Differences

This shows you the differences between two versions of the page.

--- packages [2024/04/11 06:55] – [Default Package] shankar
+++ packages [2024/05/08 08:40] (current) – [Eawag-SLUDGE] strich
@@ Line 1: / Line 1: @@
 ====== Packages ======
-  * Collection of all other objects ([[Compounds]], [[Reactions]], [[Rules]], [[Pathways]])
+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|Review]] process. This includes the [[Packages#EAWAG-BBD]], [[Packages#EAWAG-SOIL]], and [[Packages#EAWAG-SLUDGE]] packages.
+A package can be [[review|reviewed]] by the admin or a member of the reviewer [[groups|group]]. Once a package is reviewed it can not be edited anymore. A [[users|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 [[[[permissions|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.
   * All users can only see objects for which they have at least reading [[permissions|permissions]] and only edit the ones    for which they have writing [[permissions|permissions]].
   * Level to set [[license|license]], [[permissions|permissions]], and [[review|review]] status
   * All packages have an [[users|owner]] and main [[groups|group]]
-===== Review =====
-A package can be [[review|reviewed]] by the admin or a member of the reviewer [[groups|group]]. Once a package is reviewed it can not be edited anymore. A [[users|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.
-===== Permissions =====
+===== Eawag-BBD =====
+The [[https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1|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 [[http://eawag-bbd.ethz.ch/index.html|UM-BBD/PPS]] database. There are 219 biotransformation [[pathways|pathways]] contained in this package, in which there are 1399 [[compounds|compounds]] and 1480 [[reactions|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.
-Users with [[[[permissions|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.
+===== Eawag-SOIL =====
-===== Navigation =====
+The [[https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456|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 ([[https://www.efsa.europa.eu/en|EFSA]]). There are 317 [[pathways|pathways]] included in the package, with 1784 [[compounds|compounds]] and 2447 [[reactions|reactions]]. The package also contains information on different experimental conditions that are stored in [[https://envipath.org/scenario|scenarios]]. [[https://envipath.org/compound|Compounds]] in the [[https://envipath.org/pathway|pathway]] are associated with a given [[https://envipath.org/scenario|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 [[https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456|here]]
-Objects from all packages are shown when the user selects the corresponding category in the main menu (if the user has [[permissions|Permission]].READ). To view the content of a specific package you can choose it on the [[https://envipath.org/package|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 [[permissions|Permission]].WRITE.
+===== Eawag-SLUDGE =====
-=====Default Package =====
+The [[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038|EAWAG-SLUDGE]] package contains biotransformation data extracted from scientific publications for microbially mediated processes in biological wastewater treatment. There are 184 [[pathways|pathways]] included in this package, with 1070 [[compounds|compounds]] and 521 [[reactions|reactions]]. The biotransformation reaction schemes are stored as [[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/pathway|pathways]]. The experimental conditions and additional information (e. g. sludge source) are provided in [[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/scenario|scenarios]]. Any observed transformation products ([[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/compound|compounds]]) are linked to their corresponding experimental metadata ([[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/scenario|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.
-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: [[https://envipath.org/compound|compound]], [[https://envipath.org/rule|rule]], [[https://envipath.org/reaction|reaction]], [[https://envipath.org/pathway|pathway]], [[https://envipath.org/relative-reasoning|model]] and [[https://envipath.org/scenario|scenario]]). For more information see: [[users|Users]]. This also applies to users who are not logged in, those users share an account called anonymous.
-===== Eawag-BBD Package =====
-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.
+==== Navigation ====
-===== Eawag-Sludge Package =====
-The [[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038|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 [[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/pathway|pathways]]. The experimental conditions and additional information (e. g. sludge source) are collected in the [[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/scenario|scenario]] objects. Any observed transformation products ([[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/compound|compounds]]) are linked to their corresponding experimental metadata ([[https://envipath.org/package/4a3cd0f4-4d2b-4f00-b3e6-a29e721f7038/scenario|scenario]]). Kinetic parameters (rate constants and/or half-lives) including corresponding scenarios are indicated for compounds for which such data is available.
+Objects from all packages are shown when the user selects the corresponding category in the main menu (if the user has [[permissions|Permission]].READ). To view the content of a specific package you can choose it on the [[https://envipath.org/package|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 [[permissions|Permission]].WRITE.
+===Default Package ===
-===== Eawag-SOIL Package =====
+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: [[https://envipath.org/compound|compound]], [[https://envipath.org/rule|rule]], [[https://envipath.org/reaction|reaction]], [[https://envipath.org/pathway|pathway]], [[https://envipath.org/relative-reasoning|model]] and [[https://envipath.org/scenario|scenario]]). For more information see: [[users|Users]]. This also applies to users who are not logged in, those users share an account called anonymous.
-“Eawag-SOIL” package contains pathway information from soil degradation studies, stored in a biotransformation reaction scheme in the object [[https://envipath.org/pathway|pathway]]. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority ([[http://dar.efsa.europa.eu/dar-web/provision|EFSA]]). The package also contains information on different experimental conditions that are stored in the object [[https://envipath.org/scenario|scenario]]. [[https://envipath.org/compound|Compounds]] in the [[https://envipath.org/pathway|pathway]] are associated with a given [[https://envipath.org/scenario|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 [[https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456|here]]