Creating
The first step when working with any reconstruction (even for import) is to create the reconstruction. To create a new reconstruction the menu item File>New Reconstruction is used. A dialog will be displayed that allows for input of organism
information. The required information is as follows:
An identifier for the reconstruction. There is no strict rules but a common naming convention is to use an 'i' to indicate in silico, the initials of the lead author and the number of reactions in the model (i.e. Joe Blogs creates a model of 854 reactions the identifier would be iJB854). As the number of reactions would not be known for a new project Metingear provides the %n and %m metacharacters as placeholders for the number or metabolites (%m) and reactions (%n). Creating an identifier iJB-%n-%m will start as iJB-0-0 but adding a metabolite will update the identifier 'iJB-0-1'.
Note: Currently the project will always save over the starting identifier (e.g. ./iJB-0-0.mr) thus the identifier will change but not the filename of the project (which is usually the identifier). This may be changed in future releases.
The reconstruction requires full specification of taxonomic details include the name, code, tax id and kingdom. To simplify the entering of organism information the UniProt Taxonomy resource should be loaded. If the UniProt Taxonomy data has been loaded entering details into the name, code or tax id fields will provide auto completion for the other fields. All taxonomic fields must be completed with strict requirements of the code field being 5 characters (e.g. ECOLI, SALTY, STRAP) and the tax id being numeric integer.
To assist in describe the next section there are some definitions required. An (metabolic) entity is any component of a reconstruction. This includes metabolites, reaction, genes and proteins. Each entity has a name, abbreviation and an identifier. An annotated entity is an entity with one or more annotations - all entities in their basic form are unannotated. An annotated entity can also hold observations but these are used infrequently and the scope is outside of this introduction. Annotations can be added manually or automatically and there are several different types (see Annotation Types).
When creating any entity the identifier will be automatically created. The name and abbreviation need to be explicitly defined on creation of an entity. Although the names can be left blank this is no advisable as some methods depending on this naming (i.e. entering a reaction equation). The abbreviation is used less often but is still useful to quickly refer to an entry.
The menu item File>New Metabolite will open a dialog requiring a name and abbreviation for the new metabolite. The abbreviation field will attempt to provide an appropriate abbreviation from the provided name by splitting and truncating the words. You can specify a custom abbreviation after entering the name or after the entity has been created. Both the name and abbreviation can be specified after by editing the metabolite.
The File > New Reaction menu requires a name and abbreviation (see. Creating a Metabolite) and an optional reaction equation. You can specify the reaction using the names of metabolites, if a metabolite is already pressent in the reconstruction an auto complete dialog will pop-up that will allow auto-completion of that metabolite name. If you enter a metabolite name that is not currently in the reconstruction a new entity will be created with the reaction. You can specify the coefficient and compartments by prefixing and suffixing appropriate values to each participant. For example if I would like the metabolite ATP in the extracellular compartment I can suffix the compartment abbreviation in square brackets separated from the metabolite by a space ATP [e]. If the entire compartment occurs in one compartment you prefix the entire equation with [e]: ([e]: ATP -> ADP + Pi). A list of compartment supported abbreviations can be found here. Coefficients are specified by before the metabolite name, so 2 ATP specifies that there are two ATP molecules in that section of the equation. A metabolite without any coefficient will default to a coefficient value of '1' and compartment 'cytoplasm (c)'.
| Forward reaction | A -> C + D |
| Reverse reaction | A <- C + D |
| Bi-directional reaction | A <=> C + D |
| Reaction with a coefficient | (2) A <=> C + D |
| Transport reaction | A [c] <=> C [e] |
| Reaction in periplasm | A [p] <=> C [p] |
[p]: A <=> C |
You can edit the reaction after it's creation by manually editing the participants. Combined with the Copy and Paste it is possible to move a reaction to a different compartment by first duplicating it and then editing each participant.
Reaction equation auto-complete
When input a reaction equation, a suggestion dialog will pop up bellow the text field. This suggestion box helps ensure metabolites are referenced correctly. For convenience entires in ChEBI which also match the prefix are also displayed in the auto-completion list. Candidates from within the reconstruction will always be at the top of the list. If a metabolite is entered into the reaction which can not be identified a new metabolite will be created. The auto complete dialog will also help with entering compartment names and abbreviations.
To create a gene product select the File > New Gene Product. Enter the name and abbreviation (see. Creating a Metabolite) and select if you want a Protein, tRNA or rRNA. The sequence of the gene product can be added once it has been created.
| Task | Menu Item | Short Cuts | |
|---|---|---|---|
| OS X | Windows/Other | ||
| Create a reconstruction | File > New Reconstruction | ⌘N | ctrl N |
| Navigate auto-complete menu | N/A | ↑ and ↓ | |
| Confirm auto-complete menu | N/A | Ctrl space, ⏎ (Enter/Return) or Click item | |
| Create a metabolite | File > New Metabolite | ⌘⇧N | ctrl ⇧ N |
| Create a reaction | File > New Reaction | ⌘⇧R | ctrl ⇧ R |
| Create a gene product | File > New Gene Product | ⌘⇧P | ctrl ⇧ O |
| Close a dialog | Close or Cross icon | ESC | |