Packages are a collection of all relevant enviPath objects for a specific environmental compartment or practical purpose. They consist of (Compounds, Reactions, Rules, and Pathways). There are currently three curated packages in enviPath that have undergone the Review process. This includes the EAWAG-BBD, EAWAG-SOIL, and EAWAG-SLUDGE packages.
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.
The Eawag-BBD package contains information on biotransformations of organic contaminants reported in scientific literature for pure and enrichment cultures. This package contains all information provided in the legacy UM-BBD/PPS database. There are 219 biotransformation pathways contained in this package, in which there are 1399 compounds and 1480 reactions. 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, enzymes, and genes.
The Eawag-SOIL package contains data on the biotransformation of pesticides in soil reported in draft assessment reports (DARs) made publically available through the European Food Safety Authority (EFSA). There are 317 pathways included in the package, with 1784 compounds and 2447 reactions. The package also contains information on different experimental conditions that are stored in scenarios. 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. There are currently 895 compounds with half-lives provided in this package. More details concerning enviPath conventions that were used to store specific data from DAR, and their description can be found here
The EAWAG-SLUDGE package contains biotransformation data extracted from scientific publications for microbially mediated processes in biological wastewater treatment. There are 184 pathways included in this package, with 1070 compounds and 521 reactions. The biotransformation reaction schemes are stored as pathways. The experimental conditions and additional information (e. g. sludge source) are provided in scenarios. 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 provided for compounds for which such data is available. There are currently 172 compounds with reported rate constants and/or half-lives within this package.
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.