http://wiki.envipath.org/ 2026-04-14T12:14:36+00:00 http://wiki.envipath.org/ http://wiki.envipath.org/lib/exe/fetch.php?media=wiki:logo.png text/html 2025-04-14T13:19:41+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=batch_pathway_prediction&rev=1744636781&do=diff Pathway Prediction in Batch Mode text/html 2024-02-07T09:57:04+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=changelog_0.2.9&rev=1707299824&do=diff Changelog 0.2.9 * Compounds now can have multiple structures (one normalized structure is automatically generated) * Mapping servlet for mapping PPS IDs to enviPath URIs * New input masks for scenarios * Switch to Meka for Relative Reasoning text/html 2025-09-17T12:38:42+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=changelog_0.3.0&rev=1758112722&do=diff Change log 0.3.0 The following structures were corrected in November 2022: 24/11/2022 We identified some errors in compound structures within the EAWAG-SOIL package, specifically concerning the Mandipropamid and Bromoxynil pathways. As part of our corrective measures, the following changes were made: text/html 2024-03-19T13:23:23+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=compound&rev=1710854603&do=diff Compound REST Operations GET URI Parameter Accept Types Result Status Codes /compound optional parameter “delimiter” for text/csv only, default value: “,” text/html List of all compounds of all packages that the user has permission to read text/html 2024-03-22T12:08:54+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=compounds&rev=1711109334&do=diff Compounds In enviPath, a compound object stores the structure of a chemical compound. Compounds are assigned to Packages, compounds with equal structure exist only once in each package. Therefore, a compound is identified by its canonical SMILES representation (Absolute SMILES created with the CDK library). Compounds provide connections to other enviPath objects like, e.g., text/html 2024-03-15T14:52:04+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=group&rev=1710514324&do=diff Group REST Operations GET URI Parameter Accept Types Result Status Codes /group optional parameter “delimiter” for text/csv only, default value: “,” text/html List of all groups. 200 - OK application/json text/html 2024-04-11T07:18:45+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=groups&rev=1712819925&do=diff Groups Users can be organized in groups to share data and work collaborative. Users can grant permissions on packages to a group. Updating a group The user can update the following group information. * Name :The new name for the group must not be already in use. text/html 2024-07-01T08:11:07+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=license&rev=1719821467&do=diff The enviPath database and prediction system is provided under a Creative Commons license. Specifically, we offer the BBD and Soil packages under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license. You can identify the specific license used near the end of the page of each object in the license block. text/html 2024-02-13T15:17:00+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=package&rev=1707837420&do=diff Package REST Operations GET URI Parameter Accept Types Result Status Codes /package optional parameter “delimiter” for text/csv only, default value: “,” text/html List of all packages that the user has permission to read. text/html 2025-11-12T12:13:35+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=packages&rev=1762949615&do=diff Packages 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 text/html 2025-05-22T09:53:31+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=pathway_prediction_in_batch_mode&rev=1747907611&do=diff Pathway Prediction in Batch Mode Pathway prediction in enviPath can now be performed in batch mode. This feature accepts a .tsv file containing SMILES representations and compound names as input. It processes the file and returns a .tsv output containing the predicted transformation products (TPs) along with relevant metadata. Batch mode is designed to support experimentalists in generation of suspect screening lists, ideal for non-target analysis. text/html 2024-03-19T09:33:20+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=pathway_prediction&rev=1710840800&do=diff Pathway Prediction Applicable Domain For all compounds we calculate an applicability score that indicates whether the compound is similar to the training set, in terms of fingerprints and compatible rules. Additionally, all functional groups containing hetero atoms are highlighted in green (red), indicating that they are (not) sufficiently represented in the training set. The evaluation of the applicability domain criteria can be visualized in the pathway view (see example). text/html 2024-02-01T12:24:42+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=pathway&rev=1706790282&do=diff Pathway REST Operations GET URI Parameter Accept Types Result Status Codes /pathways optional parameter “delimiter” for text/csv only, default value: “,” text/html List of all pathways of all packages that the user has permission to read. text/html 2024-04-23T11:32:53+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=pathways&rev=1713871973&do=diff Pathways A pathway is a set of compounds and reactions. A pathway stores the biodegradation of compounds. A pathway can either be predicted or created manually by adding compounds and reactions. When predicting a pathway enviPath tries to apply a set of transformation rules to the compound at hand, starting with the root compound, and will add the transformation product(s) to the pathway. If two different rules predict the same compound the pathway will only have one compound but there will be… text/html 2024-04-11T07:19:26+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=permissions&rev=1712819966&do=diff Permissions There are three kind of permissions (in a hierarchical order): READ, WRITE, ALL. A user can grant permissions on a package or group to a user or a whole group. If READ permission is granted to a group an a given package all member of the group are able to see its content. text/html 2025-12-15T13:50:31+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=pfas_resources&rev=1765806631&do=diff PFAS Resources Per- and polyfluoroalkyl substances (PFASs) are a large and diverse group of synthetic chemicals characterized by strong carbon-fluorine bonds. These bonds make PFASs highly resistant to chemical, biological, and thermal degradation. As a result, PFASs are often referred to as text/html 2024-01-19T13:28:56+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=reaction&rev=1705670936&do=diff Reaction From enviPath Wiki Jump to navigation Jump to search REST Operations GET URI Parameter Accept Types Result Status Codes /reaction optional parameter “delimiter” for text/csv only, default value: text/html 2024-04-11T07:12:38+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=reactions&rev=1712819558&do=diff Reactions In enviPath, reaction objects represent biotransformation reactions from educt compound(s) to product compound(s). Reactions are directly linked to the involved compounds. A link from a rule to a reaction indicates that a reaction is in agreement with the generalized biotransformation rule. text/html 2024-09-02T12:28:52+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=references_to_external_databases&rev=1725280132&do=diff References to External Databases Compounds and reactions in enviPath can be automatically linked to external databases.At the Compound level, we've integrated links to PubChem, ChEBI, and KEGG. Reactions, on the other hand, can now be directly linked to Rhea, a curated database of biochemical reactions.This functionality is available on the package, pathway, compound, compound structure or reaction upon the selection of the “Update References” option on the “Actions” dropdown. This will trigger… text/html 2024-03-27T09:24:17+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=relative_reasoning&rev=1711531457&do=diff Relative Reasoning To limit the combinatorial explosion in pathway prediction, enviPath allows to learn and apply relative reasoning models. Rule-based relative reasoning models are available, as well as multi-label machine learning algorithms. If employed during pathway prediction, models predict probabilities for each applied text/html 2024-03-15T12:45:38+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=relative-reasoning&rev=1710506738&do=diff Relative-Reasoning REST Operations GET URI Parameter Accept Types Result Status Codes /relative-reasoning params=true text/html List of all relative-reasonings of all packages that the user has permission to read. text/html 2023-12-12T14:54:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=review&rev=1702392886&do=diff Review The enviPath system provides a Reviewing system to ensure a maximum of proven knowledge. Therefore a Reviewer group exists within the enviPath system. As default the only member of this is group is the admin. The admin can appoint other users to join the Reviewer group. Members of the Reviewer group gain the right to mark text/html 2024-03-19T15:07:13+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=rule&rev=1710860833&do=diff Rule REST Operations GET URI Parameter Accept Types Result Status Codes /rule optional parameter “delimiter” for text/csv only, default value: “,” text/html List of all rules of all packages that the user has permission to read. text/html 2024-05-03T12:38:33+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=rules&rev=1714739913&do=diff Rules In enviPath, a rule object represents a biotransformation rule. Biotransformation rules are generalizations of reactions and used for the prediction of pathways. The left-hand side of a rule represents a pattern that matches functional groups in compounds. If the functional group is matched, a transformation described via a mapping to the right-hand side of the rule is carried out. text/html 2024-03-19T13:14:18+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=scenario&rev=1710854058&do=diff Scenario REST Operations GET URI Parameter Accept Types Result Status Codes /scenario optional parameter “delimiter” for text/csv only, default value: “,” text/html List of all scenarios of all packages that the user has permission to read. text/html 2023-11-30T15:07:30+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=scenarios&rev=1701356850&do=diff Scenarios A scenario contains a collection of additional information (e.g. temperature, acidity (pH) etc.) and can be attached to other objects (pathway, rule, reaction, compound, model) of the same package. These scenarios naturally have different roles depending on the higher level object. E.g. when attached to a pathway it contains circumstances in a study, or when attached to a rule it contains the conditions when the specific rule applies. But in general, they can be used to annotate any o… text/html 2024-03-19T13:21:38+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=search&rev=1710854498&do=diff Search REST Operations GET URI Parameter Accept Types Result Status Codes /search search - the search string */* Performs a search for the given string inside the specified packages. 200 - OKpackages[] - package text/html 2025-02-10T08:18:34+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=searching_function&rev=1739175514&do=diff Searching Function The Search page enables quick and efficient data retrieval across enviPath. By default, the search is configured to include the EAWAG-BBD, EAWAG-SOIL, and EAWAG-SLUDGE packages. You can customize the selection by expanding or narrowing the set of packages using the dropdown menu. Multiple search methods are available to suit your needs: text/html 2024-03-19T13:16:11+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=setting&rev=1710854171&do=diff Setting REST Operations GET URI Parameter Accept Types Result Status Codes /setting optional parameter “delimiter” for text/csv only, default value: “,” text/html List of all settings. 200 - OK application/json text/html 2025-02-13T13:05:42+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=settings&rev=1739451942&do=diff Settings Settings are used to configure the pathway prediction, and include a list of package/s and a truncation strategy: * Packages: all available rules within the selected packages are used for pathway prediction. * Truncation strategy limits the combinatorial explosion in pathway prediction. A truncation strategy can include: text/html 2025-11-12T12:07:25+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=start&rev=1762949245&do=diff Main Page enviPath is an online, publically available database and prediction system for microbially mediated biotransformations of organic environmental contaminants. It is the successor of the University of Minnesota Biocatalysis/Biodegradation Database and Pathway Prediction System (now text/html 2024-03-12T08:33:46+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=user&rev=1710232426&do=diff User REST Operations GET URI Parameter Accept Types Result Status Codes /user optional parameter “delimiter” for text/csv only, default value: “,” text/html text/html 2024-03-27T11:39:07+00:00 Anonymous (anonymous@undisclosed.example.com) http://wiki.envipath.org/doku.php?id=users&rev=1711539547&do=diff Users Everyone is able to register a user account. The benefits of registering will be that your data will not be deleted after some time like the data provided by anonymous users. Also you can set permissions to your data and share it along with other users by adjusting the permissions on a