If you have a local installation of Sungear, you can add new experiments to
the list of experiments in the File | Load list by adding lines to the
exper.txt
file. Each line of the file describes a single experiment
as follows:
Experiment ID | File name | Description [ | species]
Experiment ID
must be unique across all experiments in the
file. File name
gives the path, relative to the data directory,
of the Sungear data file. Description
is the description displayed
in the experiment list. The optional species
designation is required
for any species other than the default arabidposis.
Adding a new species to Sungear is a fairly simple process;
however, completing the process requires either a) interaction with the
Sungear team, or b) a local installation of Sungear, along with the visdata
jar file. There are three stages to the process.
First, prepare a list of genes and descriptions as described in the Gene/Case Definition File section of the general data file documentation.
Second, a "gene-to-go" (Element-to-Group) file that associates genes with GO terms must be created. The format of this file is similar to the other Sungear files described in Creating Sungear Files. Each line of this file consists of a gene ID, followed by a delimiter, and then zero or more GO terms with which that gene is associated:
Gene ID | [GO Term ID]*
Once these files are created, they need to be processed to generate a Group-to-Element file from the Element-to-Group file. If you have a local Sungear installation, skip to local installation below. Otherwise, notify the team using the contact form on the main upload page. We will contact you and tell you how to send us the files. Once we have the files, we will translate the Element-to-Group file into our Group to Element format, which includes pre-calculated number used for on-the-fly calculation of z-scores for GO terms.
After we process this file, the new species will appear in the pull-down list on the main upload page, and any file prepared according to the Sungear Data File rules can be uploaded and viewed in Sungear.
Execute the following on the command line:
Unix: java -cp visdata.jar:sungear2.jar go.MakeGoGene
Windows: java -cp visdata.jar;sungear2.jar go.MakeGoGene
Browse to the the requested files, the click "Process" to
generate the Group-to-Element ("go2gene") file. After crreating the
new file, add a line to the species.txt
file describing the
new species. The format of the line is described below:
Species name | Gene (element) definition file | GO term (group) definition file | GO term (group) hierarchy file | GO term to gene (group to element) correspondence file
There are two steps to adding a new hierarchy (set of groups) to Sungear. The first is the creation of the two group files described in Creating Sungear Files: Group Definition File and Group Hierarchy File. Typically these will be generated programmatically (e.g., the GO hierarchy files were generated by a Java program designed to read the Gene Ontology .obo file).
The second step is to generate a new "species" by following the instructions above for adding a new species. In Sungear, the term "species" refers to a unique combination of gene (element) definitions and groups. For example, arabidopsis with TAIR annotations and the GO hierarchy would be one species; arabidopsis with TAIR annotations and the Plant Ontology hierarchy would technically be another species; and arabidopsis with the GO hierarchy and another set of annotations (e.g., UniProt vs. HGNC for human) would be a third species.