What it does: Reads and writes files in the GO Flat File Format (http://www.geneontology.org/GO.format.go.shtml). This is the format originally used by the Gene Ontology Consortium to develop the first versions of the GO. Use of this file format is NOT recommended! This file format has been officially deprecated by the GO Consortium and is included in OBO-Edit only for compatibility with old applications
Even if you need to provide your ontology in GO Flat File format for compatibility with an old tool, we suggest you develop and store your ontology in OBO 1.2 format and use a tool like obo2flat to automatically generate the GO flat files.
Supported features: This file format supports a very limited subset of OBO-Edit ontology data:
Unsupported features: OBO-Edit ontology data not supported by this file format include:
The GO Flat File adapter's basic mode conforms to the interface described in The Basic Flat File Interface, with one caveat. The GO Flat File Format stores ontology structure in one file, and definitions and comments in another. When loading files in basic mode, the paths to all structure files and the definitions file are specified together on the file path text field. You may specify as many structure files as you like, but you may load only one definition file. Ontology files can be loaded from the local disk or from a URL.
When saving in basic mode, you may only save a single structure file. Definitions and comments will be discarded. To save definitions and comments, use advanced mode.
When the "Advanced" button is pressed, the load dialog changes to look like this:
This interface allows fine control over the files to be loaded. At the top is a list of files to load. To add a new file to load, press the "Add" button. A new file with the path "<new file>" will be added.
To delete a file from the list, click the file to select it. Then press the "Del" button to remove the file from the list.
To edit a file path, click the file to select it. A path editor will appear:
To change the path, type a new path into the text box or press the "Browse" button to select a file from the disk.
To specify a definition file, type a path into the "Definition file name" text field or click the browse button.
The "Advanced Options" button allows single-character symbols to be specified for relations. This is necessary when loading very old versions of the GO Flat File Format where the file does not contain any information about relations at all. For more information about how to do this, see Specifying Relation Symbols below.
The remaining controls are a series of checkboxes:
Older versions of the GO Flat File Format specification use a single character to indicate the type of a link between two terms. When loading a very old GO Flat File (or saving for compatibility with very old tools), symbol characters must be specified for each relation in the ontology.
Realize that it is usually not necessary to specify relation symbols. This is only necessary when loading very old files, or when saving with the "Use legacy compatible types" option (see below).
To specify relation symbols, click the "Advanced Options" button from the load or save dialog. The Relation Symbol editor will appear:
To the left is a list of relations that have associated symbols. To add a new symbol association, press the "Add" button. A new association will be added for a type with the id NEWTYPE.
To delete a symbol association, click the association in the list to select it. Press the "Del" button to remove the association.
To edit a symbol association, click the association in the list to select it. The symbol association editor will appear:
There are three text editor fields:
When the "Advanced" button is pressed while saving, the save dialog looks like this:
The first component is a list of ontology nodes to save. The GO Flat File Adapter can save different branches of the ontology to different files. Each item in this list associates a branch in the ontology with a save file.
To add an ontology node to the list, press the "Add" button. A new node with the location "ROOT" will be added to the list. (See below on how to choose a different location than root).
To remove a node from the list, left-click the node to select it, and press the "Del" button.
To edit a node, left-click the node to select it. The right side of the editor panel will change to an editor that looks like this:
The top part of the panel indicates which branch to save. To save the entire ontology, select "Save at ROOT".
To save a sub-branch, select "Save at". Then, type a branch id into the text box, or click the "Browse" button. An ontology browser will appear:
Select the branch of the ontology to save by left-clicking, and press ok. The id of the selected node will appear in the "Save at" text box.
The "Filename" box contains the file path where the ontology will be saved. A path can be typed directly into the box, or a file may be chosen from the disk using the "Browse" button.
The next component in the Advanced save dialog is the definition file path. This is the path where the definitions file (containing definitions, definition dbxrefs and comments) will be saved. To specify a definition file, type a path directly into the text box or use the "Browse" button to select a file from the disk. If you would prefer not to create a definition file, this field may be left blank, but all your definitions will be lost.
The next set of controls is a series of check boxes:
The final component is the "Comment" text field. This is a freetext comment that will appear at the top of the saved file.
Press Ok to save.