Data Access
The samples collected and analyzed as part of FishPopTrace are stored in a series of carefully constructed databases. Different aspects of this data, concerning sampling, analysis, and reporting and uploading of data are accessible through 3 different interfaces provided here. Data access rights and the visibility of the data vary depending on the interface. We wish to make the scientific data generated available to non-scientific stakeholders such as fishery managers and policy makers. Meanwhile, access to some of the scientific raw data and analysis is currently restricted to FishPopTrace partners. In addition to the 3 information access interfaces, a website “Member Area” acts as an online secure file store, allowing FishPopTrace partners to collaborate on documents and to distribute files amongst each other.
Below, a short description of the database structures and the various user interfaces are given. Although the structures described below contain FishPopTrace data pertaining initially to a limited number of samples (7,500) spread over 4 commercial species, they are designed to be expanded and continually built on, to work towards building a full genetic characterization of the marine environment.
The characteristics of the fish specimen collected are stored in a central “sampling database”. This information describes the specimen age, length, weight, reproductive characteristics, location and depth of catch, storage characteristics, etc. Results and raw data for each of the genetic analysis techniques applied to these samples are stored in a series of satellite databases representing each of the techniques employed by FishPopTrace. This cross referencing approach allows results arising from SNPs, otoliths, proteomics, fatty acids and gene expression analyses to be compared for the same sample. |
Database Schema |
The primary means of information dissemination is through a publicly accessible Web-based geobrowser. Information on the samples taken during FishPopTrace, and their genetic characteristics are visualized in an interactive map. The data visible through this interface is publicly accessible and has a limited degree of access to the genetic analysis information in the databases. Environmental parameters such as sea surface temperature chlorophyll concentration and ocean currents, along with important international boundaries and economic zones are also available through this interface. This allows possible inferences regarding the effects of environmental parameters on the genetic characteristics of a species to be generated, while also considering what economic or management areas are involved. |
Geobrowser Portlet |
Access to the information describing the samples used for analysis, stored in the central sampling database, is currently provided only to the collectors of this information through a password protected Web-based portal. The interface allows scientists to check the information on samples currently in the database, edit the information and add information on new samples. The information can be queried according to numerous parameters. Records are displayed through the web-based interface, but can also be downloaded and manipulated in a spreadsheet. While access to this portal is currently highly restricted, it is envisioned to provide read-only access to a set of this information to accompany the information accessible through the geobrowser. The combined information in text and visual, map-based formats provide valuable information for informed decision making by fishery managers and policy makers. | Sampling Database Access Portlet |
The database schema above shows a series of satellite databases around the central sampling database. The Data Analysis Portlet provides access to the raw data and analysis emerging from SNPs, otoliths, proteomics, fatty acids and gene expression analyses for (a) given specimen(s). The results of each technique can be compared to those of another technique as the portlet allows users (with access rights) to see the results of each analysis type for a given sample or set of samples matching a specific criteria. For example a query could be made to show the SNP, Otolith and Faty Acid characteristics of a specific sample, or all samples of male juvenile hake taken in a particular regi | Data Analysis Portlet |
Finally, a password protected shared file repository allows members of the FishPopTrace consortium save information in a communal file store. This is a useful function for the creation of joint reports and the storage of consortium specific documents such as templates, presentations, publications and imagery for use in communications. | Member Area Fileshare Portlet |
Each of the information access “portlets” described above, which provide access to information stored in the sampling database, its satellite databases, and the member’s file repository are independent of this website. They are independent modules which can be placed anywhere, in many multiples, on any websites, providing direct links to the single instance of the underlying database structure. This gives a strong, independent data storage and access architecture, which will allow for ease of expansion of our dataset. It is intended form the foundations of a hub of genetic information which can be added to by many different sources in the future.