• Collection of all other objects (Compounds, Reactions, Rules, Pathways)
• All users can only see objects for which they have at least reading permissions and only edit the ones for which they have writing permissions.
• Level to set license, permissions, and review status
• All packages have an owner and main group

A package can be reviewed by the admin or a member of the reviewer group. Once a package is reviewed it can not be edited anymore. A user can ask for a package to be reviewed, to do that the user can click on the “Actions”-button on the webpage of the package to be reviewed.

Users with Permission.WRITE on a package can assign permissions to other users and groups. To do that click the “Actions”-button on the webpage of the package and select “Permissions”, here the user can assign the permissions to users and groups.

Objects from all packages are shown when the user selects the corresponding category in the main menu (if the user has Permission.READ). To view the content of a specific package you can choose it on the package page. Once you entered it, you have access to the objects contained within this package by clicking on the corresponding object (e.g., Compound, Rule, …). To create and add new objects to this package enter the desired category, click the “Actions”-button and select e.g. “New Compound”. Keep in mind that you can only edit existing entities or add new ones to a package if you have Permission.WRITE.

Each user owns a default package, with the same name as the username. By default, all objects that a user creates will be stored in this package (i.e. objects acreated via the following pages: compound, rule, reaction, pathway, model and scenario). For more information see: Users. This also applies to users who are not logged in, those users share an account called anonymous.

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the EAWAG-BBD is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology.

The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes.

The EAWAG-SLUDGE package contains pathways and kinetic information about microbially mediated transformation processes in biological wastewater treatment. The information was extracted from scientific publications in different journals. The biotransformation reaction schemes are stored as pathways. The experimental conditions and additional information (e. g. sludge source) are collected in the scenario objects. Any observed transformation products (compounds) are linked to their corresponding experimental metadata (scenario). Kinetic parameters (rate constants and/or half-lives) including corresponding scenarios are indicated for compounds for which such data is available.

“Eawag-SOIL” package contains pathway information from soil degradation studies, stored in a biotransformation reaction scheme in the object pathway. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA). The package also contains information on different experimental conditions that are stored in the object scenario. Compounds in the pathway are associated with a given scenario if they have been observed under the specific experimental conditions. If available, a biotransformation half-life (DT50) value is additionally associated with a given compound in the pathway and a specific scenario. More details concerning enviPath conventions that were used to store specific data from DAR, and their description can be found here