Data source
PHENOPSIS DB contains phenotypic data and experimental and environmental metadata (see additional file 1: Description of the variables stored in PHENOPSIS DB). The phenotypic data include online (i.e. automatically recorded) and offline (i.e. manually recorded) plant images and sets of offline phenotypic measurements. Metadata consist of protocols, descriptions of variables, genotype characteristics and online environmental data.
Experiment protocols and variable descriptions
Each experiment is associated with a protocol that gives information about the experimental context. Other protocols describe how variables were obtained to ensure that all experimenters use the same methods to measure a given variable.
Genotype characteristics
Arabidopsis thaliana genotypes may include ecotypes, inbred lines from specific crosses, mutants, etc. and information on the specific features of the genotype and the source of the material, i.e. the laboratory or stock center providing the seeds.
Environmental conditions
Climatic conditions (air temperature, air humidity, light intensity, vapor pressure deficit) in the PHENOPSIS growth chambers are continuously recorded during an experiment [15] and automatically sent to the server. R [16] functions check and insert them into the database. Plant watering data, i.e. the weight of individual pots before and after watering and the supplied amount of nutrient solution [15], are also automatically recorded and inserted into the database via real-time automated SQL requests.
Images
Visible and infrared images of each individual plant in PHENOPSIS [15] are automatically transferred in real-time to the server. Additional offline images are manually inserted into the database. These are produced by experimenters after the harvest of plants or plant organs for destructive measurements, including scans of different plant parts (roots, leaves, etc) (Figure 1a), or obtained after organ preparation and microscopic observations (Figure 1b).
Phenotypic data measured on plants
Non-invasive measurements, such as rosette and individual leaf area determination, plant growth stage records and transpiration measurements are performed during a growth run within PHENOPSIS. Invasive measurements, on the other hand, require the harvest of plants or plant parts and are performed at predefined dates (x days after sowing) or at given plant developmental stages. Examples are the determination of plant and organ fresh and dry weight, leaf thickness, leaf epidermal cell density and stomatal density. Both invasive and non-invasive measurements are inserted into the database via the Web interface. R functions are used to check data consistency before insertion.
Data volume
Currently, 70 experiments are stored in the database and 15 of them are publicly available. They include 87000 phenotypic measurements on 865 genotypes, of which 50000 measurements on 620 genotypes are publicly available. 600000 images are stored in the database and more than 90000 are publicly available.
PHENOPSIS DB information system
The PHENOPSIS DB has been designed for data storage, browsing and retrieval. It also provides tools for data visualisation and analysis, and image analysis. It consists of three major components: the database, the Web interface with modules developed in R or ImageJ [17], and several Web Services (Figure 2).
The database
The database was developed using the MySQL 5.0 Community Server and is composed of 15 physical tables (see additional file 2: Description of the physical data model of the PHENOPSIS DB database).
The Web interface
The Web interface was developed using XHTML, PHP, JavaScript, Jquery, Ajax and CSS. Both CSS and XHTML scripts respect the W3C [18] standards and were validated by W3C online tools [19, 20]. PHP scripts call R functions to check, insert and format data, and to perform online statistical analysis or visualisation. The RODBC package in R version 2.9.2 was used to establish the database connection.
User access
All metadata are freely available without restriction or authentication request. Metadata include: characteristics of experiments and associated protocols, list of genotypes grown in an experiment, list of variables measured in an experiment with their definition and associated protocols, comments on the experiments, micrometeorological data and plant watering data.
Images and phenotypic data from public experiments and public genotypes are also freely available without restriction or authentication request. The whole dataset associated with an experiment and/or a genotype becomes public as soon as the data have been published.
The access to images and phenotypic data from non-published experiments or confidential genotypes requires a user authentication that can be requested from the administrator in charge of the information system.
Web Services
Web Services were developed to enhance interoperability and data exchanges with other systems (information systems, stand-alone programs). The PHENOPSIS DB Web Services are based on the Tomcat/Axis solution, described using WSDL language and they apply the SOAP protocol. They were developed in the Java language.