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Annotations

johnmay edited this page Jan 21, 2013 · 24 revisions

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.

select-entry

Choose the menu item Edit > Add Annotation

annotation-menu

Select the annotation type you which to add (note chemical structure is added via Tools > Curated Cross-reference).

annotation-type

This will provide an input field for that annotation.

annotation-edit

Additional annotations can be added by selecting the green (+) icon.

annotation-edit-2

Added annotations will appear in the entity inspector on the right.

annotation-view

Annotations can also be added from the inspector. Click on the edit button in the top right.

annotation-edit-bar

Then select 'Add Annotation'.

annotation-save-bar

Deleting annotations

To delete an annotation, enter the edit mode on the inspector.

annotation-edit-bar

Which will show the edit toolbar.

annotation-save-bar

Annotations can then be deleted by clicking the (x) icon.

annotation-delete

Deleting an annotation can be undo whilst editing or after by selecting Edit > Undo.

Editing Existing Annotations

To edit an existing annotation, select the annotation in the table by double clicking and changing the value of the annotation.

annotation-edit

Click Save to store your changes, this action is undoable.

Annotation Types

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
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