to make the link between the sample and the associated data files. 1st tab: • Index: Unique id linking the analysis performed with the growth or image data files (second tab). • The first 3 fields (study site, sample type and sample code) guarantee the uniqueness of the sample code because the different partners may use the same code to different samples. This makes it possible to find the analyses carried out on a unique sample of interest. • Site: The different study sites correspond to an internal nomenclature and correspond to the study sites of the ORE DiaPFC located in Brittany and Normandy (Bresle, Oir tributary of the Selune and Scorff), to the Centre d'interprétation des captures de Salmonidés (CNICS) and to the English study sites (‘Autres’). • Type of sample: fine clip or scale. • Sample code: sample code defined by each partner. • Phenotype observed: Atlantic Salmon, Brown trout and Sea trout. • Catch number: This is used to link different samples from the same catch operation. • Catch date: this is the date when the sample was collected. • Catch site: Watercourse where the fish was caught. • Size (mm): Total length of the fish for the CNICS study sites (fish caught by anglers) and fork length for the other study sites. Measurement is in millimetres. • Weight (g): Weight of the fish, in grams. • Individual tagging: Individual mark identifier, when available. • Type of marking: Pit tag, RFID, Carlin tag, Floytag and visible implant, when available. • Protocol: Protocol of analysis that was carried out on the sample or on the fish from which the sample was taken: scale reading and growth measurement, genetic sexing, genotyping, acoustic tracking. • Result: Value of the result of the analysis for the variable of interest. • Contact: Person to contact for more information about the sample. Second tab: Attachments • Index: Unique id linking the sample to the analysis performed (first tab). • File: Link to the corresponding file. ## Description of the attached files Two types of files are attached to the sample: image files and growth data: 1. Image files in .tif format, the file name corresponds to the scale number. 2. Growth data, each sample points to a file containing measurement results. • ScaleNumber: Id of the sample which can contain several scales • Scale_N: Number of scales available in the sample ScaleNumber • Measured parameter: In italics and underlined, the "mandatory" variables measured on each scale. The value corresponds to the measurement in millimetres of the distance between the nucleus and the different points of interest on the scale. o R: "Regenerated": 1st circuli since the focus. o 1FW: end of 1st Freshwater Winter. o 2FW: end of 2nd Freshwater Winter. o 3FW: end of 3rd Freshwater Winter. o Transition: passage from river to sea. o 1SW_bg: beginning of the 1st Sea Winter band. o 1SW_end: end of the 1st sea winter band o 2SW_bg: beginning of the 2nd sea winter band o 2SW_end: end of the 2nd sea winter band o Check_bg: beginning of a zone of slow growth within the summer band o Check_end: end of a zone of slow growth within the summer band o WinterCheck_bg: beginning of a zone of fast growth within the winter band o WinterCheck_end: end of a zone of fast growth within the winter band o Spawning_mark: spawning mark, as identified by the erosion of the scale WARNING: beyond a spawning mark, scale measurement and circuli count data are no longer reliable o Circuli: each circuli except those already identified by one of the previous codes. o Edge: edge of the scale, WARNING: this is not a circuli o Edge_ER: edge of an eroded scale, WARNING: this it is not a circuli. Edge_ER replaces "Edge" if the scale is eroded on its periphery. o NR: Not filled in: data missing because illegible (concerns only "mandatory" parameters)