Editing
This page focusses on editing the basic properties of a metabolic entity and the contents of the Edit menu. Please refer to Annotations for details on editing entity annotations.
Metabolites, Reactions, Gene Products and Genes are all considered (metabolic) entities and have some values in common. All entities have a name, abbreviation and an identifier. Additionally entities can have one or more annotations and one or more observations. An annotation is a discrete piece of additional information (e.g. cross-reference, synonym, chemical structure, Gibbs free energy of formation). An observation is transient piece of information that can support an annotation, an example could be sequence homology alignments which support a functional annotation. Some annotations can be added to all types of entities whilst others can only be added to certain entities. Please refer to the Annotations wiki page for in depth details on each annotation.
Metingear divides the reconstruction between several table views. There is a view for Genes, Gene Products (protein/RNA), Metabolites and Reactions. As well as the table (yellow) there is an inspector (red) which lists more information on each entity and a sidebar (blue) for navigation.
The views can be switched between by clicking on the name in the sidebar:
Alternatively the view can be changed by selecting the toggle buttons on the toolbar. These buttons also indicate which view is currently selected.
Entries are selected by clicking on the table. Some simple data types (e.g. name) can be edited directly from the table whilst others require use of the inspector.
The name and abbreviation can be edited directly by double clicking the name and abbreviation values on the main displayed table.
The star-rating of entity can be changed by clicking on the rating and dragging the rating up or down to the required level.
The name and abbreviation can also be changed whilst the inspector is in edit mode. Selecting edit from the toolbar whilst inspecting an edit will make the abbreviation on the left and name in the middle editable.
On the metabolite table, cross-references can be added from the table view. Double clicking the cross-reference column will open a callout dialog that allows input of cross-reference identifiers. The type of the identifier is inferred automatically (if possible) but can be changed if the incorrect type is identifier. The entity will be automatically updated when you close the dialog.
Entering a KEGG Compound identifier will automatically update the type on the left.
If resource can not be inferred or is ambiguous the type can be selected from the drop down menu. This is common with identifiers which are only digits (e.g. PubChem).
Additional identifiers (up to 8) can be added by clicking the green (+) button. Cross-references can be removed to
If more identifiers are needed these can be added the same was as other annotations.
We will explore the editing by adding a hydrogen to the right of the reaction - this is semantically incorrect and only demonstrates how to added participants. Whilst viewing a single reaction, click the Edit button to the top right of the inspector.
When editing a reaction there are several options you can change. Click the right (+) icon to add a product to the right of this reaction.
Select the field of the new metabolite and enter 'H'. Please note the metabolite must existing - if it does not then you will not be able to Save the edit. Future plans include providing a drop down selection of suggested metabolites.
You may change the compartment of the new participant by selecting the compartment from the drop down box. You can also enter a value in the coefficient field, by default if the coefficient value is not specified it will be 1.0.
Clicking the Save in the top right will save the changes to the reconstruction.
It is possible to drag metabolites, reaction and proteins (genes not yet supported) between reconstructions. From a selection in the table, simply dragging the selection over to a different reconstruction in the side bar.
When switching to the other reconstruction the entities will have been copied over.
It is also possible to copy and paste beween and within reconstructions. With a selection of entities invoking ctrl C / ⌘ C will copy the selection.
You can then either switch to a different reconstruction and paste the items in, or duplicate the items in the current reconstruction (as seen below).
If the last action can be undone then these items allow regression and progression through changes made to the reconstruction. Some large actions which create a lot of data are not undoable as the memory required to store the discrete state before and after the large change. Most small changes such as name changes and adding removing annotations are supported by undo/redo.
This action will combined all selected metabolites into a single merged metabolite. All annotations which are on the individual selections will also be merged. If the metabolite appears in a reaction then all participant reactions will be updated and replaced with the new merged metabolite. By default the non-unique names of the individual metabolites will simply be concatenated with a hyphen. If desired a more appropriate name can be entered in the dialog. This action is undoable.
This action will split a metabolite into two distinct metabolites. The new metabolites are referred to as a left and right metabolite. The split metabolites are suffixed with the numbers _1 and _2
to discriminate between the newly created entities.
To split a metabolite, one must choose which reactions will use which metabolite. This is done by dragging reactions between a left and a right list. To start, all reactions are on the left. A reaction can be moved by selecting it,
dragging it over to the right hand side
dropping the reaction on the right list will remove it from the left list.
In this screenshot we will have two new metabolites. The left metabolite will maintain five of the original reactions and the right metabolite will have one reaction. This split is undoable.
The delete entities menu item will remove all selected entities from the reconstruction. If an entity is reference else where it will also be removed. As an example if a metabolite reference from a reaction is deleted then the reaction will be updated and no longer include the deleted metabolite. Any entity can be deleted, this action is undoable.
Edit > Create subset requires a selection of more or more entities
Create subset allows one to name and define a temporary subset of entities. With a selection from the active view clicking Edit > Create subset will open a dialog and request a name for the subset. Once a name has been chosen and the dialog closed the subset will apear in the sidebar under the Collections label.
Important - subsets are currently temporary and are not saved between sessions
Add annotations to the selected entities, see Annotations
This menu item will relabel all select entries with a sequential identifier (e.g. M1, M2, M3 and M4). This is useful when preparing to export a reconstruction and the identifiers are inconsistent.
Metingear is still in active development and as such may not be completely polished. The resync will force an update to the user interface which can happen if an operation fails to sent an update.
This menu item allows you clear all annotations on the selected entities. You can undo this action with Edit > Undo.
Opens the preference dialog for Metingear (see Preferences).