Edit interaction
Overview
Edit interaction window provides features including search, create, modify and delete interactions. This is the most frequently used window by curators.
Search
Users can input any string in the "interaction name" text field and then click "search" button. If there is not any input in the text field when users click the "search" button, user can continue input the string in a popup "search interaction" window.
The popup window is "search interaction" window. The MetNetDB program will search the input string in the name and synonyms of interactions, their substrates, products, enzymes, EC numbers and genes. All matched interactions will be listed in the "interaction list" table. Users can choose one of them and the detail information of the selected interaction will be displayed in the "edit interaction" window. Users can sort the list by clicking the column headers.
Create a new interaction
To create a new interaction, the user should provide the name, interaction type, location, organism, and substrates and products of the interaction. Optionally the user can provide the enzyme and EC number, pathways the interaction belongs to. When all information is ready, the user need click "insert interaction" button to create the new interaction.
Modify an existing interaction
Any information of the selected interaction is changed, the user can click "modify interaction" to change. This includes changing the pathway list that the selected interaction belongs to.
Delete an existing interaction
The user can click "delete interaction" button to delete the selected interaction.
Change pathway list that the interaction belongs to
The current pathway list that the interaction belongs to are listed in "pathway list" table. By clicking "list" button, the list is refreshed in the "pathway list" table. To add multiple existing pathways to the list, the user need click "add pathway" button and choose pathways from the popup "pathway list" window. To remove pathways from the list, the user need choose one or more pathway in the list and then click "remove" button.
Change substrates, products of the interaction
To add a new substrate or product, the user need search the entities in the "search entity" table first. Then choose one or more entities from the list. By clicking "=>from" button, the selected entities are inserted into "substrate list" table. By clicking "=>to" button, the entities are inserted into "product list" table. To remove one or more substrates, just choose them in the "substrate list" table and click "<=" button. It is also applied to remove products of the interaction. User can add enzymes by choosing one enzyme from "search entity" table and click "enzyme" button.
MetNetDB has integrated Brenda data and the user can create substrates and products by choosing EC number first and then clicking "auto" button. Since the substrate and product lists contain all possible ones for multiple enzymes of the EC number in multiple organisms, the user need to refine the list.
The entity type, location and coefficient of the substrates and products can be changed "in place". If the entity after changing does not exist in MetNetDB, the program will automatically create new one. However, the user still need search the entities first since the multiple entities may have same synonyms and the program can not infer the exact entity that user really want to specify.
In some cases, e.g., reversible interactions, the user can click "reverse direction" button to exchange the lists in the "substrate list" table and "product list" table.
Misc
All lists in the table are sortable. The user can sort them by clicking the column headers.