OMERO.editor Text Import

This page describes functionality that is currently in development (since the Beta 3.0 release). If you have any comments, or would like to try these features before the next release, please let me know...

Existing protocols can be imported into OMERO.editor by the text import function, using copy and paste.

Start by choosing Menu > Import > Import Text. This will open the text importer window. First, paste the text from a source protocol into the text import window. In this example, I will use the text from a DNA ligation protocol at OpenWetWare.org.

Some text from this web-page has been copied and pasted into the text importer...

Separate paragraphs will become individual fields, with the text as the description. If the current arrangement of paragraphs is suitable (as the first 3 paragraphs above) they may not need editing. However, the lines "Materials" and "Reagents" should be separated from the previous paragraphs, so that they form individual fields, as shown below.

The title of each field will represent the first 40 characters of the description text. If the text is less than 40 characters, this will be used for the title instead of the description. If you wish to specify a different field title, you can highlight it with the "Field Title" button. In addition, a field parameter and units can be indicated with the appropriate buttons, as shown below...

Several formatting steps have been taken in the next figure: Each numbered method of the protocol has been separated into a new paragraph, so that they are imported as separate fields in OMERO.editor. The title of steps 1 and 2 below, has been chosen from more than one section of the text. In steps 2 and 6, parameters and units have been chosen. In steps 3 and 4, text has been added (uL) and chosen as units. All of these steps will become "Number" fields, with the specified units, and the parameters (if chosen) becoming default values. NB. If a parameter is chosen without units, this will become a "Text" field, eg for storing a gene name etc.

The above text was imported into OMERO.editor and the part of the protocol represented in the previous figure appears as below. As described above, each paragraph is now a separate field. The highlighted field indicates how the field title, description, default value and units are derived from the words specified in the import window.

Finally, the imported fields can be organised hierarchically in OMERO.editor, to model the layout of the imported protocol, as shown below. The steps of the method have been indented under the "Method" field, and a similar procedure has been applied to other parts of the protocol. Further editing can be carried out as desired, in order to complete the import of the protocol.

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