# NeOn Alignment Plugin: Commands

The NeOn Alignment plugin panel is obtained by selecting "Windows" -> "Show view" -> "Others..." -> "Alignment" -> "Alignment".

The commands which can be activated through the interface are as follows:

### Online

Switch to the online mode in which the plug-in is connected to an Alignment server and can take advantage of its stored alignements and available matching methods. Only ontologies accessible on the web can be matched in this mode.

### Offline

Switch to the offline mode in which local ontologies are matched with the matching methods available within the NeOn toolkit.

### Refresh

Update the two ontology choosers (Ontology 1 and Ontology 2) with the ontology available in the toolkit.

### Match

Match the ontologies selected in the ontology choosers with the method selected in the method chooser (a new alignment is created and is available in the chooser of server alignments or local alignments depending of the mode).

### Trim (online)

Trims the correspondences in the alignment selected in the server alignment chooser whose confidence is below some threshold (a new alignment is created).

### Import (online)

The alignment selected in the server alignment chooser is imported as an ontology in the NeOn toolkit.

### Store (online)

Stores the alignment selected in the server alignment chooser on the server (it will be kept in the database and will survive any server shutdown).

### Import (offline)

The alignment selected in the local alignment chooser is imported as an ontology in the NeOn toolkit.

### Trim (offline)

Trims the correspondences in the alignment selected in the local alignment chooser whose confidence is below some threshold (a new alignment is created).

### Upload (online)

Uploads the alignment selected in the local alignment chooser on the server.

### Find alignments for ontologies (online)

Fills the server alignment chooser with all alignments available on the server.

### Find all alignments from server (online)

Fills the server alignment chooser with all alignments between the two ontologies of the ontology choosers (Ontology 1 and Ontology 2) available on the server.