From ClothoWiki

This is its icon

The Registry Importer is a tool for pulling Parts and Features from the Registry of Standard Biological Parts into Clotho. In this regard it is a very simple tool -- there are only two things you can do: You can type the name of a Registry part such as BBa_I13521 into the text box then click 'enter'. It will retrieve that part and parse into a proper Clotho object. The other thing you can do is browse the list of parts available in the Registry. Click the button to get that popup window. From this window, you can scroll down to the name of a part and it will transfer it into the text box for retrieval.

Opening Registry Importer

To open the registry importer, double click the icon. A popup window with an field to enter a part of interest, or to browse existing parts. The important thing to understand about this tool is what exactly it will import.

Using Registry Importer

Enter the part name or select a part from the browse list. Hit enter. A Sledrunner viewer will pop up with the sequence of the Part.The Registry and Clotho don't exactly describe and define Parts in the same way. You'll always get a Part object back, but you may also get Feature objects annotated onto them.

For Composite Parts, the information that the Part is indeed a Composite Part is accessible by the Importer as a composition of Basic Parts. So, the Importer will also import all its basic parts (and their features), annotate them, and then create the composite Part from them. Try it out -- type in BBa_K176170 and click enter and you'll see a composite Part.

All I see is colored text, is that it?

Yes and no. At present there aren't more detailed viewers of Parts, but the objects representing these Parts contain all the composition information, format, and author (which is now you) for the Part. If it's a composite Part, the basic Parts are in there. Also, the Features are in there. There just isn't a tool yet for visualizing such things. Currently wikitext information is not accessible through the mechanism the importer uses to retrieve data from the Registry.

Dealing with formats

One thing that cannot be easily pulled out of the Registry is the Format of the Part, and in Clotho's world all Parts have Formats. For Parts that are in the original Knight standard (for both CDS and non-CDS parts), the importer can understand that the Formats should be RFC10-CDS and RFC10, respectively. The importer can also detect and understand BglBricks parts. For standards such as Biofusion or other semi-compatible formats, it's harder to divine the Format for those parts and the importer is unlikely to create such Parts properly. So, be warned that if you know a part is in something other than the Knight Standard or BglBricks, you likely need to import them by copying and pasting sequences.

Dealing with vectors

Currently the importer will reject sequences that are "plasmids" or "vectors" from the Registry. The reason for this is that they aren't consistently described in a standard way that is unambiguously interpretable by the importer. Hopefully, an attempt to import such a thing will result in an error message instead of giving you incorrect info. However, inconsistencies in the description of such sequences could lead to them slipping through the importer's filters giving you an aberrant Part object.

This is how a part opens in sledrunner. Features of the part are highlighted

Enter a part or browse parts

Example of Registry Importer

Type in BBa_R0065 and hit enter. You'll probably get a sequence viewer like Sledrunner popping up showing you the sequence of the Part R0065 as expected. Moreover, the text will be colored. The colored region corresponds to an annotation from a Feature that was also created in the process of importing this Part. For basic parts like R0065, the Registry provides some biological information about what it is. For things like promoters and coding sequences, Clotho can understand those sequences as being Features, not Parts. Some other labels given by the Registry like "intermediate" aren't really comprehensible and they won't turn into Features. So, for Basic Parts whose part type is comprehensible, it will create a Part that is a proper Clotho Part, but it will also consider that sequence as being a Feature, and the two objects will be linked together through an annotation.