Annotations
This manual covers the manual editing of annotations. To add annotations using tools please refer to the Tools page.
To add annotation(s) a selection of one or more entities is required.
Choose the menu item Edit > Add Annotation
Select the annotation type you which to add (note chemical structure is added via Tools > Curated Cross-reference).
This will provide an input field for that annotation.
Additional annotations can be added by selecting the green (+) icon.
Added annotations will appear in the entity inspector on the right.
Annotations can also be added from the inspector. Click on the edit button in the top right.
Then select 'Add Annotation'.
To delete an annotation, enter the edit mode on the inspector.
Which will show the edit toolbar.
Annotations can then be deleted by clicking the (x) icon.
Deleting an annotation can be undo whilst editing or after by selecting Edit > Undo.
To edit an existing annotation, select the annotation in the table by double clicking and changing the value of the annotation.
Click Save to store your changes, this action is undoable.
This table details all the currently available annotations and their scope (i.e what type of entities can they be attached too).
| Name | Description | Scope | Source Code |
|---|---|---|---|
| ACP Associated | Marks a metabolite as being attached to an Acyl Carrier Protein | Metabolite | ACPAssociated |
| Chemical Structure | The chemical structure of the metabolite | Metabolite | AtomContainerAnnotation |
| Comment | Short comment that has been added by an author | AuthorAnnotation |
|
| ChEBI Cross-reference | A cross-reference specific to the ChEBI database | Metabolite | ChEBICrossReference |
| Charge | The charge of this metabolite | Metabolite | Charge |
| Citation | No description available | Citation |
|
| Classification | A cross-reference that specifically links to a classifcation identifier | Classification |
|
| Crossreference | A crossreference to an alternative identifier | CrossReference |
|
| Enzyme Classification | A cross-reference to the Enzyme Classification (E.C.) number | GeneProduct, Reaction | EnzymeClassification |
| Exact Mass | The exact mass is the sum of the masses of the atoms in a molecule using the most abundant isotope for each element | Metabolite | ExactMass |
| Executable | A parameter for an external task that describes the executable | ExecutableParameter |
|
| File | A parameter for a task (not necessarily external) that uses a local file | FileParameter |
|
| Flux Lower Bound | A lower bound for reaction flux | Reaction | FluxLowerBound |
| Flux Upper Bound | A upper bound for reaction flux | Reaction | FluxUpperBound |
| Gibbs Energy (ΔG) | Thermodynamic potential of the reaction | MetabolicReaction | GibbsEnergy |
| InChI | The IUPAC International Chemical Identifier line notation of chemical structure | Metabolite | InChI |
| KEGG Compound Cross-reference | A cross-reference that specifically links to the KEGG Compound database | Metabolite | KEGGCrossReference |
| Locus | The gene locus/association | Gene, GeneProduct, Reaction | Locus |
| Lumped | Indicate that a metabolite or reactions is not a discrete entity and rather it is an average of many entities. It is common practise to include such metabolitesas DNA/RNA/Fatty Acid Composition in biomass reactions | Metabolite, MetabolicReaction | Lumped |
| Molecular Formula | The chemical formula of a metabolite | Metabolite | MolecularFormula |
| Parameter | A parameter for a task (not necessarily external) | Parameter |
|
| SMILES | The simplified molecular-input line-entry specification representation of chemical structure | Metabolite | SMILES |
| Source | Non-semantic description of where the entity has come from | Source |
|
| Subsystem | Abstract functional role of this reaction | Reaction | Subsystem |
| Synonym | An alternative name for this entity | Synonym |
|
| Systematic Name | A systematic name for an entity | SystematicName |