Table of Contents:
- Getting started with DRG
Getting started with DRG
To upload your dataset (just before or after publication) to the DRG you can follow the brief instructions below, or look at the full set of documentation can be found here as a downloadable document.
In brief, you should
1. Download the DRG Data Template (brief directions and sample data are included with it).
2. Fill in your data. Currently, we support data primarily from gene/protein expression studies involving microarray,in-situ hybridization, PCR or immunohistochemical measurements. If your data cannot be fit into this model, please contact us (firstname.lastname@example.org).
3. The curators use controlled vocabularies linked to our ontologies in order to provide consistent use of terms. Please refer to the NIF annotation standards (small set of terms that we have chosen to use rather than the myriad of possible terms) that will be followed when reporting data, these are explained in the full documentation, but briefly:
a. Age - P54 is a reasonable age value, but check the Age classification page for our definitions of Adult, Juvenile, or Aged organisms. If your experimental organism is not defined please contribute to the discussion forums.
b. Experiment vs Control - All studies that we have entered involve a comparison between conditions, usually as a function of drug treatment, but not necessarily so. In this column, you should specify what comparison was made for the particular measurement reported. Examples, Morphine vs Saline; GRM1 Knock Out Mutant vs Wild Type Littermate
c. Conclusion: - This column captures the qualitative result of a quantitative analysis, e.g., gene expression is increased or decreased relative to specified control. Differential expression (increased or decreased) means that an appropriate statistical test was performed, and the authors found a significance level of p < 0.05. If no change is reported, the author did not find a difference; if statistics are not performed or reported, then leave this field blank.
d. Treatment - drug paradigm in the simplest terms, such as Acute Cocaine, Chronic Morphine, Methamphetamine withdrawal. This will be assigned by the NIF curator based on the Experimental paradigm.
4. Log into the wiki (getting an account should take no more than a few minutes)
5. Once the template is complete, upload the template to this wiki page. Watch here as it moves through the curation process and becomes incorporated into the database. Data are first released to our staging database to ensure that there are no errors. You will receive e-mail notification when they are available. Once the data are verified, they will be released to production.
1) The text is cut off in the Excel spreadsheet, making the instructions hard to read. How can I see all the text?
A: We have saved the sheet using the "Wrap text" function, which should display the entire contents, but sometimes with different platforms and versions, that instruction gets turned off. To turn it back on, select the entire column, go to the Format menu, select "Cells" and then "Alignment". Turn on the Wrap Text function. Alternatively, you can expand the size of the cell by positioning the cursor over the right border at the top of the sheet and dragging it to the correct size. Finally, if you click on the contents, it should display the entire text. We recommend, however, that you use the Wrap Text option.
2) Should I translate all tables into the DRG template? What makes a good table for capturing in DRG?
A: All tables are NOT suitable for inclusion in the DRG. You should only capture tables that contain data that express the results of a study. We do not bother to represent tables with demographic variables, lists of methods, or other parameters or metadata about the experimental results. That information is usually captured as part of the subject attributes or the methods. A typical table for DRG consumption includes information like the expression of a gene in a brain region or organ as a function of one or more experimental conditions. Some experimental paradigms are a lot more complicated than others. If you are not comfortable translating a particular table because you don't feel that you understand the experiment well enough, it is probably not a good table to include. However, you should always feel free to contact the NIF DRG curators (email@example.com) to see if they can help work through the example. Remember, this is a new way of reporting scientific data and we are still learning about the best way to do this.